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Journal of Chemical Theory and Computation

Stephan Mohr, Michel Masella, Laura Elizabeth Ratcliff, Luigi Genovese
We present, within Kohn-Sham Density Functional Theory calculations, a quantitative method to identify and assess the partitioning of a large quantum mechanical system into fragments. We then show how within this framework simple generalizations of other well-known population analyses can be used to extract, from first principles, reliable electrostatic multipoles for the identified fragments. Our approach reduces arbitrariness in the fragmentation procedure, and enables the possibility to assess, quantitatively, whether the corresponding fragment multipoles can be interpreted as observable quantities associated to a system's moiety...
July 21, 2017: Journal of Chemical Theory and Computation
Elvis Maradzike, Gergely Gidofalvi, Justin M Turney, Henry F Schaefer, A Eugene DePrince
Analytic energy gradients are presented for a variational two-electron reduced-density matrix (2-RDM)-driven complete active space self-consistent field (CASSCF) method. The active-space 2-RDM is determined using a semidefinite programing (SDP) algorithm built upon an augmented Lagrangian formalism. Expressions for analytic gradients are simplified by the fact that the Lagrangian is stationary with respect to variations in both the primal and dual solutions to the SDP problem. Orbital response contributions to the gradient are identical to those that arise in conventional CASSCF methods in which the electronic structure of the active space is described by a full configuration interaction (CI) wave function...
July 21, 2017: Journal of Chemical Theory and Computation
Elvira R Sayfutyarova, Qiming Sun, Garnet Kin-Lic Chan, Gerald Knizia
We introduce the atomic valence active space (AVAS), a simple and well-defined automated technique for constructing active orbital spaces for use in multi-configuration and multi-reference (MR) electronic structure calculations. Concretely, the technique constructs active molecular orbitals capable of describing all relevant electronic configurations emerging from a targeted set of atomic valence orbitals (e.g., the metal d orbitals in a redcoordination complex). This is achieved via a linear transformation of the occupied and unoccupied orbital spaces from an easily obtainable single-reference wavefunction (such as from a Hartree-Fock or Kohn-Sham calculations) based on projectors to targeted atomic valence orbitals...
July 21, 2017: Journal of Chemical Theory and Computation
Hui Li, Janamejaya Chowdhary, Lei Huang, Xibing He, Alexander D MacKerell, Benoît Roux
Additive force fields are designed to account for induced electronic polarization in a mean-field average way using effective empirical fixed charges. The limitation of this approximation is cause for serious concerns, particularly in the case of lipid membranes, where the molecular environment undergoes dramatic variations over microscopic length scales. A polarizable force field based on the classical Drude oscillator offers a practical and computationally efficient framework for an improved representation of electrostatic interactions in molecular simulations...
July 21, 2017: Journal of Chemical Theory and Computation
Siri Camee van Keulen, Alicia Solano, Ursula Rothlisberger
Rhodopsin is a photoactive G-protein-coupled receptor (GPCR) that converts dim light into a signal for the brain, leading to eyesight. Full activation of this GPCR is achieved after passing through several steps of the protein's photoactivation pathway. Key events of rhodopsin activation are the initial cis-trans photoisomerisation of the covalently bound retinal moiety followed by conformational rearrangements and deprotonation of the chromophore's protonated Schiff base (PSB), which ultimately lead to full activation in the meta II state...
July 21, 2017: Journal of Chemical Theory and Computation
A Otero-de-la-Roza, Gino A DiLabio
Recent progress in the accurate calculation of noncovalent interactions has enabled density-functional theory (DFT) to model systems relevant in biological and supramolecular chemistry. The application of DFT methods using atom-centered Gaussian basis sets to large systems is limited by the number of basis functions required to accurately model thermochemistry and, in particular, weak intermolecular interactions. Basis set incompleteness error (BSIE) arising from the use of incomplete basis sets leads to erroneous intermolecular energies, bond dissociation energies, and structures...
July 21, 2017: Journal of Chemical Theory and Computation
Dean Strotz, Julien Orts, Celestine N Chi, Roland Riek, Beat Vögeli
We have recently developed an NMR protocol to extract exact distances between nuclei in proteins from an exact interpretation of NOESY buildup intensities (eNOEs). This enabled us to calculate multi-state structural ensembles that exhibit realistic spatial sampling and long-range correlations. Our initial studies were laborious and required a deep understanding of the underlying spin dynamics. Here, we present a MatLab package that integrates all data processing steps required to convert intensities of assigned peaks in NOESY series into upper and lower distance limits for structure calculation...
July 20, 2017: Journal of Chemical Theory and Computation
Matthew John Voelker, Bogdan Barz, Brigita Urbanc
Oligomers formed by amyloid β-protein (Aβ) are central to Alzheimer's disease (AD) pathology, yet their structure remains elusive. Of the two predominant Aβ alloforms, Aβ40 and Aβ42, the latter is more strongly associated with AD. Here, we structurally characterized Aβ40 and Aβ42 monomers through pentamers which were converted from previously derived coarse-grained (DMD4B-HYDRA) simulations into all-atom conformations and subjected to explicit-solvent MD. Free energy landscapes revealed that structural differences between Aβ40 and Aβ42 conformations increase with oligomer order up to trimers...
July 20, 2017: Journal of Chemical Theory and Computation
Daniele Selli, Gianluca Fazio, Gotthard Seifert, Cristiana Di Valentin
A water/(101) anatase TiO2 interface has been investigated with the DFT-based self-consistent-charge density functional tight-binding theory (SCC-DFTB). By comparison of the computed structural, energetic, and dynamical properties with standard DFT-GGA and experimental data, we assess the accuracy of SCC-DFTB for this prototypical solid-liquid interface. We tested different available SCC-DFTB parameters for Ti-containing compounds and, accordingly, combined them to improve the reliability of the method. To better describe water energetics, we have also introduced a modified hydrogen-bond-damping function (HBD)...
July 20, 2017: Journal of Chemical Theory and Computation
Stefan Doerr, Toni Giorgino, Gerard Martinez-Rosell, João M Damas, Gianni De Fabritiis
HTMD is a programmable scientific platform intended to facilitate simulation-based research in molecular systems. This paper presents the functionalities of HTMD for the preparation of a molecular dynamics simulation starting from PDB structures, building the system using well-known forcefields and applying standardized protocols for running the simulations. We demonstrate the framework's flexibility for high-throughput molecular simulations by applying a preparation, building and simulation protocol with multiple force-fields on all of the seven hundred eukaryotic membrane proteins resolved to-date from the orientation of proteins in membranes (OPM) database...
July 19, 2017: Journal of Chemical Theory and Computation
Mauro Lapelosa
The association between the MEEVD C-terminal peptide from the heat shock protein 90 (Hsp90) and tetratricopeptide repeat A (TPR2A) domain of the heat shock organizing protein (Hop) is a useful prototype to study the fundamental molecular details about the Hop-Hsp90 interaction. We study here the mechanism of binding/unbinding, and compute the standard binding free energy and potential of mean force for the association of the MEEVD peptide to the TPR2A domain using the Adaptive Biasing Force (ABF) methodology...
July 19, 2017: Journal of Chemical Theory and Computation
Kevin J Koh, Triet S Nguyen-Beck, John Parkhill
Realtime time-dependent density-functional theory (RT-TDDFT) is one of the mostpractical techniques available to simulate electronic dynamics of molecules and mate-rials. Promising applications of RT-TDDFT to study non-linear spectra and energytransport, demand simulations of large solvated systems over long timescales, whichare computationally quite costly. In this paper, we apply an embedding techniquedeveloped for ground-state SCF methods by Manby and Miller to accelerate realtimeTDDFT. We assess the accuracy and speed of these approximations by studying theabsorption spectra of solvated and covalently split chromophores...
July 19, 2017: Journal of Chemical Theory and Computation
Gareth W Richings, Scott Habershon
We describe a method for performing nuclear quantum dynamics calculations using standard, grid-based algorithms, including the multi configurational time-dependent Hartree (MCTDH) method, where the potential energy surface (PES) is calculated ``on-the-fly''. The method of Gaussian process regression (GPR) is used to construct a global representation of the PES using values of the energy at points distributed in molecular configuration space during the course of the wavepacket propagation. We demonstrate this direct dynamics approach for both an analytical PES function describing 3-dimensional proton transfer dynamics in malonaldehyde, and for 2- and 6-dimensional quantum dynamics simulations of proton transfer in salicylaldimine...
July 18, 2017: Journal of Chemical Theory and Computation
Fernanda Bettanin, Luiz F A Ferrão, Max Pinheiro, Adelia J A Aquino, Hans Lischka, Francisco Bolivar Correto Machado, Dana Nachtigallova
In this work CASPT2 calculations of polyacenes (from naphthalene to heptacene) were performed to find a methodology suitable for calculations of the absorption spectra, in particular of the La (B2u state) and Lb (B3u state) bands, of more extended systems. The effect of the extension of the active space and of freezing  orbitals were investigated. The MCSCF excitation energy of the B2u state is not sensitive to the size of the active space used. However, the CASPT2 results depends strongly on the amount of σ orbitals frozen reflecting the ionic character of the B2u state...
July 18, 2017: Journal of Chemical Theory and Computation
Adam Philips, Alex Marchenko, Lionel Alexandre Truflandier, Jochen Autschbach
Quadrupolar NMR relaxation rates are computed for (17)O, (2)H nuclei of liquid water, and of (23)Na(+) , and (35)Cl(-) in aqueous solution, via Kohn-Sham (KS) density functional theory ab-initio molecular dynamics (aiMD) and subsequent KS electric field gradient (EFG) calculations along the trajectories. The calculated relaxation rates are within about a factor of two of experimental results, and improved over previous aiMD simulations. The relaxation rates are assessed with regard to the lengths of the simulations as well as configurational sampling...
July 18, 2017: Journal of Chemical Theory and Computation
Santanu Roy, Marcel D Baer, Christopher J Mundy, Gregory K Schenter
We present a theory for ion pair dissociation and association, motivated by the concepts of the Marcus theory of electron transfer. Despite the extensive research on ion-pairing in many chemical and biological processes, much can be learned from the exploration of collective reaction coordinates. To this end, we explore two reaction coordinates, ion pair distance and coordination number. The study of the correlation between these reaction coordinates provides a new insight into the mechanism and kinetics of ion pair dissociation and association in water...
July 17, 2017: Journal of Chemical Theory and Computation
Miguel A Caro, Olga Lopez-Acevedo, Tomi Laurila
We present a complete methodology to consistently estimate redox potentials strictly from first principles, without any experimental input. The methodology is based on (i) ab initio molecular dynamics (MD) simulations, (ii) all-atom explicit solvation, (iii) the two-phase thermodynamic (2PT) model and (iv) the use of electrostatic potentials as references for the absolute electrochemical scale. We apply the approach presented to compute reduction potentials of the following redox couples: Cr(+2/+3), V(+2/+3), Ru(NH3)6(+2/+3), Sn(+2/+4), Cu(+1/+2), FcMeOH(0/+1) and Fe(+2/+3) (in aqueous solution) and Fc(0/+1) (in acetonitrile)...
July 17, 2017: Journal of Chemical Theory and Computation
Jiří Hostaš, Jan Řezáč
Calculations of interaction energies of noncovalent interactions in small basis sets are affected by the basis set superposition error and dispersion-corrected DFT-D methods are thus usually parameterised only for triple-zeta and larger basis sets. Nevertheless, some smaller basis sets could also perform well. Among many combinations tested, we obtained excellent results with DZVP-DFT basis and newly parameterised D3 dispersion correction. The accuracy of interaction energies and geometries is close to significantly more expensive calculations...
July 17, 2017: Journal of Chemical Theory and Computation
Aliasghar Sepehri, Troy D Loeffler, Bin Chen
The Jacobian-Gaussian method, which has been recently developed for generating bending angle trials, is extended to the conformational sampling of inner segments of a long chain or a cyclic molecule where regular configurational-bias Monte Carlo was found to be very inefficient or simply incapable (i.e., for the cyclic case). For these molecules, a new conformational move would be required where one interior section is relocated while the rest of the molecule, before and after this section, is fixed. Techniques have been developed to extend the regular configurational-bias Monte Carlo to such a fixed-endpoints case by introducing a biasing probability function...
July 17, 2017: Journal of Chemical Theory and Computation
Ayako Nakata, Yasunori Futamura, Tetsuya Sakurai, David R Bowler, Tsuyoshi Miyazaki
We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, CONQUEST, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by CONQUEST and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system, and adsorbed P2 molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency...
July 17, 2017: Journal of Chemical Theory and Computation
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