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Journal of Computational Chemistry

Nils Schieschke, Roberto Di Remigio, Luca Frediani, Johannes Heuser, Sebastian Höfener
We present the explicit derivation of an approach to the multiscale description of molecules in complex environments that combines frozen-density embedding (FDE) with continuum solvation models, in particular the conductor-like screening model (COSMO). FDE provides an explicit atomistic description of molecule-environment interactions at reduced computational cost, while the outer continuum layer accounts for the effect of long-range isotropic electrostatic interactions. Our treatment is based on a variational Lagrangian framework, enabling rigorous derivations of ground- and excited-state response properties...
May 17, 2017: Journal of Computational Chemistry
Borys Szefczyk, Dawid Grabarek, Elżbieta Walczak, Tadeusz Andruniów
This study provides gas-phase S1 excited-state geometries along with emission and adiabatic energies for methylated/demethylated and ring-locked analogues of protonated Schiff base retinal models comprising system of five conjugated double bonds (PSB5), using second order multiconfiguration perturbation theory (CASPT2). CASPT2 results serve as reference data to assess the performance of CC2 (second-order approximate coupled cluster singles and doubles) and a commonly used CASSCF/CASPT2 protocol, that is, complete active space self-consistent field (CASSCF) geometry optimization followed by CASPT2 energy calculation...
May 17, 2017: Journal of Computational Chemistry
Seonghoon Kim, Jumin Lee, Sunhwan Jo, Charles L Brooks, Hui Sun Lee, Wonpil Im
Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files of the corresponding molecules are not available. To address this problem, we have developed Ligand Reader & Modeler in CHARMM-GUI. Users can upload ligand structure information in various forms (using PDB ID, ligand ID, SMILES, MOL/MOL2/SDF file, or PDB/mmCIF file), and the uploaded structure is displayed on a sketchpad for verification and further modification...
May 11, 2017: Journal of Computational Chemistry
Talapunur Vikramaditya, Shiang-Tai Lin
Accurate determination of ionization potentials (IPs), electron affinities (EAs), fundamental gaps (FGs), and HOMO, LUMO energy levels of organic molecules play an important role in modeling and predicting the efficiencies of organic photovoltaics, OLEDs etc. In this work, we investigate the effects of Hartree Fock (HF) Exchange, correlation energy, and long range corrections in predicting IP and EA in Hybrid Functionals. We observe increase in percentage of HF exchange results in increase of IPs and decrease in EAs...
May 11, 2017: Journal of Computational Chemistry
Kuan-Yu Liu, Jie Liu, John M Herbert
Analytic Hessians are often viewed as essential for the calculation of accurate harmonic frequencies, but the implementation of analytic second derivatives is nontrivial and solution of the requisite coupled-perturbed equations engenders a sizable memory footprint for large systems, given that these equations are not required for energy and gradient calculations in density functional theory. Here, we benchmark the alternative approach to harmonic frequencies based on finite differences of analytic first derivatives, a procedure that is amenable to large-scale parallelization...
May 10, 2017: Journal of Computational Chemistry
Ian L Rogers, Kevin J Naidoo
The SCC-DFTB/MIO/CHARMM free energy surface for a glycosyltransferase, TcTS, is benchmarked against a DFT/MM reaction trajectory using the same CHARMM MM force field ported to the NWChem package. The popular B3LYP functional, against which the MIO parameter set was parameterized is used to optimize TS structures and run DFT reaction dynamics. A novel approach was used to generate reaction forces from a SCC-DFTB/MIO/CHARMM reaction surface to drive B3LYP/6-31G/MM and B3LYP/6-31G(d)/MM reaction trajectories. Although TS structures compare favorably, differences stemming primarily from a minimal basis set approximation prevented a successful 6-31G(d) FEARCF reaction dynamics trajectory...
May 10, 2017: Journal of Computational Chemistry
Paul G Mezey, Zoltan Antal
With the aim of improving the performance of macromolecular quantum chemistry conformation analysis and reaction path following methods, the Adjustable Density Matrix Assembler (ADMA) method has already been combined with some faster although less accurate density matrix extrapolation methods, such as the Löwdin-Inverse-Löwdin (LIL) extrapolation along a potential energy surface, and a strategically arranged back-and-forth switching between these methods has been proven to be advantageous. Here, an alternative approach is proposed and investigated, based on several actual test calculations, where the "inexpensive" LIL density matrix extrapolation steps are replaced by only somewhat more expensive, but still ADMA-based calculations, where in the "rough-search stage," only interactions of shorter distances within the macromolecule are considered...
May 10, 2017: Journal of Computational Chemistry
Tamara Papp, László Kollár, Tamás Kégl
The coordinating properties of the trichlorostannate ligand in hydrido platinum trichlorostannato and platinum bis-trichlorostannato complexes, containing various phosphine ligands, have been elucidated by means of charge decomposition analysis, the Ziegler-Rauk Energy Decomposition with the Natural Orbitals for Chemical Valence, Domain-Averaged Fermi Hole, and natural bond orbital methods. Trichlorostannate has been found to be a strong σ-donor and a weak π-acceptor ligand with coordination properties not far from those of the cyano ligand...
May 10, 2017: Journal of Computational Chemistry
Dóra Papp, Petra Rovó, Imre Jákli, Attila G Császár, András Perczel
Non-covalent interactions between ions and aromatic rings play an important role in the stabilization of macromolecular complexes; of particular interest are peptides and proteins containing aromatic side chains (Phe, Trp, and Tyr) interacting with negatively (Asp and Glu) and positively (Arg and Lys) charged amino acid residues. The structures of the ion-aromatic-ring complexes are the result of an interaction between the large quadrupole moment of the ring and the charge of the ion. Four attractive interaction types are proposed to be distinguished based on the position of the ion with respect to the plane of the ring: perpendicular cation-π (CP⊥ ), co-planar cation-π (CP∥ ), perpendicular anion-π (AP⊥ ), and co-planar anion-π (AP∥ )...
May 10, 2017: Journal of Computational Chemistry
Daijiro Nozaki, Wolf Gero Schmidt
The current density in molecular wires connected to contacts is investigated within the nonequilibrium Green's function formalism combined with the Landauer approach. Energy-dependent and total current density through a series of molecular junctions are calculated in real space representation. A rich variety of current patterns including pronounced ring currents ("vortices") are found even in the defect-free minimal building blocks of molecular devices. The influences of contact positions, functional groups as well as atomic defects on the transport properties are examined systematically for prototypical ortho-, meta-, and para-substituted benzenes as well as heteroaromatic systems...
May 7, 2017: Journal of Computational Chemistry
Andrew L Ferguson
The weighted histogram analysis method (WHAM) is a powerful approach to estimate molecular free energy surfaces (FES) from biased simulation data. Bayesian reformulations of WHAM are valuable in proving statistically optimal use of the data and providing a transparent means to incorporate regularizing priors and estimate statistical uncertainties. In this work, we develop a fully Bayesian treatment of WHAM to generate statistically optimal FES estimates in any number of biasing dimensions under arbitrary choices of the Bayes prior...
May 5, 2017: Journal of Computational Chemistry
Swapnil Mahajan, Yves-Henri Sanejouand
The relationship between the normal modes of a protein and its functional conformational change has been studied for decades. However, using this relationship in a predictive context remains a challenge. In this work, we demonstrate that, starting from a given protein conformer, it is possible to generate in a single step model conformers that are less than 1 Å (Cα -RMSD) from the conformer which is the known endpoint of the conformational change, particularly when the conformational change is collective in nature...
May 3, 2017: Journal of Computational Chemistry
Teerapong Pirojsirikul, Andreas W Götz, John Weare, Ross C Walker, Karol Kowalski, Marat Valiev
Combined quantum mechanical molecular mechanics (QM/MM) calculations have become a popular methodology for efficient and accurate description of large molecular systems. In this work we introduce our development of a QM/MM framework based on two well-known codes-NWChem and AMBER. As an initial application area we are focused on excited state properties of small molecules in an aqueous phase using an analogue of the green fluorescent protein (GFP) chromophore as a particular test case. Our approach incorporates high level coupled cluster theory for the analysis of excited states providing a reliable theoretical analysis of effects of an aqueous solvation environment on the photochemical properties of the GFP chromophore...
May 3, 2017: Journal of Computational Chemistry
Natacha Gillet, Bernard Lévy, Vicent Moliner, Isabelle Demachy, Aurélien de la Lande
Redox potentials are essential to understand biological cofactor reactivity and to predict their behavior in biological media. Experimental determination of redox potential in biological system is often difficult due to complexity of biological media but computational approaches can be used to estimate them. Nevertheless, the quality of the computational methodology remains a key issue to validate the results. Instead of looking to the best absolute results, we present here the calibration of theoretical redox potential for quinone derivatives in water coupling QM + MM or QM/MM scheme...
May 3, 2017: Journal of Computational Chemistry
Sjoerd J de Vries, Martin Zacharias
Macromolecular docking methods can broadly be divided into geometric and atom-based methods. Geometric methods use fast algorithms that operate on simplified, grid-like molecular representations, while atom-based methods are more realistic and flexible, but far less efficient. Here, a hybrid approach of grid-based and atom-based docking is presented, combining precalculated grid potentials with neighbor lists for fast and accurate calculation of atom-based intermolecular energies and forces. The grid representation is compatible with simultaneous multibody docking and can tolerate considerable protein flexibility...
May 2, 2017: Journal of Computational Chemistry
Hiroto Tachikawa
Reactions of water dimer cation (H2O)2+ following ionization have been investigated by means of a direct ab initio molecular dynamics method. In particular, the effects of zero point vibration and zero point energy (ZPE) on the reaction mechanism were considered in this work. Trajectories were run on two electronic potential energy surfaces (PESs) of (H2O)2+: ground state ((2) A″-like state) and the first excited state ((2) A'-like state). All trajectories on the ground-state PES lead to the proton-transferred product: H2 O(+) (Wd)-H2 O(Wa) → OH(Wd)-H3 O(+) (Wa), where Wd and Wa refer to the proton donor and acceptor water molecules, respectively...
April 24, 2017: Journal of Computational Chemistry
Osvaldo Yañez, Alejandro Vásquez-Espinal, Diego Inostroza, Lina Ruiz, Ricardo Pino-Rios, William Tiznado
Theoretical studies are essential for the structural characterization of clusters, when it comes to rationalize their unique size-dependent properties and composition. However, the rapid growth of local minima on the potential energy surface (PES), with respect to cluster size, makes the candidate identification a challenging undertaking. In this article, we introduce a hybrid strategy to explore the PES of clusters. This proposal involves the use of a biased initial population of a genetic algorithm procedure...
April 24, 2017: Journal of Computational Chemistry
Jindal K Shah, Eliseo Marin-Rimoldi, Ryan Gotchy Mullen, Brian P Keene, Sandip Khan, Andrew S Paluch, Neeraj Rai, Lucienne L Romanielo, Thomas W Rosch, Brian Yoo, Edward J Maginn
Cassandra is an open source atomistic Monte Carlo software package that is effective in simulating the thermodynamic properties of fluids and solids. The different features and algorithms used in Cassandra are described, along with implementation details and theoretical underpinnings to various methods used. Benchmark and example calculations are shown, and information on how users can obtain the package and contribute to it are provided. © 2017 Wiley Periodicals, Inc.
April 24, 2017: Journal of Computational Chemistry
Athanassios C Tsipis
The (nitro)(N-methyldithiocarbamato)(trimethylphospane)nickel(II), [Ni(NO2 )(S2 CNHMe)(PMe3 )] complex catalyses efficiently the O-atom transfer reactions to CO and acetylene. Energetically feasible sequence of elementary steps involved in the catalytic cycle of the air oxidation of CO and acetylene are proposed promoted by the Ni(NO2 )(S2 CNHMe)(PMe3 )] ↔ Ni(NO2 )(S2 CNHMe)(PMe3 ) redox couple using DFT methods both in vacuum and dichloromethane solutions. The catalytic air oxidation of HC≡CH involves formation of a five-member metallacycle intermediate, via a [3 + 2] cyclo-addition reaction of HC≡CH to the Ni-N = O moiety of the Ni(NO2 )(S2 CNHMe)(PMe3 )] complex, followed by a β H-atom migration toward the Cα carbon atom of the coordinated acetylene and release of the oxidation product (ketene)...
April 24, 2017: Journal of Computational Chemistry
Premaja R Remya, Cherumuttathu H Suresh
A comprehensive density functional theory study on the dissociative and associative mechanisms of Grubbs first and second generation olefin metathesis catalysis reveals that ruthenacyclobutane intermediate (RuCB) observed in the Chauvin mechanism is not unique as it can change to a non-metathetic ruthenacyclobutane (RuCB') via the phenomenon of bond stretch isomerism (BSI). RuCB and RuCB' differ mainly in RuCα , RuCβ , and Cα Cβ bond lengths of the metallacycle. RuCB is metathesis active due to the agostic type bonding-assisted simultaneous activation of both Cα Cβ bonds, giving hypercoordinate character to Cβ whereas an absence of such bonding interactions in RuCB' leads to typical CC single bond distances and metathesis inactivity...
April 24, 2017: Journal of Computational Chemistry
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