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Journal of Molecular Modeling

Jianying Zhang, Gangling Chen, Xuedong Gong
The quantitative structure-property relationship (QSPR) methodology was applied to describe and seek the relationship between the structures and energetic properties (and sensitivity) for some common energy compounds. An extended series of structural and energetic descriptors was obtained with density functional theory (DFT) B3LYP and semi-empirical PM3 approaches. Results indicate that QSPR model constructed using quantum descriptors can be applied to verify the confidence of calculation results compared with experimental data...
June 2017: Journal of Molecular Modeling
Liu Yun-Yun, Qiu Fang-Zhou, Zhu Jun, Ren Yi, Lau Kai-Chung
The modified G4(MP2) method was applied to explore microsolvation effects on the reactivity of four solvated normal oxy-nucleophiles YO(-)(CH3OH) n=1,2 (Y = CH3, C2H5, FC2H4, ClC2H4), and five α-oxy-nucleophiles YO(-)(CH3OH) n=1,2 (Y = HO, CH3O, F, Cl, Br), in gas-phase SN2 reactions towards the substrate CH3Cl. Based on a Brønsted-type plot, our calculations reveal that the overall activation barriers of five microsolvated α-oxy-nucleophiles are obviously smaller than the prediction from the correlation line constructed by four normal microsolvated ones to different degrees, and clearly demonstrate the existence of an α-effect in the presence of one or two methanol molecule(s)...
June 2017: Journal of Molecular Modeling
Wen-Jie Wu, Wei-Jie Chi, Quan-Song Li, Ze-Sheng Li
One of the most important aims in the development of high-energy materials is to improve their stability and thus ensure that they are safe to manufacture and transport. In this work, we theoretically investigated open-chain N4B2 isomers using density functional theory in order to find the best way of stabilizing nitrogen-rich molecules. The results show that the boron atoms in these isomers are aligned linearly with their neighboring atoms, which facilitates close packing in the crystals of these materials...
June 2017: Journal of Molecular Modeling
Eberth Correa, Washington Barbosa da Silva, Patricia R P Barreto, Alessandra F Albernaz
No abstract text is available yet for this article.
June 2017: Journal of Molecular Modeling
Lalit Kumar Gautam, Mohit Yadav, Jitendra Singh Rathore
Toxin-antitoxin (TA) complexes play an important role in stress responses and programmed cell death in bacteria. The RelB-RelE toxin antitoxin system is well studied in Escherichia coli. In this study, we used combined in silico and in vitro approaches to study a novel Xn-RelT toxin from Xenorhabdus nematophila bearing its own antitoxin Xn-RelAT-a RelB homolog of E. coli. The structure for this toxin-antitoxin pair is yet unknown. We generated homology-based models of X. nematophila RelT toxin and antitoxin...
June 2017: Journal of Molecular Modeling
Qiang Zhao
Noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes were investigated using ab initio calculations at the MP2/aug-cc-pVDZ level of theory. There are four different configurations of these complexes, and the complexes are formed via hydrogen bonds, halogen bonds, π-hole interactions, or dual interactions. An examination of binding distances and interaction energies suggested that π-hole bonds are more stable than the other interactions. Molecular electrostatic potentials, electron densities, second-order stabilization energies, and electron density differences were computed to study the character of these interactions...
June 2017: Journal of Molecular Modeling
Zhengyang Gao, Yi Ding
The moisture content of coal affects the adsorption capacity of CO2 on the coal surface. Since the hydrogen bonds are formed between H2O and oxygen functional group, the H2O cluster more easily adsorbs on the coal micropore than CO2 molecule. The coal micropores are occupied by H2O molecules that cannot provide extra space for CO2 adsorption, which may leads to the reduction of CO2 adsorption capacity. However, without considering factors of micropore and oxygen functional groups, the co-adsorption mechanisms of CO2 and adsorbed H2O molecule are not clear...
June 2017: Journal of Molecular Modeling
Qiong Wu, Bo Kou, Zusheng Hang, Weihua Zhu
In this work, six (A-F) nitramino (-NHNO2)-substituted ditetrazole 2-N-oxides with different bridging groups (-CH2-, -CH2-CH2-, -NH-, -N=N-, and -NH-NH-) were designed. The six compounds were based on the parent compound tetrazole 2-N-oxide, which possesses a high oxygen balance and high density. The structure, heat of formation, density, detonation properties (detonation velocity D and detonation pressure P), and the sensitivity of each compound was investigated systematically via density functional theory, by studying the electrostatic potential, and using molecular mechanics...
June 2017: Journal of Molecular Modeling
Diego R Alcoba, Ofelia B Oña, Alicia Torre, Luis Lain, Patrick Bultinck
In this work, the dual-descriptor is studied in matrix form [Formula: see text] and both coordinates condensed to atoms, resulting in atomic and diatomic (or where applicable, bond) condensed single values. This double partitioning method of the dual-descriptor matrix is proposed within the Hirshfeld-I atoms-in-molecule framework although it is easily extended to other atoms-in-molecules methods. Diagonalizing the resulting atomic and bond dual-descriptor matrices gives eigenvalues and eigenvectors describing the reactivity of atoms and bonds...
June 2017: Journal of Molecular Modeling
Mehmet Ferdi Fellah
Hydrogen molecule adsorption on frameworks consisting of alkaline earth metal atoms (Be, Mg, or Ca) in LTL zeolite was investigated via density functional theory. A 24T zeolite cluster model was used in this study. HOMO and LUMO energy, chemical potential, chemical hardness, electronegativity, adsorption energy, and adsorption enthalpy values were calculated. The Mg-LTL and Ca-LTL clusters were found to have much lower chemical potentials and adsorption energies than those of the Be-LTL cluster. Additionally, the calculations indicated that the Mg-LTL and Ca-LTL clusters are softer (considering their lower chemical hardness values) and more chemically reactive than the Be-LTL cluster...
June 2017: Journal of Molecular Modeling
Mingfei Ji, Guodong Zheng, Xiaolong Li, Zhongqin Zhang, Guanqun Jv, Xiaowei Wang, Jialin Wang
The deregulated breakpoint cluster region (Bcr)-Abelson tyrosine kinase (Abl) fusion protein represents an attractive pharmacological target for the treatment of chronic myeloid leukemia (CML). The high affinity of monobody AS25 was designed to target the Src homology 2 (SH2) domain of Bcr-Abl, leading to allosteric inhibition of Bcr-Abl through formation of protein-protein interactions. An I164E mutation in the SH2 domain disrupts AS25 binding to the SH2 domain of Bcr-Abl. The detailed mechanisms, however, remain to be unresolved...
June 2017: Journal of Molecular Modeling
Daniel F S Machado, Rodrigo A L Silva, Ana Paula de Oliveira, Valter H Carvalho-Silva, Ricardo Gargano, Luciano Ribeiro, Heibbe C B de Oliveira
In this paper, we propose a new alternative analytical function aiming to better describe the potential energy curves of the doubly charged diatomic molecules. To achieve this goal, we modified an existing potential function in the literature to describe dicationic diatomic molecules using the deformed exponential function. We generated the potential energy curve of the testing group of dicationic diatomic molecules [Formula: see text], BH(2+), [Formula: see text] and NH(2+) by means of the CCSD(T)/aug-cc-pVQZ level of theory...
June 2017: Journal of Molecular Modeling
Adrian Calborean, Florin Graur, Vasile Bintintan
Correlations between DFT and experimental measurements on Zn(2+) and Ni(2+) chiral meso-(α,β-unsaturated)- porphyrins were performed using Kohn-Sham methodology. The exchange-correlation Becke88-Perdew86 functional was used in conjunction with double-zeta Slater basis sets. An accurate description of the electronic processes depending on the metal ion (Zn, Ni) or ligand (perilaldehyde and myrtenal) was made, confirming experimental results in terms of structural and electronic modifications. Moreover, this theoretical study provides a stronger knowledge and interpretation of the dynamical conformational features of the free base, Zn and Ni structures...
June 2017: Journal of Molecular Modeling
Yutong Feng, Jucai Yang
The neutral PrSi n (n = 12-21) species considering various spin configurations were systematically studied using PBE0 and B3LYP schemes in combination with relativistic small-core potentials (ECP28MWB) for Pr atoms and cc-pVTZ basis set for Si atoms. The total energy, growth-pattern, equilibrium geometry, relative stability, hardness, charge transfer, and magnetic moments are calculated and discussed. The results reveal that when n < 20, the ground-state structure of PrSi n evaluated to be prolate clusters...
June 2017: Journal of Molecular Modeling
Shide Hu, Weiguo Sun, Jia Fu, Lulu Zhang, Qunchao Fan, Zhanwen Zhang, Weidong Wu, Yongjian Tang
Using molecular dynamics simulations with ReaxFF reactive force field, the thermal decomposition mechanism of poly alpha-methyl styrene (PAMS) materials and the effects of heating rate and impurity fluorobenzene on PAMS thermal decompositions are studied. The results show that: 1) Pyrolysis mechanism of PAMS consists of initiation and propagation processes. In the initiation stage, random scissions of C-C backbone produce fragments, and in the propagation stage, depolymerizing reactions generate monomers and other products...
June 2017: Journal of Molecular Modeling
Miao Zhang, Ningbo Liao, Wei Xue, Ping Yang
At high temperature, silicon oxycarbide (SiCO) exhibits excellent mechanical properties and thermal stability. The incorporation of boron in SiCO results in improved performance in creep temperatures. In this work, large-scale molecular dynamics calculations were applied to obtain amorphous SiCO structures containing boron. Phase separation of C-C, B-C and Si-O was achieved for three compositions, and silicon-centered mixed-bond tetrahedrons were reproduced successfully. As the boron content increases, the boron atoms tend to form B-C and B-Si bonds in the voids, which stretches the free carbon network in some instances, causing a increase in C-C distance...
June 2017: Journal of Molecular Modeling
Xin Mao, Sufan Wang, Yongjia Shang
A series of theoretical computations were conducted via density functional theory at the B3LYP/6-31 + G(d,p) level to study the mechanism of the organocatalytic synthesis of a benzoxazine-substituted indolizine derivative. Four possible alternative pathways were considered in this work. The calculated results show that the formation of an N-ylide precursor from 4-dimethylaminopyridine (DMAP) is a key step as it provides the necessary nucleophilic centre for the subsequent H-migration and H-elimination processes...
June 2017: Journal of Molecular Modeling
Henrique O Euclides, Patricia R P Barreto
APUAMA is a free software designed to determine the reaction rate and thermodynamic properties of chemical species of a reagent system. With data from electronic structure calculations, the APUAMA determine the rate constant with tunneling correction, such as Wigner, Eckart and small curvature, and also, include the rovibrational level of diatomic molecules. The results are presented in the form of Arrhenius-Kooij form, for the reaction rate, and the thermodynamic properties are written down in the polynomial form...
June 2017: Journal of Molecular Modeling
S P Sousa, Humberto F Silva Filho, S Guerini
In this work we use the ab initio calculations to study the intercalation of lithium (Li) atoms in the channels of the single-wall boron nitride nanotube (BNNT) bundles. The relaxed structure as well as the electronic band structure were obtained. Results reveals that Li insertion modifies the band structure by shifting the Fermi energy to conduction band. The Li atoms act as electron donors and this modifies the electronic properties of the BNNT bundles due the intercalation. The electronic properties changes induced in the effects are dependent on Li atom numbers per nanotube...
June 2017: Journal of Molecular Modeling
Glenn R Morello
Accurate prediction of triplet excitation energies for transition metal complexes has proven to be a difficult task when confronted with a variety of metal centers and ligand types. Specifically, phosphorescent transition metal light emitters, typically based on iridium or platinum, often give calculated results of varying accuracy when compared to experimentally determined T1 emission values. Developing a computational protocol for reliably calculating OLED emission energies will allow for the prediction of a complex's color prior to synthesis, saving time and resources in the laboratory...
June 2017: Journal of Molecular Modeling
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