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Journal of Computational Chemistry

Karol Dyduch, Monika Srebro-Hooper, Bun Yeoul Lee, Artur Michalak
Model catalysts for CO2 /epoxide copolymerization based on Co(III) complexes were studied, with focus on the preference of their alternative isomers, cisβ vs. trans. The systems range from model structures without the co-catalyst, as derived from crystallographic data, to complex models with two (CH2 )4 N+ R3 co-catalyst chains (R = Me, Bu) grafted onto a Co(III)-salcy core. To explore the conformational space of the latter complexes, a computational protocol was developed, combining a systematic model-building approach with static and molecular dynamics calculations, and multilevel energy assessment (PM7 and DFT)...
June 11, 2018: Journal of Computational Chemistry
Jakub Krajniak, Zidan Zhang, Sudharsan Pandiyan, Eric Nies, Giovanni Samaey
We develop novel parallel algorithms that allow molecular dynamics simulations in which byproduct molecules are created and removed because of the chemical reactions during the molecular dynamics simulation. To prevent large increases in the potential energy, we introduce the byproduct molecules smoothly by changing the non-bonded interactions gradually. To simulate complete equilibrium reactions, we allow the byproduct molecules attack and destroy created bonds. Modeling of such reactions are, for instance, important to study the pore formation due to the presence of e...
June 11, 2018: Journal of Computational Chemistry
Tobias Kramer, Matthias Noack, Alexander Reinefeld, Mirta Rodríguez, Yaroslav Zelinskyy
Time- and frequency-resolved optical signals provide insights into the properties of light-harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom...
June 11, 2018: Journal of Computational Chemistry
Raman K Singh, Takeshi Iwasa, Tetsuya Taketsugu
A long-range corrected density functional theory (LC-DFT) was applied to study the geometric structures, relative stabilities, electronic structures, reactivity descriptors and magnetic properties of the bimetallic NiCun -1 and Ni2 Cun -2 (n = 3-13) clusters, obtained by doping one or two Ni atoms to the lowest energy structures of Cun , followed by geometry optimizations. The optimized geometries revealed that the lowest energy structures of the NiCun -1 and Ni2 Cun -2 clusters favor the Ni atom(s) situated at the most highly coordinated position of the host copper clusters...
May 25, 2018: Journal of Computational Chemistry
Milena Petković, Đura Nakarada, Mihajlo Etinski
Interacting Quantum Atoms methodology is used for a detailed analysis of hydrogen abstraction reaction from hydroquinone by methoxy radical. Two pathways are analyzed, which differ in the orientation of the reactants at the corresponding transition states. Although the discrepancy between the two barriers amounts to only 2 kJ/mol, which implies that the two pathways are of comparable probability, the extent of intra-atomic and inter-atomic energy changes differs considerably. We thus demonstrated that Interacting Quantum Atoms procedure can be applied to unravel distinct energy transfer routes in seemingly similar mechanisms...
May 25, 2018: Journal of Computational Chemistry
Ghazaleh Taherzadeh, Yuedong Yang, Haodong Xu, Yu Xue, Alan Wee-Chung Liew, Yaoqi Zhou
Malonylation is a recently discovered post-translational modification (PTM) in which a malonyl group attaches to a lysine (K) amino acid residue of a protein. In this work, a novel machine learning model, SPRINT-Mal, is developed to predict malonylation sites by employing sequence and predicted structural features. Evolutionary information and physicochemical properties are found to be the two most discriminative features whereas a structural feature called half-sphere exposure provides additional improvement to the prediction performance...
May 14, 2018: Journal of Computational Chemistry
Peter L Cummins, Babu Kannappan, Jill E Gready
Here, we describe a computational approach for studying enzymes that catalyze complex multi-step reactions and apply it to Ribulose 1,5-bisphosphate carboxylase-oxygenase (Rubisco), the enzyme that fixes atmospheric carbon dioxide within photosynthesis. In the 5-step carboxylase reaction, the substrate Ribulose-1,5-bisphosphate (RuBP) first binds Rubisco and undergoes enolization before binding the second substrate, CO2 . Hydration of the RuBP.CO2 complex is followed by CC bond scission and stereospecific protonation...
May 14, 2018: Journal of Computational Chemistry
Andreas Klamt, Michael Diedenhofen
A cavity construction algorithm based on the triangulation of an iso-surface is introduced as a new standard for dielectric continuum solvation calculations with the Conductor-like Screening Model COSMO. It overcomes deficiencies which have become apparent for the original COSMO standard cavity, especially in concave regions of the molecular shaped cavity. The new standard, called FINE Cavity, is described in this article with several application examples. The earlier COSMO cavity construction algorithms are described for comparison...
May 14, 2018: Journal of Computational Chemistry
Kumari Soniya, Amalendu Chandra
We have performed hybrid quantum-classical metadynamics simulations and quantum chemical calculations to investigate the free energy landscapes of intramolecular proton transfer and associated tautomeric equilibrium in pyridoxal 5 '-phosphate (PLP) Schiff Bases, namely the internal and external aldimines, at the active site of serine hydroxymethyltransferase (SHMT) enzyme in aqueous medium. It is important to determine the relative stability of the two tautomers (ketoenamine and enolimine) of the PLP aldimines to study the catalytic activity of the concerned enzyme...
May 14, 2018: Journal of Computational Chemistry
Sara Del Galdo, Giordano Mancini, Isabella Daidone, Laura Zanetti Polzi, Andrea Amadei, Vincenzo Barone
The UV-vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV-vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua-p-Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations...
May 14, 2018: Journal of Computational Chemistry
Yang Li, Junsheng Chen, Tian-Shu Chu
The sensing mechanism of a fluoride-anion probe BODIPY-amidothiourea (1c) has been elucidated through the density functional theory (DFT) and time-dependent density functional theory (TDDFT) calculations. The theoretical study indicates that in the DMSO/water mixtures the fluorescent sensing has been regulated by the fluoride complex that formed between the probe 1c/two water molecules and the fluoride anion, and the excited-state intermolecular hydrogen bond (H-B) plays an important role in the fluoride sensing mechanism...
May 11, 2018: Journal of Computational Chemistry
A Lara, M Riquelme, E Vöhringer-Martinez
Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account...
May 11, 2018: Journal of Computational Chemistry
Alexey Aleksandrov, Fang-Yu Lin, Benoît Roux, Alexander D MacKerell
In this work, we have combined the polarizable force field based on the classical Drude oscillator with a continuum Poisson-Boltzmann/solvent-accessible surface area (PB/SASA) model. In practice, the positions of the Drude particles experiencing the solvent reaction field arising from the fixed charges and induced polarization of the solute must be optimized in a self-consistent manner. Here, we parameterized the model to reproduce experimental solvation free energies of a set of small molecules. The model reproduces well-experimental solvation free energies of 70 molecules, yielding a root mean square difference of 0...
May 8, 2018: Journal of Computational Chemistry
Hiroshi Takeuchi
Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size-guided multi-seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest-energy configurations of the cluster with n - 1 molecules (seeds)...
May 8, 2018: Journal of Computational Chemistry
Jing Huang, Justin A Lemkul, Peter K Eastman, Alexander D MacKerell
Presented is the implementation of the Drude force field in the open-source OpenMM simulation package allowing for access to graphical processing unit (GPU) hardware. In the Drude model, electronic degrees of freedom are represented by negatively charged particles attached to their parent atoms via harmonic springs, such that extra computational overhead comes from these additional particles and virtual sites representing lone pairs on electronegative atoms, as well as the associated thermostat and integration algorithms...
May 4, 2018: Journal of Computational Chemistry
Dawid Grabarek, Tadeusz Andruniów
The initial S1 excited-state relaxation of retinal protonated Schiff base (RPSB) analog with central C11C12 double bond locked by eight-membered ring (locked-11.8) was investigated by means of multireference perturbation theory methods (XMCQDPT2, XMS-CASPT2, MS-CASPT2) as well as single-reference coupled-cluster CC2 method. The analysis of XMCQDPT2-based geometries reveals rather weak coupling between in-plane and out-of-plane structural evolution and minor energetical relaxation of three locked-11.8 conformers...
May 4, 2018: Journal of Computational Chemistry
Shun Sakuraba, Ikuo Fukuda
The zero-multiple summation method (ZMM) is a cutoff-based method for calculating electrostatic interactions in molecular dynamics simulations, utilizing an electrostatic neutralization principle as a physical basis. Since the accuracies of the ZMM have been revealed to be sufficient in previous studies, it is highly desirable to clarify its practical performance. In this paper, the performance of the ZMM is compared with that of the smooth particle mesh Ewald method (SPME), where the both methods are implemented in molecular dynamics software package GROMACS...
May 4, 2018: Journal of Computational Chemistry
Mohammad H Kowsari, Leila Tohidifar
The reliability of a molecular dynamics (MD) simulation study mainly depends on the accuracy of the applied force field. Unlike the ability of some potential models for reasonably predicting the thermodynamic properties of acetonitrile (ACN), simulated dynamical properties such as self-diffusion are generally underestimated compared to experimental values. The present work focuses on the evaluation and refinement of several available all-atom force fields for ACN and proposes a refined flexible six-site potential model...
May 3, 2018: Journal of Computational Chemistry
Moein Goodarzi, Fariba Nazari, Francesc Illas
Systematic addition of Li atoms to the Be2 B8 and Be2 B36 backbones has been studied by density functional theory-based calculations with the aim to investigate properties of interest on possible anode materials for Li-based batteries. For the Be2 B8 Lin (n = 1-8) and the Be2 B36 Lin (n = 1-20) systems, lithium salts are dominant whereas a clear electride feature shows up for Be2 B8 Lin (n = 9-14) and Be2 B36 Li21 . Addition of hydrogen radicals to these systems shows that the Be2 B8 Li14 electride becomes a Be2 B8 Li14 H2 hydride electride whereas Be2 B36 Li21 leads to a Be2 B36 Li21 H salt...
May 3, 2018: Journal of Computational Chemistry
Wenli Zou, Ziyu Cai, Jiankang Wang, Kunyu Xin
Based on two-component relativistic atomic calculations, a free electron density function (EDF) library has been developed for nearly all the known ECPs of the elements Li (Z = 3) up to Ubn (Z = 120), which can be interfaced into modern quantum chemistry programs to save the .wfx wavefunction file. The applicability of this EDF library is demonstrated by the analyses of the quantum theory of atoms in molecules (QTAIM) and other real space functions on HeCuF, PtO42+, OgF4 , and TlCl3 (DMSO)2 . When a large-core ECP is used, it shows that the corrections by EDF may significantly improve the properties of some density-derived real space functions, but they are invalid for the wavefunction-depending real space functions...
April 29, 2018: Journal of Computational Chemistry
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