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Journal of Chemical Theory and Computation

Kevin B Moore, Keyarash Sadeghian, C David Sherrill, Christian Ochsenfeld, Henry F Schaefer
Distinguishing the functionality of C-H···O hydrogen bonds (HBs) remains challenging, as their properties are difficult to reliably quantify. Herein, we present a study of the methane-formaldehyde complex (MFC), a case for which C-H···O HBs appear to be the predominant force. Six stationary points on the MFC potential energy surface (PES) were obtained at the CCSD(T)/ANO2 level. The CCSDT(Q)/CBS interaction energies of the conformers range from only -1.12 to -0.33 kcal mol(-1), denoting a very flat PES...
October 17, 2017: Journal of Chemical Theory and Computation
Gregoire David, Nathalie Guihery, Nicolas Ferré
Analytical expression of the interactions present in the Heisenberg Dirac van Vleck and Hubbard Hamiltonians have been derived as functions of both the energy of several broken symmetry DFT solutions and their expectation value of the S^2 spin operator. Then, following a strategy of decomposition of the magnetic exchange coupling into its main contributions (direct exchange, kinetic exchange and spin polarization) and using a recently proposed method of spin decontamination, values of these interactions have been extracted...
October 17, 2017: Journal of Chemical Theory and Computation
Aditi Krishnapriyan, Ping Yang, Anders M N Niklasson, Marc J Cawkwell
New parameterizations for semi-empirical density functional tight binding (DFTB) theory have been developed by the numerical optimization of adjustable parameters to minimize errors in the atomization energy and interatomic forces with respect to ab initio calculated data. Initial guesses for the radial dependences of the Slater-Koster bond integrals and overlap integrals were obtained from minimum basis density functional theory calculations. The radial dependences of the pair potentials and the bond and overlap integrals were represented by simple analytic functions...
October 17, 2017: Journal of Chemical Theory and Computation
Felix Plasser, Stefanie A Mewes, Andreas Dreuw, Leticia González
High-level multireference computations on electronically excited and charged states of tetracene are performed, and the results are analyzed using an extensive wave function analysis toolbox that has been newly implemented in the Molcas program package. Aside from verifying the strong effect of dynamic correlation, this study reveals an unexpected critical influence of the atomic orbital basis set. It is shown that different polarized double-ζ basis sets produce significantly different results for energies, densities, and overall wave functions, with the best performance obtained for the atomic natural orbital (ANO) basis set by Pierloot et al...
October 17, 2017: Journal of Chemical Theory and Computation
J Coleman Howard, James C Womack, Jacek Dziedzic, Chris-Kriton Skylaris, Benjamin P Pritchard, T Daniel Crawford
We present a method for computing excitation energies for molecules in solvent, based on the combination of a minimal parameter implicit solvent model and the equation-of-motion coupled-cluster singles and doubles method (EOM-CCSD). In this method, the solvent medium is represented by a smoothly varying dielectric function, constructed directly from the quantum mechanical electronic density using only two tunable parameters. The solvent-solute electrostatic interactions are computed by numerical solution of the nonhomogeneous Poisson equation and incorporated at the Hartree-Fock stage of the EOM-CCSD calculation by modification of the electrostatic potential...
October 17, 2017: Journal of Chemical Theory and Computation
X Zhang, L A Patel, O Beckwith, R Schneider, C J Weeden, J T Kindt
Micelle cluster distributions from molecular dynamics simulations of a solvent-free coarse-grained model of sodium octyl sulfate (SOS) were analyzed using an improved method to extract equilibrium association constants from small-system simulations containing one or two micelle clusters at equilibrium with free surfactants and counterions. The statistical-thermodynamic and mathematical foundations of this partition-enabled analysis of cluster histograms (PEACH) approach are presented. A dramatic reduction in computational time for analysis was achieved through a strategy similar to the selector variable method to circumvent the need for exhaustive enumeration of the possible partitions of surfactants and counterions into clusters...
October 17, 2017: Journal of Chemical Theory and Computation
Pavlína Pokorná, Miroslav Krepl, Holger Kruse, Jiri Sponer
The HutP protein from B. subtilis regulates histidine metabolism by interacting with an antiterminator mRNA hairpin in response to the binding of L-histidine and Mg(2+). We studied the functional ligand-bound HutP hexamer complexed with two mRNAs using all-atom micro-second-scale explicit-solvent MD simulations performed with the Amber force fields. The experimentally observed protein-RNA interface exhibited good structural stability in the simulations with the exception of some fluctuations in an unusual adenine-threonine interaction involving two closely-spaced H-bonds...
October 16, 2017: Journal of Chemical Theory and Computation
Richard Chudoba, Jan Heyda, Joachim Dzubiella
A temperature (T)-dependent coarse-grained (CG) Hamiltonian of polyethylene glycol/oxide (PEG/PEO) in aqueous solution is reported to be used in implicit-solvent material models in a wide temperature (i.e., solvent quality) range. The T-dependent nonbonded CG interactions are derived from a combined "bottom-up" and "top-down" approach. The pair potentials calculated from atomistic replica-exchange molecular dynamics simulations in combination with the iterative Boltzmann inversion are post-refined by benchmarking to experimental data of the radius of gyration...
October 16, 2017: Journal of Chemical Theory and Computation
Wei Hu, Lin Lin, Chao Yang
We present a new efficient way to perform hybrid density functional theory (DFT)-based electronic structure calculations. The new method uses an interpolative separable density fitting (ISDF) procedure to construct a set of numerical auxiliary basis vectors and a compact approximation of the matrix consisting of products of occupied orbitals represented in a large basis set such as the planewave basis. Such an approximation allows us to reduce the number of Poisson solves from [Formula: see text] to [Formula: see text] when we apply the exchange operator to occupied orbitals in an iterative method for solving the Kohn-Sham equations, where Ne is the number of electrons in the system to be studied...
October 13, 2017: Journal of Chemical Theory and Computation
Enrico Ronca, Zhendong Li, Carlos A Jimenez-Hoyos, Garnet Kin-Lic Chan
We study the dynamical density matrix renormalization group (DDMRG) and time-dependent density matrix renormalization group (td-DMRG) algorithms in the ab initio context to compute dynamical correlation functions of correlated systems. We analyze the strengths and weaknesses of the two methods in small model problems and propose two simple improved formulations, DDMRG(++) and td-DMRG(++), that give increased accuracy at the same bond dimension at a nominal increase in cost. We apply DDMRG(++) to obtain the oxygen core-excitation energy in the water molecule in a quadruple-zeta quality basis, which allows us to estimate the remaining correlation error in existing coupled cluster results...
October 13, 2017: Journal of Chemical Theory and Computation
Yuri A Aoto, Ana Paula de Lima Batista, Andreas Köhn, Antonio G S de Oliveira-Filho
With the objective of analyzing which kind of reference data is appropriate for benchmarking quantum chemical approaches for transition metal compounds, we present the following, (a) a collection of 60 transition metal diatomic molecules for which experimentally derived dissociation energies, equilibrium distances, and harmonic vibrational frequencies are known and (b) a composite computational approach based on coupled-cluster theory with basis set extrapolation, inclusion of core-valence correlation, and corrections for relativistic and multireference effects...
October 13, 2017: Journal of Chemical Theory and Computation
Markus Sinstein, Christoph Scheurer, Sebastian Matera, Volker Blum, Karsten Reuter, Harald Oberhofer
With the advent of efficient electronic structure methods, effective continuum solvation methods have emerged as a way to, at least partially, include solvent effects into simulations without the need for expensive sampling over solvent degrees of freedom. The multipole moment expansion (MPE) model, while based on ideas initially put forward almost 100 years ago, has recently been updated for the needs of modern electronic structure calculations. Indeed, for an all-electron code relying on localized basis sets and-more importantly-a multipole moment expansion of the electrostatic potential, the MPE method presents a particularly cheap way of solving the macroscopic Poisson equation to determine the electrostatic response of a medium surrounding a solute...
October 13, 2017: Journal of Chemical Theory and Computation
Ulf Ryde
Combined quantum mechanical and molecular mechanical (QM/MM) calculations is a popular approach to study enzymatic reactions. They are often based on a set of minimised structures obtained on snapshots from a molecular dynamics simulation to include some dynamics of the enzyme. It has been much discussed how the individual energies should be combined to obtain a final estimate of the energy, but the current consensus seems to be to use an exponential average. Then, the question is how many snapshots are needed to reach a reliable estimate of the energy...
October 12, 2017: Journal of Chemical Theory and Computation
Xingqing Xiao, Yiming Wang, Joshua N Leonard, Carol K Hall
To enhance the sampling efficiency of our computational peptide-design algorithm in conformational space, the concerted rotation (CONROT) technique is extended to enable larger conformational perturbations of peptide chains. This allows us to make relatively-large peptide conformation changes during the process of designing peptide sequences to bind with high affinity to a specific target. Searches conducted using the new algorithm identified six potential λ N(2-22) peptide variants, called B1 to B6, which bind to boxB RNA with high affinity...
October 12, 2017: Journal of Chemical Theory and Computation
Anant Dixit, Julien Claudot, Sébastien Lebègue, Dario Rocca
Within a formalism based on dielectric matrices, the electron-hole time-dependent Hartree-Fock (eh-TDHF) and the adiabatic connection second-order screened exchange (AC-SOSEX) are promising approximations to improve ground-state correlation energies by including exchange effects beyond the random phase approximation (RPA). We introduce here an algorithm based on a Gram-Schmidt orthogonalization (GSO) procedure that significantly reduce the number of matrix elements to be computed to evaluate the response functions that enter in the formulation of these two methods...
October 11, 2017: Journal of Chemical Theory and Computation
Anton V Sinitskiy, Vijay S Pande
N-methyl-D-aspartate (NMDA) receptors, key neuronal receptors playing the central role in learning and memory, are heavily glycosylated in vivo. Astonishingly little is known about the structure, dynamics and physiological relevance of glycans attached to them. We recently demonstrated that certain glycans on the ligand binding domain (LBD) of NMDA receptors (NMDARs) can serve as intramolecular potentiators, changing EC50 of NMDAR co-agonists. In this work, we use molecular dynamics trajectories, in aggregate 86...
October 11, 2017: Journal of Chemical Theory and Computation
Yang Cao, Xuehan Jiang, Wei Han
Early oligomerization during amyloid-β (Aβ) aggregation is essential for Aβ neurotoxicity. Understanding how unstructured Aβs assemble into oligomers, especially those rich in β-sheets, is essential but remains challenging as the assembly process is too transient for experimental characterization and too slow for molecular dynamics simulations. So far, atomic simulations are limited only to studies of either oligomer structures or assembly pathways for short Aβ segments. To overcome the computational challenge, we combine in this study a hybrid-resolution model and adaptive sampling techniques to perform over 2...
October 11, 2017: Journal of Chemical Theory and Computation
Bridgette Cooper, Stephen Girdlestone, Pavel Burovskiy, Georgi Gaydadjiev, Vitali Averbukh, Peter J Knowles, Wayne Luk
We demonstrate the use of data flow technology in the computation of the correlation energy in molecules at the Møller Plesset perturbation theory (MP2) level. Specifically, we benchmark density fitting (DF) - MP2 for as many as 168 atoms (in valinomycin) and show that speed ups between 3 to 3.8 times can be achieved when compared to the MOLPRO package run on a single CPU. Acceleration is achieved by offloading the matrix multiplications steps in DF-MP2 to Dataflow Engines (DFEs). We project that the acceleration factor could be as much as 24 with the next generation of DFEs...
October 11, 2017: Journal of Chemical Theory and Computation
Shuming Bai, Mario Barbatti
Photosensitized singlet oxygen generation occurring in a PS-O2 complex, where PS is a photosensitizer chromophore, is a weakly coupled intermolecular energy-transfer process, a still challenging problem for theoretical chemistry. To investigate the reaction rate directly from quantum-chemical calculations, we built a semiclassical kinetic model that minimizes the computational effort for the calculation of diabatic couplings, activation energies, and reorganization energies, which are the components of the rate...
October 11, 2017: Journal of Chemical Theory and Computation
Lukas Vlcek, Rama K Vasudevan, Stephen Jesse, Sergei V Kalinin
We describe and test theoretical principles for consistent integration of experimental and ab initio data from diverse sources into a single statistical mechanical model. The approach is based on the recently introduced concept of statistical distance between partition functions, uses a simple vector algebra formalism to describe measurement outcomes and coarse-graining operations, and takes advantage of thermodynamic perturbation expressions for fast exploration of the model parameter space. The methodology is demonstrated on a combination of thermodynamic, structural, spectroscopic, and imaging pseudoexperimental data along with ab initio-type trajectories, which are incorporated into models describing the behavior of a near-critical fluid, liquid water, thin-film mixed oxides, and binary alloys...
October 11, 2017: Journal of Chemical Theory and Computation
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