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Journal of Molecular Graphics & Modelling

Farhan Ul Haq, Asma Abro, Saad Raza, Klaus R Liedl, Syed Sikander Azam
New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods...
April 4, 2017: Journal of Molecular Graphics & Modelling
E Chigo Anota, A Bautista Hernández, A Escobedo Morales, M Castro
Design and characterization of the structural, electronic, and magnetic properties of armchair boron-nitride, BN (B27N27H18), nanosheets were performed by means of density functional theory all-electron calculations. The HSEh1PBE-GGA method together with 6-31G(d) basis sets were used. Non-stoichiometric B30N24H18 and B24N30H18 compositions: rich in boron or nitrogen atoms, forming homonuclear B or N bonds, respectively, were chosen. The obtained results reveal that these BN nanosheets reach structural stability in the anionic form, where semiconductor and magnetic behaviors are promoted...
March 30, 2017: Journal of Molecular Graphics & Modelling
Niran Aeksiri, Tippawan Jantafong
Porcine reproductive and respiratory virus (PRRSV) causes major economic concerns for the swine industry worldwide. We have performed molecular dynamics simulations (MD) and principle component analysis (PCA) to investigate the role of the catalytic triad and conformational dynamics of type I and type II of nsp4 PRRSV. The results showed that the RMSF of residues 136-142 near the active site of all models was highly flexible. Moreover, we identified the effect of single structural mutations of the catalytic triad...
March 24, 2017: Journal of Molecular Graphics & Modelling
Ping Cheng, Yongpeng Yang, Shiping Huang
Density functional theory has been performed to systematically study the interactions between RunPt13-n (n=4, 7 and 9) clusters and [BMIM](+) based ionic liquids. Ionic liquids [BMIM][Br], [BMIM][BF4], [BMIM][PF6], [BMIM][CF3SO3], and [BMIM][NTf2] have different effects on the stability of Ru7Pt6. Ionic liquids with median size anions of PF6(-) and CF3SO3(-) can better improve the stability of Ru7Pt6 than those with the small anions of Br(-) and BF4(-) and large anion of NTf2(-). Based on negative relaxation energies, the stabilities of Ru4Pt9, Ru7Pt6, and Ru9Pt4 are all enhanced after interacting with [BMIM][CF3SO3]...
March 23, 2017: Journal of Molecular Graphics & Modelling
Deepa Palanisamy, B Vijaya Pandiyan, Thirumeignanam Duraisamy, Ponmalai Kolandaivel
The present study aims to spotlight on the strength of interaction between different fatty acids with the Bovine-lactoglobulin (LGB) protein side chains along with the crystal water molecules at M062X/def2-QZVP level of theory. To analyse the role of carboxylic acid and its interaction with side chains and to reveal the significance of carboxylic acid, it was replaced by Acyl chloride (COCl), Acyl Bromide (COBr) and Acyl-Fluorine (COF) group and COS group. The ligands are linear with a straight and branched chain of carbon atoms, but extended methyl group make the ligand bend resulting in non-planar geometry...
March 22, 2017: Journal of Molecular Graphics & Modelling
Shuling Xiong, Shusen Chen, Shaohua Jin
Dihydroxylammonium 5,5'-bistetrazole-1,1'-diolate (TKX-50) is a newly synthesized energetic material with excellent comprehensive properties. Cyclotrimethylenetrinitramine (RDX) is currently one of the most widely used energetic materials in the world. TKX-50 and RDX supercell models and TKX-50/RDX cocrystal model were constructed based on their crystal cell parameters and the formation mechanism of cocrystal, respectively, then they were simulated by molecular dynamics (MD) simulations. The maximum trigger bond (NNO2) length(Lmax), binding energy (Ebind), radial distribution function (RDF), cohesive energy density(CED) and mechanical properties were simulated at different temperatures based on the simulated equilibrium structures of the models...
March 19, 2017: Journal of Molecular Graphics & Modelling
Abdulkadir Kocak, Muslum Yildiz
The disruption of aspartoacylase enzyme's catalytic activity causes fatal neurodegenerative Canavan disease. By molecular dynamics and docking methods, here we studied two deleterious mutations that have been identified in the Canavan patients' genotype E285A, F295S, and revealed the possible cause for the enzyme inhibition due to the drastic changes in active site dynamics, loss of interactions among Arg 71, Arg 168 and the substrate and pKa value of critical Glu178 residue. In addition to changes in the enzyme dynamics, free energy calculations show that the binding energy of substrate decreases dramatically up on mutations...
March 19, 2017: Journal of Molecular Graphics & Modelling
Yonglei Lv, Jianbing Li, Jianhua Fang, Xiufeng Jiao, Lumin Yan, Baifeng Shan
Human immunodeficiency virus 1 (HIV-1) protease (PR) represents one of the primary targets for developing antiviral agents for the treatment of HIV-infected patients. However, a number of multidrug-resistant mutations in the enzyme have been observed over the past decades, largely limiting the application of PR inhibitors in antiviral therapy. A systematic investigation of the intermolecular interaction between the multidrug-resistant mutants of HIV-1 PR and its substrates would help to establish a complete profile of substrate response to PR mutations and to design new antiviral agents combating drug resistance...
March 18, 2017: Journal of Molecular Graphics & Modelling
D Sam Paul, N Gautham
We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have carried out to the algorithm MOLSDOCK. iMOLSDOCK uses mutually orthogonal Latin squares (MOLS) to sample the conformation and the docking pose of the ligand and also the flexible residues of the receptor protein. The method then uses a variant of the mean field technique to analyze the sample to arrive at the optimum...
March 18, 2017: Journal of Molecular Graphics & Modelling
Erfan Lotfi, M Neek-Amal
Graphene doped with nitrogen exhibits unique properties different than perfect graphene. The temperature distribution in nitrogen-doped graphene (N-graphene) and in the graphene with grain boundary is investigated using molecular dynamics simulations. The temperature distribution in nitrogen-doped graphene nanoribbon, containing two types of grain boundaries, was found to be sensitive to the number of dopants and grain boundary. We also found that there is a remarkable temperature gap in the temperature profile of N-graphene nanoribbon-containing a grain boundary...
March 16, 2017: Journal of Molecular Graphics & Modelling
Motoyasu Ozawa, Tomonaga Ozawa, Kazuyoshi Ueda
The molecular interactions of inhibitors of bromodomains (BRDs) were investigated. BRDs are protein interaction modules that recognizing ε-N-acetyl-lysine (εAc-Lys) motifs found in histone tails and are promising protein-protein interaction (PPI) targets. First, we analyzed a peptide ligand containing εAc-Lys to evaluate native PPIs. We then analyzed tetrahydroquinazoline-6-yl-benzensulfonamide derivatives found by fragment-based drug design (FBDD) and examined their interactions with the protein compared with the peptide ligand in terms of the inter-fragment interaction energy...
March 16, 2017: Journal of Molecular Graphics & Modelling
Alireza Mansouri, Karim Mahnam
The non-covalent interaction between single-walled carbon nanotube and surfactant peptides makes them soluble in biological media to be used in nano-medicine, drug delivery and gene therapy. Pervious study has shown that two important parameters in binding peptides into nanotubes are hydrophobic effect and the number of aromatic amino acids. Ten surfactant peptides with the length of eight residue, including Lys, Trp, Tyr, Phe and Val, were designed to investigate the important parameters in binding peptides to a (6, 6) carbon nanotube...
March 14, 2017: Journal of Molecular Graphics & Modelling
Yingzhe Liu, Tao Yu, Weipeng Lai, Yiding Ma, Ying Kang, Zhongxue Ge
Molecular dynamics simulations have been performed to understand the adsorption behavior of acetone (AC) solvent at the three surfaces of 1,3,5,7-tetranitro-1,3,5,7-tetraazacyclooctan (HMX) crystal, i.e. (011), (110), and (020) faces. The simulation results show that the structural features and electrostatic potentials of crystal faces are determined by the HMX molecular packing, inducing distinct mass density distribution, dipole orientation, and diffusion of solvent molecules in the interfacial regions. The solvent adsorption is mainly governed by the van der Waals forces, and the crystal-solvent interaction energies among three systems are ranked as (020)≈(110)>(011)...
March 10, 2017: Journal of Molecular Graphics & Modelling
Jixue Sun, Yang Li, Jianping Lin
DNA nanostructures can undergo large structural fluctuations and deviate from their intended configurations. In this work, two model DNA nanostructures (i.e., Nan and Kai) were designed based on the shape of the two Chinese characters of the name of Nankai University, and additional single-stranded DNA fragments were added to interact with graphene. During four 50-ns molecular dynamic simulations in aqueous solution, the DNA nanostructures adsorbed onto graphene demonstrated more stable conformations with lower root mean square deviations and smaller coordinate changes in the z-axis direction than the DNA nanostructures that were not adsorbed onto graphene...
March 9, 2017: Journal of Molecular Graphics & Modelling
Subhankar Sardar
The singlet fission is a spin allowed and extremely fast internal conversion process involved in solar cell by which a photo-excited singlet exciton is splitted into two triplet ones. For effective singlet fission and to increase the efficiency of solar cell, designing of new molecules is an interesting area of research and our current interest. The silicon substituted oligocenes, commonly known as silaoligocenes, are found to be the efficient singlet fission material due to their special characteristics. We have shown the SF energy criteria satisfied by the singlet and triplet states of various silahexacene derivatives, and theoretically predicted whether such molecules exhibit fission properties or not...
March 8, 2017: 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
Nagakumar Bharatham, Kristin E Finch, Jaeki Min, Anand Mayasundari, Michael A Dyer, R Kiplin Guy, Donald Bashford
A virtual screening protocol involving docking and molecular dynamics has been tested against the results of fluorescence polarization assays testing the potency of a series of compounds of the nutlin class for inhibition of the interaction between p53 and Mdmx, an interaction identified as a driver of certain cancers. The protocol uses a standard docking method (AutoDock) with a cutoff based on the AutoDock score (ADscore), followed by molecular dynamics simulation with a cutoff based on root-mean-square-deviation (RMSD) from the docked pose...
February 24, 2017: Journal of Molecular Graphics & Modelling
V Nagarajan, R Chandiramouli
The electronic properties of borophane nanosheet and adsorption behavior of three distinct alcohol vapors namely methanol, ethanol and 1-propanol on borophane nanosheet is studied using density functional theory method for the first time. The state-of-the-art provides insights on to the development of new two dimensional materials with the surface passivation on boron nanostructures. The density of states spectrum provides a clear perception on charge transfer upon adsorption of alcohol vapors on borophane nanosheets...
May 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(+))...
May 2017: Journal of Molecular Graphics & Modelling
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