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Journal of Chemical Theory and Computation

Xi-Chan Gao, Qiang Hao, Chang-Sheng Wang
The polarizable dipole-dipole interaction model was formulated in our laboratory to rapidly simulate hydrogen bonding in biosystems. In this paper, this model is improved and further parametrized for stacking, T-shaped, and X-H···π interactions by adding the orbital overlap term and fitting to 19 CCSD(T)/CBS interaction energy curves of training dimers. The performance of our model is assessed through its application to more than 100 complexes, including hydrogen-bonded, stacked, T-shaped, and X-H···π complexes...
May 19, 2017: Journal of Chemical Theory and Computation
Fabian Zeller, Martin Zacharias
The aggregation of N6N9-dimethyladenine in aqueous solution into stacked oligomers represents an important model system for oligomerization processes. Molecular dynamics simulations allowed us to extract statistically converged stacking thermodynamics as well as converged association and dissociation kinetics. The simulations confirm an oligomerization mechanism according to a random isodesmic stacking model without significant cooperative effects. Multiple oligomerization and dissociation events were used to characterize stacking and unstacking processes and intermediate states in atomic detail...
May 19, 2017: Journal of Chemical Theory and Computation
Ariana Torres-Knoop, Ali Poursaeidesfahani, Thijs J H Vlugt, David Dubbeldam
Many important industrial separation processes based on adsorption operate close to saturation. In this regime, the underlying adsorption processes are mostly driven by entropic forces. At equilibrium, the entropy of adsorption is closely related to the enthalpy of adsorption. Thus, studying the behavior of the enthalpy of adsorption as a function of loading is fundamental in the understanding of the separation processes. Unfortunately, close to saturation, the enthalpy of adsorption is hard to measure experimentally and hard to compute in simulations...
May 18, 2017: Journal of Chemical Theory and Computation
Alberto Baiardi, Lorenzo Paoloni, Vincenzo Barone, Viatcheslav G Zakrzewski, Joseph Vincent Ortiz
The analysis of photoelectron spectra is usually facilitated by quantum mechanical simulations. Due to the recent improvement of experimental techniques, the resolution of experimental spectra is rapidly increasing, and the inclusion of vibrational effects is usually mandatory to obtain a reliable reproduction of the spectra. With the aim of defining a robust computational protocol, a general time-independent formulation to compute different kinds of vibrationally-resolved electronic spectra has been generalized to support also photoelectron spectroscopy...
May 18, 2017: Journal of Chemical Theory and Computation
Eloy Ramos-Cordoba, Eduard Matito
Quantitatively accurate electronic structure calculations rely on the proper description of electron correlation. A judicious choice of the approximate quantum chemistry method depends upon the importance of dynamic and nondynamic correlation, which is usually assesed by scalar measures. Existing measures of electron correlation do not consider separately the regions of the Cartesian space where dynamic or nondynamic correlation are most important. We introduce real-space descriptors of dynamic and nondynamic electron correlation that admit orbital decomposition...
May 18, 2017: Journal of Chemical Theory and Computation
Mykhaylo Krykunov, Christopher Demone, Jason W-H Lo, Tom K Woo
Periodic frameworks that possess a net charge, such as zeolites, are an important class of materials in wide use. For guest-host interactions to be simulated in these materials, partial atomic charges are often used. In this work, we investigate two methods for the generation of partial atomic charges in periodic systems having a net framework charge. We first examine the validity of generating REPEAT electrostatic potential fitted charges derived from periodic electronic structure calculations, where a constant background charge is added to neutralize the net charge on the framework...
May 18, 2017: Journal of Chemical Theory and Computation
Gert-Jan Bekker, Narutoshi Kamiya, Mitsugu Araki, Ikuo Fukuda, Yasushi Okuno, Haruki Nakamura
In order to predict the accurate binding configuration as well as the binding affinity for a flexible protein receptor and its inhibitor drug, enhanced sampling with multicanonical molecular dynamics (McMD) simulation and thermodynamic integration (TI) were combined as a general drug docking method. CDK2, cyclin-dependent kinase 2, is involved in the cell cycle regulation. Malfunctions in CDK2 can cause tumorigenesis, and thus it is a potential drug target. Here, we performed a long McMD simulation for docking the inhibitor CS3 to CDK2 starting from the unbound structure...
May 18, 2017: Journal of Chemical Theory and Computation
Barira Islam, Petr Stadlbauer, Alejandro Gil-Ley, Guillermo Pérez-Hernández, Shozeb Haider, Stephen Neidle, Giovanni Bussi, Pavel Banas, Michal Otyepka, Jiri Sponer
We have carried out a series of extended unbiased molecular dynamics (MD) simulations (up to 10 μs long, ∼162 μs in total) complemented by replica-exchange with the collective variable tempering (RECT) approach for several human telomeric DNA G-quadruplex (GQ) topologies with TTA propeller loops. We used different AMBER DNA force-field variants and also processed simulations by Markov State Model (MSM) analysis. The slow conformational transitions in the propeller loops took place on a scale of a few μs, emphasizing the need for long simulations in studies of GQ dynamics...
May 18, 2017: Journal of Chemical Theory and Computation
Wenjie Dou, Joseph E Subotnik
For a molecule with multiple electronic orbitals and many nuclear degrees of freedom near a metal surface, there is a natural embedding of the quantum-classical Liouville equation inside a classical master equation (QCLE-CME) to model nonadiabatic dynamics ( J. Chem. Phys. 2016 , 145 , 054102 ). In this paper, we propose a variety of surface hopping algorithms for solving such a QCLE-CME. We find that an augmented surface hopping (A-SH) algorithm works well for propagating such nonadiabatic dynamics (near a metal surface)...
May 18, 2017: Journal of Chemical Theory and Computation
Luning Zhao, Eric Neuscamman
We present a modification to variational Monte Carlo's linear method optimization scheme that addresses a critical memory bottleneck while maintaining compatibility with both the traditional ground state variational principle and our recently-introduced variational principle for excited states. For wave function ansatzes with tens of thousands of variables, our modification reduces the required memory per parallel process from tens of gigabytes to hundreds of megabytes, making the methodology a much better fit for modern supercomputer architectures in which data communication and per-process memory consumption are primary concerns...
May 17, 2017: Journal of Chemical Theory and Computation
Katharina Doblhoff-Dier, Joerg Meyer, Philip E Hoggan, Geert-Jan Kroes
Accurate modeling of heterogeneous catalysis requires the availability of highly accurate potential energy surfaces. Within density functional theory, these can - unfortunately - depend heavily on the exchange-correlation functional. High-level ab-initio calculations, on the other hand, are challenging due to the system size and the metallic character of the metal slab. Here, we present a quantum Monte Carlo (QMC) study of the reaction barrier for the benchmark system H2+Cu(111), focusing on the dissociative chemisorption barrier height...
May 17, 2017: Journal of Chemical Theory and Computation
Gunnar Schmitz, Christof Hattig
In recent years PNO-based local correlation based methods have gained popularity since they allow Coupled Cluster (CC) calculations with reduced computational costs. Yet, only few systematic studies concerning their accuracy are available, in particular for the explicitly correlated versions. In this work we take a deeper look at the explicitly correlated local PNO-CCSD(F12*)(T0) and PNO-CCSD(F12*)(T) methods. The first variant uses the so-called semi canonical triples correction (T0) which neglects off-diagonal elements in the occupied block of the Fock matrix...
May 17, 2017: Journal of Chemical Theory and Computation
Franco Egidi, Shichao Sun, Joshua J Goings, Giovanni Scalmani, Michael J Frisch, Xiaosong Li
We present a linear response formalism for the description of the electronic excitations of a noncollinear reference defined via Kohn-Sham spin density functional methods. A set of auxiliary variables, defined using the density and noncollinear magnetization density vector, allows the generalization of spin density functional kernels commonly used in collinear DFT to noncollinear cases, including local density, GGA, meta-GGA and hybrid functionals. Working equations and derivations of functional second derivatives with respect to the noncollinear density, required in the linear response noncollinear TDDFT formalism, are presented in this work...
May 17, 2017: Journal of Chemical Theory and Computation
Junwei Lucas Bao, Lili Xing, Donald G Truhlar
For molecules with multiple torsions, an accurate evaluation of the molecular partition function requires consideration of multiple structures and their torsional-potential anharmonicity. We previously developed a method called MS-T for this problem, and it requires an exhaustive conformational search with frequency calculations for all the distinguishable conformers; this can become expensive for molecules with a large number of torsions (and hence a large number of structures) if it is carried out with high-level methods...
May 17, 2017: Journal of Chemical Theory and Computation
Rolf David, Helene Jamet, Vincent Niviere, Yohann Moreau, Anne Milet
Superoxide reductase is a mononuclear iron enzyme involved in superoxide radical detoxification in some bacteria. Its catalytic mechanism is associated with the remarkable formation of a ferric hydroperoxide Fe3+-OOH intermediate, which is specifically protonated on its proximal oxygen to generate the reaction product H2O2. Here we present a computational study of the protonation mechanism of the Fe3+ OOH intermediate, at different level of theory. This was performed on the whole system (solvated protein) using well-tempered metadynamics at the QM/MM (B3LYP/AmberFF99SB) level...
May 16, 2017: Journal of Chemical Theory and Computation
Dominik Sidler, Michael Cristofol Clough, Sereina Riniker
Replica-exchange enveloping distribution sampling (RE-EDS) allows the efficient estimation of free-energy differences between multiple end-states from a single molecular dynamics (MD) simulation. In EDS, a reference state is sampled, which can be tuned by two kinds of parameters, i.e. smoothness parameters(s) and energy offsets, such that all end-states are sufficiently sampled. The choice of these parameters is, however, not trivial. Replica exchange (RE) or parallel tempering is a widely applied technique to enhance sampling...
May 16, 2017: Journal of Chemical Theory and Computation
Xinqiang Ding, Jonah Z Vilseck, Ryan Lee Hayes, Charles L Brooks
λ-dynamics is a generalized ensemble method for alchemical free energy calcula- tions. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator (∆Gˆ = -β(-1)ln[P(λ > λcutoff)/P (λ < 1-λcutoff)]) is utilized to approximate the free energy (∆G = -β(-1)ln[P (λ = 1)/P(λ = 0)]) based on λ trajectories, where the cutoff value of λcutoff is empirically chosen to be near 1. In the present paper, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework which we call Gibbs Sampler λ-dynamics (GSLD)...
May 16, 2017: Journal of Chemical Theory and Computation
James Shee, Shiwei Zhang, David R Reichman, Richard A Friesner
The exact and phaseless variants of auxiliary-field quantum Monte Carlo (AFQMC) have been shown to be capable of producing accurate ground-state energies for a wide variety of systems including those which exhibit substantial electron correlation effects. The computational cost of performing these calculations has to date been relatively high, impeding many important applications of these approaches. Here we present a correlated sampling methodology for AFQMC which relies on error cancellation to dramatically accelerate the calculation of energy differences of relevance to chemical transformations...
May 16, 2017: Journal of Chemical Theory and Computation
Gerhard Jung, Martin Hanke, Friederike Schmid
In recent years it has become increasingly popular to construct coarse-grained models with non-Markovian dynamics in order to account for an incomplete separation of time scales. One challenge of a systematic coarse-graining procedure is the extraction of the dynamical properties, namely the memory kernel, from equilibrium all-atom simulations. In this paper we propose an iterative method for memory reconstruction from dynamical correlation functions. Compared to previously proposed non-iterative techniques, it ensures by construction that the target correlation functions of the original fine-grained systems are reproduced accurately by the coarse-grained system, regardless of time step and discretization effects...
May 15, 2017: Journal of Chemical Theory and Computation
Tim Gould
This work proposes, justifies, and reports tests of the chemically relevant left Fukui function of Li, C, and F on a range of density functional approximations. Analysis indicates that functionals can be good at densities and bad at Fukui functions, and vice versa, analogous with energies and ionization potentials. "TPSSh", "SOGGA11X", and "B2PLYP" are star performers on both, however. Many "Minnesota functionals" fare much better here than in a recent analysis of electron densities. In this context, new optimizing strategies are mentioned...
May 15, 2017: Journal of Chemical Theory and Computation
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