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Journal of Molecular Graphics & Modelling

Bobo Cao, Jiuyao Du, Ziping Cao, Haitao Sun, Xuejun Sun, Hui Fu
To explore sustainable catalysts with innovative mechanisms, the alkylation mechanism of o-xylene with styrene was studied using DFT method in AlCl3-ionic liquid catalytic system. The reaction pathway was consisted of CC coupling and a hydrogen shift, in which two transition states were found and further discussed. The reactive energy catalyzed by superelectrophilic AlCl2(+) (12.6kcal/mol) was distinctly lower than AlCl3 (43.0kcal/mol), which was determined as the rate-determining step. Mulliken charge along IRC gave a comprehensive understanding of charge distribution and electron transfer in dynamic progress...
March 6, 2017: Journal of Molecular Graphics & Modelling
K Nejati, A Hosseinian, A Bekhradnia, E Vessally, L Edjlali
It has been recently indicated that the Li-ion batteries may be replaced by Na-ion batteries because of their low safety, high cost, and low-temperature performance, and lack of the Li mineral reserves. Here, using density functional theory calculations, we studied the potential application of B12N12 nanoclusters as anode in Na-ion batteries. Our calculations indicate that the adsorption energy of Na(+) and Na are about -23.4 and -1.4kcal/mol, respectively, and the pristine BN cage to improve suffers from a low cell voltage (∼0...
March 6, 2017: Journal of Molecular Graphics & Modelling
Mehdi D Esrafili, Soheila Asadollahi
In this work, we investigate the effect of a cation-π interaction on the cooperativity of X⋯N halogen bonds in PhX⋯NCX⋯NH3 complexes, where Ph=phenyl and X=Cl, Br, I. Molecular geometries and interaction energies of the resulting complexes are studied at the MP2/aug-cc-pVDZ(-PP) computational level. The mechanism of the cooperativity between halogen bonds is analyzed using parameters derived from the noncovalent index, quantum theory of atoms in molecules and natural bond orbital methodologies. It is found that the divalent cations (Be(2+), Mg(2+)) have a larger influence on the cooperativity of halogen bonds than monovalent ones (Li(+), Na(+))...
March 2, 2017: Journal of Molecular Graphics & Modelling
Mohammed Salah, Najia Komiha, Oum Keltoum Kabbaj, Rachida Ghailane, Khadija Marakchi
The 1,3-dipolar cycloaddition of methyl 2-trifluorobutynoate with various azides has been studied in terms of several theoretical approaches at DFT/B3LYP/6-311++G(d,p) level of theory. The mechanism of regioselectivity of these reactions was investigated through the evaluation of the potential energy surface of the cycloaddition process calculations and density DFT-based reactivity indices. These approaches were successfully applied to prediction of preferable regio-isomers for various reactions of 1,3-dipolar cycloadditions...
March 1, 2017: Journal of Molecular Graphics & Modelling
Aditi Gangopadhyay, Hirak Jyoti Chakraborty, Abhijit Datta
The dengue envelope β-OG pocket is a crucial hinge for mediating virus-host fusion via conformational changes in the envelope to the fusion-competent form. The β-OG pocket is a small molecule target site for inhibition of virus-host fusion. As of date, the only structure of the β-OG pocket known is of serotype 2. Studies of β-OG inhibition by small molecules primarily target viral serotype 2. Envelope and β-OG sequence alignments, reveal dissimilarities across serotypes. In light of protein sequence-structure-function correlation, sequence variations suggest serotypic variations in β-OG druggability...
March 1, 2017: Journal of Molecular Graphics & Modelling
Weihong Zhang, Steven C Howell, David W Wright, Andrew Heindel, Xiangyun Qiu, Jianhan Chen, Joseph E Curtis
We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody...
February 23, 2017: Journal of Molecular Graphics & Modelling
Bin Sun, Wanxu Huang, Min Liu
14α-demethylase (CYP51) is an essential metabolic enzyme for fungal survival and has been considered as an interesting target for the development of new antifungal inhibitors. Azoles antifungal inhibitors in the treatment of fungal diseases are good candidates via the interaction with the target enzyme CYP51 of fungus. In the study, we constructed the homology model for Candida albicans CYP51 (CACYP51) and analyzed the active site. In order to better understand the structural characteristics of azoles inhibitors and combination mode, the common feature pharmacophore model and the molecular docking were performed...
February 21, 2017: Journal of Molecular Graphics & Modelling
Miguel Mompeán, Mayte Villalba, Marta Bruix, Héctor Zamora-Carreras
Despite the growing number of carbohydrate-binding modules (CBMs) that are being uncovered, information on the structural determinants for the sugar-binding regions at atomic resolution is scarce. It is widely accepted that aromatic and H-bonding interactions govern these processes, and reported simulations and theoretical calculations are valuable tools to quantify and understand these interactions. We present here a computational model derived from experimental data that provide a unique atomistic picture of an uncharacterized binding mode of laminarin to the CBM family 43...
February 21, 2017: Journal of Molecular Graphics & Modelling
Hadi Alizadeh, Jamal Davoodi, Hashem Rafii-Tabar
Connexins are a 21-member membrane protein family constituting channels evolved in direct communication between adjacent cells by passaging cytoplasmic molecules and ions. Hexametrical assembly of connexin proteins in plasma membrane forms a wide aqueous pore known as connexin hemichannel. These hemichannels mediate cytoplasm and extracellular milieu communication both in many external tissues and in the central nervous system. In this study, a series of molecular dynamics simulations has been performed to investigate the effect of applied static and alternating electric fields on the stability and conformation of human connexin26 hemichannel...
February 20, 2017: Journal of Molecular Graphics & Modelling
Maciej Janicki, Marek Lozynski
(S)-3-Methyl-3-butenyl-(2R,3S)-N-benzoyl-3-phenylisoserinate is used as a model of the C-13 side chain, an essential subunit for the cytotoxicity of the diterpenoid paclitaxel, a chemotherapeutic drug used in the treatment of cancer. The potential energy surface (PES), calculated using a density functional theory method (DFT) and refined with MP2 single-point energy calculations, based on B3LYP geometries, was evaluated. Twelve intramolecular hydrogen bond patterns were identified for 103 in vacuo conformers...
February 20, 2017: Journal of Molecular Graphics & Modelling
A Hosseinian, A Bekhradnia, E Vessally, L Edjlali, M D Esrafili
Nanographenes (NGs) are a segment of graphene whose dangling bonds are saturated with hydrogen atoms, introducing different properties and promising applications. Here we investigate the electronic, thermodynamic, optical, and structural properties of four C36X3Y3H18 NGs (X=B, and Al; and Y=N, and P) based on the density functional theory calculations. It was mainly found that 1) BN-NG is planar molecule and the others are buckybowl-shaped ones, 2) The bowl-to-bowl inversion Gibbs free energies (ΔG(#)) of buckybowl shaped NGs are very huge and the rate constant is very small, hindering the inversion, 3) The relative energetic stability order based on the standard enthalpy of formation (ΔHf(°)) is as BN>AlN>BP>AlP, which the BN, and AlN doped NGs are stable at room temperature but the BP and AlP doped ones are instable, 4) The electrical conductivity order of magnitude is inverse of that of stability, 5) An exciton binding energy is predicted in the range of 0...
February 11, 2017: Journal of Molecular Graphics & Modelling
Xiaobing Chen, Bojian Xie, Liang Cao, Feng Zhu, Beibei Chen, Huifang Lv, Xingxing Fan, Lili Han, Liangyu Bie, Xinguang Cao, Xiaokun Shen, Feilin Cao
The Regorafenib is a broad-spectrum kinase inhibitor that has been approved to treat colorectal cancer (CRC). However, evidences have shown that the agent is also implicated in drug interaction with microRNA-21 (miR-21), an oncogenic miRNA which plays a key role in resisting programmed cell death in CRC cells. Here, we supposed that, instead of kinase inhibition, Regorafenib can directly bind to and then stabilize miR-21 pre-element, thus preventing RNase Dicer-meditated cleavage of the pre-element to mature miR-21...
February 10, 2017: Journal of Molecular Graphics & Modelling
Samar S Elbaramawi, Samy M Ibrahim, El-Sayed M Lashine, Mohamed E El-Sadek, Efi Mantzourani, Claire Simons
Increased resistance of MRSA (multidrug resistance Staphylococcus aureus) to anti-infective drugs is a threat to global health necessitating the development of anti-infectives with novel mechanisms of action. Phenylalanine tRNA synthetase (PheRS) is a unique enzyme of the aminoacyl-tRNA synthetases (aaRSs), which are essential enzymes for protein biosynthesis. PheRS is an (αb)2 tetrameric enzyme composed of two alpha subunits (PheS) and two larger beta subunits (PheT). Our potential target in the drug development for the treatment of MRSA infections is the phenylalanine tRNA synthetase alpha subunit that contains the binding site for the natural substrate...
February 10, 2017: Journal of Molecular Graphics & Modelling
Vivek Modi, Ramasubbu Sankararamakrishnan
The anti-apoptotic members of Bcl-2 family of proteins bind to their pro-apoptotic counterparts to induce or prevent cell death.Based on the distinct binding profiles for specific pro-apoptotic BH3 peptides, the anti-apoptotic Bcl-2 proteins can be divided into at least two subclasses. The subclass that includes Bcl-XL binds strongly to Bad BH3 peptide while it has weak binding affinity for the second subclass of Bcl-2 proteins such as Mcl-1 and A1. Anti-apoptotic Bcl-2 proteins are considered to be attractive drug targets for anti-cancer drugs...
February 9, 2017: Journal of Molecular Graphics & Modelling
Majdi M Bkhaitan, Agha Zeeshan Mirza, Hina Shamshad, Hamed I Ali
Towards the design of new class of podophyllotoxin to target topoisomerase II and tubulin as substantial target in cancer therapy, a series of isoxazolidine podophyllotoxin derivatives were designed. Topoisomerase in complex with etoposide and four β-tubulin in complex with zampanolide, taxol, vinblastine or colchicine were used as targets using GOLD5.2.2 as a docking module. The revealed key structural features of the highest fitness into tubulin domain have been explained as follows: (1) trans orientation of the lactone (ring D) with 5a-β, 8a-α configuration; (2) dioxolane in ring A; (3) free rotation of ring E; (4) α (R) or β (S) configuration has equal fitness in position 5; (5) 4'-OMe; (6) phosphoramide linkage; (7) ethylene bridge between the phosphate and isoxazolidine ring; (8) benzyl moiety at N(2)-position of isoxazolidine ring; and (9) position 5 of isoxazolidine ring accommodated with 6-bromo-9H-purine, 2-amino-6H-purin-6-one, or N-(2-oxopyrimidin-4-yl) acetamide...
February 9, 2017: Journal of Molecular Graphics & Modelling
María Font, Daniel Plano, Carmen Sanmartín, Juan Antonio Palop
A molecular modeling study has been carried out on a previously reported series of (diselanediyldibenzene-4,1-diylnide)biscarbamate derivatives that show cytotoxic and antiproliferative in vitro activity against MCF-7 human cell line; radical scavenging properties were also confirmed when these compounds were tested for their ability to scavenge DPPH and ABTS radicals. The data obtained allowed us to classify the compounds into two different groups: (a) aliphatic carbamates for which the activity could be related with a first nucleophilic attack (mediated by H2O, for example) on the selenium atoms of the central scaffold, followed by the release of the alkyl N-(4-selanylphenyl) and N-(4-selenenophenyl)carbamate moieties...
February 9, 2017: Journal of Molecular Graphics & Modelling
Abdulmujeeb T Onawole, Kazeem O Sulaiman, Rukayat O Adegoke, Temitope U Kolapo
The Zika virus (ZIKV) is a life threatening pathogen of zoonotic importance with prevalence in some parts of Africa and America. Unfortunately, there is yet to be a single approved vaccine or antiviral drug to treat the diseases and deformations being caused by the Zika virus infection. In this study, about 36 million compounds from MCULE database were virtually screened against a real matured ZIKV protein using a consensus scoring method to get improved hit rates. The consensus scoring method combined the result from the 25 top ranked molecules from both MCULE and Drug Score eXtended (DSX) docking programs which led to the selection of two hit compounds...
February 9, 2017: Journal of Molecular Graphics & Modelling
Nguyen-Quoc-Khanh Le, Trinh-Trung-Duong Nguyen, Yu-Yen Ou
The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells...
February 2, 2017: Journal of Molecular Graphics & Modelling
Mahmoud Khadem-Maaref, Faramarz Mehrnejad, Arash Phirouznia
Pyrazinamidase (PZase), a metalloenzyme, is responsible for acidic modification of pyrazinamide (PZA), a drug used in tuberculosis treatment. The metal coordination site of the enzyme is able to coordinate various divalent metal cofactors. Previous experimental studies have demonstrated that metal ions, such as Co(2+), Mn(2+), and Zn(2+), are able to reactivate metal-depleted PZase, while others including Cu(2+), Fe(2+), and Mg(2+), cannot restore activity. In this study, we investigated binding of various metal ions to the metal coordination site (MCS) of the enzyme using quantum mechanical calculations...
February 2, 2017: Journal of Molecular Graphics & Modelling
Yan Qin, Qi-Shi Du, Neng-Zhong Xie, Jian-Xiu Li, Ri-Bo Huang
An interesting possibility is explored: storing the mixture of oxygen and hydrogen in clathrate hydrate in molar ratio 1:2. The interaction energies between oxygen, hydrogen, and clathrate hydrate are calculated using high level quantum chemical methods. The useful conclusion points from this study are summarized as follows. (1) The interaction energies of oxygen-hydrogen mixed cluster are larger than the energies of pure hydrogen molecular cluster. (2) The affinity of oxygen molecules with water molecules is larger than that of the hydrogen molecules with water molecules...
February 1, 2017: Journal of Molecular Graphics & Modelling
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