UTS site search

Professor Jeffrey Reimers

Biography

So much the interest today is in interdisciplinary fields between traditional fields like chemistry, physics, biochemistry, electrical engineering, materials science, and computer science, yet so many fundamental questions remain open in each field.  My passion has always been to solve fundamental challenges, yet solving these challenges often leads to new and unexpected science and technology.

Chemistry is “The Central Science”, or so they say.  For me, this could not be truer.  How else can one be working on century-old problems like “why ammonia (NH3)  has a bond angle of 108° whilst PH3 and the rest of the series down to BiH3 have angles between 91° to 93°?” one day, how chlorophyll absorbs light the next, qubit design for quantum computing the next, the origin of intelligence the next, single-molecule device design the next, and software design for semiconductor manufacturers the next?

Many people have influenced my career, from daring and creative spectroscopists like Gad Fischer, Ian Ross, Elmars Krausz and Kent Wilson to Bob Watts and has radical ideas that classical computer simulations could model complex systems like water, to people who forged the connections between the quantum and classical universes like Rick Heller, to the inventor of electron-transfer theory and finite field computation techniques like Noel Hush and pioneers of modern chemistry like David Craig, to synthetic chemists that made functional molecules that no one could believe possible like Max Crossley, to some of the best young minds of today like Daniel Kosov, Gemma Solomon, Jun Zeng, Laura McKemmish, Lars Goerigk, and Soren Wohlthat.   In every case, I learnt the importance of putting fundamentals first.

Since moving to joint appointments at UTS and Shanghai University in 2014, I have been strengthening the links between these two young and rapidly raising institutions in the areas of chemistry, physics, and materials science.  The resources of the two universities are complimentary and provide the setting for taking on some of the most difficult challenges today facing chemical understanding and application.

My work has been widely recognized throughout the community, from distinguished fellowships such as that of the Australian Academy of Science (FAA) to the David Craig Medal for Chemistry in 2016 to national awards from the Royal Australian Chemical Institute to many citations in the popular press to being quoted by Sheldon in “The Big Bang Theory” TV show Season 3, Episode 11.

Professional

Society Membership

Fellow, Australian Academy of Science

Fellow, Royal Australian Chemical Institute

Member, Materials Australia

Member, American Chemical Society

Member, American Physical Society 

Professor, School of Mathematical and Physical Sciences
Core Member, MTEE - Materials and Technology for Energy Efficiency
B.Sc Chemistry, PhD - Dr of Philosophy Physics
 

Research Interests

Current research is based mainly at Shanghai University but presents many opportunities for involvement of UTS students.  It focuses on:

1)  Development of methods for protein structure refinement from X-ray, neutron scattering, or Cryo-EM data using quantum chemical treatment of the atoms and full atomic representations of amorphous regions.  These new methods are being implemented into the PHENIX biomolecular structure package with 15,000 worldwide users.  Experimental collaborators with new and difficult structures are encouraged.  Research projects include coding and/or development of new algorithms, and structure solution.  

2)  Understanding low-energy excited states in photosynthesis.  Most photosynthetic systems involved in solar light harvesting, including critical ones in green plants like photosystem-I and photosystem-II, show low-energy absorptions that often can contribute to primary charge separation and solar energy capture despite being too low in energy to contribute via excepted photosynthetic mechanisms.  This project involves interpreting a wide range of spectroscopic data to determine what is going on, focusing first on the simplest systems.  This work is in collaboration with Elmars Kraus at the Australian National University and with Arvi Freiberg at Tartu University in Estonia.

3)  Nuclear and electronic structure of materials and surfaces with modern applications.  This work is in collaboration with experimentalists at UTS like Milos Toth and theoreticians like Mike Ford, as well as with the theoreticians Noel Hush at Sydney University, Daniel Kosov  at James Cook University, Wei Ren, Jingzhe Chen, YongLe Li, and Liu Yi  at Shanghai University, and Hong Guo at McGill University Canada.  Surfaces can be modified in many ways through lithography techniques, and monolayers can be self assembled on them.  Diamond, graphite, silicon, and gold surfaces are all of current interest.  In many cases the surfaces conduct electricity or show interesting magnetic properties, and the connection between structure and function is always paramount.  The relationship between quantum and classical transport is critical.  

Chemical bonding, quantum chemistry, kinetics, spectroscopy, thermodynamics, optics.

Books

Reimers, J.R. 2011, Computational Methods for Large Systems: Electronic Structure Approaches for Biotechnology and Nanotechnology.
View/Download from: Publisher's site
While its results normally complement the information obtained by chemical experiments, computer computations can in some cases predict unobserved chemical phenomena Electronic-Structure Computational Methods for Large Systems gives readers a simple description of modern electronic-structure techniques. It shows what techniques are pertinent for particular problems in biotechnology and nanotechnology and provides a balanced treatment of topics that teach strengths and weaknesses, appropriate and inappropriate methods. It's a book that will enhance the your calculating confidence and improve your ability to predict new effects and solve new problems. © 2011 John Wiley & Sons, Inc.
Reimers, J.R. 2011, Preface: Choosing the Right Method for Your Problem.
View/Download from: Publisher's site

Chapters

Goerigk, L., Falklöf, O., Collyer, C.A. & Reimers, J.R. 2012, 'First steps towards quantum refinement of protein X-ray structures' in Quantum Simulations of Materials and Biological Systems, pp. 87-120.
View/Download from: Publisher's site
© Springer Science+Business Media Dordrecht 2012. Using standard force-fields and empirical restraints in protein refinement has proven to be a key tool in X-ray protein structure determination. However, detailed analysis of the resulting structural models sometimes reveals chemically unreasonable features, originating in many cases from the representation of multiple configurations using some averaged structure. Quantum chemical methods and computational capabilities have now come to the point at which full quantum refinement of protein structure is feasible, but only complete (meaning real ensembles of) chemical structures may be considered. Density functional theory (DFT) is currently the most popular quantum chemical approach but a large number of approximate functionals are available and most of these do not correctly describe the biologically important London dispersion effects. For small molecules it has been shown that efficient dispersion corrections can overcome this problem, without additional computational effort. We show that this is also the case using linear-scaling dispersion-corrected DFT to refine protein X-ray structures. The study considers the effect on the R factors (i.e. the agreement between modeled and observed diffraction data) when DFT is used to optimize atomic coordinates from the traditionally refined X-ray structure of triclinic hen egg white lysozyme, resolved to 0.65… This particular system was chosen as an ensemble of 8 chemically realistic structures, which are used for the representation of observed structural variability within the crystallographic unit cell and which has been recently published [Falklöf et al. in Theor. Chem. Acc. 131:1076, 2012]. Optimizing only isolated residues within the protein for which all neighboring functional groups are fully identified, we show that in many cases dispersion-corrected DFT (and also Hartree-Fock) optimization competes with conventional refinement techniques. Significant correlations ...
Reimers, J.R. & Hush, N.S. 2006, 'The Nature of the Special-pair Radical Cation Produced by Primary Charge Separation During Photosynthesis' in Artificial Photosynthesis: From Basic Biology to Industrial Application, pp. 109-126.
View/Download from: Publisher's site
Bili, A., Reimers, J.R. & Hush, N.S. 2006, 'Functionalization of semiconductor surfaces by organic layers: Concerted cycloaddition versus stepwise free-radical reaction mechanisms' in Properties of Single Organic Molecules on Crystal Surfaces, pp. 333-360.
View/Download from: Publisher's site
© 2006 by Imperial College Press. All rights reserved. In the age when the miniaturization trend that has driven the semiconductor industry is reaching its limits, organic modification of semiconductors is emerging as a field that could give much-needed impetus. We review the current state of understanding of the functionalization of C(100), Si(100), and Ge(100) surfaces through chemisorption of alkenes and alkynes, focusing on adsorbate structural control. While reactions on C(100) show most of the properties expected for concerted cycloaddition reactions such as [2+2] and [4+2] (Diels–Alder) processes, reactions on Si(100) present a wide range of variant behavior, including in some cases the prominence of non-cycloaddition products. More general stepwise free-radical addition processes are seen to provide a better description of reactions on Si(100), their prominence being attributed to either the non-existence or ineffectiveness of bonding within surface silicon dimers. The investigations of these systems provide not only insight into driving mechanisms for chemisorption but also motivation for the development of new techniques of organic functionalization on semiconductors.

Conferences

Reimers, J.R., Cai, Z.L., Kobayashi, R., Ratsep, M., Freiberg, A. & Krausz, E. 2014, 'The Role of High-Level Calculations in the Assignment of the Q-Band Spectra of Chlorophyll', AIP Conference Proceedings, International Conference of Computational Methods in Sciences and Engineering 2014, American Institute of Physics, Athens, GREECE, pp. 18-22.
View/Download from: Publisher's site
We recently established a novel assignment of the visible absorption spectrum of chlorophyll-a that sees the two components Q(x) and Q(y) of the low-energy Q band as being intrinsically mixed by non-adiabatic coupling. This ended 50 years debate as to the nature of the Q bands, with prior discussion poised only in the language of the Born-Oppenheimer and Condon approximations. The new assignment presents significant ramifications for exciton transport and quantum coherence effects in photosystems. Results from state of the art electronic structure calculations have always been used to justify assignments, but quantitative inaccuracies and systematic failures have historically limited usefulness. We examine the role of CAM-B3LYP time-dependent density-functional theory (TD-DFT) and Symmetry Adapted Cluster-Configuration Interaction (SAC-CI) calculations in first showing that all previous assignments were untenable, in justifying the new assignment, in making some extraordinary predictions that were vindicated by the new assignment, and in then identifying small but significant anomalies in the extensive experimental data record.
Reimers, J.R. 2013, 'Computational strategies for tackling complex electron-transfer related problems in biology and nanotechnology: Applications to natural photosynthesis and artificial solar-energy harvesting', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY.
McKemmish, L.K., Reimers, J.R., McKenzie, R.H., Marks, A.E. & Hush, N.S. 2013, 'Electron transfer, biological phonon condensates, and the "Quantum Consciousness" hypothesis', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY.
McKemmish, L.K., McKenzie, R.H., Hush, N.S. & Reimers, J.R. 2011, 'Electron-vibration quantum entanglement in chemical bonding', Optics InfoBase Conference Papers, pp. 737-739.
A simple model for chemical reactions is applied to examine electron-vibration entanglement in terms of both its potential usefullness for quantum computation and what it reveals about basic chemical processes. © 2011 AOS.
McKemmish, L.K., Kedziora, D.J., White, G.R., Hush, N.S. & Reimers, J.R. 2011, 'Molecular design principles for linearly scalable, frequency-based, universal quantum computers', Optics InfoBase Conference Papers, pp. 734-736.
Minimizing of the number of strong couplings between qubits is shown to facilitate frequencybased universal quantum computers with two-qubit-gate construction difficulty that scales linearly with increasing register size, matching that known already for one-qubit gates. © 2011 AOS.
Martelli, C., Canning, J., Reimers, J.R., Sintic, M., Stocks, D., Crossley, M.J. & IEEE 2008, 'Molecular Electronics inside Optical Fibres', 2008 JOINT CONFERENCE OF THE OPTO-ELECTRONICS AND COMMUNICATIONS CONFERENCE AND THE AUSTRALIAN CONFERENCE ON OPTICAL FIBRE TECHNOLOGY, VOLS 1 AND 2, pp. 361-362.
Pecchia, A., Gagliardi, A., Solomon, G., Di Carlo, A., Frauenheim, T. & Reimers, J.R. 2006, 'Incoherent tunneling and heat dissipation in molecular bridges', Progress in Nonequilibrium Green's Functions III, pp. 349-356.
View/Download from: Publisher's site
Gagliardi, A., Solomon, G.C., Pecchia, A., Di Carlo, A., Frauenheim, T., Reimers, J.R. & Hush, N.S. 2006, 'Simulations of inelastic tunnelling in molecular bridges', Nonequilibrium Carrier Dynamics in Semiconductors Proceedings, pp. 183-186.
Kanchanawong, P., Dahlbom, M., Treynor, T.P., Reimers, J.R., Hush, N.S. & Boxer, S.G. 2005, 'Intervalence band stark effects of special pair radical cations in mutant photosynthetic reaction centers with altered hydrogen bonding interactions', BIOPHYSICAL JOURNAL, pp. 510A-510A.
Reimers, J.R., Solomon, G.C. & Hush, N.S. 2004, 'Advantages of the use of semiempirical methods in molecular electronics.', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, pp. U1028-U1028.
Reimers, J., Picconatto, C., Ellenbogen, J. & Shashidhar, R. 2003, 'Molecular electronics III: Preface', Annals of the New York Academy of Sciences.
REIMERS, J., CRAW, J. & HUSH, N. 1992, 'SOLITON, CHARGE-DENSITY WAVE STRUCTURE AND BAND-GAPS IN ODD POLYENE AND SYMMETRICAL POLYMETHINECYANINE (BROOKER) IONS AND IN TERT-POLYACETYLENE - IMPLICATIONS FOR MOLECULAR ELECTRONICS', MOLECULAR ELECTRONICS - SCIENCE AND TECHNOLOGY, pp. 11-27.
REIMERS, J. & HUSH, N. 1991, 'ELECTRIC-FIELD PERTURBATION OF ELECTRONIC (VIBRONIC) ABSORPTION ENVELOPES - APPLICATION TO CHARACTERIZATION OF MIXED-VALENCE STATES', MIXED VALENCY SYSTEMS : APPLICATIONS IN CHEMISTRY, PHYSICS AND BIOLOGY, pp. 29-50.
REIMERS, J. & HUSH, N. 1990, 'FORMALISM FOR ELECTRON-TRANSFER AND ENERGY-TRANSFER IN BRIDGED SYSTEMS', ELECTRON TRANSFER IN BIOLOGY AND THE SOLID STATE, pp. 27-63.

Journal articles

Reimers, J.R., Ford, M.J. & Goerigk, L. 2016, 'Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism', Molecular Simulation, vol. 42, no. 6-7, pp. 494-510.
View/Download from: UTS OPUS or Publisher's site
© 2015 Taylor & Francis. The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual-Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual-Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future.
Reimers, J.R., Panduwinata, D., Visser, J., Chin, Y., Tang, C., Goerigk, L., Ford, M.J., Baker, M., Sum, T.J., Coenen, M.J.J., Hendriksen, B.L.M., Elemans, J.A.A.W., Hush, N.S. & Crossley, M.J. 2016, 'From chaos to order: Chain-length dependence of the free energy of formation of meso-tetraalkylporphyrin self-assembled monolayer polymorphs', Journal of Physical Chemistry C, vol. 120, no. 3, pp. 1739-1748.
View/Download from: UTS OPUS or Publisher's site
© 2016 American Chemical Society. We demonstrate that systematic errors can be reduced and physical insight gained through investigation of the dependence of free energies for meso-tetraalkylporphyrin self-assembled monolayers (SAMs) polymorphism on the alkyl chain length m. These SAMs form on highly ordered pyrolytic graphite (HOPG) from organic solution, displaying manifold densities and atomic structures. SAMs with m = 11-19 are investigated experimentally while those with m = 6-28 are simulated using density-functional theory (DFT). It is shown that, for m = 15 or more, the alkyl chains crystallize to dominate SAM structure. Meso-tetraalkylporphyrin SAMs of length less than 11 have never been observed, a presumed effect of inadequate surface attraction. Instead, we show that free energies of SAM formation actually enhance as the chain length decreases. The inability to image regular SAMs stems from the appearance of many polymorphic forms of similar free energy, preventing SAM ordering. We also demonstrate a significant odd/even effect in SAM structure arising from packing anomalies. Comparison of the chain-length dependence of formation free energies allows the critical dispersion interactions between molecules, solvent, and substrate to be directly examined. Interpretation of the STM data combined with measured enthalpies indicates that Grimme's D3 explicit-dispersion correction and the implicit solvent correction of Floris, Tomasi and Pascual Ahuir are both quantitatively accurate and very well balanced to each other.
Reimers, J.R., Ford, M.J., Halder, A., Ulstrup, J. & Hush, N.S. 2016, 'Gold surfaces and nanoparticles are protected by Au(0)-thiyl species and are destroyed when Au(I)-thiolates form.', Proceedings of the National Academy of Sciences of the United States of America, vol. 113, no. 11, pp. E1424-E1433.
The synthetic chemistry and spectroscopy of sulfur-protected gold surfaces and nanoparticles is analyzed, indicating that the electronic structure of the interface is Au(0)-thiyl, with Au(I)-thiolates identified as high-energy excited surface states. Density-functional theory indicates that it is the noble character of gold and nanoparticle surfaces that destabilizes Au(I)-thiolates. Bonding results from large van der Waals forces, influenced by covalent bonding induced through s-d hybridization and charge polarization effects that perturbatively mix in some Au(I)-thiolate character. A simple method for quantifying these contributions is presented, revealing that a driving force for nanoparticle growth is nobleization, minimizing Au(I)-thiolate involvement. Predictions that Brust-Schiffrin reactions involve thiolate anion intermediates are verified spectroscopically, establishing a key feature needed to understand nanoparticle growth. Mixing of preprepared Au(I) and thiolate reactants always produces Au(I)-thiolate thin films or compounds rather than monolayers. Smooth links to O, Se, Te, C, and N linker chemistry are established.
Reimers, J.R., Biczysko, M., Bruce, D., Coker, D.F., Frankcombe, T.J., Hashimoto, H., Hauer, J., Jankowiak, R., Kramer, T., Linnanto, J., Mamedov, F., Müh, F., Rätsep, M., Renger, T., Styring, S., Wan, J., Wang, Z., Wang-Otomo, Z.Y., Weng, Y.X., Yang, C., Zhang, J.P., Freiberg, A. & Krausz, E. 2016, 'Challenges facing an understanding of the nature of low-energy excited states in photosynthesis.', Biochimica et biophysica acta, vol. 1857, no. 9, pp. 1627-1640.
View/Download from: UTS OPUS
While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding.
Lee, S.H., Blake, I.M., Larsen, A.G., McDonald, J.A., Ohkubo, K., Fukuzumi, S., Reimers, J.R. & Crossley, M.J. 2016, 'Synthetically tuneable biomimetic artificial photosynthetic reaction centres that closely resemble the natural system in purple bacteria', Chemical Science, vol. 7, no. 10, pp. 6534-6550.
View/Download from: UTS OPUS or Publisher's site
© 2016 The Royal Society of Chemistry.Porphyrin-based photosynthetic reaction centre (PRC) mimics, ZnPQ-Q2HP-C60 and MP2Q-Q2HP-C60 (M = Zn or 2H), designed to have a similar special-pair electron donor and similar charge-separation distances, redox processes and photochemical reaction rates to those in the natural PRC from purple bacteria, have been synthesised and extensive photochemical studies performed. Mechanisms of electron-transfer reactions are fully investigated using femtosecond and nanosecond transient absorption spectroscopy. In benzonitrile, all models show picosecond-timescale charge-separations and the final singlet charge-separations with the microsecond-timescale. The established lifetimes are long compared to other processes in organic solar cells or other organic light harvesting systems. These rigid, synthetically flexible molecules provide the closest mimics to the natural PRC so far synthesised and present a future direction for the design of light harvesters with controllable absorption, redox, and kinetics properties.
Reimers, J.R., Chi, Q., Ford, M.J., Halder, A., Hush, N.S., Ulstrup, J. & Zhang, J. 2016, 'En ny historie om guld og svovl', Dansk Kemi, vol. 97, no. 8, pp. 20-23.
View/Download from: UTS OPUS
- guld-svovlbindingen i thiolers adsorption på guldnanopartikler og plane guldoverflader En netop publiceret større australsk-dansk undersøgelse giver ny indsigt i, hvordan thioldækkede Au-overflader er opbygget. Det har betydning for design, syntese og dannelsesmekanismer for Au-nanopartikler og Au-overflader med skræddersyede fysiske og kemiske egenskaber
Hansen, C.S., Blanksby, S.J., Chalyavi, N., Bieske, E.J., Reimers, J.R. & Trevitt, A.J. 2015, 'Ultraviolet photodissociation action spectroscopy of the N-pyridinium cation.', The Journal of chemical physics, vol. 142, no. 1, p. 014301.
View/Download from: UTS OPUS
The S1S0 electronic transition of the N-pyridinium ion (C5H5NH(+)) is investigated using ultraviolet photodissociation (PD) spectroscopy of the bare ion and also the N2-tagged complex. Gas-phase N-pyridinium ions photodissociate by the loss of molecular hydrogen (H2) in the photon energy range 37,000-45,000 cm(-1) with structurally diagnostic ion-molecule reactions identifying the 2-pyridinylium ion as the exclusive co-product. The photodissociation action spectra reveal vibronic details that, with the aid of electronic structure calculations, support the proposal that dissociation occurs through an intramolecular rearrangement on the ground electronic state following internal conversion. Quantum chemical calculations are used to analyze the measured spectra. Most of the vibronic features are attributed to progressions of totally symmetric ring deformation modes and out-of-plane modes active in the isomerization of the planar excited state towards the non-planar excited state global minimum.
Ouyang, R., Yan, J., Jensen, P.S., Ascic, E., Gan, S., Tanner, D., Mao, B., Niu, L., Zhang, J., Tang, C., Hush, N.S., Reimers, J.R. & Ulstrup, J. 2015, 'Intermixed Adatom and Surface-Bound Adsorbates in Regular Self-Assembled Monolayers of Racemic 2-Butanethiol on Au(111)', CHEMPHYSCHEM, vol. 16, no. 5, pp. 928-932.
View/Download from: UTS OPUS or Publisher's site
Kobayashi, R. & Reimers, J.R. 2015, 'Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents', Molecular Physics, vol. 113, no. 13-14, pp. 1648-1654.
View/Download from: UTS OPUS or Publisher's site
The coordination of bases to chlorophyll magnesium modifies spectroscopic properties in solution as well as in situ in reaction centres. We evaluate the free energies of complexation of one or two pyridine, 1-propanol, diethyl ether or water solvent molecules at 298 and 150 K to rationalise observed phenomena. Various a priori dispersion-corrected density functional theory calculations are performed as well as second-order Møller–Plesset calculations, focusing on the effects of dispersion modifying the intermolecular interactions, of dispersion modifying solvation energies, of entropy, and of basis-set superposition error. A process of particular interest is magnesium complexation in ether at low temperature that is often exploited to assign the Q-band visible absorption spectrum of chlorophyll. Recently, we demonstrated that trace water interferes with this process, but the nature of the resulting complex could not be uniquely determined; here, it is identified as ether.Chlorophyll-a.H2O, consistent with interpretations based on our authoritative 2013 assignment.
McKemmish, L.K., McKenzie, R.H., Hush, N.S. & Reimers, J.R. 2015, 'Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy.', Physical chemistry chemical physics : PCCP, vol. 17, no. 38, pp. 24666-24682.
View/Download from: UTS OPUS
Entanglement is sometimes regarded as the quintessential measure of the quantum nature of a system and its significance for the understanding of coupled electronic and vibrational motions in molecules has been conjectured. Previously, we considered the entanglement developed in a spatially localized diabatic basis representation of the electronic states, considering design rules for qubits in a low-temperature chemical quantum computer. We extend this to consider the entanglement developed during high-energy processes. We also consider the entanglement developed using adiabatic electronic basis, providing a novel way for interpreting effects of the breakdown of the Born-Oppenheimer (BO) approximation. We consider: (i) BO entanglement in the ground-state wavefunction relevant to equilibrium thermodynamics, (ii) BO entanglement associated with low-energy wavefunctions relevant to infrared and tunneling spectroscopies, (iii) BO entanglement in high-energy eigenfunctions relevant to chemical reaction processes, and (iv) BO entanglement developed during reactive wavepacket dynamics. A two-state single-mode diabatic model descriptive of a wide range of chemical phenomena is used for this purpose. The entanglement developed by BO breakdown correlates simply with the diameter of the cusp introduced by the BO approximation, and a hierarchy appears between the various BO-breakdown correction terms, with the first-derivative correction being more important than the second-derivative correction which is more important than the diagonal correction. This simplicity is in contrast to the complexity of BO-breakdown effects on thermodynamic, spectroscopic, and kinetic properties. Further, processes poorly treated at the BO level that appear adequately treated using the Born-Huang adiabatic approximation are found to have properties that can only be described using a non-adiabatic description. For the entanglement developed between diabatic electronic states and the nuclear motion...
Reimers, J.R. 2015, 'The importance of motions that accompany those occurring along the reaction coordinate', Australian Journal of Chemistry, vol. 68, no. 8, pp. 1202-1212.
View/Download from: UTS OPUS or Publisher's site
© CSIRO 2015. The reaction coordinate is a well known quantity used to define the motions critical to chemical reactions, but many other motions always accompany it. These other motions are typically ignored but this is not always possible. Sometimes it is not even clear as to which motions comprise the reaction coordinate: spectral measurements that one may assume are dominated by the reaction coordinate could instead be dominated by the accompanying modes. Examples of different scenarios are considered. The assignment of the visible absorption spectrum of chlorophyll-a was debated for 50 years, with profound consequences for the understanding of how light energy is transported and harvested in natural and artificial solar-energy devices. We recently introduced a new, comprehensive, assignment, the centrepiece of which was determination of the reaction coordinate for an unrecognized photochemical process. The notion that spectroscopy and reactivity are so closely connected comes directly from Hush's adiabatic theory of electron-transfer reactions. Its basic ideas are reviewed, similarities to traditional chemical theories drawn, key analytical results described, and the importance of the accompanying modes stressed. Also highlighted are recent advances that allow this theory to be applied to general transformations including isomerization processes, hybridization, aromaticity, hydrogen bonding, and understanding why the properties of first-row molecules such as NH3 (bond angle 108°) are so different to those of PH3-BiH3 (bond angles 90-93°). Historically, the question of what is the reaction coordinate and what is just an accompanying motion has not commonly been at the forefront of attention. In our new approach in which all chemical processes are described using the same core theory, this question becomes thrust forward as always being the most important qualitative feature to determine.
Reimers, J.R., McKemmish, L.K., McKenzie, R.H. & Hush, N.S. 2015, 'A unified diabatic description for electron transfer reactions, isomerization reactions, proton transfer reactions, and aromaticity', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24598-24617.
View/Download from: UTS OPUS or Publisher's site
This journal is &copy; the Owner Societies 2015. While diabatic approaches are ubiquitous for the understanding of electron-transfer reactions and have been mooted as being of general relevance, alternate applications have not been able to unify the same wide range of observed spectroscopic and kinetic properties. The cause of this is identified as the fundamentally different orbital configurations involved: charge-transfer phenomena involve typically either 1 or 3 electrons in two orbitals whereas most reactions are typically closed shell. As a result, two vibrationally coupled electronic states depict charge-transfer scenarios whereas three coupled states arise for closed-shell reactions of non-degenerate molecules and seven states for the reactions implicated in the aromaticity of benzene. Previous diabatic treatments of closed-shell processes have considered only two arbitrarily chosen states as being critical, mapping these states to those for electron transfer. We show that such effective two-state diabatic models are feasible but involve renormalized electronic coupling and vibrational coupling parameters, with this renormalization being property dependent. With this caveat, diabatic models are shown to provide excellent descriptions of the spectroscopy and kinetics of the ammonia inversion reaction, proton transfer in N<inf>2</inf>H<inf>7</inf><sup>+</sup>, and aromaticity in benzene. This allows for the development of a single simple theory that can semi-quantitatively describe all of these chemical phenomena, as well as of course electron-transfer reactions. It forms a basis for understanding many technologically relevant aspects of chemical reactions, condensed-matter physics, chemical quantum entanglement, nanotechnology, and natural or artificial solar energy capture and conversion.
Reimers, J.R., McKemmish, L.K., McKenzie, R.H. & Hush, N.S. 2015, 'Non-adiabatic effects in thermochemistry, spectroscopy and kinetics: The general importance of all three Born-Oppenheimer breakdown corrections', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24641-24665.
View/Download from: UTS OPUS or Publisher's site
This journal is &copy; the Owner Societies 2015. Using a simple model Hamiltonian, the three correction terms for Born-Oppenheimer (BO) breakdown, the adiabatic diagonal correction (DC), the first-derivative momentum non-adiabatic correction (FD), and the second-derivative kinetic-energy non-adiabatic correction (SD), are shown to all contribute to thermodynamic and spectroscopic properties as well as to thermal non-diabatic chemical reaction rates. While DC often accounts for >80% of thermodynamic and spectroscopic property changes, the commonly used practice of including only the FD correction in kinetics calculations is rarely found to be adequate. For electron-transfer reactions not in the inverted region, the common physical picture that diabatic processes occur because of surface hopping at the transition state is proven inadequate as the DC acts first to block access, increasing the transition state energy by ()<sup>2</sup>/16J<sup>2</sup> (where is the reorganization energy, J the electronic coupling and the vibration frequency). However, the rate constant in the weakly-coupled Golden-Rule limit is identified as being only inversely proportional to this change rather than exponentially damped, owing to the effects of tunneling and surface hopping. Such weakly-coupled long-range electron-transfer processes should therefore not be described as "non-adiabatic" processes as they are easily described by Born-Huang ground-state adiabatic surfaces made by adding the DC to the BO surfaces; instead, they should be called just "non-Born-Oppenheimer" processes. The model system studied consists of two diabatic harmonic potential-energy surfaces coupled linearly through a single vibration, the "two-site Holstein model". Analytical expressions are derived for the BO breakdown terms, and the model is solved over a large parameter space focusing on both the lowest-energy spectroscopic transitions and the quantum dynamics of coherent-state wavepackets. BO breakdown is i...
Reimers, J.R., McKemmish, L.K., McKenzie, R.H. & Hush, N.S. 2015, 'Bond angle variations in XH3 [X = N, P, As, Sb, Bi]: The critical role of Rydberg orbitals exposed using a diabatic state model', Physical Chemistry Chemical Physics, vol. 17, no. 38, pp. 24618-24640.
View/Download from: UTS OPUS or Publisher's site
&copy; 2015 the Owner Societies. Ammonia adopts sp<sup>3</sup> hybridization (HNH bond angle 108&deg;) whereas the other members of the XH<inf>3</inf> series PH<inf>3</inf>, AsH<inf>3</inf>, SbH<inf>3</inf>, and BiH<inf>3</inf> instead prefer octahedral bond angles of 90-93&deg;. We use a recently developed general diabatic description for closed-shell chemical reactions, expanded to include Rydberg states, to understand the geometry, spectroscopy and inversion reaction profile of these molecules, fitting its parameters to results from Equation of Motion Coupled-Cluster Singles and Doubles (EOM-CCSD) calculations using large basis sets. Bands observed in the one-photon absorption spectrum of NH<inf>3</inf> at 18.3 eV, 30 eV, and 33 eV are reassigned from Rydberg (formally forbidden) double excitations to valence single-excitation resonances. Critical to the analysis is the inclusion of all three electronic states in which two electrons are placed in the lone-pair orbital n and/or the symmetric valence antibonding orbital. An illustrative effective two-state diabatic model is also developed containing just three parameters: the resonance energy driving the high-symmetry planar structure, the reorganization energy opposing it, and HXH bond angle in the absence of resonance. The diabatic orbitals are identified as sp hybrids on X; for the radical cations XH<inf>3</inf><sup>+</sup> for which only 2 electronic states and one conical intersection are involved, the principle of orbital following dictates that the bond angle in the absence of resonance is acos(-1/5) = 101.5&deg;. The multiple states and associated multiple conical intersection seams controlling the ground-state structure of XH<inf>3</inf> renormalize this to acos[3sin<sup>2</sup>(2<sup>1/2</sup>atan(1/2))/2 - 1/2] = 86.7&deg;. Depending on the ratio of the resonance energy to the reorganization energy, equilibrium angles can vary from these limiting values up to 120&deg;, and the anomalously large bond angle in NH<inf>3</inf>...
Reimers, J.R., Panduwinata, D., Visser, J., Chin, Y., Tang, C., Goerigk, L., Ford, M.J., Sintic, M., Sum, T.J., Coenen, M.J.J., Hendriksen, B.L.M., Elemans, J.A.A.W., Hush, N.S. & Crossley, M.J. 2015, 'A priori calculations of the free energy of formation from solution of polymorphic self-assembled monolayers', Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 45, pp. E6101-E6110.
View/Download from: UTS OPUS or Publisher's site
First-principles free energy calculations, characterizing polymorphism of self-assembled monolayers (SAMs) of porphyrin molecules formed from solution onto graphite, are performed using efficient methods previously applied only to small-molecule reactivity. SAM structures are typically optimized in the absence of solvent using density functional theory embodying explicit dispersion corrections. Added then are dispersion-dominated implicit solvation energies and SAM formation entropies derived from both molecular and phonon vibration frequencies. Scanning tunneling microscopy (STM) images are measured, and polymorph formation free energies are approximated. Close parallels between experiment and theory support the hypothesis that the first seconds of SAM formation are under thermodynamic control, despite formed SAMs being kinetically trapped. Polymorphism is associated with large opposing changes to entropy and substratemolecule and solventmolecule interaction energies.
Reimers, J.R., Cai, Z., Kobayashi, R., Ratsep, M., Freiberg, A. & Krausz, E. 2014, 'Formation Of Water-Chlorophyll Clusters In Dilute Samples Of Chlorophyll-A In Ether At Low Temperature', Physical Chemistry Chemical Physics, vol. 16, no. 6, pp. 2323-2330.
View/Download from: UTS OPUS or Publisher's site
Reimers, J.R., McKemmish, L.K., McKenzie, R.H., Mark, A.E. & Hush, N.S. 2014, 'The revised Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not scientifically justified Comment on "Consciousness in the universe: A review of the 'Orch OR' theory" by Hameroff and Penrose', Journal of Migration and Society, vol. 11, no. 1, pp. 101-103.
View/Download from: Publisher's site
Reimers, J.R. & Krausz, E.R. 2014, 'An analytical data inversion method for magnetic circular dichroism spectra dominated by the "B-term"', Physical Chemistry Chemical Physics, vol. 16, no. 6, pp. 2315-2322.
View/Download from: UTS OPUS or Publisher's site
A simple procedure is developed enabling the analytical inversion of an (unpolarized) absorption spectrum combined with a Magnetic Circular Dichroism (MCD) spectrum to resolve two overlapping bands of orthogonal polarization. This method is appropriate when (i) the overlapping transitions are well isolated from other bands, and (ii) when their electronic spacing is large enough so that the "A-term'' and "C-term'' contributions to the MCD spectrum can be ignored and hence only the "B-term'' contribution need be considered. We apply this procedure to assign the Q-band system of chlorophylls, though similar challenges also commonly arise throughout both conventional and X-ray MCD (XMCD) spectroscopy. Analytical data inversion has not previously been possible as the inversion process is two-fold underdetermined. We show that the assumptions of isolated spectra and "B-term'' dominance yields one generally valid constraint, leaving only one quantity unspecified by the experimental data. For some systems, an approximation leading to equal but opposite sign B-term magnitudes of the two components may be reasonable, but for chlorophyllides we find this constraint to be inappropriate. Instead, we constrain a bounded variable controlling the relative absorption strengths. Derived spectral bandshapes of the individual components are shown to be insensitive to its particular value, allowing weak spectral components of one polarization overlapped by intense components of the other to be immediately exposed. This is demonstrated for the chlorophylls, molecules for which the failure to detect such weak features historically led to incorrect proposals for the Q-band assignments
Goerigk, L., Collyer, C.A. & Reimers, J.R. 2014, 'Recommending Hartree-Fock theory with London-dispersion and basis-set-superposition corrections for the optimization or quantum refinement of protein structures.', The journal of physical chemistry. B, vol. 118, no. 50, pp. 14612-14626.
View/Download from: UTS OPUS
We demonstrate the importance of properly accounting for London dispersion and basis-set-superposition error (BSSE) in quantum-chemical optimizations of protein structures, factors that are often still neglected in contemporary applications. We optimize a portion of an ensemble of conformationally flexible lysozyme structures obtained from highly accurate X-ray crystallography data that serve as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but also, for the first time, demonstrate how London dispersion and BSSE influence crystallographic R factors. Our conclusions parallel recent recommendations for the optimization of small gas-phase peptide structures made by some of the present authors: Hartree-Fock theory extended with Grimme's recent dispersion and BSSE corrections (HF-D3-gCP) is superior to popular density functional theory (DFT) approaches. Not only are statistical errors on average lower with HF-D3-gCP, but also the convergence behavior is much better. In particular, we show that the BP86/6-31G* approach should not be relied upon as a black-box method, despite its widespread use, as its success is based on an unpredictable cancellation of errors. Using HF-D3-gCP is technically straightforward, and we therefore encourage users of quantum-chemical methods to adopt this approach in future applications.
Yan, J., Ouyang, R., Jensen, P.S., Ascic, E., Tanner, D., Mao, B., Zhang, J., Tang, C., Hush, N.S., Ulstrup, J. & Reimers, J.R. 2014, 'Controlling the stereochemistry and regularity of butanethiol self-assembled monolayers on au(111).', Journal of the American Chemical Society, vol. 136, no. 49, pp. 17087-17094.
View/Download from: UTS OPUS
The rich stereochemistry of the self-assembled monolayers (SAMs) of four butanethiols on Au(111) is described, the SAMs containing up to 12 individual C, S, or Au chiral centers per surface unit cell. This is facilitated by synthesis of enantiomerically pure 2-butanethiol (the smallest unsubstituted chiral alkanethiol), followed by in situ scanning tunneling microscopy (STM) imaging combined with density functional theory molecular dynamics STM image simulations. Even though butanethiol SAMs manifest strong headgroup interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the headgroup itself, whether it takes on the adatom-bound motif RS(*)Au(0)S(*)R or involves direct binding of RS(*) to face-centered-cubic or hexagonal-close-packed sites. Binding as RS(*) produces large, organizationally chiral domains even when R is achiral, while adatom binding leads to rectangular plane groups that suppress long-range expression of chirality. Binding as RS(*) also inhibits the pitting intrinsically associated with adatom binding, desirably producing more regularly structured SAMs.
Coenen, M., Den Boer, D., Van Den Bruele, F., Habets, T., Timmers, K., Van Der Maas, M., Khoury, T., Panduwinata, D., Crossley, M., Reimers, J.R., Van Enckevort, W., Hendriksen, B., Elemans, J. & Speller, S. 2013, 'Polymorphism In Porphyrin Monolayers: The Relation Between Adsorption Configuration And Molecular Conformation', Physical Chemistry Chemical Physics, vol. 15, no. 30, pp. 12451-12458.
View/Download from: UTS OPUS or Publisher's site
Self-assembled monolayers of meso-5,10,15,20-tetrakis(undecyl)porphyrin copper(II) on a graphite/1-octanoic acid interface have been studied by Scanning Tunnelling Microscopy. Four distinct polymorphs were observed, varying in their unit cell size. Arrays of unit cells of the various polymorphs seamlessly connect to each other via shared unit cell vectors. The monolayers are not commensurate, but coincident with the underlying graphite substrate. The seamless transition between the polymorphs is proposed to be the result of an adaptation of the molecular conformations in the polymorphs and at the boundaries, which is enabled by the conformational freedom of the alkyl tails of these molecules.
Goerigk, L. & Reimers, J.R. 2013, 'Finding efficient Methods For The Quantum Chemical Treatment Of Protein Structures: The Effects Of London-Dispersion And Basis-Set Incompleteness On Peptide And Water-Cluster Geometries', Journal Of Chemical Theory And Computation, vol. 9, no. 7, pp. 3240-3251.
View/Download from: UTS OPUS or Publisher's site
We demonstrate how quantum chemical Hartree-Fock (HF) or density functional theory (DFT) optimizations with small basis sets of peptide and water cluster structures are decisively improved if London-dispersion effects, the basis-set-superposition error (BSSE), and other basis-set incompleteness errors are addressed. We concentrate on three empirical corrections to these problems advanced by Grimme and co-workers that lead to computational strategies that are both accurate and efficient. Our analysis encompasses a reoptimized version of Hobzas P26 set of tripeptide structures, a new test set of conformers of cysteine dimers, and isomers of the water hexamer. These systems reflect features commonly found in protein crystal structures. In all cases, we recommend Grimmes DFT-D3 correction for London-dispersion. We recommend usage of large basis sets such as cc-pVTZ whenever possible to reduce any BSSE effects and, if this is not possible, to use Grimmes gCP correction to account for BSSE when small basis sets are used. We demonstrate that S-S and C-S bond lengths are very prone to basis-set incompleteness and that polarization functions should always be used on S atoms. At the double-zeta level, the PW6B95-D3-gCP DFT method combined with the SVP and 6-31G* basis sets yields accurate results. Alternatively, the HF-D3-gCP/SV method is recommended, with inclusion of polarization functions for S atoms only. Minimal basis sets offer an intriguing route to highly efficient calculations, but due to significant basis-set incompleteness effects, calculated bond lengths are seriously overestimated, making applications to large proteins very difficult, but we show that Grimmes newest HF-3c correction overcomes this problem and so makes this computational strategy very attractive. Our results provide a useful guideline for future applications to the optimization, quantum refinement, and dynamics of large proteins.
Reimers, J.R., Cai, Z., Kobayashi, R., Ratsep, M., Freiberg, A. & Krausz, E. 2013, 'Assignment Of The Q-Bands Of The Chlorophylls: Coherence Loss Via Q(X) - Q(Y) Mixing', Scientific Report, vol. 3, pp. 1-8.
View/Download from: UTS OPUS or Publisher's site
We provide a new and definitive spectral assignment for the absorption, emission, high-resolution fluorescence excitation, linear dichroism, and/or magnetic circular dichroism spectra of 32 chlorophyllides in various environments. This encompases all data used to justify previous assignments and provides a simple interpretation of unexplained complex decoherence phenomena associated with Q(x)-> Q(y) relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Q(x) (S-2) and Q(y) (S-1), strong vibronic coupling inseparably mixes these states in chlorophyll-a. This spreads x-polarized absorption intensity over the entire Q-band system to influence all exciton-transport, relaxation and coherence properties of chlorophyll-based photosystems. The fraction of the total absorption intensity attributed to Q(x) ranges between 7% and 33%, depending on chlorophyllide and coordination, and is between 10% and 25% for chlorophyll-a. CAM-B3LYP density-functional-theory calculations of the band origins, relative intensities, vibrational Huang-Rhys factors, and vibronic coupling strengths fully support this new assignment.
Lambropoulos, N., Reimers, J.R., Crossley, M., Hush, N. & Silverbrook, K. 2013, 'A Multiscale Simulation Technique For Molecular Electronics: Design Of A Directed Self-Assembled Molecular N-Bit Shift Register Memory Device', Nanotechnology, vol. 24, no. 50.
View/Download from: UTS OPUS or Publisher's site
A general method useful in molecular electronics design is developed that integrates modelling on the nano-scale (using quantum-chemical software) and on the micro-scale (using finite-element methods). It is applied to the design of an n-bit shift register memory that could conceivably be built using accessible technologies. To achieve this, the entire complex structure of the device would be built to atomic precision using feedback-controlled lithography to provide atomic-level control of silicon devices, controlled wet-chemical synthesis of molecular insulating pillars above the silicon, and controlled wet-chemical self-assembly of modular molecular devices to these pillars that connect to external metal electrodes (leads). The shift register consists of n connected cells that read data from an input electrode, pass it sequentially between the cells under the control of two external clock electrodes, and deliver it finally to an output device. The proposed cells are trimeric oligoporphyrin units whose internal states are manipulated to provide functionality, covalently connected to other cells via dipeptide linkages. Signals from the clock electrodes are conveyed by oligoporphyrin molecular wires, and mu-oxo porphyrin insulating columns are used as the supporting pillars. The developed multiscale modelling technique is applied to determine the characteristics of this molecular device, with in particular utilization of the inverted region for molecular electron-transfer processes shown to facilitate latching and control using exceptionally low energy costs per logic operation compared to standard CMOS shift register technology.
Lee, S., Larsen, A., Ohkubo, K., Cai, Z., Reimers, J.R., Fukuzumi, S. & Crossley, M. 2012, 'Long-Lived Long-Distance Photochemically Induced Spin-Polarized Charge Separation In Beta,Beta '-Pyrrolic Fused Ferrocene-Porphyrin-Fullerene Systems', Chemical Science, vol. 3, no. 1, pp. 257-269.
View/Download from: UTS OPUS or Publisher's site
The exceptionally long lived charge separation previously observed in a b,b'-pyrrolic-fused ferrocene-porphyrin-fullerene triad (lifetime 630 mu s) and related porphyrin-fullerene dyad (lifetime 260 mu s) is attributed to the production of triplet charge-separated states. Such molecular excited-state spin polarization maintained over distances of up to 23 angstrom is unprecedented and offers many technological applications. Electronic absorption and emission spectra, femtosecond and nanosecond time-resolved transient absorption spectra, and cyclic voltammograms of two triads and four dyads are measured and analyzed to yield rate constants, donor-acceptor couplings, free-energy changes, and reorganization energies for charge-separation and charge-recombination processes. Production of long-lived intramolecular triplet states is confirmed by electron-paramagnetic resonance spectra at 77-223 K, as is retention of spin polarization in p-conjugated ferrocenium ions. The observed rate constants were either first predicted (singlet manifold) or later confirmed (triplet manifold) by a priori semiclassical kinetics calculations for all conceivable photochemical processes, parameterized using density-functional theory and complete-active-space self-consistent-field calculations. Identified are both a ps-timescale process attributed to singlet recombination and a mu s-timescale process attributed to triplet recombination.
Falklof, O., Collyer, C. & Reimers, J.R. 2012, 'Toward Ab Initio Refinement Of Protein X-Ray Crystal Structures: Interpreting And Correlating Structural Fluctuations', Theoretical Chemistry Accounts, vol. 131, no. 1.
View/Download from: UTS OPUS or Publisher's site
Mckemmish, L., Kedziora, D., White, G., Hush, N. & Reimers, J.R. 2012, 'Frequency-Based Quantum Computers From A Chemist'S Perspective', Australian Journal Of Chemistry, vol. 65, no. 5, pp. 512-519.
View/Download from: UTS OPUS or Publisher's site
Quantum computer elements are often designed and tested using molecular or nanoscopic components that form registers of qubits in which memory is stored and information processed. Often such registers are probed and manipulated using frequency-based techniques such as nuclear-magnetic resonance spectroscopy. A major challenge is to design molecules to act as these registers. We provide a basis for rational molecular design through consideration of the generic spectroscopic properties required for quantum computing, bypassing the need for intricate knowledge of the way these molecules are used spectroscopically. Designs in which two-qubit gate times scale similarly to those for one-qubit gates are presented. The specified spectroscopic requirements are largely independent of the type of spectroscopy used (e. g. magnetic resonance or vibrational) and are often independent of technical details of the application (e.g. broadband or high-resolution spectroscopy). This should allow the design of much larger quantum registers than have currently been demonstrated.
Reimers, J.R. & Cai, Z. 2012, 'Hydrogen Bonding And Reactivity Of Water To Azines In Their S-1 (N,Pi*) Electronic Excited States In The Gas Phase And In Solution', Physical Chemistry Chemical Physics, vol. 14, no. 25, pp. 8791-8802.
View/Download from: UTS OPUS or Publisher's site
Yin, S., Li, L., Yang, Y. & Reimers, J.R. 2012, 'Challenges For The Accurate Simulation Of Anisotropic Charge Mobilities Through Organic Molecular Crystals: The Beta Phase Of Mer-Tris(8-Hydroxyquinolinato)Aluminum(Iii) (Alq3) Crystal', Journal Of Physical Chemistry C, vol. 116, no. 28, pp. 14826-14836.
View/Download from: UTS OPUS or Publisher's site
Trevitt, A.J., Reimers, J.R., Clarke, R.J. & Vandenberg, J.I. 2012, 'BIOPHYSCHEM2011: A Joint Meeting of the Australian Society for Biophysics and the RACI Physical Chemistry Division Foreword', AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 65, no. 5, pp. 439-441.
View/Download from: Publisher's site
Ratsep, M., Cai, Z., Reimers, J.R. & Freiberg, A. 2011, 'Demonstration And Interpretation Of Significant Asymmetry In The Low-Resolution And High-Resolution Q(Y) Fluorescence And Absorption Spectra Of Bacteriochlorophyll A', Journal of Chemical Physics, vol. 134, no. 2.
View/Download from: UTS OPUS or Publisher's site
Low- and high-resolution absorption and fluorescence emission Qy spectra of bacteriochlorophyll a (BChl a) were recorded, along with homogeneous band line shapes, revealing significant asymmetry between the absorption and emission profiles that are interpreted using a priori spectral calculations. The spectra were recorded in a range of organic solvents facilitating both penta- and hexa-coordination of Mg at ambient and cryogenic temperatures. Detailed vibrational structure in the ground electronic state, virtually independent of Mg coordination, was revealed at 4.5 K by a hole-burning fluorescence line-narrowing technique, complementing the high-resolution spectrum of the excited state measured previously by hole burning to provide the first complete description of the Qy absorption and fluorescence spectra of BChl a. Spectral asymmetry persists from 4.5 to 298 K. Time-dependent density-functional theory calculations of the gas-phase absorption and emission spectra obtained using the CAM-B3LYP density functional, curvilinear coordinates, and stretch-bend-torsion scaling factors fitted to data for free-base porphyrin quantitatively predict the observed frequencies of the most-significant vibrational modes as well as the observed absorption/emission asymmetry. Most other semi-empirical, density-functional, and ab initio computational methods severely overestimate the electron-vibrational coupling and its asymmetry. It is shown that the asymmetry arises primarily through Duschinsky rotation.
Chin, Y., Panduwinata, D., Sintic, M., Sum, T., Hush, N., Crossley, M. & Reimers, J.R. 2011, 'Atomic-Resolution Kinked Structure Of An Alkylporphyrin On Highly Ordered Pyrolytic Graphite', Journal of Physical Chemistry Letters, vol. 2, no. 2, pp. 62-66.
View/Download from: UTS OPUS or Publisher's site
The atomic structures of the chains of an alkyl porphyrin (5, 10, 15, 20- tetranonadecylporphyrin) self-assembled monolayer (SAM) at the solid/liquid interface of highly ordered pyrolytic graphite (HOPG) and 1-phenyloctane is resolved using calibrated scanning tunneling microscopy (STM), density functional theory (DFT) image simulations, and ONIOM-based geometry optimizations. While atomic structures are often readily determined for prophyrin SAMs, the determination of the structure of alkyl-chain connections has not previously been possible A graphical calibration procedure is introduced, allowing accurate observation of SAM lattice parameters, and of the many possible atomic structure modeled, only the lowest-energy structure obtained was found to predict the observed lattice parameters and image topography. Hydrogen atoms are shown to provide the conduit for the tunneling current through the alkyl chains.
Wang, Y., Chi, Q., Hush, N., Reimers, J.R., Zhang, J. & Ulstrup, J. 2011, 'Gold Mining By Alkanethiol Radicals: Vacancies And Pits In The Self-Assembled Monolayers Of 1-Propanethiol And 1-Butanethiol On Au(111)', Journal Of Physical Chemistry C, vol. 115, no. 21, pp. 10630-10639.
View/Download from: UTS OPUS or Publisher's site
Thomas, G., Hsieh, Y., Chun, C., Cai, Z., Reimers, J.R. & Payne, R. 2011, 'Peptide Ligations Accelerated By N-Terminal Aspartate And Glutamate Residues', Organic Letters, vol. 13, no. 18, pp. 4770-4773.
View/Download from: UTS OPUS or Publisher's site
A novel application of intramolecular base catalysis confers enhanced reaction rates for aminolysis ligations between peptide thioesters and peptides bearing N-terminal aspartate or glutamate residues. The broad scope of this process and its application in the total synthesis of the diabetes drug exenatide is demonstrated.
Wang, Y., Chi, Q., Zhang, J., Hush, N., Reimers, J.R. & Ulstrup, J. 2011, 'Chain-Branching Control Of The Atomic Structure Of Alkanethiol-Based Gold-Sulfur Interfaces', Journal Of The American Chemical Society, vol. 133, no. 38, pp. 14856-14859.
View/Download from: UTS OPUS or Publisher's site
Density functional theory structure calculations at 0 K and simulations at 300 K of observed high-resolution in situ scanning tunneling microscopy (STM) images reveal three different atomic-interface structures for the self-assembled monolayers (SAMs) of three isomeric butanethiols on Au(111): direct binding to the Au (111) surface without pitting, binding to adatoms above a regular surface with extensive pitting, and binding to adatoms with local surface vacancies and some pitting. Thermal motions are shown to produce some observed STM features, with a very tight energy balance controlling the observed structures. Variation of the degree of substitution on the a carbon is found to significantly change the relative energies for interaction of the different types of adatom structures with the surface, while the nature of the surface cell, controlled primarily by inter-adsorbate steric interactions, controls substrate reorganization energies and adsorbate distortion energies. Most significantly, by manipulating these features, chemical control of the adsorbate can produce stable interfaces with surface pitting eliminated, providing new perspectives for technological applications of SAMs.
Wohlthat, S., Solomon, G., Hush, N. & Reimers, J.R. 2011, 'Interference-Induced Electron- And Hole-Conduction Asymmetry', Theoretical Chemistry Accounts, vol. 130, no. 4-Jun, pp. 815-828.
View/Download from: UTS OPUS or Publisher's site
Principles established by Shephard and Paddon-Row for optimizing and controlling intramolecular electron transport through the modulation of interfering pathways are employed to design new molecules for steady-state conduction experiments aimed at manifesting electron-hole conduction asymmetry in a unique way. First, a review of the basic principles is presented through application to a pertinent model system in which a molecule containing donor and acceptor terminal linking groups with an internal multiple-pathway bridge is used to span two metal electrodes. Different interference patterns are produced depending on whether the through-molecule coupling pathways are symmetric or antisymmetric with respect to a topological bisecting plane, giving rise to asymmetric electron and hole conductances at the tight-binding (Huckel) level; this process is also described from a complementary molecular-orbital viewpoint. Subsequently, a new molecular system based on organic polyradicals is designed to allow such asymmetry to be realized in single-molecule conduction experiments. These polyradicals are analyzed using analogous simple models, density-functional theory (DFT) calculations of steady-state transmission, and intermediate neglect of differential overlap (INDO) calculations of intramolecular connectivity, verifying that polyradicals at low temperatures should show experimentally measureable electron-hole conduction asymmetry. A key feature of this system is that the polyradicals form a narrow partially occupied band of orbitals that lie within and well separated from the HOMO and LUMO orbitals of the surrounding molecular scaffold, allowing for holes and electrons to be transported through the same molecular band.
Mckemmish, L., Mckenzie, R., Hush, N. & Reimers, J.R. 2011, 'Quantum Entanglement Between Electronic And Vibrational Degrees Of Freedom In Molecules', Journal of Chemical Physics, vol. 135, no. 24.
View/Download from: UTS OPUS or Publisher's site
We consider the quantum entanglement of the electronic and vibrational degrees of freedom in molecules with tendencies towards double welled potentials. In these bipartite systems, the von Neumann entropy of the reduced density matrix is used to quantify the electron-vibration entanglement for the lowest two vibronic wavefunctions obtained from a model Hamiltonian based on coupled harmonic diabatic potential-energy surfaces. Significant entanglement is found only in the region in which the ground vibronic state contains a density profile that is bimodal (i.e., contains two separate local maxima). However, in this region two distinct types of density and entanglement profiles are found: one type arises purely from the degeneracy of energy levels in the two potential wells and is destroyed by slight asymmetry, while the other arises through strong interactions between the diabatic levels of each well and is relatively insensitive to asymmetry. These two distinct types are termed fragile degeneracy-induced entanglement and persistent entanglement, respectively. Six classic molecular systems describable by two diabatic states are considered: ammonia, benzene, BNB, pyridine excited triplet states, the Creutz-Taube ion, and the radical cation of the "special pair" of chlorophylls involved in photosynthesis. These chemically diverse systems are all treated using the same general formalism and the nature of the entanglement that they embody is elucidated.
Heine, K.B., Clegg, J.K., Heine, A., Gloe, K., Gloe, K., Henle, T., Bernhard, G., Cai, Z.-.L., Reimers, J.R., Lindoy, L.F., Lach, J. & Kersting, B. 2011, 'Complexation, Computational, Magnetic, and Structural Studies of the Maillard Reaction Product Isomaltol Including Investigation of an Uncommon pi Interaction with Copper(II)', INORGANIC CHEMISTRY, vol. 50, no. 4, pp. 1498-1505.
View/Download from: UTS OPUS or Publisher's site
Reimers, J.R., Wang, Y., Cankurtaran, B.O. & Ford, M.J. 2010, 'Chemical Analysis Of The Superatom Model For Sulfur-Stabilized Gold Nanoparticles', Journal of the American Chemical Society, vol. 132, no. 24, pp. 8378-8384.
View/Download from: UTS OPUS or Publisher's site
The superatom model for nanoparticle structure is shown to be inadequate for the prediction of the thermodynamic stability of gold nanoparticles. The observed large HOMO-LUMO gaps for stable nanoparticles predicted by this model are, for sulfur-stabilize
Wohlthat, S., Reimers, J.R. & Hush, N. 2010, 'Accurate And Computationally Efficient Third-Nearest-Neighbor Tight-Binding Model For Large Graphene Fragments', Physical Review B, vol. 81, no. 19, p. 195125.
View/Download from: UTS OPUS or Publisher's site
Owing to the large sizes involved, most calculations of the electronic properties of graphene and its fragments involve empirical tight-binding models restricted to nearest-neighbor interactions only. Such approaches fail to predict key electronic and magnetic properties, however, and rely on assumed geometries. While alternative approaches based on density-functional theory are much more successful in predicting properties, they are often computationally prohibitive to apply. We introduce a simple third-nearest-neighbor pi-only tight-binding approach that maintains the computational efficiency of the empirical method while achieving the accuracy of the density-functional methods to which it is parametrized. It yields both nuclear geometries and electronic structures of graphene fragments, providing an efficient and accurate replacement for traditional tight-binding models of graphene.
Politzer, P., Reimers, J.R., Murray, J. & Toro-labbe, A. 2010, 'Reaction Force And Its Link To Diabatic Analysis: A Unifying Approach To Analyzing Chemical Reactions', Journal of Physical Chemistry Letters, vol. 1, no. 19, pp. 2858-2862.
View/Download from: UTS OPUS or Publisher's site
The reaction force F(R) and the reaction force constant kappa(R) provide a rigorously based approach to characterizing a chemical process. The energies associated with its different stages are presented and discussed for a number of examples. Analysis of these suggests an alternative modified expression for the Hammond-Leffler postulate. We show that diabatic analysis leads to a description of the process that is qualitatively very similar to that coming from F(R) and kappa(R), quantitatively so for proton-transfer reactions. Reaction force analysis provides a unifying framework that can encompass a variety of independent concepts relating to chemical processes.
Zhu, B., Zhang, Q., Zhang, Y., Tao, Z., Clegg, J., Reimers, J.R., Lindoy, L. & Wei, G. 2009, 'Polymeric Di- And Discrete Trinuclear Silver(I) Assemblies Incorporating Gamma-Carbon Bonded, Neutral Acetylacetone-Imine Motifs Assembled From Racemic And Diastereopure N,N '-Bis(Acetylacetone)Cyclohexanediimine Units', Dalton Transactions, vol. -, no. 25, pp. 4896-4900.
View/Download from: UTS OPUS or Publisher's site
Diastereopure (1R,2R)-N,N'-bis(acetylacetone)cyclohexanedi-imine L(1) and its corresponding (1R,2R)L(1)/(1S,2S)L(2) enantiomeric mixture react with AgNO(3) to yield the unusual coordination polymer [Ag(2)(L(1))(L(2))(NO(3))(2)](n) (1) and the unique trimetallic discrete species {[Ag(3)(L(1))(3)(mu(3)-O,O,O-NO(3))(H(2)O)(3)](2)(NO(3))}(NO(3))(3)center dot 8.5H(2)O (2) which incorporates a symmetrical mu(3)-bridging nitrato group that gives rise to a C(3)-symmetric triskelion motif; both species also feature gamma-carbon eta(1) aryl-like coordination of neutral bridging acetylacetone-imine units to the respective Ag(I) centres.
Martelli, C., Canning, J., Reimers, J.R., Sintic, M., Stocks, D., Khoury, T. & Crossley, M. 2009, 'Evanescent-Field Spectroscopy Using Structured Optical Fibers: Detection Of Charge-Transfer At The Porphyrin-Silica Interface', Journal of the American Chemical Society, vol. 131, no. 8, pp. 2925-2933.
View/Download from: UTS OPUS or Publisher's site
The fabrication of porphyrin thin films derived from dichloro[5,10,15,20-tetra(heptyl)porphyrinato]tin(IV) [Cl-Sn(THP)-Cl] in the holes of photonic crystal fibers over 90 cm in length is described. Evanescent field spectroscopy (EFS) is used to investigate the interfacial properties of the films, with the high surface optical intensity and the long path length combining to produce significant absorption. By comparison with results obtained for similar films formed from Cl-Sn(THP)-Cl inside fused-silica cuvettes and on glass slides, the film is shown to be chemisorbed as a surface Si-O-Sn(THP)-X (X = Cl or OH) species. In addition to the usual porphyrin Q and Soret bands, new absorptions in the in-fiber films are observed by EFS at 445 nm and between 660-930 nm. The 660-930 nm band is interpreted as a porphyrin to silicon charge-transfer transition and postulated to arise following chemisorption at mechanical-strain induced defect sites on the silica surface. Such defect sites are caused by the optical fiber production process and are less prevalent on other glass surfaces. EFS within optical fibers therefore offers new ways for understanding interface phenomena such as surface adsorbates on glass. Such understanding will benefit all devices that exploit interface phenomena, both in optical fibers and other integrated waveguide forms. They may be directly exploited to create ultrasensitive molecular detectors and could yield novel photonic devices.
Reimers, J.R., Mckemmish, L., Mckenzie, R., Mark, A. & Hush, N. 2009, 'Weak, Strong, And Coherent Regimes Of Frohlich Condensation And Their Applications To Terahertz Medicine And Quantum Consciousness', Proceedings of The National Academy of Sciences of the United States of America, vol. 106, no. 11, pp. 4219-4224.
View/Download from: UTS OPUS or Publisher's site
In 1968, Frohlich showed that a driven set of oscillators can condense with nearly all of the supplied energy activating the vibrational mode of lowest frequency. This is a remarkable property usually compared with Bose-Einstein condensation, superconductivity, lasing, and other unique phenomena involving macroscopic quantum coherence. However, despite intense research, no unambiguous example has been documented. We determine the most likely experimental signatures of Frohlich condensation and show that they are significant features remote from the extraordinary properties normally envisaged. Frohlich condensates are classified into 3 types: weak condensates in which profound effects on chemical kinetics are possible, strong condensates in which an extremely large amount of energy is channeled into 1 vibrational mode, and coherent condensates in which this energy is placed in a single quantum state. Coherent condensates are shown to involve extremely large energies, to not be produced by the Wu-Austin dynamical Hamiltonian that provides the simplest depiction of Frohlich condensates formed using mechanically supplied energy, and to be extremely fragile. They are inaccessible in a biological environment. Hence the Penrose-Hameroff orchestrated objective-reduction model and related theories for cognitive function that embody coherent Frohlich condensation as an essential element are untenable. Weak condensates, however, may have profound effects on chemical and enzyme kinetics, and may be produced from biochemical energy or from radio frequency, microwave, or terahertz radiation. Pokorny's observed 8.085-MHz microtubulin resonance is identified as a possible candidate, with microwave reactors (green chemistry) and terahertz medicine appearing as other feasible sources.
Mckemmish, L., Reimers, J.R., Mckenzie, R., Mark, A. & Hush, N. 2009, 'Penrose-Hameroff Orchestrated Objective-Reduction Proposal For Human Consciousness Is Not Biologically Feasible', Physical Review E, vol. 80, no. 2.
View/Download from: UTS OPUS or Publisher's site
Penrose and Hameroff have argued that the conventional models of a brain function based on neural networks alone cannot account for human consciousness, claiming that quantum-computation elements are also required. Specifically, in their Orchestrated Objective Reduction (Orch OR) model [R. Penrose and S. R. Hameroff, J. Conscious. Stud. 2, 99 (1995)], it is postulated that microtubules act as quantum processing units, with individual tubulin dimers forming the computational elements. This model requires that the tubulin is able to switch between alternative conformational states in a coherent manner, and that this process be rapid on the physiological time scale. Here, the biological feasibility of the Orch OR proposal is examined in light of recent experimental studies on microtubule assembly and dynamics. It is shown that the tubulins do not possess essential properties required for the Orch OR proposal, as originally proposed, to hold. Further, we consider also recent progress in the understanding of the long-lived coherent motions in biological systems, a feature critical to Orch OR, and show that no reformation of the proposal based on known physical paradigms could lead to quantum computing within microtubules. Hence, the Orch OR model is not a feasible explanation of the origin of consciousness.
Saraireh, S., Smith, P., King, B., Reimers, J.R., Wallace, B. & Crossley, M. 2009, 'Norbornadiene-Based Molecules For Functionalizing The Si(001) Surface', Journal of Physical Chemistry C, vol. 113, no. 36, pp. 16094-16103.
View/Download from: UTS OPUS or Publisher's site
One of the fundamental requirements in the development of silicon-based molecular electronic devices is the ability to attach organic molecules to silicon surfaces to form well-defined structures that are stable and possess specific characteristics. Previous work has shown that, although norbornadiene (NBE) forms very stable structures on the Si(001) surface with its apex CH(2) group pointing outward from the surface, these structures cannot be resolved in scanning tunneling microscopy. In this paper, we report the results of density functional theory calculations of the interaction with the Si(001) surface of 7-trifluoroacetoxy-norbornadiene (7-TFA-NBE) in which a hydrogen atom of the apex CH(2) group is substituted by the trifluoroacetoxy OC(O)CF(3) group. This molecule is shown to form very stable structures with the trifluoroacetoxy group sitting well above the surface. Moreover, in contrast to NBE, we find that the different 7-TFA-NBE chemisorption structures should be distinguishable in high-resolution scanning tunneling microscopy experiments. This raises the exciting possibility of employing norbornadiene-based molecules with appropriately chosen functional groups to create molecular structures on Si(001) that are stable and experimentally distinguishable and yield the requisite atomic and electronic properties.
Wang, Y., Chi, Q., Hush, N., Reimers, J.R., Zhang, J. & Ulstrup, J. 2009, 'Scanning Tunneling Microscopic Observation Of Adatom-Mediated Motifs On Gold-Thiol Self-Assembled Monolayers At High Coverage', Journal Of Physical Chemistry C, vol. 113, no. 45, pp. 19601-19608.
View/Download from: UTS OPUS or Publisher's site
Self-assembled monolayers (SAMs) formed by chemisorption of a branched-chain alkanethiol, 2-methyl-1-propanethiol, on Au(111) surfaces were Studied by in situ scanning tunneling microscopy (STM) under electrochemical potential control and analyzed using extensive density functional theory (DFF) calculations. The SAM forms in the unusual (8 x root 3)-4 superlattice, producing a very complex STM image. Seventy possible structures were considered for the SAM, with the calculated lowest-energy configuration in fact predicting the details of the unusual observed STM image. The most stable structure involves two R-S-Au-S-R adatom-mediated motifs per surface cell, with steric-induced variations in the adsorbate alignment inducing the observed STM image contrasts. Observed pits covering 5.6 +/- 0.5% of the SAM surface are consistent with this structure. These results provide the missing link from the structural motifs observed on Surfaces at low coverage and on gold nanoparticles to the observed spectroscopic properties of high-coverage SAMs formed by methanethiol. However, the significant role attributed to intermolecular steric packing effects suggests a lack of generality for the adatom-mediated motif at high coverage.
Wohlthat, S., Kirchner, T. & Reimers, J.R. 2009, 'N-Silylamine Junctions For Molecular Wires To Gold: The Effect Of Binding Atom Hybridization On The Electronic Transmission', Journal Of Physical Chemistry C, vol. 113, no. 47, pp. 20458-20462.
View/Download from: UTS OPUS or Publisher's site
In molecular conduction studies, amine groups are often used as linkers between molecules and gold surfaces. We demonstrate using density functional theory (DFT) that N-silyl substitution of 1,4-benzenediamine (BDA) produces a highly polarizable junction with a conductance and electrostatic profile that depends strongly on the local hybridization. In BDA itself, a forced change in hybridization from sp(3) to sp(2) is predicted to increase the conductivity by an order of magnitude. N-silyl Substitution is shown to make this effect accessible while maintaining a 5-fold conductance ratio and Sufficient binding strength to allow junctions to spontaneously assemble. Hence N-silylamines are predicted to form useful, externally controllable molecular junctions.
McKemmish, L.K., Reimers, J.R., McKenzie, R.H., Mark, A.E. & Hush, N.S. 2009, 'Penrose-Hameroff orchestrated objective-reduction proposal for human consciousness is not biologically feasible.', Physical review. E, Statistical, nonlinear, and soft matter physics, vol. 80, no. 2 Pt 1, p. 021912.
View/Download from: Publisher's site
Penrose and Hameroff have argued that the conventional models of a brain function based on neural networks alone cannot account for human consciousness, claiming that quantum-computation elements are also required. Specifically, in their Orchestrated Objective Reduction (Orch OR) model [R. Penrose and S. R. Hameroff, J. Conscious. Stud. 2, 99 (1995)], it is postulated that microtubules act as quantum processing units, with individual tubulin dimers forming the computational elements. This model requires that the tubulin is able to switch between alternative conformational states in a coherent manner, and that this process be rapid on the physiological time scale. Here, the biological feasibility of the Orch OR proposal is examined in light of recent experimental studies on microtubule assembly and dynamics. It is shown that the tubulins do not possess essential properties required for the Orch OR proposal, as originally proposed, to hold. Further, we consider also recent progress in the understanding of the long-lived coherent motions in biological systems, a feature critical to Orch OR, and show that no reformation of the proposal based on known physical paradigms could lead to quantum computing within microtubules. Hence, the Orch OR model is not a feasible explanation of the origin of consciousness.
Reimers, J.R., Lee, S.H., Larsen, A.G., Kotani, H., Ohkubo, K., Fukuzumi, S. & Crossley, M.J. 2009, 'The nature of long-lived photo-induced charge separation in ferrocene-porphyrin-fullerene molecules', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 238.
Crossley, M., Sheehan, C., Khoury, T., Reimers, J.R. & Sintic, P. 2008, 'Construction Of Building Blocks For Extended Porphyrin Arrays By Nitration Of Porphyrin-2,3-Diones And Quinoxalino[2,3-B]Porphyrins', New Journal of Chemistry, vol. 32, no. 2, pp. 340-352.
View/Download from: UTS OPUS or Publisher's site
Nitration of metal(II) porphyrin-2,3-diones 3 - 5 and quinoxalino[2,3-b] porphyrins 13 - 15 with nitrogen dioxide gave a mixture of beta-pyrrolic functionalised nitro-porphyrin isomers in relative abundance of 7-nitro-> 12- nitro-> 8-nitro. The large selectivity for reaction at the 7-position over the adjacent 8-position (> 5 to 1 in the diones 3 - 5 and about 3 to 1 in the quinoxalinoporphyrins 13 - 15) is especially striking. This selectivity results mainly from electronic effects and is consistent with a mechanism involving a porphyrin pi-cation radical intermediate. A key step incorporated into the isomer separation sequence was to make use of the different chromatographic polarity of metalated compounds compared to unmetalated compounds coupled with the observation that introduction of a nitro group to the 7-position of free-base porphyrindione greatly increases its rate of metalation while introduction of the nitro group at the 12-position greatly decreases its rate of metalation, relative to the unsubstituted parent. Thus demetalation of zinc(II) nitro-porphyrin-dione isomers, which are difficult to separate, allows for highly selective remetalation of the 7-isomer and its very easy separation from the unmetalated 12-nitro-porphyrin-dione. These nitrated compounds are useful building blocks for more elaborate systems.
Sintic, P., E, W., Ou, Z., Shao, J., Mcdonald, J., Cai, Z., Kadish, K., Crossley, M. & Reimers, J.R. 2008, 'Control Of The Site And Potential Of Reduction And Oxidation Processes In Pi-Expanded Quinoxalinoporphyrins', Physical Chemistry Chemical Physics, vol. 10, no. 4, pp. 515-527.
View/Download from: UTS OPUS or Publisher's site
Quinoxalino[2,3-b']porphyrins are pi-expanded porphyrins, having a quinoxaline fused to a beta,beta'-pyrrolic position of the porphyrin. They are used as components in systems proposed as 'molecular wires'. Knowledge of their redox properties is of value in the design of electron- or hole-conduction systems. In particular, the location of the charge density in the radical anions of quinoxalinoporphyrins can be modulated by peripheral functionalization. New theoretical treatments of electrochemical potentials are developed that identify the site of reduction in both the anions and the dianions of 33 quinoxalinoporphyrins. These molecules include free-base and metallated macrocycles substituted on the quinoxaline with electron- withdrawing groups ( NO(2), Cl, Br) and/or electron-donating groups ( NH(2), OCH(3)). Spectroelectrochemistry, density-functional theory calculations, and substituent-parameter models are used to verify the analysis. Five distinct patterns are observed for the locations of the first and second reductions; some of these patterns involve delocalized charges. Nitroquinoxalinoporphyrins with the nitro groups at the 5- and 6-quinoxaline positions are found to have quite different properties owing to distortions caused by peri interactions that force the nitro group of the 5- nitro regioisomer out of conjugation. Charge localization on the nitroquinoxaline fragment is found for some molecules, and this is attributed to ion-pairing with the 0.1 M tetrabutylammonium perchlorate electrolyte used, leading to the verified prediction that electron- paramagnetic resonance spectra of these molecules taken without the electrolyte yield delocalized anions. These properties enable the control of conduction through molecular wires synthesised from quinoxalinoporphyrins.
Reimers, J.R., Wallace, B. & Hush, N. 2008, 'Towards A Comprehensive Model For The Electronic And Vibrational Structure Of The Creutz-Taube Ion', Royal Society of London. Philosophical Transactions A. Mathematical, Physical and Engineering Sciences, vol. 366, no. 1862, pp. 15-31.
View/Download from: UTS OPUS or Publisher's site
Since the synthesis of the Creutz-Taube ion, the nature of its charge localization has been of immense scientific interest, this molecule providing a model system for the understanding of the operation of biological photosynthetic and electron-transfer processes. However, recent work has shown that its nature remains an open question. Many systems of this type, including photosynthetic reaction centres, are of current research interest, and thereby the Creutz-Taube ion provides an important chemical paradigm: the key point of interest is the details of how such molecules behave. We lay the groundwork for the construction of a, comprehensive model for its chemical and spectroscopic properties. Advances are described in some of the required areas including: simulation of electronic absorption spectra; quantitative depiction of the large interaction of the ion's electronic description with solvent motions; and the physics of Ru-NH3 spectator-mode vibrations. We show that details of the solvent electron-phonon coupling are critical in the interpretation of the spectator-mode vibrations, as these strongly mix with solvent motions when 0.75 < 2J/lambda < 1. In this regime, a, double-well potential exists which does not support localized zero-point vibration, and many observed properties of the Creutz-Taube ion are shown to be consistent with the hypothesis that the ion has this character.
Wenbo, E., Kadish, K., Sintic, P., Khoury, T., Govenlock, L., Ou, Z., Shao, J., Ohkubo, K., Reimers, J.R., Fukuzumi, S. & Crossley, M. 2008, 'Control Of The Orbital Delocalization And Implications For Molecular Rectification In The Radical Anions Of Porphyrins With Coplanar 90 Degrees And 180 Degrees Beta,Beta '-Fused Extensions', Journal of Physical Chemistry A, vol. 112, no. 3, pp. 556-570.
View/Download from: UTS OPUS or Publisher's site
Through-porphyrin electronic communication is investigated using "linear-type" and "corner-type" bis(quinoxalino)porphyrins in free-base form and their Zn-II, Cu-II, Ni-II, and Pd-II derivatives. These compounds are porphyrins with quinoxalines fused on opposite or adjacent beta,beta'-pyrrolic positions; they were synthesized from 5,10,15,20-tetrakis(3,5-di-tert-butylphenyl)-porphyrin-2,3,12,13- and -2,3,7,8-tetraone, respectively, by reaction with 1,2-phenylenediamine. The degree of electron spin delocalization into the fused rings in the pi-radical anions of the free-base and metal(II) bisquinoxalinoporphyrins was elucidated by electrochemistry, UV-vis absorption, and electron spin resonance (ESR) spectra of the singly reduced species and density functional theory calculations. Hyperfine splitting patterns in the ESR spectra of the pi-radical anions show that symmetric molecules have delocalized electron spin, indicating, that significant inter-quinoxaline interactions are mediated through the central porphyrin unit, these interactions being sufficient to guarantee through-molecule conduction. However, when molecular symmetry is broken by tautomeric exchange of the inner nitrogen hydrogens in the free-base porphyrin with a corner-type quinoxaline substitution pattern, the pi-radical anion becomes confined so that one quinoxaline group is omitted from spin delocalization. This indicates the appearance of a unidirectional barrier to through-molecule conduction, suggesting a new motif for chemically controlled rectification.
Wohlthat, S., Pauly, F. & Reimers, J.R. 2008, 'The Conduction Properties Of Alpha,Omega-Diaminoalkanes And Hydrazine Bridging Gold Electrodes', Chemical Physics Letters, vol. 454, no. 4-6, pp. 284-288.
View/Download from: UTS OPUS or Publisher's site
The conduction properties of alpha,omega-diaminoalkanes and hydrazine bridging gold electrodes are investigated using density functional theory in combination with Green's function techniques and group theory. We show that more than 99% of the current at low bias is carried by one channel of A' symmetry whose form is invariant to both the alkane chain length and realistic changes of the injection energy. The total conductance decreases exponentially with a decay constant of 0.73 angstrom(-1) with increasing chain length while the calculated gold- amine contact resistance is ca. 150 k Omega.
Wohlthat, S., Pauly, F. & Reimers, J.R. 2008, 'Two-Dimensional, Phenanthroline-Based, Extended Pi-Conjugated Molecules For Single-Molecule Conduction', Journal Of Physics: Condensed Matter, vol. 20, no. 29, p. 295208.
View/Download from: UTS OPUS or Publisher's site
The conduction properties of phenanthroline-terminated, polycyclic extended pi-conjugated molecular wires are investigated using density functional theory (DFT) in combination with Green's function techniques and group theory. While these molecules could possibly be thought of as accessible graphene-like fragments, they are calculated to conduct poorly. The decay constant for their exponential decrease of conductance with length is in excess of 0.6 angstrom(-1) for the addition of internal fused quinoxaline groups and in excess of 0.9 angstrom(-1) for the addition of internal pyrazine-fused pyrene groups. Furthermore, while the bidentate phenanthroline connectors adhere strongly to gold, they are sometimes predicted to be less conductive than related monodentate connectors. Careful design is thus required for any graphene-like extended pi-system intended for single-molecule conduction applications.
Sintic, P.J., E, W., Ou, Z., Shao, J., McDonald, J.A., Cai, Z.-.L., Kadish, K.M., Crossley, M.J. & Reimers, J.R. 2008, 'Control of the site and potential of reduction and oxidation processes in pi-expanded quinoxalinoporphyrins', PHYSICAL CHEMISTRY CHEMICAL PHYSICS, vol. 10, no. 4, pp. 515-527.
View/Download from: Publisher's site
Sintic, P.J., Wenbo, E., Ou, Z., Shao, J., McDonald, J.A., Cai, Z.L., Kadish, K.M., Crossley, M.J. & Reimers, J.R. 2008, 'Control of the site and potential of reduction and oxidation processes in -expanded quinoxalinoporphyrins (Physical Chemistry Chemical Physics (2008) 10, (268-280) DOI: 10.1039/b711320j)', Physical Chemistry Chemical Physics, vol. 10, no. 48, p. 7328.
View/Download from: Publisher's site
Curiel, D., Ohkubo, K., Reimers, J.R., Fukuzumi, S. & Crossley, M. 2007, 'Photoinduced Electron Transfer In A Beta,Beta '-Pyrrolic Fused Ferrocene-(Zinc Porphyrin)-Fullerene', Physical Chemistry Chemical Physics, vol. 9, no. 38, pp. 5260-5266.
View/Download from: Publisher's site
Cai, Z. & Reimers, J.R. 2007, 'The Lowest Singlet (N,Pi*) And (Pi,Pi*) Excited States Of The Hydrogen-Bonded Complex Between Water And Pyrazine', Journal Of Physical Chemistry A, vol. 111, no. 5, pp. 954-962.
View/Download from: Publisher's site
Ren, W., Reimers, J.R., Hush, N., Zhu, Y., Wang, J. & Guo, H. 2007, 'Models For The Structure And Electronic Transmission Of Carbon Nanotubes Covalently Linked By A Molecular Bridge Via Amide Couplings', Journal Of Physical Chemistry C, vol. 111, no. 9, pp. 3700-3704.
View/Download from: Publisher's site
Gagliardi, A., Solomon, G., Pecchia, A., Frauenheim, T., Di Carlo, A., Hush, N. & Reimers, J.R. 2007, 'A Priori Method For Propensity Rules For Inelastic Electron Tunneling Spectroscopy Of Single-Molecule Conduction', Physical Review B, vol. 75, no. 17.
View/Download from: Publisher's site
Wang, Y., Hush, N. & Reimers, J.R. 2007, 'Simulation Of The Au(111)-(22 X Root 3) Surface Reconstruction', Physical Review B, vol. 75, no. 23.
View/Download from: Publisher's site
Leiger, K., Freiberg, A., Dahlbom, M., Hush, N. & Reimers, J.R. 2007, 'Pressure-Induced Spectral Changes For The Special-Pair Radical Cation Of The Bacterial Photosynthetic Reaction Center', Journal Of Chemical Physics, vol. 126, no. 21.
View/Download from: Publisher's site
Xia, S., Pan, G., Cai, Z., Wang, Y. & Reimers, J.R. 2007, 'The Manganite-Water Interface', Journal Of Physical Chemistry C, vol. 111, no. 28, pp. 10427-10437.
View/Download from: Publisher's site
Wang, Y., Hush, N. & Reimers, J.R. 2007, 'Understanding The Chemisorption Of 2-Methyl-2-Propanethiol On Au(111)', Journal Of Physical Chemistry C, vol. 111, no. 29, pp. 10878-10885.
View/Download from: Publisher's site
Kadish, K., Wenbo, E., Sintic, P., Ou, Z., Shao, J., Ohkubo, K., Fukuzumi, S., Govenlock, L., Mcdonald, J., Try, A., Cai, Z., Reimers, J.R. & Crossley, M. 2007, 'Quinoxalino[2,3-B']Porphyrins Behave As Pi-Expanded Porphyrins Upon One-Electron Reduction: Broad Control Of The Degree Of Delocalization Through Substitution At The Macrocycle Periphery', Journal Of Physical Chemistry B, vol. 111, no. 30, pp. 8762-8774.
View/Download from: Publisher's site
Yin, S., Dahlbom, M., Canfield, P., Hush, N., Kobayashi, R. & Reimers, J.R. 2007, 'Assignment Of The Q(Y) Absorption Spectrum Of Photosystem-I From Thermosynechococcus Elongatus Based On Cam-B3Lyp Calculations At The Pw91-Optimized Protein Structure', Journal Of Physical Chemistry B, vol. 111, no. 33, pp. 9923-9930.
View/Download from: Publisher's site
Wang, Y., De Gironcoli, S., Hush, N. & Reimers, J.R. 2007, 'Successful A Priori Modeling Of Co Adsorption On Pt(111) Using Periodic Hybrid Density Functional Theory', Journal Of The American Chemical Society, vol. 129, no. 34, pp. 10402-10407.
View/Download from: Publisher's site
Dastoor, P., Mcneill, C., Frohne, H., Foster, C., Dean, B., Fell, C., Belcher, W., Canipbell, W., Officer, D., Blake, I., Thordarson, P., Crossley, M., Hush, N. & Reimers, J.R. 2007, 'Understanding And Improving Solid-State Polymer/C-60-Fullerene Bulk-Heterojunction Solar Cells Using Ternary Porphyrin Blends', Journal Of Physical Chemistry C, vol. 111, no. 42, pp. 15415-15426.
View/Download from: Publisher's site
Cafe, P., Larsen, A., Yang, W., Bilic, A., Blake, I., Crossley, M., Zhang, J., Wackerbarth, H., Ulstrup, J. & Reimers, J.R. 2007, 'Chemisorbed And Physisorbed Structures For 1,10-Phenanthroline And Dipyrido[3,2-A : 2 ',3 '-C]Phenazine On Au(111)', Journal Of Physical Chemistry C, vol. 111, no. 46, pp. 17285-17296.
View/Download from: Publisher's site
Reimers, J.R., Solomon, G., Gagliardi, A., Bilic, A., Hush, N., Frauenheim, T., Di Carlo, A. & Pecchia, A. 2007, 'The Green'S Function Density Functional Tight-Binding (Gdftb) Method For Molecular Electronic Conduction', JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, no. 26, pp. 5692-5702.
View/Download from: Publisher's site
Cai, Z., Lopez, P., Reimers, J.R., Cui, Q. & Elstner, M. 2007, 'Application Of The Computationally Efficient Self-Consistent-Charge Density-Functional Tight-Binding Method To Magnesium-Containing Molecules', JOURNAL OF PHYSICAL CHEMISTRY A, vol. 111, no. 26, pp. 5743-5750.
View/Download from: Publisher's site
Wang, Y., Hush, N.S. & Reimers, J.R. 2007, 'Formation of gold-methanethiyl self-assembled monolayers', JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, vol. 129, no. 47, pp. 14532-+.
View/Download from: Publisher's site
Bilic, A., Reimers, J.R., Hush, N., Hoft, R.C. & Ford, M. 2006, 'Adsorption of benzene on copper, silver, and gold surfaces', Journal Of Chemical Theory And Computation, vol. 2, no. 4, pp. 1093-1105.
View/Download from: UTS OPUS or Publisher's site
The adsorption of benzene on the Cu(111), Ag(111), Au(111), and Cu(110) surfaces at low coverage is modeled using density-functional theory (DFT) using periodic-slab models of the surfaces as well as using both DFT and complete-active-space self-consiste
Canfield, P., Dahlbom, M., Hush, N. & Reimers, J.R. 2006, 'Density-Functional Geometry Optimization Of The 150 000-Atom Photosystem-I Trimer', Journal Of Chemical Physics, vol. 124, no. 2.
View/Download from: Publisher's site
Solomon, G., Gagliardi, A., Pecchia, A., Frauenheim, T., Di Carlo, A., Reimers, J.R. & Hush, N. 2006, 'Understanding The Inelastic Electron-Tunneling Spectra Of Alkanedithiols On Gold', Journal Of Chemical Physics, vol. 124, no. 9.
View/Download from: Publisher's site
Kriplani, N., Nackashi, D., Amsinck, C., Di Spigna, N., Steer, M., Franzon, P., Rick, R., Solomon, G. & Reimers, J.R. 2006, 'Physically Based Molecular Device Model In A Transient Circuit Simulator', Chemical Physics, vol. 326, no. 1, pp. 188-196.
View/Download from: Publisher's site
Bilic, A., Reimers, J.R., Hush, N., Hoft, R.C. & Ford, M. 2006, 'Adsorption Of Benzene On Copper, Silver, And Gold Surfaces', Journal Of Chemical Theory And Computation, vol. 2, no. 4, pp. 1093-1105.
View/Download from: Publisher's site
Cai, Z., Crossley, M., Reimers, J.R., Kobayashi, R. & Amos, R. 2006, 'Density Functional Theory For Charge Transfer: The Nature Of The N-Bands Of Porphyrins And Chlorophylls Revealed Through Cam-B3Lyp, Caspt2, And Sac-Ci Calculations', Journal Of Physical Chemistry B, vol. 110, no. 31, pp. 15624-15632.
View/Download from: Publisher's site
Kanchanawong, P., Dahlbom, M., Treynor, T., Reimers, J.R., Hush, N. & Boxer, S. 2006, 'Charge Delocalization In The Special-Pair Radical Cation Of Mutant Reaction Centers Of Rhodobacter Sphaeroides From Stark Spectra And Nonadiabatic Spectral Simulations', Journal Of Physical Chemistry B, vol. 110, no. 37, pp. 18688-18702.
View/Download from: Publisher's site
Solomon, G., Gagliardi, A., Pecchia, A., Frauenheim, T., Di Carlo, A., Reimers, J.R. & Hush, N. 2006, 'Molecular Origins Of Conduction Channels Observed In Shot-Noise Measurements', Nano Letters, vol. 6, no. 11, pp. 2431-2437.
View/Download from: Publisher's site
Solomon, G., Gagliardi, A., Pecchia, A., Frauenheim, T., Di Carlo, A., Reimers, J.R. & Hush, N. 2006, 'The Symmetry Of Single-Molecule Conduction', Journal Of Chemical Physics, vol. 125, no. 18.
View/Download from: Publisher's site
Reimers, J.R., Solomon, G.C., Cai, Z.-.L., Hush, N.S., Gagliardi, A., Frauenheim, T., Pecchia, A. & Di Carlo, A. 2006, 'Application of DFTB in molecular electronics', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 232, pp. 263-263.
Reimers, J.R., Ulstrup, J., Meyer, T.J. & Solomon, G.C. 2006, '"The molecules and methods of chemical, biochemical, and nanoscale electron transfer" - Preface', CHEMICAL PHYSICS, vol. 324, no. 1, pp. 1-2.
View/Download from: Publisher's site
Reimers, J.R., Ulstrup, J., Meyer, T.J. & Solomon, G.C. 2006, 'Preface - "The molecules and methods of chemical, biochemical, and nanoscale electron transfer"', CHEMICAL PHYSICS, vol. 326, no. 1, pp. 1-2.
View/Download from: Publisher's site
Dahlbom, M. & Reimers, J.R. 2005, 'Successes And Failures Of Time-Dependent Density Functional Theory For The Low-Lying Excited States Of Chlorophylls', Molecular Physics, vol. 103, no. 6-Aug, pp. 1057-1065.
View/Download from: Publisher's site
Cai, Z. & Reimers, J.R. 2005, 'First Singlet (N,Pi) Excited State Of Hydrogen-Bonded Complexes Between Water And Pyrimidine', Journal Of Physical Chemistry A, vol. 109, no. 8, pp. 1576-1586.
View/Download from: Publisher's site
Solomon, G., Reimers, J.R. & Hush, N. 2005, 'Overcoming Computational Uncertainties To Reveal Chemical Sensitivity In Single Molecule Conduction Calculations', Journal Of Chemical Physics, vol. 122, no. 22.
View/Download from: Publisher's site
Zhang, J., Bilic, A., Reimers, J.R., Hush, N. & Ulstrup, J. 2005, 'Coexistence Of Multiple Conformations In Cysteamine Monolayers On Au(111)', Journal Of Physical Chemistry B, vol. 109, no. 32, pp. 15355-15367.
View/Download from: Publisher's site
Reimers, J.R., Cai, Z. & Hush, N. 2005, 'A Priori Evaluation Of The Solvent Contribution To The Reorganization Energy Accompanying Intramolecular Electron Transfer: Predicting The Nature Of The Creutz-Taube Ion', Chemical Physics, vol. 319, no. 1-Mar, pp. 39-51.
View/Download from: Publisher's site
Bilic, A., Reimers, J.R. & Hush, N. 2005, 'The Structure, Energetics, And Nature Of The Chemical Bonding Of Phenylthiol Adsorbed On The Au(111) Surface: Implications For Density-Functional Calculations Of Molecular-Electronic Conduction 1.1850455G', JOURNAL OF CHEMICAL PHYSICS, vol. 122, no. 9.
View/Download from: Publisher's site
Jordanides, X., Scholes, G., Shapley, W., Reimers, J.R. & Fleming, G. 2004, 'Electronic Couplings And Energy Transfer Dynamics In The Oxidized Primary Electron Donor Of The Bacterial Reaction Center', Journal Of Physical Chemistry B, vol. 108, no. 5, pp. 1753-1765.
View/Download from: Publisher's site
Bilic, A., Reimers, J.R., Hofer, W. & Hush, N. 2004, 'Adsorption Sites Of Maleic Anhydride On Si(100) Revisited: Inter- Versus Intra-Row Attachment', Chemical Physics Letters, vol. 385, no. 5-Jun, pp. 341-344.
View/Download from: Publisher's site
Wang, B., Zheng, X., Michl, J., Foley, E., Hersam, M., Bilic, A., Crossley, M., Reimers, J.R. & Hush, N. 2004, 'An Azanorbornadiene Anchor For Molecular-Level Construction On Silicon(100)', Nanotechnology, vol. 15, no. 3, pp. 324-332.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 2004, 'Hamiltonian Operators Including Both Symmetric And Antisymmetric Vibrational Modes For Vibronic Coupling And Intervalence Charge-Transfer Applications', Chemical Physics, vol. 299, no. 1, pp. 79-82.
View/Download from: Publisher's site
Bilic, A., Reimers, J.R. & Hush, N. 2004, 'Dissociated Water On Si(100): Relation Between Stm Topograph And Actual Geometry', Surface Review And Letters, vol. 11, no. 2, pp. 185-190.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 2004, 'Unified Description Of The Electrochemical, Charge Distribution, And Spectroscopic Properties Of The Special-Pair Radical Cation In Bacterial Photosynthesis', Journal Of The American Chemical Society, vol. 126, no. 13, pp. 4132-4144.
View/Download from: Publisher's site
Lambropoulos, N., Reimers, J.R. & Hush, N. 2004, 'Flanged Nanotube-Electrode Junctions', Nanotechnology, vol. 15, no. 9, pp. 1226-1232.
View/Download from: Publisher's site
Antolovich, M., Lindoy, L. & Reimers, J.R. 2004, 'Explanation Of The Anomalous Complexation Of Silver(I) With Ammonia In Terms Of The Poor Affinity Of The Ion For Water', Journal Of Physical Chemistry A, vol. 108, no. 40, pp. 8434-8438.
View/Download from: Publisher's site
Solomon, G., Reimers, J.R. & Hush, N. 2004, 'Single Molecule Conductivity: The Role Of Junction-Orbital Degeneracy In The Artificially High Currents Predicted By Ab Initio Approaches', Journal Of Chemical Physics, vol. 121, no. 14, pp. 6615-6627.
View/Download from: Publisher's site
Wallace, B. & Reimers, J.R. 2004, 'Wavepacket Propagation Using Time-Sliced Semiclassical Initial Value Methods', Journal Of Chemical Physics, vol. 121, no. 24, pp. 12208-12216.
View/Download from: Publisher's site
Reimers, J.R., Bilic, A., Cai, Z., Dahlbom, M., Lambropoulos, N., Solomon, G., Crossley, M. & Hush, N. 2004, 'Molecular Electronics: From Basic Chemical Principles To Photosynthesis To Steady-State Through-Molecule Conductivity To Computer Architectures', AUSTRALIAN JOURNAL OF CHEMISTRY, vol. 57, no. 12, pp. 1133-1138.
View/Download from: Publisher's site
Crossley, M., Sintic, P., Walton, R. & Reimers, J.R. 2003, 'Synthesis And Physical Properties Of Biquinoxalinyl Bridged Bis-Porphyrins: Models For Aspects Of Photosynthetic Reaction Centres', Organic & Biomolecular Chemistry, vol. 1, no. 15, pp. 2777-2787.
View/Download from: Publisher's site
Fischer, G., Cai, Z., Reimers, J.R. & Wormell, P. 2003, 'Singlet And Triplet Valence Excited States Of Pyrimidine', Journal Of Physical Chemistry A, vol. 107, no. 17, pp. 3093-3106.
View/Download from: Publisher's site
Nieuwenburg, P., Clarke, R., Cai, Z., Chen, M., Larkum, A., Cabral, N., Ghiggino, K. & Reimers, J.R. 2003, 'Examination Of The Photophysical Processes Of Chlorophyll D Leading To A Clarification Of Proposed Uphill Energy Transfer Processes In Cells Of Acaryochloris Marina', Photochemistry And Photobiology, vol. 77, no. 6, pp. 628-637.
View/Download from: 2.0.CO;2">Publisher's site
Bilic, A., Reimers, J.R. & Hush, N. 2003, 'Modeling The Adsorption Of Norbornadiene On The Si(001) Surface: The Predominance Of Non-[2+2]-Cycloaddition Products', Journal Of Chemical Physics, vol. 119, no. 2, pp. 1115-1126.
View/Download from: Publisher's site
Reimers, J.R., Shapley, W. & Hush, N. 2003, 'Modelling The Bacterial Photosynthetic Reaction Center. V. Assignment Of The Electronic Transition Observed At 2200 Cm(-1) In The Special-Pair Radical-Cation As A Second-Highest Occupied Molecular Orbital To Highest Occupied Molecular Orbital Transit', Journal Of Chemical Physics, vol. 119, no. 6, pp. 3240-3248.
View/Download from: Publisher's site
Reimers, J.R., Shapley, W., Rendell, A. & Hush, N. 2003, 'Modelling The Bacterial Photosynthetic Reaction Center. Vi. Use Of Density-Functional Theory To Determine The Nature Of The Vibronic Coupling Between The Four Lowest-Energy Electronic States Of The Special-Pair Radical Cation', Journal Of Chemical Physics, vol. 119, no. 6, pp. 3249-3261.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 2003, 'Modeling The Bacterial Photosynthetic Reaction Center. Vii. Full Simulation Of The Intervalence Hole-Transfer Absorption Spectrum Of The Special-Pair Radical Cation', Journal Of Chemical Physics, vol. 119, no. 6, pp. 3262-3277.
View/Download from: Publisher's site
Binstead, R., Reimers, J.R. & Hush, N. 2003, 'Inter-Porphyrin Coupling: Rotation-Modulation Of Inter-Ring Coupling In A Mu-Oxo-Silicon Phthalocyanine Dimer', Chemical Physics Letters, vol. 378, no. 5-Jun, pp. 654-659.
View/Download from: Publisher's site
Reimers, J.R., Cai, Z., Bilic, A. & Hush, N. 2003, 'The Appropriateness Of Density-Functional Theory For The Calculation Of Molecular Electronics Properties', MOLECULAR ELECTRONICS III, vol. 1006, pp. 235-251.
View/Download from: Publisher's site
Reimers, J.R., Hush, N. & Crossley, M. 2002, 'Inter-Porphyrin Coupling: How Strong Should It Be For Molecular Electronics Applications?', Journal Of Porphyrins And Phthalocyanines, vol. 6, no. 11-Dec, pp. 795-805.
Bilic, A., Reimers, J.R., Hush, N. & Hafner, J. 2002, 'Adsorption Of Ammonia On The Gold(111) Surface', Journal Of Chemical Physics, vol. 116, no. 20, pp. 8981-8987.
View/Download from: Publisher's site
Lambropoulos, N., Reimers, J.R. & Hush, N. 2002, 'Binding To Gold(0): Accurate Computational Methods With Application To Aunh3', Journal Of Chemical Physics, vol. 116, no. 23, pp. 10277-10286.
View/Download from: Publisher's site
Sendt, K., Johnston, L., Hough, W., Crossley, M., Hush, N. & Reimers, J.R. 2002, 'Switchable Electronic Coupling In Model Oligoporphyrin Molecular Wires Examined Through The Measurement And Assignment Of Electronic Absorption Spectra', Journal Of The American Chemical Society, vol. 124, no. 31, pp. 9299-9309.
View/Download from: Publisher's site
Cai, Z. & Reimers, J.R. 2002, 'The First Singlet (N,Pi*) And (Pi,Pi*) Excited States Of The Hydrogen-Bonded Complex Between Water And Pyridine', Journal Of Physical Chemistry A, vol. 106, no. 37, pp. 8769-8778.
View/Download from: Publisher's site
Cai, Z., Sendt, K. & Reimers, J.R. 2002, 'Failure Of Density-Functional Theory And Time-Dependent Density-Functional Theory For Large Extended Pi Systems', Journal Of Chemical Physics, vol. 117, no. 12, pp. 5543-5549.
View/Download from: Publisher's site
Shapley, W., Reimers, J.R. & Hush, N. 2002, 'Indo/S Parameters For Gold', International Journal Of Quantum Chemistry, vol. 90, no. 1, pp. 424-438.
View/Download from: Publisher's site
Reimers, J.R., Shapley, W., Lambropoulos, N. & Hush, N. 2002, 'An Atomistic Approach To Conduction Between Nanoelectrodes Through A Single Molecule', MOLECULAR ELECTRONICS II, vol. 960, pp. 100-130.
Reimers, J.R., Hush, N.S. & Crossley, M.J. 2002, 'Inter-porphyrin coupling: how strong should it be for molecular electronics applications?', JOURNAL OF PORPHYRINS AND PHTHALOCYANINES, vol. 6, no. 11-12, pp. 795-805.
Bilic, A., Reimers, J.R. & Hush, N.S. 2002, 'Adsorption of pyridine on the gold(111) surface: Implications for "alligator clips" for molecular wires', JOURNAL OF PHYSICAL CHEMISTRY B, vol. 106, no. 26, pp. 6740-6747.
View/Download from: Publisher's site
Hambley, T., Lindoy, L., Reimers, J.R., Turner, P., Wei, G. & Widmer-cooper, A. 2001, 'Macrocyclic Ligand Design. X-Ray, Dft And Solution Studies Of The Effect Of N-Methylation And N-Benzylation Of 1,4,10,13-Tetraoxa-7,16-Diazacyclooctadecane On Its Affinity For Selected Transition And Post-Transition Metal Ions', Journal Of The Chemical Society-Dalton Transactions, no. 5, pp. 614-620.
View/Download from: Publisher's site
Widmer-cooper, A., Lindoy, L. & Reimers, J.R. 2001, 'The Effect Of Alkylation Of N- And O-Donor Atoms On Their Strength Of Coordination To Silver(I)', Journal Of Physical Chemistry A, vol. 105, no. 26, pp. 6567-6574.
View/Download from: Publisher's site
Hughes, J., Hutter, M., Reimers, J.R. & Hush, N. 2001, 'Modeling The Bacterial Photosynthetic Reaction Center. 4. The Structural, Electrochemical, And Hydrogen-Bonding Properties Of 22 Mutants Of Rhodobacter Sphaeroides', Journal Of The American Chemical Society, vol. 123, no. 35, pp. 8550-8563.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 2001, 'The Need For Quantum-Mechanical Treatment Of Capacitance And Related Properties Of Nanoelectrodes', Journal Of Physical Chemistry B, vol. 105, no. 37, pp. 8979-8988.
View/Download from: Publisher's site
Reimers, J.R. 2001, 'A Practical Method For The Use Of Curvilinear Coordinates In Calculations Of Normal-Mode-Projected Displacements And Duschinsky Rotation Matrices For Large Molecules', Journal Of Chemical Physics, vol. 115, no. 20, pp. 9103-9109.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N.S. 2001, 'The need for quantum-mechanical treatment of capacitance and related properties of nanoelectrodes', Journal of Physical Chemistry B, vol. 105, no. 37, pp. 8979-8988.
View/Download from: Publisher's site
Capacitance and other properties of large metal clusters proposed for use as nanoelectrodes in complex molecular-electronic devices, or as cores of the monolayer-passivated nanoparticles studied by Murray (J. Phys. Chem. B 1999, 103, 9996), are discussed using atomistic formalisms based on classical electrostatics as well as INDO electronic structure theory. Using classical electrostatics, both finite-size and atomicity effects are found to be important for properties such as the surface charge distribution but unimportant for other properties such as the electric field profile between electrodes. The INDO and classical atomistic charge distributions are found to be strikingly different, with both departing from textbook expectations based on theorems of classical continuum electrostatics such as Gauss' law. For linear chains of metallic atoms, ab initio full configuration interaction as well as density-functional (DFT) calculations validate the INDO/S picture in which both positively and negatively charged atoms appear within a chain of net positive charge, contrary to the classical treatment that permits only distribution of the net charge. Examination of the form of the INDO/S Hamiltonian reveals that a key aspect of the failure of classical atomistic electrostatics arises from its treatment of self-energy (the energy required to store a finite charge in the finite atomic volume). Exchange operators present in the quantum approaches halve the classical self-energy contributions, facilitating charging. Even the requirement that atomic charges be distributed across the width of a surface atomic plane is found to significantly modify the classical self-energy and hence induce large short-range deviations from standard capacitance relationships. For large clusters, the INDO/S results are shown to depict qualitatively reasonable properties by comparison with published DFT calculations. INDO/S may prove an efficient computational scheme for the study of a wide range...
Hambley, T.W., Lindoy, L.F., Reimers, J.R., Turner, P., Wei, G. & Widmer-Cooper, A.N. 2001, 'Macrocyclic ligand design. X-Ray, DFT and solution studies of the effect of N-methylation and N-benzylation of 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane on its affinity for selected transition and post-transition metal ions', Journal of the Chemical Society, Dalton Transactions, no. 5, pp. 633-638.
Potentiometric titration in 95% methanol (I = 0.1 mol dm-3, Et4NClO4) has been employed to investigate the effect of N-methylation and N-benzylation of 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane 1 on the binding of all three rings to cobalt(II), nickel(II), copper(II), zinc(II), cadmium(II), silver(I) and lead(II). The results show that enhanced selectivity for silver(I) is exhibited by the di-N-benzylated derivative 3 while the analogous dimethylated derivative 2 discriminates for both silver(I) and lead(II). The crystal structures of [Ag(1)]PF6, [Ag(2)]PF 6, [Ag(3)]PF6 and [Pb(1)(NO3)2] have been determined. In the silver complexes the NH hydrogens of 1 and the N-methyl and N-benzyl substituents of the dialkylated derivatives 2 and 3 were found to lie on the same side of the mean donor planes of the co-ordinated macrocycles ('cis' arrangements). Density functional theory has been employed to model the silver complexes in both their energy-minimised 'cis' and 'trans' configurations. In accordance with the X-ray evidence, the calculations predict that the 'cis' arrangement is the more stable in each case. The crystal structure of the lead complex of 1 shows a 'trans' arrangement of its NH groups. &copy; The Royal Society of Chemistry 2001.
Cai, Z. & Reimers, J.R. 2000, 'Application Of Time-Dependent Density-Functional Theory To The (3)Sigma(-)(U) First Excited State Of H(2)', Journal Of Chemical Physics, vol. 112, no. 2, pp. 527-530.
View/Download from: Publisher's site
Hall, L., Reimers, J.R., Hush, N. & Silverbrook, K. 2000, 'Formalism, Analytical Model, And A Priori Green'S-Function-Based Calculations Of The Current-Voltage Characteristics Of Molecular Wires', Journal Of Chemical Physics, vol. 112, no. 3, pp. 1510-1521.
View/Download from: Publisher's site
Reimers, J.R., Hall, L. & Hush, N. 2000, 'Tautomerization Of Nucleobase Model Compounds: The 4-Pyridinol And 4(1H)-Pyridinone Monomers And Their Dimers', Journal Of Physical Chemistry A, vol. 104, no. 21, pp. 5087-5092.
View/Download from: Publisher's site
Cai, Z. & Reimers, J.R. 2000, 'The Low-Lying Excited States Of Pyridine', Journal Of Physical Chemistry A, vol. 104, no. 36, pp. 8389-8408.
View/Download from: Publisher's site
Reimers, J.R., Hughes, J. & Hush, N. 2000, 'Modeling The Bacterial Photosynthetic Reaction Center 3: Interpretation Of Effects Of Site-Directed Mutagenesis On The Special-Pair Midpoint Potential', Biochemistry, vol. 39, no. 51, pp. 16185-16189.
View/Download from: Publisher's site
Reimers, J.R., Hutter, M., Hughes, J. & Hush, N. 2000, 'Nature Of The Special-Pair Radical Cation In Bacterial Photosynthesis', INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, vol. 80, no. 6, pp. 1224-1243.
View/Download from: 3.0.CO;2-W">Publisher's site
Hush, N. & Reimers, J.R. 2000, 'Solvent Effects On The Electronic Spectra Of Transition Metal Complexes', CHEMICAL REVIEWS, vol. 100, no. 2, pp. 775-786.
View/Download from: Publisher's site
Cai, Z., Tozer, D. & Reimers, J.R. 2000, 'Time-Dependent Density-Functional Determination Of Arbitrary Singlet And Triplet Excited-State Potential Energy Surfaces: Application To The Water Molecule', JOURNAL OF CHEMICAL PHYSICS, vol. 113, no. 17, pp. 7084-7096.
View/Download from: Publisher's site
Reimers, J.R. & Hall, L. 1999, 'The Solvation Of Acetonitrile', Journal Of The American Chemical Society, vol. 121, no. 15, pp. 3730-3744.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1999, 'Electron And Energy Transfer Through Bridged Systems. 9. Toward A Priori Evaluation Of The Intermetallic Coupling In Bis-Metal Complexes', Journal Of Physical Chemistry A, vol. 103, no. 16, pp. 3066-3072.
View/Download from: Publisher's site
Hurst, J., Wormell, P., Reimers, J.R. & Lacey, A. 1999, 'Nature Of Nonbonding Molecular Orbitals: Application To Two Symmetric Tetraazanaphthalenes', Journal Of Physical Chemistry A, vol. 103, no. 16, pp. 3089-3096.
View/Download from: Publisher's site
Reimers, J.R., Hall, L., Crossley, M. & Hush, N. 1999, 'Rigid Fused Oligoporphyrins As Potential Versatile Molecular Wires. 2. B3Lyp And Scf Calculated Geometric And Electronic Properties Of 98 Oligoporphyrin And Related Molecules', Journal Of Physical Chemistry A, vol. 103, no. 22, pp. 4385-4397.
View/Download from: Publisher's site
Hutter, M., Hughes, J., Reimers, J.R. & Hush, N. 1999, 'Modeling The Bacterial Photosynthetic Reaction Center. 2. A Combined Quantum Mechanical Molecular Mechanical Study Of The Structure Of The Cofactors In The Reaction Centers Of Purple Bacteria', Journal Of Physical Chemistry B, vol. 103, no. 23, pp. 4906-4915.
View/Download from: Publisher's site
Weber, P. & Reimers, J.R. 1999, 'Ab Initio And Density Functional Calculations Of The Energies Of The Singlet And Triplet Valence Excited States Of Pyrazine', Journal Of Physical Chemistry A, vol. 103, no. 48, pp. 9821-9829.
View/Download from: Publisher's site
Weber, P. & Reimers, J.R. 1999, 'Ab Initio And Density-Functional Calculations Of The Vibrational Structure Of The Singlet And Triplet Excited States Of Pyrazine', Journal Of Physical Chemistry A, vol. 103, no. 48, pp. 9830-9841.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1999, 'Vibrational Stark Spectroscopy 3. Accurate Benchmark Ab Initio And Density Functional Calculations For Co And Cn-', Journal Of Physical Chemistry A, vol. 103, no. 49, pp. 10580-10587.
View/Download from: Publisher's site
Hutter, M., Reimers, J.R. & Hush, N. 1998, 'Modeling The Bacterial Photosynthetic Reaction Center. 1. Magnesium Parameters For The Semiempirical Am1 Method Developed Using A Genetic Algorithm', Journal Of Physical Chemistry B, vol. 102, no. 41, pp. 8080-8090.
View/Download from: Publisher's site
Hush, N., Reimers, J.R., Hall, L., Johnston, L. & Crossley, M. 1998, 'Optimization And Chemical Control Of Porphyrin-Based Molecular Wires And Switches', MOLECULAR ELECTRONICS: SCIENCE AND TECHNOLOGY, vol. 852, pp. 1-21.
View/Download from: Publisher's site
Reimers, J.R., Hall, L., Hush, N. & Silverbrook, K. 1998, 'Chemical Control Of Tautomerization-Based Molecular Electronic And Color Switches', MOLECULAR ELECTRONICS: SCIENCE AND TECHNOLOGY, vol. 852, pp. 38-53.
View/Download from: Publisher's site
Reimers, J.R., Hutter, M. & Hush, N. 1998, 'The Spectroscopy Of The Low-Lying Bands In The Special-Pair Radical-Cations Of Photosynthetic Reaction Centres', PHOTOSYNTHESIS RESEARCH, vol. 55, no. 2-Mar, pp. 163-171.
View/Download from: Publisher's site
Hush, N. & Reimers, J.R. 1998, 'Solvent Effects On Metal To Ligand Charge Transfer Excitations', COORDINATION CHEMISTRY REVIEWS, vol. 177, pp. 37-60.
View/Download from: Publisher's site
Hush, N.S., Hutter, M. & Reimers, J.R. 1998, 'Low-lying vibronic transitions as source of microscopic parameters of electron transfer in the 'special pairs' of bacterial photosynthetic reaction centres.', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 215, pp. U189-U189.
Hush, N.S., Zeng, J., Reimers, J.R. & Craw, J.S. 1998, 'The primary process in photooxidation of Fe2+(H2O)6 in water', Advances in Chemistry Series, vol. 254, pp. 263-277.
When aqueous solutions containing Fe2+ ions are irradiated at <250 nm, photooxidation to Fe3+occurs and molecular hydrogen is generated. This plwtoprocess has been studied extensively for over 60 years, but without agreement being reached about the nature of the primary step. Possible initial steps include metal-to-ligand charge transfer (MLCT), internal Fe2+ 3d4s absorption, direct electron photodetachment producing a partially solvated electron in a pre-existing solvent cavity, and polaron-type charge transfer to solvent (CTTS) absorption. We consider the energetics and solvent shift of the first three of these processes, concluding that the MLCT band is too high in energy, the 3d -4s excitation could participate, and the direct photodetachment band is at the correct energy and intensity to account for all that is (as yet) observed of the absorption band. In general, a rather complicated picture of this process in inorganic complexes emerges. In this work, we apply a general method tue have developed for estimating the effects of solvents on transitions of species that have strong specific interactions (e.g., hydrogen bonding) with the solvent molecules. &copy; 1998 American Chemical Society.
Hayward, J. & Reimers, J.R. 1997, 'Unit Cells For The Simulation Of Hexagonal Ice', Journal Of Chemical Physics, vol. 106, no. 4, pp. 1518-1529.
View/Download from: Publisher's site
Bacskay, G., Reimers, J.R. & Nordholm, S. 1997, 'The Mechanism Of Covalent Bonding', Journal Of Chemical Education, vol. 74, no. 12, pp. 1494-1502.
View/Download from: Publisher's site
Reimers, J.R., Bacskay, G. & Nordholm, S. 1997, 'The Basics Of Covalent Bonding', Journal Of Chemical Education, vol. 74, no. 12, pp. 1503-1503.
Reimers, J.R., Zeng, J. & Hush, N. 1996, 'Vibrational Stark Spectroscopy .2. Application To The Cn Stretch In Hcn And Acetonitrile', Journal Of Physical Chemistry, vol. 100, no. 5, pp. 1498-1504.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1996, 'Solvent Effects On Molecular And Ionic Spectra .7. Modeling The Absorption And Electroabsorption Spectra Of Pentaammine-Ruthenium(Ii) Pyrazine And Its Conjugate Acid In Water', Journal Of The American Chemical Society, vol. 118, no. 8, pp. 2059-2068.
View/Download from: Publisher's site
Armstrong, R., Gallagher, S., Lay, P., Reimers, J.R. & Reed, C. 1996, 'Solvent Effects On The Electronic Spectrum Of C-60 - Reply', Journal Of Physical Chemistry, vol. 100, no. 13, pp. 5604-5604.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1996, 'Solvent Effects On Molecular And Ionic Spectra .8. The (1)(N,Pi*) Excited States Of Pyridazine In Water', Journal Of Physical Chemistry, vol. 100, no. 22, pp. 9561-9567.
View/Download from: Publisher's site
Reimers, J.R., Lu, T., Crossley, M. & Hush, N. 1996, 'Molecular Electronic Properties Of Fused Rigid Porphyrin-Oligomer Molecular Wires', Chemical Physics Letters, vol. 256, no. 4-May, pp. 353-359.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1996, 'The Effects Of Couplings To Symmetric And Antisymmetric Modes And Minor Asymmetry On The Spectral Properties Of Mixed-Valence And Related Charge-Transfer Systems', Chemical Physics, vol. 208, no. 2, pp. 177-193.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1996, 'Solvent Effects On Molecular And Ionic Spectra Ix: The Change In Dipole Moment Accompanying Metal To Ligand Charge Transfer Absorption In Pentaaminopyridylruthenium(Ii)', Journal Of Physical Chemistry, vol. 100, no. 50, pp. 19292-19294.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1996, 'Analytic Solutions To Resonant And Non-Resonant Through-Bridge Electronic Coupling', Nanotechnology, vol. 7, no. 4, pp. 417-423.
View/Download from: Publisher's site
Reimers, J.R., Lu, T., Crossley, M. & Hush, N. 1996, 'Molecular Electronic Properties Of Fused Rigid Porphyrin-Oligomer Molecular Wires', Nanotechnology, vol. 7, no. 4, pp. 424-429.
View/Download from: Publisher's site
Armstrong, R.S., Gallagher, S.H., Lay, P.A., Reimers, J.R. & Reed, C.A. 1996, 'Reply to comment on "solvent effects on the electronic spectrum of C60"', Journal of Physical Chemistry, vol. 100, no. 13, p. 5604.
Reimers, J.R. & Hush, N. 1995, 'The Nature Of The Near-Infrared Electronic Absorption At 1250 Nm In The Spectra Of The Radical Cations Of The Special Pairs In The Photosynthetic Reaction Centers Of Rhodobacter-Sphaeroides And Rhodopseudomonas-Viridis', Journal Of The American Chemical Society, vol. 117, no. 4, pp. 1302-1308.
View/Download from: Publisher's site
Reimers, J.R., Lu, T., Crossley, M. & Hush, N. 1995, 'The Mechanism Of Inner-Hydrogen Migration In Free-Base Porphyrin - Ab-Initio Mp2 Calculations', Journal Of The American Chemical Society, vol. 117, no. 10, pp. 2855-2861.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1995, 'Solvent Effects On Molecular And Ionic Spectra .5. Development Of A Method For Simulation Of The Liquid Structure And Solvatochromic Shift Of Inorganic Complexes Such As Pentaaminopyridylruthenium(Ii) In Water', Journal Of Physical Chemistry, vol. 99, no. 26, pp. 10459-10470.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1995, 'Nature Of The Ground And First Excited-States Of The Radical Cations Of Photosynthetic Bacterial Reaction Centers', Chemical Physics, vol. 197, no. 3, pp. 323-332.
View/Download from: Publisher's site
Zeng, J., Woywod, C., Hush, N. & Reimers, J.R. 1995, 'Solvent Effects On Molecular And Ionic Spectra .6. Hydrogen-Bonding And The Delocalized Nature Of The First (1)(N,Pi-Asterisk) Excited-State Of Pyrazine', Journal Of The American Chemical Society, vol. 117, no. 33, pp. 8618-8626.
View/Download from: Publisher's site
Hush, N. & Reimers, J.R. 1995, 'Vibrational Stark Spectroscopy .1. Basic Theory And Application To The Co Stretch', Journal Of Physical Chemistry, vol. 99, no. 43, pp. 15798-15805.
View/Download from: Publisher's site
Reimers, J.R., Craw, J., Bacskay, G. & Hush, N. 1995, 'Towards Efficient Molecular Wires And Switches - The Brooker Ions', Biosystems, vol. 35, no. 2-Mar, pp. 107-111.
View/Download from: Publisher's site
Reimers, J.R., Craw, J.S., Bacskay, G.B. & Hush, N.S. 1995, 'Towards efficient molecular wires and switches: the Brooker ions.', Bio Systems, vol. 35, no. 2-3, pp. 107-111.
View/Download from: Publisher's site
In search of materials which may function as molecular wires or switches, analytical models have suggested that the Brooker ions should be particularly interesting. We study them in detail using ab initio, semi-empirical and specially-designed empirical techniques, predicting molecular geometries, charge distributions, and conductivities. Provided molecular symmetry is maintained, odd polyenes and Brooker ions NH2-(CH)+ 2n - 1 - NH2 are shown to conduct significantly better than even polyenes, but the advantage becomes a simple multiplicative factor once solitons form (chains of length ca 20 A). Symmetry lowering is predicted to dramatically decrease the conductivity but introduces the possibility that the Brooker ions may function as molecular switches, having greatly enhanced, switchable, non-linear optical properties.
ZENG, J., REIMERS, J. & HUSH, N. 1995, 'THE PRIMARY PROCESS IN PHOTOOXIDATION OF FE2+ IN WATER', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 209, pp. 446-INOR.
Reimers, J.R. & Hush, N. 1994, 'Electron-Transfer And Energy-Transfer Through Bridged Systems .3. Tight-Binding Linkages With Zero Or Nonzero Asymptotic Band-Gap', Journal Of Photochemistry And Photobiology A-Chemistry, vol. 82, no. 1-Mar, pp. 31-46.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1994, 'The Influence Of Spin-Forbidden Monomer Excitations On Spin-Allowed Electron-Transfer And Electron-Localized States Of Mixed-Valence And Single-Valence Dimeric Systems', Inorganica Chimica Acta, vol. 226, no. 1-Feb, pp. 33-42.
View/Download from: Publisher's site
Lu, T., Reimers, J.R., Crossley, M. & Hush, N. 1994, 'Rigid Fused Oligoporphyrins As Potential Versatile Molecular Wires .1. Geometry And Connectivity Of 1,4,5,8-Tetraazaanthracene-Bridged Systems', Journal Of Physical Chemistry, vol. 98, no. 46, pp. 11878-11884.
View/Download from: Publisher's site
Zeng, J., Craw, J., Hush, N. & Reimers, J.R. 1994, 'Solvent Effects On Molecular And Ionic Spectra .4. Photochemistry Of Fe2+(H2O)(6) In Water Revisited - Possible Mechanisms For The Primary Absorption Process Leading To Electron Ejection', JOURNAL OF PHYSICAL CHEMISTRY, vol. 98, no. 43, pp. 11075-11088.
View/Download from: Publisher's site
Reimers, J.R., Craw, J. & Hush, N. 1993, 'Solitons In Finite And Infinite Length Negative-Defect Transpolyacetylene And The Corresponding Brooker (Polymethinecyanine) Cations .3. Relation Between Predicted Soliton Charge-Density Wave Structure Of Odd Polyene Anions And C-13 Nmr Chemical-Shif', Journal Of Physical Chemistry, vol. 97, no. 11, pp. 2778-2787.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1993, 'Enthalpy Of Hydration And Partial Molar Specific Volume As Criteria For Evaluation Of Intermolecular Potentials - Npt-Ensemble Monte-Carlo Calculations For Dilute Neon In Water', Chemical Physics Letters, vol. 206, no. 1-Apr, pp. 318-322.
View/Download from: Publisher's site
Zeng, J., Craw, J., Hush, N. & Reimers, J.R. 1993, 'Medium Effects On Molecular And Ionic Electronic-Spectra - Application To The Lowest 1(N, Pi-Asterisk) State Of Dilute Pyridine In Water', Chemical Physics Letters, vol. 206, no. 1-Apr, pp. 323-328.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1993, 'Solvent Effects On Molecular-Spectra .2. Simulations Of Hydrated Clusters And Dilute-Solutions Of Pyrimidine In Its Lowest (N,Pi-Asterisk) Singlet Excited-State', Journal Of Chemical Physics, vol. 99, no. 3, pp. 1496-1507.
View/Download from: Publisher's site
Zeng, J., Hush, N. & Reimers, J.R. 1993, 'Solvent Effects On Molecular-Spectra .3. Absorption To And Emission From The Lowest Singlet (N,Pi-Asterisk) State Of Dilute Pyrimidine In Water', Journal Of Chemical Physics, vol. 99, no. 3, pp. 1508-1521.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1993, 'Hole, Electron And Energy-Transfer Through Bridged Systems .8. Soliton Molecular Switching In Symmetry-Broken Brooker (Polymethinecyanine) Cations', Chemical Physics, vol. 176, no. 2-Mar, pp. 407-420.
View/Download from: Publisher's site
Reimers, J.R., Craw, J., Wong, A., Bacskay, G. & Hush, N. 1993, 'Comparison Of Soliton Geometry And Charge-Density-Wave Structure, And Band-Gaps, Between Odd Polyene And Symmetrical Polymethine Cyanine (Brooker) Ions And T-Polyacetylene-Scf And Model Hamiltonian Approaches With Implications For Molecular Wires And', Molecular Crystals And Liquid Crystals Science And Technology Section A-Molecular Crystals And Liquid Crystals, vol. 234, pp. 51-57.
View/Download from: Publisher's site
Zeng, J., Craw, J., Hush, N. & Reimers, J.R. 1993, 'Solvent Effects On Molecular-Spectra .1. Normal-Pressure And Temperature Monte-Carlo Simulations Of The Structure Of Dilute Pyrimidine In Water', JOURNAL OF CHEMICAL PHYSICS, vol. 99, no. 3, pp. 1482-1495.
View/Download from: Publisher's site
Reimers, J.R., Craw, J.S. & Hush, N.S. 1993, 'Relation between predicted soliton charge-density wave structure of odd polyene anions and 13C NMR chemical shifts', Journal of Physical Chemistry, vol. 97, no. 11, pp. 2778-2787.
The charge-density wave and geometric soliton structures of ,-diphenyl odd polyene ions (C6H5)2(CH)2n+1- with chain length 2n + 1 = 1-21, 29, 31, and 41 are calculated using AM1. Qualitatively, the effects of a phenyl end group on a polyene chain are predicted to be similar to the effects of extending the chain by three CH units. Hence, phenyl substitution is not expected to affect the properties of an infinite chain; the predicted geometric soliton bond-length alternation is ri = 0.095 &plusmn; 0.002 &Aring; and half-width is l = 7.0 &plusmn; 0.2 while the entire net ionic charge is localized on the soliton whose charge-density-wave half-width is l = 9.1 &plusmn; 0.3. For the shorter ions, experimental estimates of the charge-density-wave properties are made assuming various 13C NMR atomic chemical shift to atomic charge correlations. Use of the O'Brien postulate, according to which individual charges and shifts correlate in the same way as do their averages, is shown to be suspect by the AM1 calculations and predicts l = 13 &plusmn; 1.5; other correlations which relate the observed chemical shifts to AMI charges predict that l could be as low as 7. It is demonstrated that it is important not to consider individual atomic charges and chemical shifts, which are affected by the problems associated with determining CC bond polarizations (or bond ionicities), but rather to combine atomic charges into average bond charges and atomic chemical shifts into average bond chemical shifts. Given this, the Su-Schrieffer-Heeger soliton model is shown to provide an excellent description of the deduced charge-density wave. &copy; 1993 American Chemical Society.
Craw, J., Reimers, J.R., Bacskay, G., Wong, A. & Hush, N. 1992, 'Solitons In Finite-Length And Infinite-Length Negative-Defect Transpolyacetylene And The Corresponding Brooker (Polymethinecyanine) Cations .1. Geometry', Chemical Physics, vol. 167, no. 1-Feb, pp. 77-99.
View/Download from: Publisher's site
Craw, J., Reimers, J.R., Bacskay, G., Wong, A. & Hush, N. 1992, 'Solitons In Finite-Length And Infinite-Length Negative-Defect Transpolyacetylene And The Corresponding Brooker (Polymethinecyanine) Cations .2. Charge-Density Wave', Chemical Physics, vol. 167, no. 1-Feb, pp. 101-109.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1991, 'Electronic-Properties Of Transition-Metal Complexes Determined From Electroabsorption (Stark) Spectroscopy .2. Mononuclear Complexes Of Ruthenium(Ii)', Journal Of Physical Chemistry, vol. 95, no. 24, pp. 9773-9781.
View/Download from: Publisher's site
Hush, N., Wong, A., Bacskay, G. & Reimers, J.R. 1990, 'Electron And Energy-Transfer Through Bridged Systems .6. Molecular Switches - The Critical-Field In Electric-Field Activated Bistable Molecules', Journal Of The American Chemical Society, vol. 112, no. 11, pp. 4192-4197.
View/Download from: Publisher's site
Reimers, J.R., Hush, N., Sammeth, D. & Callis, P. 1990, '2-Photon Fluorescence Excitation Spectrum Of A Naphthalene Norbornylog - Implications For Electron-Transfer', Chemical Physics Letters, vol. 169, no. 6, pp. 622-626.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1990, 'Electron-Transfer And Energy-Transfer Through Bridged Systems .2. Tight-Binding Linkages With Zero Asymptotic Band-Gap', Chemical Physics, vol. 146, no. 1-Feb, pp. 89-103.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1990, 'Spectroscopic Evidence For Electronically Forbidden But Vibronically Allowed Long-Range Electron-Transfer In Norbornylog-Bridged Naphthalene-Diacyanoethylene Systems', Chemical Physics, vol. 146, no. 1-Feb, pp. 105-114.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1990, 'Electron-Transfer And Energy-Transfer Through Bridged Systems .4. Intermetallic Coupling And Electronic-Spectra Of The Bis(Pentaammineruthenium) Complexes Of Alpha,Omega-Dipyridyl Trans-Polyenes In D2O', Inorganic Chemistry, vol. 29, no. 19, pp. 3686-3697.
View/Download from: Publisher's site
Reimers, J.R. & Hush, N. 1990, 'Electron-Transfer And Energy-Transfer Through Bridged Systems .5. Intermetallic Coupling And Electronic-Spectra Of The Bis(Pentaammineruthenium) Complexes Of Alpha,Omega-Dipyridyl Trans-Polyenes In Nitrobenzene', Inorganic Chemistry, vol. 29, no. 22, pp. 4510-4513.
View/Download from: Publisher's site
HUSH, N. & REIMERS, J. 1990, 'BRIDGING LIGANDS AS ELECTRON-TRANSFER MEDIATORS', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 200, pp. 49-INOR.
REIMERS, J. & HUSH, N. 1990, 'FORMALISM FOR ELECTRON-TRANSFER AND ENERGY-TRANSFER IN BRIDGED SYSTEMS', ADVANCES IN CHEMISTRY SERIES, no. 226, pp. 27-63.
HUSH, N. & REIMERS, J. 1990, 'RAPID ELECTRONICALLY FORBIDDEN BUT VIBRONICALLY ALLOWED ELECTRON-TRANSFER', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 200, pp. 87-PHYS.
Reimers, J.R. & Hush, N. 1989, 'Electron-Transfer And Energy-Transfer Through Bridged Systems .1. Formalism', Chemical Physics, vol. 134, no. 2-Mar, pp. 323-354.
View/Download from: Publisher's site
Reimers, J.R. & Heller, E. 1988, 'On The Relationship Between The Classical, Semiclassical, And Quantum Dynamics Of A Morse Oscillator', Journal Of Physical Chemistry, vol. 92, no. 11, pp. 3225-3235.
View/Download from: Publisher's site
Heller, E., Reimers, J.R. & Drolshagen, G. 1987, 'Classical And Semiclassical Approximations For Incoherent Neutron-Scattering', Physical Review A, vol. 36, no. 6, pp. 2613-2627.
View/Download from: Publisher's site
Bergsma, J., Edelsten, P., Gertner, B., Huber, K., Reimers, J.R., Wilson, K., Wu, S. & Hynes, J. 1986, 'Dynamics Of The A + Bc Reaction In Solution', Chemical Physics Letters, vol. 123, no. 5, pp. 394-398.
View/Download from: Publisher's site
Mills, M., Reimers, J.R. & Watts, R. 1986, 'Monte-Carlo Simulation Of The Oh Stretching Spectrum Of Solutions Of Kcl, Kf, Licl And Lif In Water', Molecular Physics, vol. 57, no. 4, pp. 777-791.
View/Download from: Publisher's site
Reimers, J.R. & Heller, E. 1986, 'The Exact Eigenfunctions And Eigenvalues Of A Particle In A Box Obtained Using Gaussian Wavepacket Dynamics', Journal Of Physics A-Mathematical And General, vol. 19, no. 13, pp. 2559-2571.
View/Download from: Publisher's site
Bergsma, J., Reimers, J.R., Wilson, K. & Hynes, J. 1986, 'Molecular-Dynamics Of The A+Bc Reaction In Rare-Gas Solution', Journal Of Chemical Physics, vol. 85, no. 10, pp. 5625-5643.
View/Download from: Publisher's site
WILSON, K., BERGSMA, J., EDELSTEN, P., GERTNER, B., REIMERS, J., ALI, D. & HYNES, J. 1986, 'MOLECULAR-DYNAMICS OF CHARGE AND ATOM TRANSFER-REACTIONS', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 191, pp. 204-PHYS.
Reimers, J.R., Wilson, K., Heller, E. & Langhoff, S. 1985, 'Casscf-Wave Packet Abinitio Prediction Of Electronic And Vibrational-Spectra - Application To The A(2Pi)[-X(2Sigma+) Absorption Of C2H At 3000-K', Journal Of Chemical Physics, vol. 82, no. 11, pp. 5064-5077.
View/Download from: Publisher's site
Reimers, J.R. & Heller, E. 1985, 'The Exact Eigenfunctions And Eigenvalues Of A Two-Dimensional Rigid Rotor Obtained Using Gaussian Wave Packet Dynamics', Journal Of Chemical Physics, vol. 83, no. 2, pp. 511-515.
View/Download from: Publisher's site
Reimers, J.R. & Heller, E. 1985, 'The Exact Thermal Rotational Spectrum Of A Two-Dimensional Rigid Rotor Obtained Using Gaussian Wave Packet Dynamics', Journal Of Chemical Physics, vol. 83, no. 2, pp. 516-520.
View/Download from: Publisher's site
BERGSMA, J., EDELSTEN, P., GERTNER, B., HUBER, K., REIMERS, J., WILSON, K., WU, S. & HYNES, J. 1985, 'DYNAMICS OF THE A+BC REACTION IN SOLUTION', ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, vol. 190, no. SEP, pp. 118-PHS.
Reimers, J.R. & Watts, R. 1984, 'The Structure And Vibrational-Spectra Of Small Clusters Of Water-Molecules', Chemical Physics, vol. 85, no. 1, pp. 83-112.
View/Download from: Publisher's site
Reimers, J.R. & Watts, R. 1984, 'The Structure, Thermodynamic Properties And Infrared-Spectra Of Liquid Water And Ice', Chemical Physics, vol. 91, no. 2, pp. 201-223.
View/Download from: Publisher's site
Reimers, J.R. & Watts, R. 1984, 'A Local Mode Potential Function For The Water Molecule', Molecular Physics, vol. 52, no. 2, pp. 357-381.
View/Download from: Publisher's site
Reimers, J.R. & Watts, R.O. 1984, 'The structure and vibrational spectra of small clusters of water molecules', Chemical Physics, vol. 85, no. 1, pp. 83-112.
View/Download from: Publisher's site
A potential surface for deformable water molecules is constructed using an accurate local-mode intramolecular model together with a realistic semi-empirical intermolecular interaction. Locally stable structures for (H2O)n, n = 2, 3 and 4, are reported and their vibrational frequencies calculated using both normal-mode analysis with variational corrections for anharmonicities, and local-mode analysis. It is shown that experimentally observed changes in vibrational frequencies on cluster formation arise from anharmonic terms in the monomer potential that become significant due to distortions to the equilibrium geometry. Inhomogeneous line shapes are calculated using rigid-rotor theory, linear response theory, non-equilibrium molecular dynamics and a semi-classical method based on classical Monte Carlo trajectory propagation and local-mode spectral analysis. The last method gives a satisfactory description of the density of states in the intramolecular vibrational region of the spectrum. Dipole moment functions including polarisation give infrared intensities in good agreement with available experimental data. &copy; 1984 Elsevier Science Publishers B.V.
Reimers, J.R. & Watts, R. 1983, 'Analysis Of The Oh Bend And Stretch Region In The Vibrational-Spectrum Of Water', Chemical Physics Letters, vol. 94, no. 2, pp. 222-226.
View/Download from: Publisher's site
Reimers, J.R., Wilson, K. & Heller, E. 1983, 'Complex Time-Dependent Wave Packet Technique For Thermal-Equilibrium Systems - Electronic-Spectra', Journal Of Chemical Physics, vol. 79, no. 10, pp. 4749-4757.
View/Download from: Publisher's site
Coker, D., Reimers, J.R. & Watts, R. 1982, 'The Infrared-Absorption Spectrum Of Water', Australian Journal Of Physics, vol. 35, no. 5, pp. 623-638.
View/Download from: Publisher's site
Reimers, J.R., Watts, R. & Klein, M. 1982, 'Intermolecular Potential Functions And The Properties Of Water', Chemical Physics, vol. 64, no. 1, pp. 95-114.
View/Download from: Publisher's site
Fischer, G., Reimers, J.R. & Ross, I. 1981, 'Cndo-Calculation Of 2Nd-Order Vibronic Coupling In The 1B2U-1A1G Transition Of Benzene', Chemical Physics, vol. 62, no. 1-Feb, pp. 187-193.
View/Download from: Publisher's site
Chappell, P., Fischer, G., Reimers, J.R. & Ross, I. 1981, 'Electronic-Spectrum Of 1,5-Naphthyridine - Theoretical Treatment Of Vibronic Coupling', Journal Of Molecular Spectroscopy, vol. 87, no. 2, pp. 316-330.
View/Download from: Publisher's site

International Centre for Quantum and Molecular Structures, Shanghai University.