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Journal of Computational Chemistry

Yan Ying Liang, Bo Li, Xuan Xu, Feng Long Gu, Chaoyuan Zhu
In this work, we investigated the nonlinear optical (NLO) properties of excess electron electride molecules of M[Cu(Ag)@(NH3 )n ](M = Be, Mg and Ca; n = 1-3) using density functional theory (DFT). This electride molecules consist of an alkaline-earth (Be, Mg and Ca) together with transition metal (Cu and Ag) doped in NH3 cluster. The natural population analysis of charge and their highest occupied molecular orbital suggests that the M[Cu(Ag)@(NH3 )n ] compound has excess electron like alkaline-earth metal form double cage electrides molecules, which exhibit a large static first hyperpolarizability ( <mml:math xmlns:mml="http://www...
November 16, 2018: Journal of Computational Chemistry
Jahanzeb Khan, Yunpeng Liu, Tianqi Zhao, Hua Geng, Wei Xu, Zhigang Shuai
Metal organic coordination polymers (MOCPs) provide an intriguing platform to design functional thermoelectric materials through modifying metal atoms, organic ligands, etc. Based on density functional theory (DFT) coupled with Boltzmann transport theory, the thermoelectric properties of several MOCPs, which is designed by intercalating organic linkers ranging from benzene to pentacene between two inorganic units, have been investigated. We found that the interplay of d orbital of Ni atom and π orbitals of the organic linkers play an important role in band engineering and then thermoelectric efficiency...
November 15, 2018: Journal of Computational Chemistry
Cen-Feng Fu, Ruiqi Zhang, Qiquan Luo, Xingxing Li, Jinlong Yang
The direct Z-scheme system constructed by two-dimensional (2D) materials is an efficient route for hydrogen production from photocatalytic water splitting. In the present work, the 2D van der Waals (vdW) heterojunctions of MoSe2 /SnS2 , MoSe2 /SnSe2 , MoSe2 /CrS2 , MoTe2 /SnS2 , MoTe2 /SnSe2 , and MoTe2 /CrS2 are proposed to be promising candidates for direct Z-scheme photocatalysts and verified by first principles calculations. Perpendicular electric field is induced in these 2D vdW heterojunctions, which enhances the efficiency of solar energy utilization...
November 15, 2018: Journal of Computational Chemistry
Cheng Shang, Si-Da Huang, Zhi-Pan Liu
The potential energy surface (PES) calculation is the bottleneck for modern material simulation. The high-dimensional neural network (HDNN) technique emerged recently appears to be a problem solver for fast and accurate PES computation. The major cost of the HDNN lies at the computation of the structural descriptors that capture the geometrical environment of atoms. Here, we introduce a massive parallelization strategy optimized for our recently developed power-type structural descriptor. The method involves three-levels: from the top to the bottom the parallelization is over atoms first, then, over structural descriptors and finally over the n-body functions...
November 10, 2018: Journal of Computational Chemistry
Subhamoy Mahajan, Tian Tang
As a polycation with diverse applications in biomedical and environmental engineering, polyethylenimine (PEI) can be synthesized with varying degrees of branching, polymerization, and can exist in different protonation states. There have been some interests in molecular modeling of PEI at all-atom or coarse-grained (CG) levels, but present CG models are limited to linear PEIs. Here we present the methodology to systematically categorize bond lengths, bond angles and dihedral angles, which allows us to model branched PEIs...
November 10, 2018: Journal of Computational Chemistry
Iori Harada, Akira Nakayama, Jun-Ya Hasegawa
A structure optimization method with ionization energy constraint is developed to explore structures with specific ionization energy. The Levine-Coe-Martínez penalty function (J Phys Chem B 2008, 112, 405) was adopted, and the penalty function includes a predefined core-ionization energy and inner-shell ionization energy. For an SN 2 reaction, isomerization of a platinum complex, a proton transfer reaction, and carbon monoxide adsorption on a palladium cluster, the present method was tested, and the targeted energy minima were obtained as designated by the input ionization energy...
November 10, 2018: Journal of Computational Chemistry
Miho Hatanaka, Tomonari Wakabayashi
The 4f-4f emissions from lanthanide trication (Ln3+ ) complexes are widely used in bioimaging probes. The emission intensity from Ln3+ depends on the surroundings, and thus, the design of appropriate photo-antenna ligands is indispensable. In this study, we focus on two probes for detecting hydrogen peroxide, for which emission intensities from Tb3+ are enhanced chemo-selectively by the H2 O2 -mediated oxidation of ligands. To understand the mechanism, the Gibbs free energy profiles of the ground and excited states related to emission and quenching are computed by combining our approximation-called the energy shift method-and density functional theory...
November 10, 2018: Journal of Computational Chemistry
Yoshitake Sakae, John E Straub, Yuko Okamoto
We propose a molecular simulation method using genetic algorithm (GA) for biomolecular systems to obtain ensemble averages efficiently. In this method, we incorporate the genetic crossover, which is one of the operations of GA, to any simulation method such as conventional molecular dynamics (MD), Monte Carlo, and other simulation methods. The genetic crossover proposes candidate conformations by exchanging parts of conformations of a target molecule between a pair of conformations during the simulation. If the candidate conformations are accepted, the simulation resumes from the accepted ones...
November 10, 2018: Journal of Computational Chemistry
Tomoaki Yagi, Hirofumi Sato
A simple model of a lipid membrane, a binary mixture of saturated lipids and unsaturated lipids, was studied using an integral equation theory. The planar membrane is modeled as mixture of linear and bent molecules in two-dimensional space, and site-site radial distribution function, Kirkwood-Buff (KB) integral and related quantities were computed over the whole range of the molar fraction to understand their mixing behavior. We found that a close packing of linear molecules is enhanced as the fraction of bent molecules increases, but a long range correlation between the linear molecules is weakened...
November 5, 2018: Journal of Computational Chemistry
Naveen K Dandu, Olajumoke Adeyiga, Dipak Panthi, Shaina A Bird, Samuel O Odoh
Methane-to-methanol conversion (MMC) can be facilitated with high methanol selectivities by copper-exchanged zeolites. There are however two open questions regarding the use of these zeolites to facilitate the MMC process. The first concerns the possibility of operating the three cycles in the stepwise MMC process by these zeolites in an isothermal fashion. The second concerns the possibility of improving the methanol yields by systematic substitution of some copper centers in these active sites with other earth-abundant transition metals...
October 31, 2018: Journal of Computational Chemistry
Varinia Bernales, Robert D Froese
DFT and CCSD(T) methods were used to examine 61 different rhodium catalysts for the hydroformylation of ethylene. The carbon monoxide (CO) stretching frequency was a key electronic parameter to understand the π-accepting nature of the ligand. Normally, π-accepting ligands lead to increased CO stretching frequencies and a reduction in CO dissociation energy. There was no relationship between CO dissociation energy and CO stretching frequency. However, a clear relationship exists between the ethylene insertion barrier (from the rhodium dicarbonyl hydride resting state) and the CO stretching frequency as stronger π-accepting ligands systematically led to a reduction in the barrier...
October 31, 2018: Journal of Computational Chemistry
Igor Ying Zhang, Jianming Wu, Xin Xu
Polycyclic saturated hydrocarbons (PSHs) are attractive candidates as hydrocarbon propellants. To assess their potential values, one of the key factors is to determine their energy contents, such as to calculate their heats of formation (HOF). In this work, we have calculated HOFs for a set of 36 PSHs including exo-Tricyclo[,6) ] decane, the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. The results from B3LYP, B3LYP-D3BJ, M06-2X, B2PLYP, B2PLYP-D3BJ, and the XYG3 type of doubly hybrid (xDH) functionals are presented...
October 31, 2018: Journal of Computational Chemistry
Ya-Ting Wang, Xiang-Yang Liu, Wei-Hai Fang
In the present work, mechanism of the O2 (1 Δg ) generation from the reaction of the dissolved Cl2 with H2 O2 in basic aqueous solution has been explored by the combined ab initio calculation and nonadiabatic dynamics simulation, together with different solvent models. Three possible pathways have been determined for the O2 (1 Δg ) generation, but two of them are sequentially downhill processes until formation of the OOCl- complex with water, which are of high exothermic character. Once the complex is formed, singlet molecular oxygen is easily generated by its decomposition along the singlet-state pathway...
October 31, 2018: Journal of Computational Chemistry
Nozomi Takagi, Masayuki Nakagaki, Kazuya Ishimura, Ryoichi Fukuda, Masahiro Ehara, Shigeyoshi Sakaki
Experimentally observed NO dimerization on Cu and Ag surfaces is surprising because binding energy of NO dimer is very small in gas phase. MRMP2, MP2 to MP4, CCSD(T), and DFT studies of NO dimerization on Ag2 and Cu2 clusters disclosed that the CCSD(T) method could be applied to this reaction on Ag2 and Cu2 unlike NO dimerization in gas phase which exhibits significantly large nondynamical electron correlation effect. Charge-transfer (CT) from Ag2 and Cu2 to NO moieties plays important role in NN bond formation between two NO molecules...
October 31, 2018: Journal of Computational Chemistry
Hui Li, Di Wang, Xin Zhao, Li-Nan Lu, Cui Liu, Li-Dong Gong, Dong-Xia Zhao, Zhong-Zhi Yang
Nitrosylation reaction mechanisms of the hydrolysates of NAMI-A and hydrolysis reactions of ruthenium nitrosyl complexes were investigated in the triplet state and the singlet state. Activation free energies were calculated by combining the QM/MM(ABEEM) method with free energy perturbation theory, and the explicit solvent environment was simulated by an ABEEMσπ polarizable force field. Our results demonstrate that nitrosylation reactions of the hydrolysates of NAMI-A occur in both the triplet and the singlet states...
October 30, 2018: Journal of Computational Chemistry
Dan Hu, Xiaoqing Guan, Yukun Wang
Free energy calculation is an efficient way for studying rare event dynamics. For a complex rare event dynamics, multiple reaction coordinates may be required to describe the transition path between equilibrium states. Theoretically, a one-dimensional sampling along the transition path can provide sufficient information to calculate the potential of mean force (PMF) along the transition path. In the widely used free energy analysis method Wham, the sample data are divided into a series of bins to calculate PMF...
October 30, 2018: Journal of Computational Chemistry
Shreyas Malpathak, Xinyou Ma, William L Hase
In Density Functional Theory (DFT) direct dynamics simulations with Unrestricted Hartree Fock (UHF) theory, triplet instability often emerges when numerically integrating a classical trajectory. A broken symmetry initial guess for the wave function is often used to obtain the unrestricted DFT potential energy surface (PES), but this is found to be often insufficient for direct dynamics simulations. An algorithm is described for obtaining smooth transitions between the open-shell and the closed-shell regions of the unrestricted PES, and thus stable trajectories, for direct dynamics simulations of dioxetane and its •OCH2 -CH2 O• singlet diradical...
October 26, 2018: Journal of Computational Chemistry
Paul Jerabek, Peter Schwerdtfeger, Gernot Frenking
Quantum chemical calculations using density functional theory at the BP86-D3(BJ)/def2-TZVPP level of theory are reported for transition metal compounds [TM]-L in high and low oxidation states involving carbene, carbyne, alkene, and alkyne ligands L. The nature of the [TM]-L bond is analyzed with the energy decomposition analysis - natural orbitals for chemical valence (EDA-NOCV) method. The calculations reveal that transition metal compounds with ligands, that are typically classified as donor-acceptor complexes possessing dative bonds (Fischer-type carbenes and carbynes, alkene, and alkyne complexes) or as TM compounds with electron-sharing bonds (Schrock-type carbenes and carbynes, metallacyclopropanes, and metallacyclopropenes), exhibit significant differences between the orbital interactions when closed-shell or open shell fragments are used...
October 26, 2018: Journal of Computational Chemistry
Titus Adrian Beu, Andrada-Elena Ailenei, Alexandra Farcaş
We present a revised version of our previously published atomistic Chemistry at Harvard Macromolecular Mechanics (CHARMM) force field for polyethyleneimine (PEI). It is based on new residue types (with symmetric CNC backbone), whose integer charges and bonded parameters are derived from ab initio calculations on an enlarged set of model polymers. The force field is validated by extensive molecular dynamics simulations on solvated PEI chains of various lengths and protonation patterns. The profiles of the gyration radius, end-to-end distance, and diffusion coefficient fine-tune our previous results, while the simulated diffusion coefficients excellently reproduce experimental findings...
October 26, 2018: Journal of Computational Chemistry
Vivek Gavane, Shruti Koulgi, Vinod Jani, Mallikarjunachari V N Uppuladinne, Uddhavesh Sonavane, Rajendra Joshi
Lead optimization is one of the crucial steps in the drug discovery pipeline. After identifying the lead molecule and obtaining its 2D geometry, understanding the best conformation it would attain in 3D still remains one of the most challenging steps in drug discovery. There have been multiple methods and algorithms that are directed toward achieving best conformation for the lead molecules. TANGO focuses on conformation generation and its optimization using semiempirical energy calculations. The conformation generation is based on torsion angle rotation of the exocyclic bonds...
October 26, 2018: Journal of Computational Chemistry
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