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Journal of Molecular Modeling

Nadia Melo Borges, Geraldo Rodrigues Sartori, Jean F R Ribeiro, Josmar R Rocha, João B L Martins, Carlos A Montanari, Ricardo Gargano
The main purpose of this study was to address the performance of virtual screening methods based on ligands and the protein structure of acetylcholinesterase (AChE) in order to retrieve novel human AChE (hAChE) inhibitors. In addition, a protocol was developed to identify novel hit compounds and propose new promising AChE inhibitors from the ZINC database with 10 million commercially available compounds. In this sense, 3D similarity searches using rapid overlay of chemical structures and similarity analysis through comparison of electrostatic overlay of docked hits were used to retrieve AChE inhibitors from collected databases...
January 13, 2018: Journal of Molecular Modeling
Cheng Shen, Pengcheng Wang, Ming Lu
In this paper, four series of benzoheterocycle based energetic materials (EMs) have been designed to plan out a strategy to improve the density and safety of EMs, such as combining the insensitive group with aminobenzene ring and the high energetic nitramine explosives, benzo-heterocycle mother ring, designing multi-nitrogen heterocycles with a conjugated system containing N-N and C-N high energy bonds, and hydrogen bonding. Their optimized structure and detonation properties were first calculated and discussed using DFT methods...
January 11, 2018: Journal of Molecular Modeling
Sławomir J Grabowski
MP2/aug-cc-pVTZ calculations were performed for complexes linked by hydrogen bonds. Three types of proton donating species were taken into account: H2O, CCl3H, and H3O+. These calculations are supported by the natural bond orbital (NBO) method and the quantum theory of atoms in molecules (QTAIM) approach. Numerous correlations between parameters of H-bonded systems were found. The most important are those which show the response of the system on the H-bond formation; for example, the increase of polarization of the A-H bond correlates with the strength of the hydrogen bond...
January 8, 2018: Journal of Molecular Modeling
Macon Magno, Frank Hagelberg
The transport properties of zigzag graphene nanoribbons (zGNRs) were studied by density functional theory (DFT) in conjunction with Green's function analysis. In particular, spin transport through a zGNR (12,0) device was investigated under the constraint of ferromagnetic coordination of the ribbon edges. Several configurations with two vacant sites in the edge and the bulk region of the zGNR device were derived from this system. For all structures, magnetocurrent ratios (MCRs) were recorded as a function of the bias as well as the amount of strain applied longitudinally to the devices...
January 8, 2018: Journal of Molecular Modeling
Alexandre Costa, Elizama Ramos Costa, Adilson Luís Pereira Silva, Auro Atsushi Tanaka, Jaldyr de Jesus Gomes
This paper presents a theoretical study of the effects of substituents (F, Cl, Br, CH3, and CN) on the aromaticity of borazine (B3N3H6), using density functional theory (DFT) and the Hartree-Fock (HF) method. The calculations to optimize the geometries, structural properties, and vibrational frequencies were performed using the same 6-311G(d,p) and 6-311++G(d,p) basis sets, comparing the methods with experimental results. In the analysis of the NICSZZ values, it was found that that replacing the hydrogen atoms by halogen atoms (F, Cl, and Br) and CH3 reduced the aromaticity of the borazine molecule, while use of the CN group resulted in NICSZZ values (0...
January 8, 2018: Journal of Molecular Modeling
Patrick Scilabra, Vijith Kumar, Maurizio Ursini, Giuseppe Resnati
Modeling indicates the presence of a region of low electronic density (a "σ-hole") on group 14 elements, and this offers an explanation for the ability of these elements to act as electrophilic sites and to form attractive interactions with nucleophiles. While many papers have described theoretical investigations of interactions involving carbon and silicon, such investigations of the heavier group 14 elements are relatively scarce. The purpose of this review is to rectify, to some extent, the current lack of experimental data on interactions formed by germanium and tin with nucleophiles...
January 8, 2018: Journal of Molecular Modeling
Victor Hugo Malamace da Silva, Daniel Garcez S Quattrociocchi, Stanislav R Stoyanov, José Walkimar de Mesquita Carneiro, Leonardo Moreira da Costa, Glaucio Braga Ferreira
A series of B3LYP/6-311+G(d,p) calculations of the affinity of monodentate ligands for [Cd(H2O)3]2+ are performed. Three types of ligands containing O (phosphine oxide, lactam, amide, carboxylic acid, ester, ketone, aldehyde, ether, halohydrin, enol, furan), N (thiocyanate, amine, ammonia, azide), and S (thioester, thioketone, thiol, thiophene, disulfide) interacting atoms are investigated. The results show that phosphine oxide has the largest affinity for the cadmium cation due to the polarization of the P=O bond...
January 8, 2018: Journal of Molecular Modeling
Milad Radiom, Plinio Maroni, Tomasz A Wesolowski
Using MP2, CCSD, and B3LYP methods of computational chemistry, we show length dependence in the intrinsic elastic properties of short alkane fragments. For isolated alkane fragments of finite length in the gas phase and zero temperature, the intrinsic elasticity constants are found to vary with the number of carbon atoms and its parity. From extrapolation of the elasticity constants calculations to infinite chain length, and by comparing with in-situ elasticity constant of single poly(ethylene) molecule obtained with atomic force microscopy, we estimate the softening effect of environment on the extension response of the polymer...
January 8, 2018: Journal of Molecular Modeling
Diana Yepes, Jorge I Martínez-Araya, Pablo Jaque
In this work, we computationally evaluated the influence of six different molecular solvents, described as a polarizable continuum model at the M06-2X/6-31+G(d,p) level, on the activation barrier/reaction rate, overall energy change, TS geometry, and degree of (a)synchronicity of two concerted Diels-Alder cycloadditions of acrolein (R1) and its complex with Lewis acid acrolein···BH3 (R2) to cyclopentadiene. In gas-phase, we found that both exothermicity and activation barrier are only reduced by about 2...
December 29, 2017: Journal of Molecular Modeling
Luciano Almeida Leal, Leonardo Evaristo de Sousa, Patrick Pascoal de Brito, Bernhard Georg Enders Neto, Artemis Marti Ceschin, Wiliam Ferreira da Cunha, Luiz Antonio Ribeiro, Demétrio Antonio da Silva Filho
The optical properties of systems composed of the polymers PolyeraActivInk™ N2200 and P3HT are experimentally and theoretically investigated using UV-Vis spectroscopy and time-dependent density functional theory calculations, respectively. From a theoretical point of view, we carried out an analysis considering several functionals and model oligomers of different sizes to mimic the polymers. As our studies were performed with and without solvents, a first important result regards the fact that, by considering solvent effects, a better agreement between theoretical and experimental results could be achieved...
December 28, 2017: Journal of Molecular Modeling
Jorge I Martínez-Araya, Diana Yepes, Pablo Jaque
Six organometallic compounds coming from a basic Mo-based complex were analyzed from the perspective of the dual descriptor in order to detect subtle influences that a substituent group could exert on the reactive core at a long range. Since the aforementioned complexes are open-shell systems, the used operational formula for the dual descriptor is that one defined for those aforementioned systems, which was then compared with spin density. In addition, dual descriptor was decomposed into two terms, each of which was also applied on every molecular system...
December 27, 2017: Journal of Molecular Modeling
Chonticha Suwattanasophon, Napat Songtawee, Peter Wolschann, Kiattawee Choowongkomon
The family of human epidermal growth factor receptors (HER) is involved in tumor cell growth. Homodimerization and heterodimerization of the HER family are important for activation of these receptors. The structures of homodimer conformation are well characterized, while the structures of heterodimer conformations, especially between HER1 and HER2, are not completely understood. In this study, two models of possible asymmetric HER1/HER2 kinase domains were built. Molecular dynamics simulations and molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) methods were applied to examine the possibility of these two-heterodimer interactions...
December 26, 2017: Journal of Molecular Modeling
Xintao Huang, Jucai Yang
The most stable structures and electronic properties of TmSi n (n = 3-10) clusters and their anions have been probed by using the ABCluster global search technique combined with the PBE, TPSSh, and B3LYP density functional methods. The results revealed that the most stable structures of neutral TmSi n and their anions can be regarded as substituting a Si atom of the ground state structure of Si n + 1 with a Tm atom. The reliable AEAs, VDEs and simulated PES of TmSi n (n = 3-10) are presented. Calculations of HOMO-LUMO gap revealed that introducing Tm atom to Si cluster can improve photochemical reactivity of the cluster...
December 26, 2017: Journal of Molecular Modeling
Martyna Chojnacka, Mikolaj Feliks, Wiktor Beker, W Andrzej Sokalski
Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has been successfully applied to predict catalytic effects resulting from intermolecular interactions with individual water molecules constituting the first hydration shell, aminoacid mutations in enzymes or Si→Al substitutions in zeolites. In this contribution, hydrogen to fluorine (H→F) substitution effects for two model reactions have been examined indicating qualitative applicability of the catalytic field concept in the case of systems involving intramolecular interactions...
December 22, 2017: Journal of Molecular Modeling
Jesús Sánchez-Márquez, David Zorrilla, Víctor García, Manuel Fernández
In the present work, a new methodology defined for obtaining reactivity indices (philicities) is proposed. This is based on reactivity functions such as the Fukui function or the dual descriptor, and makes it possible to project the information from reactivity functions onto molecular orbitals, instead of onto the atoms of the molecule (atomic reactivity indices). The methodology focuses on the molecules' natural bond orbitals (bond reactivity indices) because these orbitals have the advantage of being localized, allowing the reaction site of an electrophile or nucleophile to be determined within a very precise molecular region...
December 22, 2017: Journal of Molecular Modeling
Dinushka Herath, Tandabany Dinadayalane
Density functional theory (DFT) calculations were performed to study doping of two nitrogen atoms at different positions on a finite-sized graphene model of C82H24. We examined 21 structures of double nitrogen doped graphene to calculate their relative stabilities. The structure with two nitrogen atoms located apart is the most stable among the positional isomers considered in this study. For double nitrogen doping within a six-membered ring, the 1,4-position is more preferred than 1,3- or 1,2-positions for the finite-sized single layer graphene sheet...
December 22, 2017: Journal of Molecular Modeling
Piotr Talaga, Mateusz Z Brela, Artur Michalak
The analysis of the electronic-structure changes along IRC paths for double-proton-transfer reactions in the formamide dimer (R1), formamide-thioformamide system (R2), and the thioformamide dimer (R3) was performed based on the extended-transition-state natural orbitals for chemical valence (ETS-NOCV) partitioning of the reaction force, considering the intra-fragments strain and the inter-fragments interaction terms, and further-the electrostatic, Pauli-repulsion and orbital interaction components, with the latter being decomposed into the NOCV components...
December 22, 2017: Journal of Molecular Modeling
Hasan Özsoy, Nevin Uras-Aytemiz, F Mine Balcı
Nine minima were found on the intermolecular potential energy surface for the ternary system HNO3(CH3OH)2 at the MP2/aug-cc-pVDZ level of theory. The cooperative effect, which is a measure of the hydrogen-bonding strength, was probed in these nine conformations of HNO3…(CH3OH)2. The results are discussed here in terms of structures, energetics, infrared vibrational frequencies, and topological parameters. The cooperative effect was observed to be an important contributor to the total interaction energies of the cyclic conformers of HNO3…(CH3OH)2, meaning that it cannot be neglected in simulations in which the pair-additive potential is applied...
December 21, 2017: Journal of Molecular Modeling
Samuel Bekoe, Manasseh Kusi Osei, Richard Tia, Evans Adei
This work reports a detailed DFT study on the generation of trimethylenemethanes (TMMs) from the ring opening of dialkoxymethylenecyclopropane (DMCP), methylenecyclopropanethioacetal (MCPT), and substituted derivatives of DMCP and MCPT, as well as follow-up reactions of the TMMs. The singlet DMCP and MCPT were found to be 51.32 and 53.77 kcal mol-1 more stable than the triplet DMCP and MCPT respectively, corresponding to triplet:singlet population ratios of 1:1038 and 1:1040, respectively, at 25 °C using Boltzmann distribution, implying that the proportion of the triplet species is negligible at 25 °C...
December 21, 2017: Journal of Molecular Modeling
Bing-Xing Yang, Yong Luo, Li-Ping Ye
The surface structures, O2 adsorption, and CO oxidation reaction properties of Ce6O12/Cu(111) have been investigated using density functional theory including on-site Coulomb corrections (DFT + U). Results show that the supported ceria nanoparticles would gain electrons from the Cu(111) surface, and the Ce4+ are reduced to Ce3+. In addition, the oxygens at the interface have been largely activated, resulting in much low formation energy of O vacancies. For the CO oxidation reaction, two possible pathways are investigated, CO reacts with the O2 molecule adsorbed on Ce3+ and the lattice O at the interface, respectively...
December 20, 2017: Journal of Molecular Modeling
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