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Journal of Computational Chemistry

Hieu Thanh Nguyen, Tam Van-Thanh Mai, Lam Kim Huynh
Based on our modified classification of elemental species, a framework for automatic generation of multilevel Homodesmotic fragment-separation (mHDFS) reactions for chemical species was proposed. Combined the mHDFS framework with a database of heat of formation (HoF) and the calculated electronic structure data for the elemental mHD species, the mHDFS-HoF program was constructed in C/C++ language to calculate heat of formation for a species of interest on-the-fly. Using the electronic structure data calculated at CBS-QB3 level of theory for the elemental mHD species, applications and robustness of the code were discussed with several acyclic hydrocarbon systems including neutral and radical species...
February 20, 2019: Journal of Computational Chemistry
Markus Höhnerbach, Paolo Bientinesi
Despite initiatives to improve the quality of scientific software, there still is a large presence of legacy code. The focus of such code is usually on domain-science features, rather than maintainability or highest performance. Additionally, architecture specific optimizations often result in less maintainable code. In this article, we focus on the AIREBO potential from LAMMPS, which exhibits large and complex computational kernels, hindering any systematic optimization. We suggest an approach based on complexity-reducing refactoring and hardware abstraction and present the journey from the C++ port of a previous Fortran code to performance-portable, KNC-hybrid, vectorized, scalable, and optimized code supporting full and reduced precision...
February 19, 2019: Journal of Computational Chemistry
Zhifang Yang, Yanping Zheng, Wenliang Li, Jingping Zhang
Density functional theory calculations are performed to investigate electronic properties and Li/Na storage capability of Hf3 C2 and its derivatives (uniform passivated: Hf3 C2 T2 [T = F, O, OH] and hybrid passivated: Hf3 C2 Fx O2-x and Hf3 C2 Ox (OH)2-x [x = 1.0, 1.5]). For Hf3 C2 monolayer, it has excellent performance, such as good conductivity, low diffusion energy barrier, low open circuit voltage, and high storage capacities (Li(1034.70 mAh g-1 ), Na(444.90 mAh g-1 )), providing the most prospective as anode material...
February 18, 2019: Journal of Computational Chemistry
Haixin Wei, Ray Luo, Ruxi Qi
Immersed interface method (IIM) is a promising high-accuracy numerical scheme for the Poisson-Boltzmann model that has been widely used to study electrostatic interactions in biomolecules. However, the IIM suffers from instability and slow convergence for typical applications. In this study, we introduced both analytical interface and surface regulation into IIM to address these issues. The analytical interface setup leads to better accuracy and its convergence closely follows a quadratic manner as predicted by theory...
February 18, 2019: Journal of Computational Chemistry
Miao Yan, Hai-Ru Li, Xin-Xin Tian, Yue-Wen Mu, Hai-Gang Lu, Si-Dian Li
Detailed molecular orbital and bonding analyses reveal the existence of both fluxional σ- and π-bonds in the global minima Cs <mml:math xmlns:mml=""> <mml:msubsup> <mml:mi>B</mml:mi> <mml:mn>18</mml:mn> <mml:mrow> <mml:mn>2</mml:mn> <mml:mo>-</mml:mo> </mml:mrow> </mml:msubsup> </mml:math> (1) and Cs MB18 (3) and transition states Cs <mml:math xmlns:mml=""> <mml:msubsup> <mml:mi>B</mml:mi> <mml:mn>18</mml:mn> <mml:mrow> <mml:mn>2</mml:mn> <mml:mo>-</mml:mo> </mml:mrow> </mml:msubsup> </mml:math> (2) and Cs <mml:math xmlns:mml="http://www...
February 18, 2019: Journal of Computational Chemistry
Oscar A Douglas-Gallardo, David Adrian Saez, Stefan Vogt-Geisse, Esteban Vöhringer-Martinez
Carboxylation reactions represent a very special class of chemical reactions that is characterized by the presence of a carbon dioxide (CO2 ) molecule as reactive species within its global chemical equation. These reactions work as fundamental gear to accomplish the CO2 fixation and thus to build up more complex molecules through different technological and biochemical processes. In this context, a correct description of the CO2 electronic structure turns out to be crucial to study the chemical and electronic properties associated with this kind of reactions...
February 16, 2019: Journal of Computational Chemistry
Sergey A Samsonov, Martin Zacharias, Isaure Chauvot de Beauchene
Glycosaminoglycans (GAGs), a major constituent of the extracellular matrix, participate in cell-signaling by binding specific proteins. Structural data on protein-GAG interactions are crucial to understand and modulate these signaling processes, with potential applications in regenerative medicine. However, experimental and theoretical approaches used to study GAG-protein systems are challenged by GAGs high flexibility limiting the conformational sampling above a certain size, and by the scarcity of GAG-specific docking tools compared to protein-protein or protein-drug docking approaches...
February 15, 2019: Journal of Computational Chemistry
Sandra Romero-Molina, Yasser B Ruiz-Blanco, Mirja Harms, Jan Münch, Elsa Sanchez-Garcia
The prediction of peptide-protein or protein-protein interactions (PPI) is a challenging task, especially if amino acid sequences are the only information available. Machine learning methods allow us to exploit the information content in PPI datasets. However, the numerical codification of these datasets often influences the performance of data mining approaches. Here, we introduce a procedure for the general-purpose numerical codification of polypeptides. This procedure transforms pairs of amino acid sequences into a machine learning-friendly vector, whose elements represent numerical descriptors of residues in proteins...
February 15, 2019: Journal of Computational Chemistry
Xiaohui Wang, Xingzhao Tu, Boming Deng, John Z H Zhang, Zhaoxi Sun
The equilibrium and nonequilibrium adaptive alchemical free energy simulation methods optimum Bennett's acceptance ratio and optimum crooks' equation (OCE), based on the statistically optimal bidirectional reweighting estimator named Bennett's Acceptance Ratio or Crooks' equation, perform initial sampling in the staging alchemical transformation and then determine the importance rank of different states via the time-derivative of the variance. The method is proven to give speedups compared with the equal time rule...
February 14, 2019: Journal of Computational Chemistry
Isuru R Ariyarathna, Evangelos Miliordos
Bonding mechanisms, potential energy curves, accurate structures, energetics, and electron affinities are obtained for all M(CX)1-3 species with M = Li, Na, and X = O, S, Se, Te, and Po, at the coupled-cluster level with triple-ζ quality basis sets. We discuss and rationalize the trends within different molecular groups. For example, we found larger binding energies for M = Li, for CX = CPo, and for the tri-coordinated (n = 3) complexes. All three facts are explained by the fact that the global minimum of the titled complexes originate from the first excited 2 P (2p1 for Li or 3p1 for Na) state of the metal, with each ligand forming a dative bond with the metal...
February 12, 2019: Journal of Computational Chemistry
Dongdong Wang, Jingwei Weng, Wenning Wang
In conventional "Venus Flytrap" mechanism, substrate-binding proteins (SBPs) interconvert between the open and closed conformations. Upon ligand binding, SBPs form a tightly closed conformation with the ligand bound at the interface of two domains. This mechanism was later challenged by many type III SBPs, such as the vitamin B12 -binding protein BtuF, in which the apo- and holo-state proteins adopt very similar conformations. Here, we combined molecular dynamics simulation and Markov state model analysis to study the conformational dynamics of apo- and B12 -bound BtuF...
February 12, 2019: Journal of Computational Chemistry
Andrew S Rosen, Justin M Notestein, Randall Q Snurr
Metal-organic frameworks (MOFs) are a class of nanoporous materials with highly tunable structures in terms of both chemical composition and topology. Due to their tunable nature, high-throughput computational screening is a particularly appealing method to reduce the time-to-discovery of MOFs with desirable physical and chemical properties. In this work, a fully automated, high-throughput periodic density functional theory (DFT) workflow for screening promising MOF candidates was developed and benchmarked, with a specific focus on applications in catalysis...
February 4, 2019: Journal of Computational Chemistry
Nguyen Tien Trung, Pham Ngoc Khanh, Alfredo J Palace Carvalho, Minh Tho Nguyen
Thirty-six stable complexes of formic acid with formaldehydes and thioformaldehydes were determined on the potential energy surface, in which the XCHO···HCOOH complexes are found to be more stable than the XCHS···HCOOH counterparts, with X = H, F, Cl, Br, CH3 , NH2 . All complexes are stabilized by hydrogen bonds, and their contribution to the total stabilization energy of the complexes increases in going from C-H···S to C-H···O to O-H···S and finally to O-H···O. Remarkably, a significant blueshift of Csp2 -H bond by 81-96 cm-1 in the Csp2 -H···O hydrogen bond has hardly ever been reported, and a considerable redshift of O-H stretching frequency by 206-544 cm-1 in the O-H···O/S hydrogen bonds is also predicted...
February 4, 2019: Journal of Computational Chemistry
Florent Réal, Valérie Vallet, Michel Masella
We propose a general strategy to remediate force-field artifacts in describing pairwise interactions among similar molecules M in the vicinity of another chemical species, C, like water molecules interacting at short distance from a monoatomic ion. This strategy is based on introducing a three-body potential energy term that alters the pairwise interactions among M-type molecules when they lie at short range from the species C. In other words the species C is the center of a space domain where the pairwise interactions among the molecules M is altered...
January 31, 2019: Journal of Computational Chemistry
Arghya Chakravorty, Emilio Gallicchio, Emil Alexov
A novel grid-based method is presented, which in conjunction with a smooth Gaussian-based model of atoms, is used to compute molecular volume (MV) and surface area (MSA). The MV and MSA are essential for computing nonpolar component of free energies. The objective of our grid-based approach is to identify solute atom pairs that share overlapping volumes in space. Once completed, this information is used to construct a rooted tree using depth-first method to yield the final volume and SA by using the formulations of the Gaussian model described by Grant and Pickup (J...
January 30, 2019: Journal of Computational Chemistry
Wenhong Yang, Zhifeng Ma, Jun Yi, Sadia Ahmed, Wen-Hua Sun
The two-dimensional and three-dimensional quantitative structure-property relationship (2D- and 3D-QSPR) approaches are applied to investigate the catalytic performance for a total data set of 55 bis(imino)pryridine iron and cobalt complexes, including the catalytic activity, molecular weight, and melting temperature of the product. The obtained models for the catalytic performance of interest exhibit good results by both 2D- and 3D-QSPR modeling, meanwhile higher predictive and validation powers observed in the 3D type...
January 29, 2019: Journal of Computational Chemistry
Laura J S Lopes, Tony Lelièvre
We apply the adaptive multilevel splitting (AMS) method to the C eq → C ax transition of alanine dipeptide in vacuum. Some properties of the algorithm are numerically illustrated, such as the unbiasedness of the probability estimator and the robustness of the method with respect to the reaction coordinate. We also calculate the transition time obtained via the probability estimator, using an appropriate ensemble of initial conditions. Finally, we show how the AMS method can be used to compute an approximation of the committor function...
January 29, 2019: Journal of Computational Chemistry
Stefan Mattsson, Beate Paulus
We employ density functional theory with Hubbard U correction or hybrid functionals to study the series of magnetic 3d metal trifluorides MF3 (M = Ti-Ni). Experimental lattice parameters are reproduced with an error margin of 0.5%-4.3%. Cooperative Jahn-Teller distortions are reproduced for MnF3 , but also found in TiF3 and CoF3 at smaller levels compared to MnF3 . Trends in electronic structure with respect to positions of the d bands are linked to the magnetic properties where M = Ti-Cr are weak magnetic Mott-Hubbard insulators, M = Fe-Ni are strong magnetic charge-transfer insulators and MnF3 falls in between...
January 29, 2019: Journal of Computational Chemistry
Kelly N Tran, Shuqiang Niu, Toshiko Ichiye
Respiratory complex I facilitates electron transfer from NADH to quinone over ~95 Å through a chain of seven iron-sulfur (Fe-S) clusters in the respiratory chain. In this study, the reduction potentials of the Fe-S clusters in Thermus thermophilus complex I are calculated using a Density Functional Theory + Poisson-Boltzmann method. Our results indicate that the reduction potentials are influenced by a variety of factors including the clusters being deeply buried in the complex and the protonation state of buried ionizable residues...
January 29, 2019: Journal of Computational Chemistry
Mengyu Liu, Yanli Zeng, Zheng Sun, Lingpeng Meng
The "windmill" pattern cyclic halogen polymers (XBr)3 (X = Cl, Br, I) and (BrY)n (n = 3-6, Y = Cl, Br, I) have been investigated using the density functional theory. Due to the anisotropic distribution of its electron density, the halogen atom can form halogen-bonded interactions by functioning as both electron donor sites and electron acceptor sites. For (XBr)3 (X = Cl, Br, I) trimers, the Cl···Cl interaction is the weakest, and the I···I interaction is the strongest. For (BrY)n (n = 3-6, Y = Cl, Br, I), the Br···Br halogen bonds are the strongest in (BrY)4 tetramers...
January 24, 2019: Journal of Computational Chemistry
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