Jeffrey R. Reimers

University of Sydney, Sydney, New South Wales, Australia

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Publications (167)494.89 Total impact

  • [Show abstract] [Hide abstract]
    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; · 4.20 Impact Factor
  • 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; · 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. · 3.84 Impact Factor
  • Physics of Life Reviews 11/2013; · 6.58 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; · 5.39 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; · 4.20 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 01/2013; 3:2761. · 5.08 Impact Factor
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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.
  • 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. · 4.20 Impact Factor
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    ABSTRACT: 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.
    The Journal of Chemical Physics 12/2011; 135(24):244110. · 3.12 Impact Factor
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    ABSTRACT: The exceptionally long lived charge separation previously observed in a β,β′-pyrrolic-fused ferrocene-porphyrin-fullerene triad (lifetime 630 μs) and related porphyrin-fullerene dyad (lifetime 260 μs) is attributed to the production of triplet charge-separated states. Such molecular excited-state spin polarization maintained over distances of up to 23 Å 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 π-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 μs-timescale process attributed to triplet recombination.
    Chemical Science 11/2011; 3(1):257-269. · 8.31 Impact Factor
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    ABSTRACT: 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.
    International Quantum Electronics Conference; 08/2011
  • International Quantum Electronics Conference; 08/2011
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    ABSTRACT: 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 α 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.
    Journal of the American Chemical Society 08/2011; 133(38):14856-9. · 10.68 Impact Factor
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    ABSTRACT: 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.
    Organic Letters 08/2011; 13(18):4770-3. · 6.14 Impact Factor
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    ABSTRACT: Scanning-tunneling microscopy (STM) under electrochemical control (in situ STM) in aqueous solution, combined with a priori density functional theory (DFT) image simulations at room temperature, reveals the atomic nature of the interface between Au(111) and self-assembled monolayers (SAMs) of 1-propanethiol and 1-butanethiol. Use of single-crystal gold substrates allows for both high-resolution images of the surface cell internal structure and the evaluation of pit densities on large surface terraces, while room-temperature STM image simulations facilitate discrimination between possible atomic interface structures. For both adsorbates, the high-coverage c(4 × 2) phase is identified as (3 × 2√3)-4, while the medium-coverage striped phase of 1-propanethiol SAMs is identified as (7 × √3)-4. All of these structures contain two adatom-bound adsorbates of the form RS–Au–SR (R = CnH2n+1S•) per surface unit cell. The observed pit coverages of 2.8–4.0% are much less than those typically found for methanethiol SAMs (ca. 12–20%), indicating that one of the two gold adatoms per cell in 1-propanethiol and 1-butanethiol SAMs is extracted to form a local surface vacancy rather than a coalesced surface pit. The surface vacancy appears free to diffuse within each cell on the STM time scale, with only small STM image changes associated with vacancy localization. Significantly, the c(4 × 2) phases of 1-propanethiol and 1-butanethiol SAMs give quite different STM images. 1-Butanethiol SAMs show characteristics similar to those of longer linear alkanethiols with four bright spots per cell, while the 1-propanethiol SAM displays five bright spots organized in a different pattern. These differences are rationalized by a more uniform vacancy distribution and rigid structure for 1-butanethiol SAMs, compared to the different diffusionally labile vacancy configurations and higher lateral S–C–C–C conformational flexibility found for 1-propanethiol. Also, the differences in interface structure from that of methanethiol SAMs are rationalized in terms of varying pit coalescence energies. These subtle differences underline the striking diversity in the electronic and molecular structural packing even within a single class of closely related molecular adsorbates.
    The Journal of Physical Chemistry C 05/2011; 115:10630-10639. · 4.84 Impact Factor
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    ABSTRACT: The metal complexation properties of the naturally occurring Maillard reaction product isomaltol HL(2) are investigated by measurement of its stability constants with copper(II), zinc(II), and iron(III) using potentiometric pH titrations in water, by structural and magnetic characterization of its crystalline complex, [Cu(L(2))(2)]·8H(2)O, and by density functional theory calculations. Strong complexation is observed to form the bis(isomaltolato)copper(II) complex incorporating copper in a typical (pseudo-)square-planar geometry. In the solid state, extensive intra- and intermolecular hydrogen bonding involving all three oxygen functions per ligand assembles the complexes into ribbons that interact to form two-dimensional arrays; further hydrogen bonds and π interactions between the furan moiety of the anionic ligands and adjacent copper(II) centers connect the complexes in the third dimension, leading to a compact polymeric three-dimensional (3D) arrangement. The latter interactions involving copper(II), which represent an underappreciated aspect of copper(II) chemistry, are compared to similar interactions present in other copper(II) 3D structures showing interactions with benzene molecules; the results indicate that dispersion forces dominate in the π system to chelated copper(II) ion interactions.
    Inorganic Chemistry 02/2011; 50(4):1498-505. · 4.59 Impact Factor
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    ABSTRACT: Low- and high-resolution absorption and fluorescence emission Q(y) 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 Q(y) 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.
    The Journal of Chemical Physics 01/2011; 134(2):024506. · 3.12 Impact Factor
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    ABSTRACT: The atomic structure 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 porphyrin 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 structures 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.
    Journal of Physical Chemistry Letters 12/2010; 2(2):62–66. · 6.59 Impact Factor

Publication Stats

1k Citations
494.89 Total Impact Points

Institutions

  • 1989–2013
    • University of Sydney
      • School of Chemistry
      Sydney, New South Wales, Australia
  • 2011
    • Griffith University
      • Center for Clean Environment and Energy
      Southport, Queensland, Australia
  • 2008
    • University of New South Wales
      • School of Chemistry
      Kensington, New South Wales, Australia
  • 2007–2008
    • University of Houston
      • Department of Chemistry
      Houston, TX, United States
    • University of Tartu
      • Institute of Physics
      Tartu, Tartumaa, Estonia
  • 2006
    • University of Queensland
      Brisbane, Queensland, Australia
  • 2005
    • Australian National University
      Canberra, Australian Capital Territory, Australia
    • Technical University of Denmark
      • Department of Chemistry
      Copenhagen, Capital Region, Denmark
  • 2004
    • University of Liverpool
      • Surface Science Research Centre
      Liverpool, England, United Kingdom
    • Charles Sturt University
      Уогга Уогга, New South Wales, Australia