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Journal of Chemical Theory and Computation

Mangesh I Chaudhari, Jijeesh R Nair, Lawrence R Pratt, Fernando A Soto, Perla B Balbuena, Susan Rempe
Lithium ion solvation and diffusion properties in ethylene carbonate (EC) and propylene carbonate (PC) are studied by molecular simulation, experiments, and electronic structure calculations. Studies carried out in water provide a reference for interpretation. Classical molecular dynamics simulation results are compared to ab initio molecular dynamics to as- sess non-polarizable force field parameters for solvation structure of the carbonate solvents. Quasi-chemical theory (QCT) is adapted to take advantage of four-fold occupancy of the near-neighbor solvation structure observed in simulations, and used to calculate solvation free energies...
October 21, 2016: Journal of Chemical Theory and Computation
Petr Stadlbauer, Liuba Mazzanti, Tristan Cragnolini, David J Wales, Philippe Derreumaux, Samuela Pasquali, Jiri Sponer
G-quadruplexes are the most important non-canonical DNA architectures. Many quadruplex-forming sequences, including the human telomeric sequence d(GGGTTA)n, have been investigated due to their implications in cancer and other diseases, and because of their potential in DNA-based nanotechnology. Despite availability of atomistic structural studies of folded G-quadruplexes, their folding pathways remain mysterious, and mutually contradicting models of folding coexist in the literature. Recent experiments convincingly demonstrated that G-quadruplex folding often takes days to reach the thermodynamics equilibrium...
October 21, 2016: Journal of Chemical Theory and Computation
Nathan A Bernhardt, Wenhui Xi, Wei Wang, Ulrich H E Hansmann
Recent experiments suggest that an amino acid sequence encodes not only the native fold of a protein but also other forms essential for its function, or important during folding or association. These various forms populate a multi-funnel folding and association landscape where mutations, changes in environment or interaction with other molecules switch between the encoded folds. We introduce replica-exchange-with- tunneling as a way to simulate efficiently switching between distinct folds of proteins and protein aggregates...
October 21, 2016: Journal of Chemical Theory and Computation
Hahnbeom Park, Philip Bradley, Per Greisen, Yuan Liu, Vikram Khipple Mulligan, David E Kim, David Baker, Frank DiMaio
Most biomolecular modeling energy functions for structure prediction, sequence design, and molecular docking, have been parameterized using existing macromolecular structural data; this contrasts molecular mechanics force fields which are largely optimized using small-molecule data. In this study, we describe an integrated method that enables optimization of a biomolecular modeling energy function simultaneously against small-molecule thermodynamic data and high-resolution macromolecular structural data. We use this approach to develop a next-generation Rosetta energy function that utilizes a new anisotropic implicit solvation model, and an improved electrostatics and Lennard-Jones model, illustrating how energy functions can be considerably improved in their ability to describe large-scale energy landscapes by incorporating both small-molecule and macromolecule data...
October 21, 2016: Journal of Chemical Theory and Computation
Michel Alain Cuendet, Harel Weinstein, Michael V LeVine
Allostery plays a fundamental role in most biological processes. However, little theory is available to describe it outside of two-state models. Here we use a statistical mechanical approach to show that the allosteric coupling between two collective variables is not a single number, but instead a two-dimensional thermodynamic coupling function that is directly related to the mutual information from information theory and the copula density function from probability theory. On this basis, we demonstrate how to quantify the contribution of specific energy terms to this thermodynamic coupling function, enabling an approximate decomposition that reveals the mechanism of allostery...
October 21, 2016: Journal of Chemical Theory and Computation
Fabien Brieuc, Yael Bronstein, Hichem Dammak, Philippe Depondt, Fabio Finocchi, Marc Hayoun
The quantum thermal bath (QTB) has been presented as an alternative to path-integral based methods to introduce nuclear quantum effects in molecular dynamics simulations. The method has proved to be efficient, yielding accurate results for various systems. However, the QTB method is prone to zero-point energy leakage (ZPEL) in highly anharmonic systems. This is a well known problem in methods based on classical trajectories where part of the energy of the high frequency modes is transferred to the low frequency modes leading to a wrong energy distribution...
October 21, 2016: Journal of Chemical Theory and Computation
Thomas E Gartner, Thomas H Epps, Arthi Jayaraman
We describe an extension of the Gibbs ensemble molecular dynamics (GEMD) method for studying phase equilibria. Our modifications to GEMD allow for direct control over particle transfer between phases and improve the method's numerical stability. Additionally, we found that the modified GEMD approach had advantages in computational efficiency in comparison to a hybrid Monte Carlo (MC)/MD Gibbs ensemble scheme in the context of the single component Lennard-Jones fluid. We note that this increase in computational efficiency does not compromise the close agreement of phase equilibrium results between the two methods...
October 21, 2016: Journal of Chemical Theory and Computation
Chang Woo Kim, Young Min Rhee
Constructing a reliable potential energy surface (PES) is a key step toward computationally studying chemical dynamics of any molecular system. The interpolation scheme is a useful tool that can closely follow the accuracy of quantum chemical means at a dramatically reduced computational cost. However, applying interpolation for building a PES of a large molecule is not a straightforward black-box approach, as it frequently encounters practical difficulties associated with its large dimensionality. Here, we present detailed courses of applying interpolation toward building a PES of a large chromophore molecule...
October 19, 2016: Journal of Chemical Theory and Computation
Han Wang, Xingyu Gao, Jun Fang
The smooth particle mesh Ewald (SPME) method is the standard method for computing the electrostatic interactions in the molecular simulations. In this work, we develop the multiple staggered mesh Ewald (MSME) method, which averages the SPME forces computed on, e.g. M, staggered meshes. We prove, from a theoretical perspective, that the MSME is as accurate as the SPME, but uses M(2) times less mesh points in a certain parameter range. In the complementary parameter range, the MSME is as accurate as the SPME with twice of the interpolation order...
October 19, 2016: Journal of Chemical Theory and Computation
Aude Giard, Jean-Sébastien Filhol, Franck Jolibois, Florine Cavelier, Dorothée Berthomieu
The determination of pKa values for molecules containing multiple acidic groups in solution is challenging both experimentally and theoretically. We propose a general method to obtain these values by combining a graphical analysis based on a predominance diagram, for amino acids and nicotianamine polyacid with first principle DFT calculations. Implicit and semi-explicit water solvent models were included to account for solvation. This strategy enables the investigation of the protonation states of compounds containing acidic moities in solution depending on the pH domain...
October 19, 2016: Journal of Chemical Theory and Computation
André Anda, Luca De Vico, Thorsten Hansen, Darius Abramavicius
The modelling of vibrations in optical spectra rely heavily on the simplifications brought about by using harmonic oscillators. Realistic molecular systems, however, can deviate substantially from this description. We develop two methods which show that the extension to arbitrarily shaped potential energy surfaces is not only straightforward, but also efficient. These methods are applied to an electronic two-level system with potential energy surfaces of polynomial form, and used to study anharmonic features such as the zero-phonon line shape and mirror symmetry breaking between absorption and fluorescence spectra...
October 19, 2016: Journal of Chemical Theory and Computation
Craig Waitt, Nashali M Ferrara, Henk Eshuis
The performance of the random phase approximation (RPA) is tested for ther- mochemistry and geometries of transition metal chemistry using various benchmarks obtained either computationally or experimentally. Comparison is made to popular (semi-)local, meta- and hybrid density functionals as well as to second-order Møller- Plesset perturbation theory (MP2) and its spin-component-scaled derivatives. The benchmarks sets include reaction energies, barrier heights and dissociation energies of prototype bond-activation reactions, dissociation energies for a set of large transition metal complexes, bond lengths and dissociation energies of metal hydride ions, and bond lengths and angles of a set of closed-shell first-row transition metal complexes...
October 17, 2016: Journal of Chemical Theory and Computation
David Williams-Young, Joshua J Goings, Xiaosong Li
Solutions of the real-time time-dependent density functional theory (RT-TDDFT) equations provide an affordable route to understanding the electronic dynamics that underpins many spectroscopic techniques. From the solutions of the RT-TDDFT equations it is possible to extract optical absorption and circular dichroism spectra, as well as descriptions of charge transfer and charge transport dynamics. In order to apply RT-TDDFT to increasingly large systems, it is necessary to develop methods to overcome computational bottlenecks...
October 17, 2016: Journal of Chemical Theory and Computation
Shibing Chu, Emanuele Coccia, Matteo Barborini, Leonardo Guidoni
Electron correlation plays a crucial role in the energetics of reactions catalyzed by transition metal complexes, such as water splitting. In the present work we exploit the performance of various methods to describe the thermodynamics of a simple but representative model of water splitting reaction, based on a single cobalt ion as catalyst. Density Functional Theory (DFT) calculations show a significant dependance on the the adopted functional and not negligible differences with respect to CSSD(T) findings are found along the reaction cycle...
October 17, 2016: Journal of Chemical Theory and Computation
Marko Melander, Elvar Örn Jónsson, Jens Jørgen Mortensen, Tejs Vegge, Juan María García Lastra
Combining constrained density function theory (cDFT) with Marcus theory is an efficient and promising way to address charge transfer reactions. Here, we present a general and robust implementation of cDFT within the projector augmented wave (PAW) framework. PAW pseudopotentials offer a reliable frozen-core electron description across the whole periodic table, with good transferability, as well as facilitate the extraction of all-electron quantities. The present implementation is applicable to two different wave function representations -- atomic centred basis sets (LCAO) and the finite-difference (FD) approximation utilizing real-space grids...
October 17, 2016: Journal of Chemical Theory and Computation
Adam Fouda, Ulf Ryde
We have examined how the self-interaction error in density-functional theory (DFT) calculations affects energies calculated on large systems (600-1000 atoms) involving several charged groups. We employ 18 different quantum mechanical (QM) methods, including Hartree-Fock, as well as pure, hybrid, and range-separated DFT methods. They are used to calculate reaction and activation energies for three different protein models in vacuum, in a point-charge surrounding, or with a continuum-solvent model. We show that pure DFT functionals give rise to a significant delocalisation of the charges in charged groups in the protein, typically by ~0...
October 17, 2016: Journal of Chemical Theory and Computation
Kaito Miyamoto, Thomas F Miller, Frederick R Manby
We introduce Fock-corrected density-functional theory (FCDFT), a semi-empirical minimal-basis method part way between density-functional tight binding (DFTB) and DFT. FCDFT contains DFTB-like Fock-matrix contributions calculated using simple pairwise formulae and Slater-Koster transformations. But it also contains the full Kohn-Sham treatment of Coulombic electrostatics. The resulting method is better suited than either minimal-basis DFT or DFTB for modelling the low-level subsystem in embedded mean-field theory (EMFT), improving over the former by correcting for basis-set incompleteness, and over the latter by properly accounting for electrostatics...
October 17, 2016: Journal of Chemical Theory and Computation
Darya N Komsa, Viktor N Staroverov
Standard density-functional approximations often incorrectly predict that heteronuclear diatomic molecules dissociate into fractionally charged atoms. We demonstrate that these spurious charges can be eliminated by adapting the shape-correction method for Kohn-Sham potentials that was originally introduced to improve Rydberg excitation energies [Phys. Rev. Lett. 2012, 108, 253005]. Specifically, we show that if a suitably determined fraction of electron charge is added to or removed from a frontier Kohn-Sham orbital level, the approximate Kohn-Sham potential of a stretched molecule self-corrects by developing a semblance of step structure; if this potential is used to obtain the electron density of the neutral molecule, charge delocalization is blocked and spurious fractional charges disappear beyond a certain internuclear distance...
October 17, 2016: Journal of Chemical Theory and Computation
Saeed Izadi, Ramu Anandakrishnan, Alexey V Onufriev
Molecular Dynamics (MD) simulations based on the implicit solvent generalized Born (GB) models can provide significant computational advantages over the traditional explicit solvent simulations. However, the standard GB becomes prohibitively expensive for all-atom simulations of large structures; the model scales poorly, ~n^2, with the number of solute atoms. Here we combine our recently developed Optimal Point Charge Approximation (OPCA) with the Hierarchical Charge Partitioning (HCP) approximation to present an ~n log n multi-scale, yet fully atomistic, GB model (GB-HCPO)...
October 17, 2016: Journal of Chemical Theory and Computation
Fanny Vazart, Danilo Calderini, Cristina Puzzarini, Dimitrios Skouteris, Vincenzo Barone
We describe an integrated computational strategy aimed at providing reliable thermochemical and kinetic information on the formation processes of astrochemical complex organic molecules. The approach involves state-of-the-art quantum-mechanical computations, second-order vibrational perturbation theory, and kinetic models based on capture and transition state theory together with the master equation approach. Notably, tunneling, quantum reflection, and leading anharmonic contributions are accounted for in our model...
October 14, 2016: Journal of Chemical Theory and Computation
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