Jeffrey R. Reimers

Shanghai University, Shanghai, Shanghai Shi, China

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Publications (138)588.89 Total impact

  • Jeffrey Robert Reimers · Ross H McKenzie · Laura K McKemmish · Noel S Hush
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    ABSTRACT: 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 (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 investigated pertinent to: ammonia inversion, aromaticity in benzene, the Creutz-Taube ion, the bacterial photosynthetic reaction centre, BNB, the molecular conductor Alq3, and inverted-region charge recombination in a ferrocene-porphyrin-fullerene triad photosynthetic model compound. Throughout, the fundamental nature of BO breakdown is linked to the properties of the Cusp Catastrophe: the cusp diameter is shown to determine the magnitudes of all couplings, numerical basis-set and trajectory-integration requirements, and to determine the transmission coefficient  used to understand deviations from transition-state theory.
    Physical Chemistry Chemical Physics 07/2015; DOI:10.1039/C5CP02238J · 4.20 Impact Factor
  • Jeffrey Robert Reimers · Laura K McKemmish · Ross H McKenzie · Noel S Hush
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    ABSTRACT: 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 N2H7+, 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.
    Physical Chemistry Chemical Physics 07/2015; DOI:10.1039/C5CP02236C · 4.20 Impact Factor
  • Laura K McKemmish · Ross H McKenzie · Noel S Hush · Jeffrey Robert Reimers
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    ABSTRACT: 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, qualitatively differently behavior is found compared to traditional properties of the density matrix and hence entanglement provides new information about system properties. For chemical reactions, this type of entanglement simply builds up as the transition-state region is crossed. It is robust to small changes in parameter values and is therefore more attractive for making quantum qubits than is the related fragile ground-state entanglement, provided that coherent motion at the transition state can be sustained.
    Physical Chemistry Chemical Physics 07/2015; DOI:10.1039/C5CP02239H · 4.20 Impact Factor
  • Jeffrey Robert Reimers · Laura K McKemmish · Ross H McKenzie · Noel S Hush
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    ABSTRACT: Ammonia adopts sp3 hybridization (HNH bond angle 108) whereas the other members of the XH3 series PH3, AsH3, SbH3, and BiH3 instead prefer octahedral bond angles of 90-93. 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 NH3 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 XH3+ 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 = 101.5. The multiple states and associated multiple conical intersection seams controlling the ground-state structure of XH3 renormalize this to = 86.7. Depending on the ratio of the resonance energy to the reorganization energy, equilibrium angles can vary from these limiting values up to 120, and the anomalously large bond angle in NH3 arises because the resonance energy is unexpectedly large. This occurs as the ordering of the lowest Rydberg orbital and the * orbital swap, allowing Rydbergization to compresses * to significantly increase the resonance energy. Failure of both the traditional and revised versions of the valence-shell electron-pair repulsion (VSEPR) theory to explain the ground-state structures in simple terms is attributed to exclusion of this key physical interaction.
    Physical Chemistry Chemical Physics 07/2015; DOI:10.1039/C5CP02237A · 4.20 Impact Factor
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    ABSTRACT: In situ scanning tunneling microscopy combined with density functional theory molecular dynamics simulations reveal a complex structure for the self-assembled monolayer (SAM) of racemic 2-butanethiol on Au(111) in aqueous solution. Six adsorbate molecules occupy a (10×√3)R30° cell organized as two RSAuSR adatom-bound motifs plus two RS species bound directly to face-centered-cubic and hexagonally close-packed sites. This is the first time that these competing head-group arrangements have been observed in the same ordered SAM. Such unusual packing is favored as it facilitates SAMs with anomalously high coverage (30 %), much larger than that for enantiomerically resolved 2-butanethiol or secondary-branched butanethiol (25 %) and near that for linear-chain 1-butanethiol (33 %).
    ChemPhysChem 02/2015; 16(5). DOI:10.1002/cphc.201402904 · 3.36 Impact Factor
  • Rika Kobayashi · Jeffrey R. Reimers
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    ABSTRACT: 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.
    Molecular Physics 01/2015; DOI:10.1080/00268976.2014.1003620 · 1.64 Impact Factor
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    ABSTRACT: The S1←S0 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.
    The Journal of Chemical Physics 01/2015; 142(1):014301. DOI:10.1063/1.4904267 · 3.12 Impact Factor
  • Lars Goerigk · Charles A. Collyer · Jeffrey R. Reimers
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    ABSTRACT: 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 serves as a reliable benchmark. We not only analyze root-mean-square deviations from the experimental Cartesian coordinates, but, for the first time, also 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 its 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.
    The Journal of Physical Chemistry B 11/2014; 118:14612. DOI:10.1021/jp510148h · 3.30 Impact Factor
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    ABSTRACT: The rich stereochemistry of the self-assembled monolayers (SAMs) of the four butanethiols on Au(111) is described, 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 (DFT) molecular dynamics STM-image simulations. Even though butanethiol SAMs manifest strong head-group interactions, steric interactions are shown to dominate SAM structure and chirality. Indeed, steric interactions are shown to dictate the nature of the head-group itself: whether it takes on the adatom-bound motif RS•Au(0)S•R or else involves direct binding of RS• to face-centered cubic (FCC) or hexagonal close-packed (HCP) 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.
    Journal of the American Chemical Society 11/2014; 136(49). DOI:10.1021/ja508100c · 11.44 Impact Factor
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    ABSTRACT: Simultaneously measured absorption (ABS) and magnetic circular dichroism (MCD) spectra of the Q-bands of chlorophyll-a (Chl-a) in ether over 150-186 K reveal that the species that forms at low temperature is a chlorophyll hydrate rather than a diether complex. We have recently proposed a new assignment paradigm for the spectra of chlorophillides which, for the first time, quantitatively accounts for a wide range of observed data. Observations performed at low temperature in ether have historically been very important for the interpretation of the spectra of Chl-a. While our assignment for this system initially anticipated only small spectral changes as the temperature is lowered, significant changes are known to occur. Extensive CAM-B3LYP time-dependent density-functional theory (TD-DFT) calculations verify that the observed spectra of the hydrated species conforms to expectations based on our new assignment, as well as supporting the feasibility of the proposed hydration reactions.
    Physical Chemistry Chemical Physics 12/2013; 16(6). DOI:10.1039/c3cp53729c · 4.20 Impact Factor
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    Jeffrey R Reimers · Elmars Krausz
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    ABSTRACT: 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.
    Physical Chemistry Chemical Physics 12/2013; 16(6). DOI:10.1039/c3cp53730g · 4.20 Impact Factor
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    ABSTRACT: 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 μ-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.
    Nanotechnology 11/2013; 24(50):505202. DOI:10.1088/0957-4484/24/50/505202 · 3.67 Impact Factor
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    Physics of Life Reviews 11/2013; 11(1). DOI:10.1016/j.plrev.2013.11.003 · 9.48 Impact Factor
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    ABSTRACT: 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 Qx → Qy relaxation. Whilst most chlorophylls conform to the Gouterman model and display two independent transitions Qx (S2) and Qy (S1), 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 Qx 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.
    Scientific Reports 09/2013; 3:2761. DOI:10.1038/srep02761 · 5.58 Impact Factor
  • Lars Goerigk · Jeffrey R. Reimers
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    ABSTRACT: 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 Hobza’s 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 Grimme’s 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 Grimme’s 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-ζ 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 Grimme’s 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.
    Journal of Chemical Theory and Computation 06/2013; 9(7). DOI:10.1021/ct400321m · 5.31 Impact Factor
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    ABSTRACT: 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.
    Physical Chemistry Chemical Physics 04/2013; 15(30). DOI:10.1039/c3cp50829c · 4.20 Impact Factor
  • Lars Goerigk · Olle Falklöf · Charles A. Collyer · Jeffrey R. Reimers
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    ABSTRACT: 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 Å. 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 are found between method quality, perceived from small-molecule studies and changes in the R factor, indicating both the high quality of the original refinement but also indicating which methods will be most useful in subsequent full-protein refinements using imbedded DFT constraints.
    08/2012: chapter 6: pages 87-120; Springer.
  • Shiwei Yin · Lanlan Li · Yongmei Yang · Jeffrey R. Reimers
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    ABSTRACT: Quantitative agreement has been found between observed and calculated charge mobilities through organic conductors, despite the use of many assumptions in the calculations, including: the relative strength of the intermolecular electronic coupling to the reorganization energy driving charge localization, the treatment of site variability in the material, the involvement of tunneling processes during charge hopping between sites, the use of weak-coupling-based perturbation theory to determine hopping rates, the residence times for charges on sites, the effect of the large field strengths used in experimental studies, the general appropriateness of simple one-dimensional diffusion modeling approaches, and the involvement of molecular excited states of the ions. We investigate the impact of these assumptions, concluding that all may be very significant. In some cases, methodological options are considered, and optimum procedures are determined, showing that (i) the use of Koopmans' theorem to estimate intermolecular couplings in solids is problematic and (ii) the correct expression for the residence lifetime of a charge on a crystal site. These conclusions are drawn from simulations of anisotropic charge mobilities through the β phase of mer-tris(8-hydroxyquinolinato)aluminum(III) (Alq3) crystal, a material commonly used in OLED applications. Calculations are compared that determine mobilities at finite applied field from drift velocities through either semianalytical solutions of the master equation or else kinetic Monte Carlo simulations, as well as those that determine mobilities from multidimensional diffusion coefficients at zero field by Monte Carlo and those that analytically solve simplified one-dimensional diffusion models. For crystalline Alq3 itself, the calculations predict electron mobilities that are 4–6 orders of magnitude larger than those predicted by similar methods for amorphous Alq3, in agreement with experimental findings. This work vindicates recent theories describing the poor mobilities of the amorphous material, forming a complete basic picture for Alq3 conductivity.
    The Journal of Physical Chemistry C 07/2012; 116(28):14826–14836. DOI:10.1021/jp303724r · 4.77 Impact Factor
  • Jeffrey R Reimers · Zheng-Li Cai
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    ABSTRACT: A unified picture is presented of water interacting with pyridine, pyridazine, pyrimidine, and pyrazine on the S(1) manifold in both gas-phase dimers and in aqueous solution. As (n,π*) excitation to the S(1) state removes electrons from the ground-state hydrogen bond, this analysis provides fundamental understanding of excited-state hydrogen bonding. Traditional interpretations view the excitation as simply breaking hydrogen bonds to form dissociated molecular products, but reactive processes such as photohydrolysis and excited-state proton coupled electron transfer (PCET) are also possible. Here we review studies performed using equations-of-motion coupled-cluster theory (EOM-CCSD), multireference perturbation theory (CASPT2), time-dependent density-functional theory (TD-DFT), and excited-state Monte Carlo liquid simulations, adding new results from symmetry-adapted-cluster configuration interaction (SAC-CI) and TD-DFT calculations. Invariably, gas-phase molecular dimers are identified as stable local minima on the S(1) surface with energies less than those for dissociated molecular products. Lower-energy biradical PCET minima are also identified that could lead to ground-state recombination and hence molecular dissociation, dissociation into radicals or ions, or hydration reactions leading to ring cleavage. For pyridine.water, the calculated barriers to PCET are low, suggesting that this mechanism is responsible for fluorescence quenching of pyridine.water at low energies rather than accepted higher-energy Dewar-benzene based "channel three" process. Owing to (n,π*) excitation localization, much higher reaction barriers are predicted for the diazines, facilitating fluorescence in aqueous solution and predicting that the as yet unobserved fluorescence from pyridazine.water and pyrimidine.water should be observable. Liquid simulations based on the assumption that the solvent equilibrates on the fluorescence timescale quantitatively reproduce the observed spectral properties, with the degree of (n,π*) delocalization providing a critical controlling factor.
    Physical Chemistry Chemical Physics 04/2012; 14(25):8791-802. DOI:10.1039/c2cp24040h · 4.20 Impact Factor
  • Olle Falklöf · Charles A. Collyer · Jeffrey R. Reimers
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    ABSTRACT: The refinement of protein crystal structures currently involves the use of empirical restraints and force fields that are known to work well in many situations but nevertheless yield structural models with some features that are inconsistent with detailed chemical analysis and therefore warrant further improvement. Ab initio electronic structure computational methods have now advanced to the point at which they can deliver reliable results for macromolecules in realistic times using linear-scaling algorithms. The replacement of empirical force fields with ab initio methods in a final refinement stage could allow new structural features to be identified in complex structures, reduce errors and remove computational bias from structural models. In contrast to empirical approaches, ab initio refinements can only be performed on models that obey basic qualitative chemical rules, imposing constraints on the parameter space of existing refinements, and this in turn inhibits the inclusion of unlikely structural features. Here, we focus on methods for determining an appropriate ensemble of initial structural models for an ab initio X-ray refinement, modeling as an example the high-resolution single-crystal X-ray diffraction data reported for the structure of lysozyme (PDB entry “2VB1”). The AMBER force field is used in a Monte Carlo calculation to determine an ensemble of 8 structures that together embody all of the partial atomic occupancies noted in the original refinement, correlating these variations into a set of feasible chemical structures while simultaneously retaining consistency with the X-ray diffraction data. Subsequent analysis of these results strongly suggests that the occupancies in the empirically refined model are inconsistent with protein energetic considerations, thus depicting the 2VB1 structure as a deep-lying minimum in its optimized parameter space that actually embodies chemically unreasonable features. Indeed, density-functional theory calculations for one specific nitrate ion with an occupancy of 62% indicate that water replaces this ion 38% of the time, a result confirmed by subsequent crystallographic analysis. It is foreseeable that any subsequent ab initio refinement of the whole structure would need to locate a globally improved structure involving significant changes to 2VB1 which correct these identified local structural inconsistencies.
    Theoretical Chemistry Accounts 01/2012; 131(1). DOI:10.1007/s00214-011-1076-8 · 2.14 Impact Factor

Publication Stats

3k Citations
588.89 Total Impact Points

Institutions

  • 2015
    • Shanghai University
      Shanghai, Shanghai Shi, China
  • 2014
    • University of Technology Sydney
      • School of Physics and Advanced Materials
      Sydney, New South Wales, Australia
  • 1993–2013
    • University of Sydney
      • School of Chemistry
      Sydney, New South Wales, Australia
  • 2008
    • University of New South Wales
      • School of Chemistry
      Kensington, New South Wales, Australia
  • 2007
    • Massey University
      Palmerston North City, Manawatu-Wanganui, New Zealand
    • University of Houston
      • Department of Chemistry
      Houston, TX, United States
    • Ocean University of China
      • College of Chemistry and Chemical Engineering
      Tsingtao, Shandong Sheng, China
  • 2006–2007
    • Universität Bremen
      Bremen, Bremen, Germany
    • University of North Carolina at Chapel Hill
      • Department of Chemistry
      North Carolina, United States
  • 2005–2007
    • Technical University of Denmark
      • Department of Chemistry
      Lyngby, Capital Region, Denmark
  • 2004
    • Charles Sturt University
      Уогга Уогга, New South Wales, Australia