Efficient methods for the quantum chemical treatment of protein structures: The effects of London-dispersion and basis-set incompleteness on peptide and water-cluster geometries

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. © 2013 American Chemical Society

Free energies for the coordination of ligands to the magnesium of chlorophyll-a in solvents

© 2015 Taylor & Francis. 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 quantum cellular automata cell design trade-offs: latching vs. power dissipation.

The use of molecules to enact quantum cellular automata (QCA) cells has been proposed as a new way for performing electronic logic operations at sub-nm dimensions. A key question that arises concerns whether chemical or physical processes are to be exploited. The use of chemical reactions allows the state of a switch element to be latched in molecular form, making the output of a cell independent of its inputs, but costs energy to do the reaction. Alternatively, if purely electronic polarization is manipulated then no internal latching occurs, but no power is dissipated provided the fields from the inputs change slowly compared to the molecular response times. How these scenarios pan out is discussed by considering calculated properties of the 1,4-diallylbutane cation, a species often used as a paradigm for molecular electronic switching. Utilized are results from different calculation approaches that depict the ion either as a charge-localized mixed-valence compound functioning as a bistable switch, or else as an extremely polarizable molecule with a delocalized electronic structure. Practical schemes for using molecular cells in QCA and other devices emerge

Relating transition-state spectroscopy to standard chemical spectroscopic processes

© 2017 Elsevier B.V. Transition-state spectra are mapped out using generalized adiabatic electron-transfer theory. This simple model depicts diverse chemical properties, from aromaticity, through bound reactions such as isomerizations and atom-transfer processes with classic transition states, to processes often described as being “non-adiabatic”, to those in the “inverted” region that become slower as they are made more exothermic. Predictably, the Born-Oppenheimer approximation is found inadequate for modelling transition-state spectra in the weak-coupling limit. In this limit, the adiabatic Born-Huang approximation is found to perform much better than non-adiabatic surface-hopping approaches. Transition-state spectroscopy is shown to involve significant quantum entanglement between electronic and nuclear motion

Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism

© 2015 Taylor & Francis. The recent advent of dispersion-corrected density-functional theory (DFT) methods allows for quantitative modelling of molecular self-assembly processes, and we consider what is required to develop applications to the formation of large self-assembled monolayers (SAMs) on hydrophobic surfaces from organic solution. Focus is on application of the D3 dispersion correction of Grimme combined with the solvent dispersion model of Floris, Tomasi and Pascual-Ahuir to simulate observed scanning-tunnelling microscopy (STM) images of various polymorphs of tetraalkylporphyrin SAMs on highly oriented pyrolytic graphite surfaces. The most significant problem is identified as the need to treat SAM structures that are incommensurate with those of the substrate, providing a challenge to the use of traditional periodic-imaging boundary techniques. Using nearby commensurate lattices introduces non-systematic errors into calculated lattice constants and free energies of SAM formation that are larger than experimental uncertainties and polymorph differences. Developing non-periodic methods for polymorph interface simulation also remains a challenge. Despite these problems, existing methods can be used to interpret STM images and SAM atomic structures, distinguishing between multiple feasible polymorph types. They also provide critical insight into the factors controlling polymorphism. All this stems from a delicate balance that the intermolecular D3 and solvent Floris, Tomasi and Pascual-Ahuir corrections provide. Combined optimised treatments should yield fully quantitative approaches in the future

Single-photon emitters in hexagonal boron nitride: a review of progress.

This report summarizes progress made in understanding properties such as zero-phonon-line energies, emission and absorption polarizations, electron-phonon couplings, strain tuning and hyperfine coupling of single photon emitters in hexagonal boron nitride. The primary aims of this research are to discover the chemical nature of the emitting centres and to facilitate deployment in device applications. Critical analyses of the experimental literature and data interpretation, as well as theoretical approaches used to predict properties, are made. In particular, computational and theoretical limitations and challenges are discussed, with a range of suggestions made to overcome these limitations, striving to achieve realistic predictions concerning the nature of emitting centers. A symbiotic relationship is required in which calculations focus on properties that can easily be measured, whilst experiments deliver results in a form facilitating mass-produced calculations

Decomposition of Ferrocene on Pt(111) and Its Effect on Molecular Electronic Junctions

© 2019 American Chemical Society. From dilute vapor, ferrocene encountering Pt(111) decomposes, producing bound cyclopentadienyl rings, in contrast to its legendary stability in solution electrochemistry. We propose that decomposition occurs through initial chemisorption, making a Pt-C bond to a ferrocenium hydride, followed by step-edge catalyzed decomposition leading to migration of the Fe atom inside the Pt bulk. These conclusions are based on results from density functional theory (DFT) calculations. When Pt(111) approaches ferrocene tethered to a self-assembled monolayer, only the first, spontaneous but mechanically reversible chemisorption is predicted. Nonequilibrium Green's function calculations utilizing DFT predict that chemisorption increases molecular junction conductivities by a factor of 2-5. This could contribute to the extremely high conductivities observed in junctions supporting rectification up to unprecedented high-frequency cutoffs of ∼520 GHz, though squashed junctions at half monolayer coverage are predicted to conduct 104 times better

Asymmetry in the Qy Fluorescence and Absorption Spectra of Chlorophyll <i>a</i> Pertaining to Exciton Dynamics.

Significant asymmetry found between the high-resolution Q y emission and absorption spectra of chlorophyll-a is herein explained, providing basic information needed to understand photosynthetic exciton transport and photochemical reactions. The Q y spectral asymmetry in chlorophyll has previously been masked by interference in absorption from the nearby Q x transition, but this effect has recently been removed using extensive quantum spectral simulations or else by analytical inversion of absorption and magnetic circular dichroism data, allowing high-resolution absorption information to be accurately determined from fluorescence-excitation spectra. To compliment this, here, we measure and thoroughly analyze the high-resolution differential fluorescence line narrowing spectra of chlorophyll-a in trimethylamine and in 1-propanol. The results show that vibrational frequencies often change little between absorption and emission, yet large changes in line intensities are found, this effect also being strongly solvent dependent. Among other effects, the analysis in terms of four basic patterns of Duschinsky-rotation matrix elements, obtained using CAM-B3LYP calculations, predicts that a chlorophyll-a molecule excited into a specific vibrational level, may, without phase loss or energy relaxation, reemit the light over a spectral bandwidth exceeding 1,000 cm-1 (0.13 eV) to influence exciton-transport dynamics

Getting Past the Language Gap: Innovations in Machine Translation

In this chapter, we will be reviewing state of the art machine translation systems, and will discuss innovative methods for machine translation, highlighting the most promising techniques and applications. Machine translation (MT) has benefited from a revitalization in the last 10 years or so, after a period of relatively slow activity. In 2005 the field received a jumpstart when a powerful complete experimental package for building MT systems from scratch became freely available as a result of the unified efforts of the MOSES international consortium. Around the same time, hierarchical methods had been introduced by Chinese researchers, which allowed the introduction and use of syntactic information in translation modeling. Furthermore, the advances in the related field of computational linguistics, making off-the-shelf taggers and parsers readily available, helped give MT an additional boost. Yet there is still more progress to be made. For example, MT will be enhanced greatly when both syntax and semantics are on board: this still presents a major challenge though many advanced research groups are currently pursuing ways to meet this challenge head-on. The next generation of MT will consist of a collection of hybrid systems. It also augurs well for the mobile environment, as we look forward to more advanced and improved technologies that enable the working of Speech-To-Speech machine translation on hand-held devices, i.e. speech recognition and speech synthesis. We review all of these developments and point out in the final section some of the most promising research avenues for the future of MT

Electron-vibration entanglement in the Born-Oppenheimer description of chemical reactions and spectroscopy

This journal is © the Owner Societies. 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