[Show abstract][Hide abstract] 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; · 11.44 Impact Factor
[Show abstract][Hide abstract] 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. · 3.38 Impact Factor
[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
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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. · 4.84 Impact Factor
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] ABSTRACT: We have modeled the dissociative chemisorption of water on the Si(100)-(2×1) surface using a generalized gradient approximation of density functional theory and a periodic slab model of the surface. For the energetically favorable structures, scanning tunneling microscope topographs of the filled states are simulated. These exhibit distinctively dark characteristics where water "islands" are formed, in agreement with experimental findings. In addition, they indicate that the hydrogen-atom and hydroxyl-radical adducts display somewhat different contrasts. Furthermore, in the case of a partial saturation of a Si dimer a prominent brightness is predicted for the unsaturated Si atoms if their dimer-forming counterparts are saturated by hydroxyl species, while in the case of hydrogen saturation the contrast is rather dim.
Surface Review and Letters 01/2012; 11(02). · 0.37 Impact Factor
[Show abstract][Hide abstract] 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.
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] ABSTRACT: 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 (Hückel) 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.
[Show abstract][Hide abstract] 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. · 8.60 Impact Factor
[Show abstract][Hide abstract] 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
[Show abstract][Hide abstract] 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. · 11.44 Impact Factor