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Journal of Molecular Modeling

Mingzhu Xia, Yuting Chu, Tianyi Wang, Wu Lei, Fengyun Wang
As a kind of promising energetic materials, the double furazan-based and furoxan-based compounds have raised concerns of many researchers in recent years. In this paper, the optimized structures, energetic properties, heat of formation (HOF), detonation properties, and bond dissociation energies of these compounds were calculated by density functional theory (DFT) method. The results show that the N-O bond, which is close to the adjacent coordinated oxygen atom in furoxan ring, is more fragile than the other N-O bonds in the ring...
November 2016: Journal of Molecular Modeling
Navnit Kumar Mishra, Anil Kumar Sharma, Tapan Kumar Mukherjee
Melanoma is a cancer associated with melanocytes of epidermis. There has been a consistent increase in the number of melanoma patients because of the depletion of the ozone layer which makes it of paramount importance to explore the immunogenic potential of various peptides in melanoma therapy. In the current study, a mutated decapeptide (ELAGIGILTV) epitope ID 12941 was taken from the melanoma antigen recognized by T-cells. This epitope displayed relatively better affinity for histocompatibility leukocyte antigen influencing the proliferation of cytotoxic T-cells...
November 2016: Journal of Molecular Modeling
Chandresakaran Prathipa, Lakshminarayanan Akilandeswari
There are eight possible pathways for the iron-tricarbonyl-assisted thermal electrocyclic ring opening of fluorocyclobutene due to variations in the orientation of the binding of Fe(CO)3 relative to the fluorine substituent (R1 or R2), stereoselectivity (conrotatory or disrotatory, i.e., C or D), and the torquoselectivity of fluorine (inward-facing or outward-facing, i.e., in or out). A density functional study revealed that the energetically favored pathway is R1 Din. Not only is the D mode favored energetically, but the in configuration was observed to be the lowest-lying mode of R1, despite the general tendency of fluorine substituents to prefer an out configuration...
November 2016: Journal of Molecular Modeling
Houmam Belaidi, Salah Belaidi, Claudine Katan, Camille Latouche, Abdou Boucekkine
The electronic and optical properties of six iridium imidazolylidene complexes (1a, 1b, 2, 2b, 3, 3b) that are strong candidates for use in OLED systems were investigated theoretically. Computations using DFT and TD-DFT methods were performed to explain the observed optical properties of these complexes. Observed absorption bands were assigned and the lowest triplet excited states were computed. Whereas complexes 1a and 1b are nonemissive in solution, the simulated phosphorescence spectra of complexes 2, 2b, 3, and 3b were in good agreement with the observed spectra when the vibrational contributions to the electronic transitions were taken into account...
November 2016: Journal of Molecular Modeling
Vinodhkumar Vijayakumar, Ramadoss Vijayaraj, Günther H Peters
The stability of cyclic peptide assemblies (CPs) forming a macromolecular nanotube structure was investigated in solvents of different polarity using computational methods. The stability and structure of the complexes were studied using traditional molecular dynamics (MD). Energy of dissociation was estimated from steered MD in combination with umbrella sampling simulations. A cyclic peptide nanotube (CPNT) was constructed by stacking of eight cyclo[(D-Trp-L-Gln-D-Trp-L-Glu)2], and hereafter is referred to as (WQWE)8...
November 2016: Journal of Molecular Modeling
Adèle D Laurent, Edwin Otten, Boris Le Guennic, Denis Jacquemin
In this work, we investigate the ground- and excited-state structures as well as the optical properties of a series of five formazanate dyes using state-of-the-art density-based and wavefunction-based methods. The present work is the first to evaluate the properties of formazanate-BF2 dyes with wavefunction-correlated schemes. Firstly, we show that CC2 provides more twisted ground-state geometries than DFT while both approaches lead to planar excited-state structures. Secondly, we demonstrate that the differences between the transition energies computed at TD-DFT, CIS(D), SOS-CIS(D), ADC(2), and CC2 levels are large and that the optical spectra also significantly depend on the selected geometries...
November 2016: Journal of Molecular Modeling
M C Bacchus-Montabonel, F Calvo
Solvation effects are of major interest in the context of radiation damage, due to their potential applications in cancer therapy. Reliable modeling of the solvent is, however, quite challenging, and numerous studies have been devoted to isolated biomolecules and stepwise-hydrated molecules in which the amount of solvent is controlled one molecule at a time. The influence of stepwise hydration on radiation damage is investigated here using the example of proton-induced charge transfer in two biomolecular targets...
November 2016: Journal of Molecular Modeling
Paul A Sibbald
Phosphine-borane adducts are a well-known moiety in synthetic and coordination chemistry. These complexes form a dative bond in which the Lewis basic phosphorus atom donates electron density into an empty p-orbital of the Lewis acidic boron atom. However, donation of the phosphorus lone pair is not the only stabilizing interaction, as hyperconjugation and electrostatic interaction also play important roles in bonding. This paper describes a detailed density functional theory level (B3LYP) study completed to determine the impact electron-donating and withdrawing substituents have on phosphine-borane bonds through the investigation of a series of para-substituted PAr3-BH3 and PH3-BAr3 phosphine-borane adducts...
November 2016: Journal of Molecular Modeling
Marina Laine, Nuno A Barbosa, Robert Wieczorek, Mikhail Ya Melnikov, Aleksander Filarowski
A number of fluorescent dyes based on BODIPY (4,4'-difluoro-4-bora-3a,4a-diaza-s-indacene) have been studied theoretically. This paper presents the results of calculations of these BODIPY dyes in their ground and excited states, performed using DFT and TD-DFT methods, respectively. The influences of N,N-dimethylaminobenzyl, ortho-fluorophenol, and methyl substituents as well as the solvent polarity on the positions of the absorption and emission bands of the dyes were analyzed. The computational data obtained in this work were compared to the corresponding experimental data...
November 2016: Journal of Molecular Modeling
James J P Stewart
A new method for predicting the energy contributions to substrate binding and to specificity has been developed. Conventional global optimization methods do not permit the subtle effects responsible for these properties to be modeled with sufficient precision to allow confidence to be placed in the results, but by making simple alterations to the model, the precisions of the various energies involved can be improved from about ±2 kcal mol(-1) to ±0.1 kcal mol(-1). This technique was applied to the oxidized nucleotide pyrophosphohydrolase enzyme MTH1...
November 2016: Journal of Molecular Modeling
Guillaume Chevrot, Eudes Eterno Fileti, Vitaly V Chaban
Using molecular dynamics simulations, we investigated the thermal stability and real-time denaturation of a model mini-protein in four solvents: (1) water, (2) 1-ethyl-3-methylimidazolium alaninate [EMIM][ALA] (5 mol% in water), (3) methioninate [EMIM][MET] (5 mol% in water), and (4) tryptophanate [EMIM][TRP] (5 mol% in water). Upon analyzing the radius of gyration, the solvent-accessible surface area, root-mean-squared deviations, and inter- and intramolecular hydrogen bonds, we found that the mini-protein remains stable at 30-40 K higher temperatures in aqueous amino acid based ionic liquids (AAILs) than in water...
November 2016: Journal of Molecular Modeling
Yan-Zhen Zheng, Yu Zhou, Qin Liang, Da-Fu Chen, Rui Guo
Flavonoids are among the most important bioactive compounds responsible for the medical properties of honey and propolis. Water is the solvent most commonly used to extract flavonoids from honey and propolis. Hydrogen-bonding interactions are of great importance in the extraction process. In this work, hydrogen-bonding interactions between a representative flavonoid, luteolin, and water were investigated by density functional theory (DFT) from a theoretical viewpoint. The following conclusions were drawn: first, the molecular structure of luteolin is non-planar...
November 2016: Journal of Molecular Modeling
A V Raevsky, M Sharifi, D A Samofalova, P A Karpov, Y B Blume
Histone lysine acetylation is a reversible post-translational modification that does not involve changes in DNA sequences. Enzymes play an important role in developmental processes and their deregulation has been linked to the progression of diverse disorders. The HAT enzyme family fulfills an important role in various developmental processes mediated by the state of chromatin, and have been attributed to its deregulation. To understand acetylation mechanisms and their role in cell signaling, transcriptional regulation, and apoptosis, it is crucial to identify and analyze acetylation sites...
November 2016: Journal of Molecular Modeling
Rogério V A Júnior, Gustavo L C Moura, Nathalia B D Lima
We evaluated a group of phthalimide derivatives, which comprise a convenient test set for the study of the multiple factors involved in the energetics of hydrogen bond formation. Accordingly, we carried out quantum chemical calculations on the hydrogen bonded complexes formed between a sample of phthalimide derivatives with formic acid with the intent of identifying the most important electronic and structural factors related to how their strength and spontaneity vary across the series. The geometries of all species considered were fully optimized at DFT B3LYP/6-31++G(d,p), RM1, RM1-DH2, and RM1-D3H4 level, followed by frequency calculations to determine their Gibbs free energies of hydrogen bond formation using Gaussian 2009 and MOPAC 2012...
November 2016: Journal of Molecular Modeling
J C Espinoza-Hicks, J M Nápoles-Duarte, G V Nevárez-Moorillón, A Camacho-Dávila, L M Rodríguez-Valdez
Novel chalcone derivatives with different substituents attached to A and B-rings: hydroxyl, methoxyl, geranyl, and prenyl groups were synthesized. The obtained compounds were characterized by NMR, HRMS, UV-Vis, IR, and MS. The theoretical analysis was carried out in all the compounds using density functional theory (DFT) with the B3LYP, PBE0, and M06-2X functionals in combination with the 6-311G(d,p) Pople-type basis set. The excited state properties were calculated by time dependent density functional theory (TD-DFT) using the same methodology applied for the ground state properties...
October 2016: Journal of Molecular Modeling
Liangzhi Xia, Qing Liu, Fengling Wang, Jinming Lu
Based on the structure of MOF-808, different substituents were introduced to replace hydrogen atom on the phenyl ring of MOF-808. The GCMC method was used to study the effect of functional groups on the hydrogen storage properties of MOF-808-X (X = -OH, -NO2, -CH3, -CN, -I). The H2 uptakes and isosteric heat of adsorption were simulated at 77 K. The results indicate that all these substituents have favorable impact on the hydrogen storage capacity, and -CN is found to be the most promising substituent to improve H2 uptake...
October 2016: Journal of Molecular Modeling
Borko Bošković, Janez Brest
This paper presents a differential evolution algorithm that is adapted for the protein folding optimization on a three-dimensional AB off-lattice model. The proposed algorithm is based on a self-adaptive differential evolution that improves the algorithm efficiency and reduces the number of control parameters. A mutation strategy for the fast convergence is used inside the algorithm. A temporal locality is used in order to speed up the algorithm convergence additionally and to find amino-acid conformations with the lowest free energy values...
October 2016: Journal of Molecular Modeling
Michal Malček, Lukáš Bučinský, Zuzana Barbieriková, Sandra Dorotíková, Dana Dvoranová, Vlasta Brezová, Peter Rapta, Stanislav Biskupič
Protonation in the two-electron/two-proton reduction processes of 2,6-dichlorophenolindophenolate (DCIP) is investigated combining density functional theory (DFT) and molecular dynamics (MD) methods. DCIP (anion), DCIP(•-) (radical anion), and DCIP(2-) (dianion) are considered, including the electronic structure analysis from the prospective of quantum theory of atoms and molecules (QTAIM). It is shown that oxygen on the indophenolate moiety and nitrogen are the first and/or the second proton acceptor sites and their energetic order depends on the total charge of the system...
October 2016: Journal of Molecular Modeling
Mario Vincenzo La Rocca, Malvina Rutkowski, Stéphanie Ringeissen, Jérôme Gomar, Marie-Céline Frantz, Saliou Ngom, Carlo Adamo
The overall objective was to identify an accurate computational electronic method to virtually screen phenolic compounds through their antioxidant and free-radical scavenging activity. The impact of a key parameter of the density functional theory (DFT) approach was studied. Performances of the 21 most commonly used exchange-correlation functionals are thus detailed in the evaluation of the main energetic parameters related to the activities of two prototype antioxidants, namely quercetin and edaravone, is reported...
October 2016: Journal of Molecular Modeling
Ken-Peng Song, Fu-de Ren, Shu-Hai Zhang, Wen-Jing Shi
A molecular dynamics method was employed to study the binding energies associated with the cocrystallization (at selected crystal planes) of either 1,3,5-triamino-2,4,6-trinitro-benzene (TATB), 1,1-diamino-2,2-dinitroethylene, 3-nitro-1,2,4-triazol-5-one (TATB, FOX-7, and NTO, respectively, all of which are explosives), or N,N-dimethylformamide (DMF, a nonenergetic solvent) in various molar ratios with 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane in its α and β conformations (α-HMX and β-HMX, respectively)...
October 2016: Journal of Molecular Modeling
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