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Journal of Molecular Modeling

Carlos E T de Magalhães, Ranylson M L Savedra, Karina S Dias, Rodrigo Ramos, Melissa F Siqueira
The chromism observed in the MEH-PPV polymer in tetrahydrofuran (THF) solution is discussed as a function of the structural morphology of the backbone chains. To evaluate this phenomenon, we carried out simulations employing a hybrid methodology using molecular dynamics and quantum mechanical approaches. Our results support the hypothesis that the morphological order-disorder transition is related to the change from red to blue phase observed experimentally. The morphological disorder is associated with total or partial twisted arrangements in the polymer backbone, which induces an electronic conjugation length more confined to shorter segments...
March 2017: Journal of Molecular Modeling
Sabahuddin Ahmad, Mohammad Imran Siddiqi
Cathepsin S has been demonstrated to play a crucial role in the remodeling of extracellular matrix proteins such as elastin and collagen, which in turn contribute to the structural integrity of the cardiovascular wall. Atherosclerotic lesions, aneurysm formation, plaque rupture, thrombosis, and calcification are some of the cardiovascular disorders related to cathepsin S. A highly selective inhibitor of human as well as animal cathepsin S, RO5444101, was recently reported to attenuate the progression of atherosclerotic lesions...
March 2017: Journal of Molecular Modeling
Félix Moncada, Roberto Flores-Moreno, Andrés Reyes
We propose a scheme to estimate hydrogen isotope effects on molecular polarizabilities. This approach combines the any-particle molecular orbital method, in which both electrons and H/D nuclei are described as quantum waves, with the auxiliary density perturbation theory, to calculate analytically the polarizability tensor. We assess the performance of method by calculating the polarizability isotope effect for 20 molecules. A good correlation between theoretical and experimental data is found. Further analysis of the results reveals that the change in the polarizability of a X-H bond upon deuteration decreases as the electronegativity of X increases...
March 2017: Journal of Molecular Modeling
Marcelo Lopes Pereira Junior, Luiz Antonio Ribeiro Junior
The polaron stability in organic molecular crystals is theoretically investigated in the scope of a two-dimensional Holstein-Peierls model that includes lattice relaxation. Particularly, the investigation is focused on designing a model Hamiltonian that can address properly the polaron properties in different model oligoacene crystals. The findings showed that a suitable choice for a set of parameters can play the role of distinguishing the model crystals and, consequently, different properties related to the polaron stability in these systems are observed...
March 2017: Journal of Molecular Modeling
Snehasis Bhunia, Ajeet Singh, Animesh K Ojha
Complexes of the dipeptide phenylalanine-phenylalanine (Phe-Phe) with divalent metal cations (Cu(2+), Zn(2+), Ca(2+) and Ba(2+)) were studied at the B3LYP and MP2 levels of theory with the basis sets 6-311++G(d,p) and 6-31 + G(d) in the gas phase. The relative energies of these complexes indicated that cation-π bidentate/tridentate conformations are more favourable than other conformations with uncoordinated rings. These findings were confirmed by the calculated values of thermodynamic parameters such as the Gibbs free energy...
March 2017: Journal of Molecular Modeling
Rhuiago M de Oliveira, Luiz F Roncaratti, Luiz Guilherme M de Macedo, Ricardo Gargano
This investigation generated rovibrational energies and spectroscopic constants for systems of CCl4 with Ng (Ng = He, Ne, Ar), O2, D2O and ND3 from scattering experimental data, and the results presented are of interest for microwave spectroscopy studies of small halogenated molecules. The rovibrational spectra were obtained through two different approaches (Dunham and DVR) within the improved Lennard Jones (ILJ) model. Spectra were also generated within ordinary Lennard Jones and deviations suggest that the ILJ model should be preferred due to interactions beyond dispersion forces presented in these systems...
March 2017: Journal of Molecular Modeling
Nadezhda A Andreeva, Vitaly V Chaban
Efficient design of ionic compounds requires a systematic understanding of cation-anion interactions. Weakening of electrostatic attraction is essential to increase the liquid range of the ionic compound and decrease its melting point. Here, we report simulations of the closest-approach cation-anion distances in a variety of ion pairs containing the tetrakis(pentafluorophenyl)borate (TFPB(-)) anion. Small alkali cations (Li(+), Na(+)) penetrate the TFPB(-) core, whereas K(+) and larger organic cations do not...
March 2017: Journal of Molecular Modeling
Fabian E Olazarán, Carlos A García-Pérez, Debasish Bandyopadhyay, Isaias Balderas-Rentería, Angel D Reyes-Figueroa, Lars Henschke, Gildardo Rivera
In this work, through a docking analysis of compounds from the ZINC chemical library on human β-tubulin using high performance computer cluster, we report new polycyclic aromatic compounds that bind with high energy on the colchicine binding site of β-tubulin, suggesting three new key amino acids. However, molecular dynamic analysis showed low stability in the interaction between ligand and receptor. Results were confirmed experimentally in in vitro and in vivo models that suggest that molecular dynamics simulation is the best option to find new potential β-tubulin inhibitors...
March 2017: Journal of Molecular Modeling
Alexander A Kantardjiev
Graphical Abstract Subtle.Nets.Finder is a workflow of algorithms for identification of subtly interacting groups in DNA/RNA/protein complexes. It is founded on detailed and sophisticated evaluation of the self-consistency in the cooperative network of residue interactions via a combination of advanced calculations (fast multipole method and statistical mechanics) supplemented with graph-theoretical procedures.
March 2017: Journal of Molecular Modeling
Quanyu Wang, Zhuan Ji, Bo Han
Glycidyl fatty acid esters (GEs) are by-products of edible oil refinement that have attracted attention globally due to concerns over their possible harmful effects on human health when consumed. It is thus important to improve our understanding of GE formation if we are to suppress GE production during edible oil refinement. In this paper, a first-principles density functional theory study of the formation mechanism of GEs was performed. Triglycerides undergo a self-condensation reaction between two adjacent ester groups to yield GEs and an anhydride as a by-product...
March 2017: Journal of Molecular Modeling
Masoomeh Omidi, Hamid Reza Shamlouei, Motahareh Noormohammadbeigi
Density functional theory (DFT) calculations were used to study the effect of scandium doping on the structural, energetic, electronic, linear and nonlinear optical (NLO) properties of Be12O12, Mg12O12 and Ca12O12 nanoclusters. Scandium (Sc) doping on nanoclusters leads to narrowing of their E g, which enhances their conductance greatly. Also, the polarizability (α) and first hyperpolarizability (β0) of nanoclusters were dramatically increased as Be, Mg or Ca atoms are substituted with a Sc atom. Among all clusters, α and β0 values for Sc-doped Ca12O12 were the largest...
March 2017: Journal of Molecular Modeling
Leonid Gorb, Manoj K Shukla
A computational chemistry investigation was undertaken to shed light on the facilitatory role played by Fe(3+) and Al(3+) cations in the adsorption of anionic As(V) species by humic acids through the formation of so-called cationic bridges. Geometric and energetic parameters were obtained using density functional theory at the B3LYP/6-31G(d,p) level in conjunction with the polarizable continuum model (to account for the influence of bulk water). We found that, despite their similar molecular geometries, the adsorption energies of the As(V) species AsO4(3-) and H2AsO(4-) differ when Fe(3+), FeOH(2+), Al(3+), and AlOH(2+) participate in the bridge...
March 2017: Journal of Molecular Modeling
Hai-Peng Li, Ze-Tong Bi, Wen-Yue Fu, Run-Feng Xu, Yi Zhang, Xiao-Peng Shen, Ming-Xue Li, Gang Tang, Kui Han
We investigate the molecular structure, vibrational and electronic absorption spectra, and electronic hyperpolarizabilities of trans and cis isomers of 4-hydroxyazobenzene (HOAB) via density functional theory. Results show that the azo dye exhibits a high third-order nonlinear optical response and good optical transparency. Both the basis set and the functional are important influences on the results obtained when calculating the absorption spectrum and NLO response. We also study the effect of the solvent on the electronic absorption spectrum to assess the ability of the functional to reproduce the experimental spectrum in combination with a suitable solvent model...
March 2017: Journal of Molecular Modeling
Ángel Sánchez-González, Francisco J Martín-Martínez, J A Dobado
Lignin is the most abundant natural polymer composed by aromatic moieties. Its chemical composition and its abundance have focused efforts to unlock its potential as a source of aromatic compounds for many years. The lack of a proper way for lignin de-polymerization has hampered its success as a natural solution for commodity aromatic chemicals, which is also due to the lack of understanding of the underlying mechanisms of lignin polymerization. A fuller fundamental understanding of polymerization mechanisms could lead to improvements in de-polymerization strategies, and therefore a proper methodology and a predictive theoretical framework are required for such purpose...
March 2017: Journal of Molecular Modeling
Roobee Garla, Narinder Kaur, Mohinder Pal Bansal, Mohan Lal Garg, Biraja Prasad Mohanty
Exposure to inorganic arsenic (As) is one of the major health concerns in several regions around the world. Binding of As(III) with thiols is central to the mechanisms related to its toxicity, detoxification, and therapeutic effects. Due to its high thiol content, metallothionein (MT) is presumed to play an important role in case of arsenic toxicity. Consequences of these As-thiol interactions are not yet clear due to various difficulties in the characterization of arsenic bound proteins by spectroscopic techniques...
March 2017: Journal of Molecular Modeling
Allaa R Hilal, Rifaat Hilal
The photo dissociation of nitrosyl fluorite, FONO, a potential source of atmospheric fluorine, underlies its active role in ozone depletion and other activities in the troposphere. In the present work, the electronic structure of FONO is revisited at high level of ab initio and density functional theory (DFT) theoretical levels. Several different post SCF methods were used to compute excited states, vertical excitation energies and intensities, namely configuration interaction with single excitations (CIS), equation of motion coupled cluster with single and double excitations (EOM-CCSD), and symmetry adopted cluster configuration interaction (SAC-CI) methods...
March 2017: Journal of Molecular Modeling
Hongxia Zhao, Jiaping Liu, Qianping Ran, Yong Yang, Xin Shu
Comb-like polycarboxylate ether (PCE) molecules with different content of methyl groups substituted on backbone and different location of methyl groups substituted on the side chains, respectively, were designed and were studied in explicit salt solutions by all-atom molecular dynamics simulations. Methyl groups substituted on the backbone of PCE have a great effect on the conformation of PCE. Stiffness of charged backbone was not only affected by the rotational freedom but also the electrostatic repulsion between the charged COO(-) groups...
March 2017: Journal of Molecular Modeling
Jeremy W Prokop, Jozef Lazar, Gabrielle Crapitto, D Casey Smith, Elizabeth A Worthey, Howard J Jacob
Protein modeling and molecular dynamics hold a unique toolset to aide in the characterization of clinical variants that may result in disease. Not only do these techniques offer the ability to study under characterized proteins, but they do this with the speed that is needed for time-sensitive clinical cases. In this paper we retrospectively study a clinical variant in the XIAP protein, C203Y, while addressing additional variants seen in patients with similar gastrointestinal phenotypes as the C203Y mutation...
March 2017: Journal of Molecular Modeling
Yun Zhang, Hong Huang, Zhiling Liang, Houhe Liu, Ling Yi, Jinhong Zhang, Zhiqiang Zhang, Cheng Zhong, Yugang Huang, Guodong Ye
The free radical addition reaction is very important in UV curing. The benzoyl radical is the most commonly observed radical. In the addition process, the benzoyl radical adds to an acrylate monomer, forming a primary radical that has great value for subsequent research. In this article, a quantum chemical method was used to study the microscopic progression from the reactive complex to the saddle point. The reactions of three monomers (amylene, allyl methyl ether and methyl acrylate) with a benzoyl radical were evaluated in terms of geometry and energy...
March 2017: Journal of Molecular Modeling
Guangren Yu, Xiaomin Liu, Xiaochun Zhang, Xiaochun Chen, Zhiping Liu, Ahmed A Abdeltawab
1,3-Dimethylimidazolium dimethylphosphate ([C1mim][DMP]) was observed experimentally to be able to eliminate the atmospheric azeotropic point of acetone and methanol, which is an important azeotrope generally encountered in furfural production and the Fischer-Tropsch process. Here, we employed ab initio calculation to understand the underlying mechanism of [C1mim][DMP] in eliminating the azeotropic point of acetone and methanol. Structure, energy and interaction in binary-, ternary- and quaternary-clusters composed of methanol, acetone, [C1mim](+) or/and [DMP]‾ were calculated...
March 2017: Journal of Molecular Modeling
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