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Journal of Molecular Modeling

Linda-Lucila Landeros-Martínez, Daniel Glossman-Mitnik, Norma Flores-Holguín
Here, we report theoretical research into the interaction of the drug tamoxifen drug with tripeptides found in the tumor environment-specifically, asparagine-glycine-arginine (NGR) and arginine-glycine-aspartic acid (RGD). Reactivity parameters of these tripeptides were calculated and their intrinsic reactivities and cross-reactivities were analyzed. The interactions of the tripeptides with the nanodiamond-tamoxifen (ND-TAM) complex where the nanodiamond acts as a nanocarrier were also examined theoretically...
November 9, 2018: Journal of Molecular Modeling
Chaofu Wu
All-atomistic (AA) molecular dynamics (MD) is considered as one of the desirable methods for studying glass transition temperatures (Tg) of specific polymers. However, heavy computational efforts are generally required, and the simulated Tg values are not always in good agreement with the experimental data. In this work, a multiscale scheme is proposed: first, the structural and volumetric properties based multiscale modeling is employed to parameterize the coarse-grained (CG) potentials against the AA simulations of an oligomeric melt; with the CG potentials, MD simulations are then carried out on a serial of oligomer bulks and polymer systems of interests, for which the dynamical Tg values are determined...
November 8, 2018: Journal of Molecular Modeling
Hao Li, Yue Yu, Xuyan Xue, Ju Xie, Hongzong Si, Jin Yong Lee, Aiping Fu
First principles calculations have been performed to investigate the structural, electronic, and optical properties of germanene/MoS2 heterostructures. The results show that a weak van der Waals coupling between germanene and MoS2 layers can lead to a considerable band-gap opening (53 meV) as well as the preserved Dirac cone with a linear band dispersion of germanene. The applied external electric filed can not only enhance the interaction strength between two layers, but also linearly control the charge transfer between germanene and MoS2 layers, and consequently lead to a tunable band gap...
November 6, 2018: Journal of Molecular Modeling
Peter Politzer, Jane S Murray
The term "chemical hardness" refers to the resistance to deformation of the electronic density of a system; the greater this resistance, the "harder" the system. Polarizability, a physical property, is an inverse measure of resistance to deformation and thus should be inversely related to hardness. This is indeed generally accepted. Hardness has been postulated to be the second derivative of a system's energy with respect to its number of electrons, despite the fact that this involves the differentiation of a noncontinuous function...
November 6, 2018: Journal of Molecular Modeling
Yasaman Nobakht, Nematollah Arshadi
The aldol reaction in the presence of L-proline acting as an organocatalyst is a well-known example of asymmetric synthesis. Many theoretical and experimental studies have been carried out to probe the mechanism of this reaction. In this work, two levels of density functional theory in the gas phase and DMSO were used to elucidate the best pathways for this reaction, with the enamine and enol considered intermediates and L-proline considered either a reactant or a facilitator. The calculations indicated that both intermediates are formed simultaneously in the reaction medium...
November 6, 2018: Journal of Molecular Modeling
Cristina Coquis, Arlette Richaud, Francisco Méndez
The methylxanthines have attracted interest due to the changes on their biological activities and physicochemical properties in terms of the number and position of the methyl groups present in the xanthine moiety. We report a theoretical study of the influence of the methyl substituent in the basicity and reactivity of xanthine and its methylated derivatives. Our results provide that when the xanthine increases the number of methyl substituents, the gas phase basicity increases (reactivity to proton increases), and the global hardness decreases...
November 3, 2018: Journal of Molecular Modeling
Rajan Vohra, Ravinder Singh Sawhney
The feasibility of electron transport conduction through a guanine base of DNA was investigated and then compared with another component of DNA, i.e., cytosine. A mathematical approach based on the jellium model using non-equilibrium Green's function combined with semi empirical extended Huckel theory was applied using the Atomistik Tool Kit. This was further used to measure significant transport parameters such as current, conductance, transmission spectra and the HOMO-LUMO gap of the suggested molecular system...
November 1, 2018: Journal of Molecular Modeling
Ewa Dresler, Agnieszka Kącka-Zych, Magdalena Kwiatkowska, Radomir Jasiński
Reaction paths for [3 + 2] cycloaddition (32CA) between 2-methyl-1-nitroprop-1-ene and (Z)-C-aryl-N-phenylnitrones were explored in detail at the B3LYP/6-31G(d) level of theory. All of the 32CA processes considered were found to be initiated by the attack of the most nucleophilic oxygen atom in the nitrone molecule on the most electrophilic carbon atom (Cβ) in the nitroethylene moiety. This type of interaction favors the formation of 4-nitro-substituted cycloadducts. Additionally, based on a molecular electron density theory (MEDT) study, the 32CA processes of interest should be considered polar processes with asynchronous transition states (TSs)...
October 30, 2018: Journal of Molecular Modeling
Khodayar Gholivand, Mohammad Kahnouji, Yazdan Maghsoud, Ehsan Masumian, Mahdieh Hosseini
The selectivity of phosphoryl P(O)R3 , sulfoxide S(O)R2 , and carbonyl C(O)R2 (R = NH2 , CH3 , OH, and F) derivatives with lanthanide cations (La3+ , Eu3+ , Lu3+ ) was studied by density functional theory calculations. Theoretical approaches were also used to investigate energy and the nature of metal-ligand interaction in the model complexes. Atoms in molecules and natural bond orbital (NBO) analyses were accomplished to understand the electronic structure of ligands, L, and the related complexes, L-Ln3+ ...
October 29, 2018: Journal of Molecular Modeling
Salima Lakehal, Aicha Lakehal, Malika Bouchagour, Christophe Morell, Henry Chermette
In this work, the nature of the chemical interactions between the metalloid atom (M = Si, Ge, As, Sb, Te, Po) and the nitrogen atoms in the bora-amidinate (bam) complexes (Cln M[PhB(Nt Bu)2 ]) are investigated, mainly via density-based indices. The descriptors used are derived using the quantum theory of atoms in molecules and natural orbitals for chemical valence approaches. It is shown that the strongest interaction is achieved with silicon. Indeed, it is generally the lightest metalloid in a particular group of the periodic table (i...
October 29, 2018: Journal of Molecular Modeling
Mei Wen, Zhuo Zhe Li, An Yong Li
Quantum chemistry computations were performed at the MP2 and B3LYP levels of theory using the basis sets aug-cc-pVDZ and def2-TZVPPD to study the noble gas (Ng) compounds formed by insertion of a Ng atom (Kr, Xe, Rn) into the B-H/F and N-H/F bonds of inorganic benzene B3 N3 H6 and its fluorine derivative B3 N3 F6 . The geometrical structures were optimized and vibrational analysis was carried out to demonstrate these structures being local minima on the potential energy surface. The thermodynamic properties of the formation process of Ng compounds were calculated...
October 27, 2018: Journal of Molecular Modeling
Lixin Shi, Qiang Han
Molecular dynamics (MD) simulations were employed to study the influence of solvents on the structure and mechanical properties of physically crosslinked poly(vinyl alcohol) (PVA) gels. Firstly, three kinds of PVA precursor gels were made by adding water, dimethyl sulfoxide (DMSO) and a mixture of DMSO and water (4:1 by weight), respectively. The solvents in the precursor gels were then exchanged with water to obtain three kinds of PVA hydrogels. Solvent in the precursor gel with a mixture of DMSO and water was also exchanged with ethanol and DMSO, respectively...
October 27, 2018: Journal of Molecular Modeling
Rabia Hameed, Tanja van Mourik, Afsar Khan
A complete set of NMR coupling constants (1 JC-H , 2 JC-H , 3 JC-H , and 3 JH-H ) were calculated for the eight stereoisomers of quinic acid, at the B3LYP/6-311G(d,p)/PCM(methanol) level of theory. The Fermi contact term of the coupling constants was computed with a modified, uncontracted, version of the 6-311G(d,p) basis set, with additional tight polarization functions. 1 H and 13 C NMR chemical shifts were determined at the same level using the gauge-invariant atomic orbital (GIAO) method. The magnitude of the spin-spin coupling constants was found to be affected by the orientation (axial or equatorial) of the coupling proton and the orientation of the hydroxy group on the coupling carbon, whereas the chemical shifts depend on the presence or absence of electron-withdrawing hydroxy groups attached to the carbon atoms involved...
October 26, 2018: Journal of Molecular Modeling
Hongxia Zhao, Yong Yang, Yanwei Wang, Xin Shu, Shishan Wu, Qianping Ran, Jiaping Liu
This work investigated interactions between calcium cations (Ca2+ ) and three common types of oxygen-based functional groups of concrete superplasticizers using density functional theory (DFT) calculations and all-atom molecular dynamics (MD) simulations. The three common types of oxygen-based functional groups were modeled as three hypothetical, low-molecular-weight organic molecules, each containing a methyl-terminated oxyethylene dimer and an adsorbing head of two oxygen-based functional groups, and are referred to as carboxylate, sulfonate, and phosphate groups, respectively, following the usual terminology in the field of concrete admixtures...
October 24, 2018: Journal of Molecular Modeling
Youtao Zhu, Zhe Han, Lijun Fu, Chengbu Liu, Dongju Zhang
Understanding the mechanism for the catalyzed cleavage of the β-O-4 ether linkage in lignin is crucial to developing efficient strategies for depolymerizing lignin. In this work, veratrylglycerol-β-guaiacyl ether (VG) was used as a lignin model compound in a theoretical investigation of the mechanism for the cleavage of the β-O-4 bond as catalyzed by the acidic ionic liquid (IL) 1-H-3-methylimidazolium chloride ([HMIM]Cl). The reaction was found to involve two processes-dehydration and hydrolysis-in which the cation functions as a Brønsted acid (donating a proton) and the anion acts as a nucleophile (promoting dehydration) or interacts with the substrate through hydrogen bonding, stabilizing the intermediate...
October 24, 2018: Journal of Molecular Modeling
F N Tomilin, A S Fedorov, P V Artyushenko, S G Ovchinnikov, T M Ovchinnikova, P E Tsikalova, V G Soukhovolsky
The correlation between the kinetic stability of molecules against temperature and variations in their geometric structure under optical excitation is investigated by the example of different organic pheromone molecules sensitive to temperature or ultraviolet radiation using the density functional theory. The kinetic stability is determined by the previously developed method based on the calculation of the probability of extension of any structural bond by a value exceeding the limit value Lмах corresponding to the breaking of the bond under temperature excitation...
October 24, 2018: Journal of Molecular Modeling
Juan Dang, Qingzhu Zhang
Polycyclic aromatic hydrocarbons (PAHs) have induced large-scale and long-term environmental contamination due to heavy emissions, toxicity, and persistence. The investigation of the ultimate sink of PAHs in the atmosphere is very important. In this work, using quantum chemistry methods, the reaction mechanism of hydroxyl radical-initiated oxidation of benzo[a]anthracene (BaA) in the atmosphere was studied. The products resulted from the gas-phase reaction of BaA with hydroxyl radical include benzo[a]anthracenols, dialdehydes, ketones, epoxides, etc...
October 23, 2018: Journal of Molecular Modeling
Xingyong Wang, Haibo Yu
Density functional theory calculations were carried out to investigate the formation mechanism of the thymine-thymine (6-4) dimer ((6-4)TT), which is one of the main DNA lesions induced by ultraviolet radiation and is closely related to skin cancers. The DNA backbone was found to have nonnegligible effects on the triplet reaction pathway, particularly the reaction steps involving substantial base rotations. The mechanism for the isomerization from (6-4)TT to its Dewar valence isomer (DewarTT) was also explored, confirming the necessity of absorbing a second photon...
October 23, 2018: Journal of Molecular Modeling
Pankaj Kumar Singh, Om Silakari
To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC-a natural product database-was employed. The work presented here is based on the previously explored fact that pharmacophore-based parallel screening is a reliable in silico protocol to predict the possible biological activities of any compound, or any compound library, by screening it with a number of pharmacophore models...
October 20, 2018: Journal of Molecular Modeling
Julio E Terán, Cesar H Zambrano, Jose R Mora, L Rincón, F J Torres
Theoretical calculations focusing on the cleavage of the C-X bond in methyl halides (CH3 X; X = Cl, Br, I) as mediated by CoI -based systems have been carried out using the hybrid functional ωB97-XD together with the basis set 6-311++G(2d,2p). A total of seven CoI -based compounds were evaluated: cob[I]alamin (CoI Cbl) in its base-on form and cobaloxime (CoI Cbx) with either no ligand or different ligands (either pyridine (PYR), tributylphosphine (TBP), dimethyl sulfide (DMS), cyclohexylisocyanide (CI), or 5,6-dimethylbenzimidazole (DMB)) at the lower axial position...
October 18, 2018: Journal of Molecular Modeling
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