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Journal of Molecular Modeling

Yan-Zhen Zheng, Jing Xu, Qin Liang, Da-Fu Chen, Rui Guo, Zhong-Min Fu
Ethanol is one of the most commonly used solvents to extract flavonoids from propolis. Hydrogen bonding interactions play an important role in the properties of liquid system. The main objective of the work is to study the hydrogen bonding interactions between flavonoid and ethanol. Luteolin is a very common flavonoid that has been found in different geographical and botanical propolis. In this work, it was selected as the representative flavonoid to do detailed research. The study was performed from a theoretical perspective using density functional theory (DFT) method...
August 2017: Journal of Molecular Modeling
Vladimir S Naumov, Stanislav K Ignatov
The GROMOS 56ACARBO force field for the description of carbohydrates was modified for calculations of chitosan (poly-1,4-(N-acetyl)-β-D-glucopyranosamine-2) with protonated and non-protonated amino groups and its derivatives. Additional parameterization was developed on the basis of quantum chemical calculations. The modified force field (56ACARBO_CHT) allows performing the molecular dynamic calculations of chitosans with different degrees of protonation corresponding to various acidity of medium. Test calculations of the conformational transitions in the chitosan rings and polymeric chains as well as the chitosan nanocrystal dissolution demonstrate good agreement with experimental data...
August 2017: Journal of Molecular Modeling
Harry Ramanantoanina, Claude Daul
The ligand field density functional theory (LFDFT) algorithm is extended to treat the electronic structure and properties of systems with three-open-shell electron configurations, exemplified in this work by the calculation of the core and semi-core 1s, 2s, and 3s one-electron excitations in compounds containing transition metal ions. The work presents a model to non-empirically resolve the multiplet energy levels arising from the three-open-shell systems of non-equivalent ns, 3d, and 4p electrons and to calculate the oscillator strengths corresponding to the electric-dipole 3d (m)  → ns (1)3d (m) 4p (1) transitions, with n = 1, 2, 3 and m = 0, 1, 2, …, 10 involved in the s electron excitation process...
August 2017: Journal of Molecular Modeling
Jianhua Hou, Zhixiong Yang, Zhiru Li, Haoyu Chai, Ruiqi Zhao
We designed nine endohedral dodecahedrane heterodimers H@C20Hn-C20Hn@M (M = Cu, Ag, and Au, n = 15, 18, and 19) that may act as single-molecule spin switches, and we predicted theoretically that the ground states of the dimmers shift from low-spin states (S = 0) to the high-spin states (S = 1) under an external electric field applied parallel or perpendicular to the molecular symmetry axes, consisting well with the analyses of Stark effect. Molecular orbitals analyses provide an intuitive insight into the spin crossover behavior...
August 2017: Journal of Molecular Modeling
Sumita Karan, Vipin K Kashyap, Syed Shafi, Ajay K Saxena
Mycobacterium tuberculosis decaprenylphosphoryl-β-D-ribose oxidase (MtbDprE1) acts in concert with decaprenylphosphoryl-β-D-ribose 2-epimerase (MtbDprE2) and catalyzes the epimerization of DPR into DPA. DPA is the sole precursor for synthesis of arabinogalactan and lipoarabinomannan in the mycobacterial cell wall. MtbDprE1 is a unique antimalarial drug target and many covalent and non-covalent inhibitors against MtbDprE1 have been studied for their antituberculosis activities. In the current study, we have purified MtbDprE1 enzyme and synthesized six sulfur-rich 2-mercaptobenzothiazole and 1, 2, 3-triazole conjugated ligands and performed binding analysis with MtbDprE1...
August 2017: Journal of Molecular Modeling
John F Moxnes, Øyvind Frøyland, Tallak Risdal
This work is a study of 5-amino-3-nitro-1,2,4-triazole (ANTA), 3-nitro-1,2,4-triazol-5-one (NTO), and nitrated derivatives of ANTA and NTO. RDX and TNT were studied for comparison. ANTA and NTO are low-sensitive high explosives with detonation properties comparable to 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitroperhydro-1,3,5-triazine (RDX). We showed previously that nitrated NTO and ANTA compounds, when used in a glycidyl azide polymer (GAP) matrix in rocket propellants, could give impulses above 2600 m/s and that the oxygen balance is positive...
August 2017: Journal of Molecular Modeling
Akhil Kumar, Gaurava Srivastava, Swati Srivastava, Seema Verma, Arvind S Negi, Ashok Sharma
BACE-1 and GSK-3β are potential therapeutic drug targets for Alzheimer's disease. Recently, both the targets received attention for designing dual inhibitors for Alzheimer's disease. Until now, only two-scaffold triazinone and curcumin have been reported as BACE-1 and GSK-3β dual inhibitors. Docking, molecular dynamics, clustering, binding energy, and network analysis of triazinone derivatives with BACE-1 and GSK-3β was performed to get molecular insight into the first reported dual inhibitor. Further, we designed and evaluated a naphthofuran series for its ability to inhibit BACE-1 and GSK-3β with the computational approaches...
August 2017: Journal of Molecular Modeling
Mirosław Kwiatkowski, Bassim H Hameed
The paper presents the results of research devoted to reliability evaluation of the analysis of results of the porous structure of activated carbons based on incomplete nitrogen adsorption isotherms using the BET, t-plot, and NLDFT methods, as well as the LBET method comprising the unique numerical fast multivariant procedure of adsorption system identification. The research involved the application of the nitrogen adsorption isotherms obtained for five samples of activated carbons produced from waste materials of organic origin by way of chemical activation with potassium hydroxide, sodium hydroxide, and potassium carbonate with the use of microwave heating...
August 2017: Journal of Molecular Modeling
Rui-Hong Meng, Xiong Cao, Shuang-Qi Hu, Li-Shuang Hu
The cooperativity effects of the H-bonding interactions in HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane)∙∙∙HMX∙∙∙FA (formamide), HMX∙∙∙HMX∙∙∙H2O and HMX∙∙∙HMX∙∙∙HMX complexes involving the chair and chair-chair HMX are investigated by using the ONIOM2 (CAM-B3LYP/6-31++G(d,p):PM3) and ONIOM2 (M06-2X/6-31++G(d,p):PM3) methods. The solvent effect of FA or H2O on the cooperativity effect in HMX∙∙∙HMX∙∙∙HMX are evaluated by the integral equation formalism polarized continuum model...
August 2017: Journal of Molecular Modeling
Ramón Alain Miranda-Quintana, Marco Martínez González, David Hernández-Castillo, Luis A Montero-Cabrera, Paul W Ayers, Christophe Morell
The regioselectivity of the 1,3-dipolar cycloaddition of a model nitrone with a set of dipolarophiles, presenting diverse electronic effects, is analyzed using conceptual density functional theory (DFT) methods. We deviate from standard approaches based on frontier molecular orbitals and formulations of the local hard/soft acid/base principle and use instead the dual descriptor. A detailed analysis is carried out to determine the influence of the way to calculate the dual descriptor, the computational procedure, basis set and choice of method to condensate the values of this descriptor...
August 2017: Journal of Molecular Modeling
Shaohui Zheng, Mengyue Xiao, Yongping Tian, Xue Chen
Knowledge of the charge (electron) transfer process at the donor-acceptor interface is required to understand the working mechanisms of different organic photovoltaic materials. Investigating the lowest charge-transfer state in organic donor-acceptor solar cells is important as it allows the destruction/formation of excitons and polarons to be studied, and is directly related to the open circuit voltage. By performing low-cost and feasible calculations of ground-state electronic structures using the Mulliken rule as well as the optimally tuned range-separated hybrid (OTRSH) density functional and a regular long-range corrected functional, the lowest charge-transfer (CT) state energies of a series of dimers containing functionalized anthracene (the donor) and tetracyanoethylene (the acceptor) were obtained...
August 2017: Journal of Molecular Modeling
Nery Villegas-Escobar, Alejandro Toro-Labbé, Marcos Becerra, Misael Real-Enriquez, Jose R Mora, Luis Rincon
This contribution presents a computational study aimed at understanding factors affecting barriers associated with the activation of the H-H bond in molecular hydrogen and the H-CH3 bond in methane mediated by intermolecular Frustrated Lewis Pairs (FLPs). The classical phosphine P(t-Bu)3 Lewis base in conjunction with two Lewis acids, B(C6F5)3 and Al(C6F5)3, were used as representative models of intermolecular FLPs. DFT calculations were performed using the dispersion corrected ωB97x-D functional, including toluene as a solvent through the PCM-SMD implicit solvent scheme...
August 2017: Journal of Molecular Modeling
S U A Ramjauny, I A Alswaidan, N B Jaufeerally-Safee, L Rhyman, P Ramasami
The characterization of the seleno-sulfide-bromo systems and the isomerization process on the [H, S, Se, Br] potential energy surface were investigated using state-of-the-art theoretical methods. The CCSD(T) and the MP2 levels of theory were employed along with the series of correlation consistent basis sets extrapolated to the complete basis set (CBS) limit in the optimization of the geometrical parameters and computation of electronic energies. The relative stability, in kcal mol(-1), at the CCSD(T)/CBS follows the trend: HSSeBr (0) > HSeSBr (9...
August 2017: Journal of Molecular Modeling
Bo Lu, Xueying Zhang, Lingpeng Meng, Yanli Zeng
Similar to σ-hole interactions, the π-hole interaction has attracted much attention in recent years. According to the positive electrostatic potentials above and below the surface of inorganic heterocyclic compounds S2N2 and three SN2P2 isomers (heterocyclic compounds 1-4), and the negative electrostatic potential outside the X atom of XH3 (X = N, P, As), S2N2/SN2P2⋯XH3 (X = N, P, As) complexes were constructed and optimized at the MP2/aug-cc-pVTZ level. The X atom of XH3 (X = N, P, As) is almost perpendicular to the ring of the heterocyclic compounds...
August 2017: Journal of Molecular Modeling
Qing Li, Chun-Min Li, Hong-Liang Xu, Zhong-Min Su
A graphene nanoflake (GNF) is a polycyclic aromatic hydrocarbon (PAH) with a huge two-dimensional π-conjugated carbon material in which a central benzene ring is surrounded by identical benzene-type rings through infinite alternant method. In this paper, we explore the structure-aromaticity relationship of the GNFs and the GNFs with hollow sites (GNFHs) by combining the nucleus-independent chemical shifts (NICS) with the anisotropy of the current induced density (ACID). Firstly, the benzene is a typical aromatic molecule (NICS = -9...
August 2017: Journal of Molecular Modeling
Przemysław Czeleń
A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of such enzyme inhibition as analyzed by an indoline sulfamylophenyl derivative (CHEMBL410072). Previous work has shown that such compounds exhibit selective properties towards their biological targets...
August 2017: Journal of Molecular Modeling
Alia Méjri, Fabien Picaud, Mohammed El Khalifi, Tijani Gharbi, Bahoueddine Tangour
The oxidative addition of primary amine on a monocyclic phospholane was studied in confined conditions. This one-step chemical reaction has been investigated using the DFT technique to elucidate the role of confinement in carbon nanotubes on the reaction. Calculations were carried out by a progressive increase of the nanotube diameters from 10 Å to 15 Å in order to highlight the dependence of the reactivity on the nanotube diameter. First, single point investigations were dedicated to the study of reactants, transition states, and products placed in the different nanotubes while keeping their optimized structure as free compounds...
August 2017: Journal of Molecular Modeling
Jelena Tamuliene, Jonas Sarlauskas, Svajone Bekesiene
This study presents an investigation of the effects of adding extra nitro group substituents to N-(3,5-dimethyl-2,4,6-trinitrophenyl)-1H-1,2,4-triazol-3-amine (HEM-II) on its thermal and chemical stability as well as its explosive performance. An analysis of the thermal stabilities of HEM-II and HEM-II-based molecules based on an investigation of the binding energy per atom for each molecule was performed. The values of the gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) as well as those of the chemical hardness and softness for HEM-II and the HEM-II-based molecules were studied to determine the chemical stabilities of these molecules...
August 2017: Journal of Molecular Modeling
Kamolrat Somboon, Jitti Niramitranon, Prapasiri Pongprayoon
Pseudomonas aeruginosa is an important nosocomial human pathogen. The major difficulty in the fight against this pathogen is the relative impermeability of its outer membrane (OM). Only specific substrates can penetrate through the OM of P. aeruginosa via substrate-specific porins, so this has become one of the most problematic drug-resistant pathogens. Carbapenems are the most effective drugs for treating P. aeruginosa infections. One such carbapenem that is applied in cases of P. aeruginosa infection is imipenem (IMI), which uses outer membrane carboxylate channel D1 (OccD1) as a point of entry into the pathogen...
August 2017: Journal of Molecular Modeling
Sangeeta Kundu, Sanchita Mukherjee, Dhananjay Bhattacharyya
Genomic DNA of higher organisms exists as extremely long polymers, while in bacteria and other lower organisms it is circular with no terminal base pairs. Temperature-induced melting of the DNA double helix by localized strand separation has been unattainable by molecular dynamic simulations due to more rapid fraying of the terminal base pairs in oligomeric DNA. However, local-sequence-dependent unfolding of the DNA double helix is extremely important for understanding various biochemical phenomena, and can be addressed by simulating a model polymeric DNA duplex...
August 2017: Journal of Molecular Modeling
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