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Journal of Molecular Modeling

Zuzana Sochorová Vokáčová, Iztok Turel, Jaroslav V Burda
Based on experimental work, 12 half-sandwich organoruthenium(II) complexes with p-cymene and various substituted β-diketonates (acac) modified by several functional groups were explored. These complexes were optimized at the B3PW91/6-31 + G(d)/PCM/UFF computational level with the Ru atom described by Stuttgart pseudopotentials. The electron density analysis was performed using the B3LYP/ 6-311++G(2df,2pd)/DPCM/scaled-UAKS model. Electrostatic and averaged local ionization potential were explored and extremes on 0...
March 20, 2018: Journal of Molecular Modeling
Gui-Yun Hang, Wen-Li Yu, Tao Wang, Zhen Li
In this work, a CL-20/DNB cocrystal explosive model was established and six different kinds of fluoropolymers, i.e., PVDF, PCTFE, F2311 , F2312 , F2313 and F2314 were added into the (1 0 0), (0 1 0), (0 0 1) crystal orientations to obtain the corresponding polymer bonded explosives (PBXs). The influence of fluoropolymers on PBX properties (energetic property, stability and mechanical properties) was investigated and evaluated using molecular dynamics (MD) methods. The results reveal a decrease in engineering moduli, an increase in Cauchy pressure (i...
March 19, 2018: Journal of Molecular Modeling
Raj Chawla, Sumit Sharma
Styrene-butadiene rubber is a copolymer widely used in making car tires and has excellent abrasion resistance. The Young's modulus and tribology of pure styrene butadiene rubber (SBR) polymer and carbon nanotube reinforced polymer composites have been investigated using molecular dynamics simulations. The mechanism of enhanced tribology properties using carbon nanotube has been studied and discussed. The obtained Young's modulus shows the enhancement in mechanical properties of SBR polymer when carbon nanotubes are used as reinforcement...
March 18, 2018: Journal of Molecular Modeling
Gurleen Kaur Walia, Deep Kamal Kaur Randhawa
The adsorption behavior of sulfur-based toxic gases (H2 S and SO2 ) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restricting its dimensions into one dimension, construction of nanoribbons, and by introduction of a defect, its band gap can be tuned. Pristine armchair silicene nanoribbons (P-ASiNRs) have a very low sensitivity to gas molecules...
March 16, 2018: Journal of Molecular Modeling
Qi Gao, Chao Lu, Xiao-Wen Wang, Jun-Wei Zhang, Youtao Song, You-Lin Xue
Irisin is found closely associated with promoting the browning of beige fat cells in white adipose tissue. The crystal structure reveals that irisin forms a continuous inter-subunit β-sheet dimer. Here, molecular dynamics (MD) simulation and steered molecular dynamics (SMD) simulation were performed to investigate the dissociation process and the intricate interactions between the two irisin monomers. In the process of MD, the interactions between the monomers were roughly analyzed through the average numbers of both hydrophobic contacts and H-bonds...
March 16, 2018: Journal of Molecular Modeling
Noorakmar Jusoh, Hasanuddin Zainal, Azzmer Azzar Abdul Hamid, Noraslinda M Bunnori, Khairul Bariyyah Abd Halim, Shafida Abd Hamid
Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (PDB ID: 3TI6) using molecular docking. The design is based on structural resemblance with the commercial inhibitor, oseltamivir (OTV), ligand polarity, and amino acid residues in the NA active sites...
March 15, 2018: Journal of Molecular Modeling
Gérard A Ndongo, Marthe O Boyomo, Pierre A Owono
The photophysical properties of some 3-hydroxychromones (3-HC) and 3-hydroxyquinolones (3-HQ) derivatives are investigated in polar and non-polar aprotic solvents using the TDDFT method and the PCM formalism. In acetonitrile and n-hexane, 2-(2-benzothienyl)-3-HC) (BTHC), 2-furyl-3-HQ (FHQ), and 1-methyl-2-furyl-3-HQ (MFHQ) have exhibited dual emission bands due to the excited state intramolecular proton transfer (ESIPT) reaction, leading to a single excited tautomer form. Our results indicate a very high BTHC light absorption efficiency and radiative rate constant...
March 14, 2018: Journal of Molecular Modeling
Lijun Fu, Xueli Mu, Baiqing Li
A new method for the syn-dichlorination of alkenes at room temperature has been proposed by Denmark et al. The method uses diselenide (PhSeSePh) as the precatalyst, benzyltriethylammonium chloride (BnEt3 NCl) as the source of chlorine, and an N-fluoropyridinium salt as the oxidant to recover the catalyst. This approach has achieved exquisite diastereocontrol on a number of alkene substrates. In this paper, we report the results of DFT calculations we performed to study the mechanism of this reaction. We were able to identify a reasonable reaction path, including the intermediate and transition-state structures...
March 13, 2018: Journal of Molecular Modeling
Marjan A Nejad, Herbert M Urbassek
We study the influence of surface functionalization of a silica surface on insulin adsorption using accelerated molecular dynamics simulation. Three different functional groups are studied, CH3 , OH, and COOH. Due to the partial charges of these groups, the surface polarity of silica is strongly altered. We find that the adsorption energies of insulin change in agreement with the decreasing surface polarity. Conformational changes in the adsorbed protein and the magnitude of the molecular dipole moment in the adsorbed state are consistent with this result...
March 9, 2018: Journal of Molecular Modeling
Zhao Tan, An Yong Li
A novel type of trivalent BNg five-membered cational species B5 Ngn 3+ (Ng = He~Rn, n = 1~5) has been found and investigated theoretically using the B3LYP and MP2 methods with the def2-QZVPPD and def2-TZVPPD basis sets. The geometry, harmonic vibrational frequencies, bond energies, charge distribution, bond nature, aromaticity, and energy decomposition analysis of these structures were reported. The calculated B-Ng bond energy is quite large (the averaged bond energy is in the range of 209.2~585.76 kJ mol-1 ) for heavy rare gases and increases with the Ng atomic number...
March 9, 2018: Journal of Molecular Modeling
Alain Minguirbara, Mama Nsangou
The B3LYP/6-31++G* theoretical level was used to study the influence of various hexahydrated monovalent (Li+ , Na+ , K+ ) and divalent (Mg2+ ) metal counterions in interaction with the charged PO2 - group, on the geometrical and vibrational characteristics of the DNA fragments of 3',5'-dDSMP, represented by four conformers (g+ g+ , g+ t, g- g- and g- t). All complexes were optimized through two solvation models [the explicit model (6H2 O) and the hybrid model (6H2 O/Continuum)]. The results obtained established that, in the hybrid model, counterions (Li+ , Na+ , K+ , Mg2+ ) always remain in the bisector plane of the O1-P-O2 angle...
March 7, 2018: Journal of Molecular Modeling
K Vijay Reddy, Snehanshu Pal
The dependence of creep deformation behavior of nickel bicrystal specimens on grain boundary (GB) complexion was investigated by performing a simulated bending creep test using molecular dynamics methods. Strain burst phenomena were observed during the low temperature [500 K, i.e., <0.3 * melting point of nickel (Tm )] bending creep process. Atomic strain and dislocation analyses showed that the time of occurrence of strain burst depends on how easily GB migration happens in bicrystal specimens. Specimens with kite monolayer segregation GB complexion were found to be stable at low temperature (500 K), whereas specimens with split-kite GB complexion were stable at a comparatively higher temperature (900 K)...
March 7, 2018: Journal of Molecular Modeling
Lili Dong, Ruirui Feng, Jiawei Bi, Shengqiang Shen, Huizhe Lu, Jianjun Zhang
Human sodium-dependent glucose co-transporter 2 (hSGLT2) is a crucial therapeutic target in the treatment of type 2 diabetes. In this study, both comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were applied to generate three-dimensional quantitative structure-activity relationship (3D-QSAR) models. In the most accurate CoMFA-based and CoMSIA-based QSAR models, the cross-validated coefficients (r2 cv ) were 0.646 and 0.577, respectively, while the non-cross-validated coefficients (r2 ) were 0...
March 6, 2018: Journal of Molecular Modeling
Saad Raza, Syed Sikander Azam
Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented...
March 6, 2018: Journal of Molecular Modeling
Fang Bao, Gongzheng Zhang, Shaohua Jin, Yuping Zhang, Qinghai Shu, Lijie Li
The heats of formation (HOFs), detonation properties, and bond dissociation energies (BDEs) of a series of energetic bis-1,2,4-trizaole compounds with different substituents were studied using density functional theory at the 6-311 + G(2df, 2p) level. The HOF results indicated that the presence of the substituents -NH2 , -NO2 , -NHNO2 , and -N3 markedly increases the HOFs of bis-1,2,4-trizaole compounds. The calculated detonation velocities and detonation pressures indicated that the presence of the substituents -NH2 , -NO2 , -NHNO2 , -CH(NO2 )2 , and -OH strongly enhances the detonation properties of bis-1,2,4-trizaole compounds...
March 6, 2018: Journal of Molecular Modeling
Xiaoning Li, Wenli Guo, Yibo Wu, Wei Li, Liangfa Gong, Xiaoqian Zhang, Shuxin Li, Yuwei Shang, Dan Yang, Hao Wang
To identify ionic liquids (ILs) that could be used as solvents in isobutylene (IB) polymerization, the interactions between IB and eight different ILs based on the 1-butyl-3-methylimidazolium cation ([Bmim]+ ) were investigated using density functional theory (DFT). The anions in the ILs were chloride, hexafluorophosphate, tetrafluoroborate, bis[(trifluoromethyl)sulfonyl]imide, tetrachloroaluminate ([AlCl4 ]- ), tetrachloroferrate, acetate, and trifluoroacetate. The interaction geometries were explained by changes in the total energy, intermolecular distances, Hirshfeld charges, and the electrostatic potential surface...
March 6, 2018: Journal of Molecular Modeling
Milanpreet Kaur, Ravinder Singh Sawhney, Derick Engles
Using the smallest non-classical fullerene, we investigate the impact of endohedral fullerene molecules on the quantum transport through molecular junctions, and then compared this with the pure C20 -based molecular junction. By employing the density functional theory combined with the non-equilibrium Green's function, we contemplated different electronic parameters, namely, density of states, transmission coefficient, energy levels, molecular orbitals, conduction gaps, electron density and their charge transfer...
March 4, 2018: Journal of Molecular Modeling
Nikhat Saba, Alpana Seal
Vinca alkaloids are chemotherapeutic agents used in the treatment of both pediatric and adult cancer patients. Cytochrome P450 3A5 (CYP3A5) is 9- to 14-fold more efficient at clearing vincristine than cytochrome P450 3A4 (CYP3A4) is. However, patients who express an inactive form of the polymorphic CYP3A5 enzyme suffer from severe neurotoxicity during vincristine treatment, resulting in chemotherapy failure. Previous studies have found that the addition of new features to the parent drug can enhance its binding affinity to tubulin manyfold and could therefore yield novel anticancer drugs...
March 4, 2018: Journal of Molecular Modeling
Rajani R Joshi
In this paper, diversity and conservation in the 'landscape' of random variation of protein tertiary structures are explored for quantitative feature-vector models of major types of functionally important 3D structural motifs. For this, I have deployed a recently developed nonparametric regression (NPR)-based multidimensional copula method of simulation. Apart from improved accuracy of multidimensional random sample generation, the simulation provides additional insight into diversity in the protein structural landscape in terms of random variation in the feature-vector...
March 2, 2018: Journal of Molecular Modeling
Xiangxiang Shi, Jun Zheng, Tingting Yan
Human respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in infants and young children. Here, the RSV fusion (F) glycoprotein epitope FFL was redesigned based on its complex crystal structure with motavizumab, an mAb drug in development for the prevention of RSV infections, aiming to obtain therapeutic peptide vaccines with high affinity to induce RSV-specific neutralizing antibodies. Computational modeling and analysis found that only a small region covering the helix-turn-helix (HTH) motif of FFL can directly interact with motavizumab and confer stability and specificity to the complex system, while the rest of the epitope primarily serves as a structural scaffold that stabilizes the HTH conformation of motavizumab-binding site...
March 2, 2018: Journal of Molecular Modeling
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