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Journal of Molecular Modeling

A Z de Oliveira, I B Ferreira, C T Campos, F E Jorge, P A Fantin
Nonrelativistic and relativistic (Douglas-Kroll-Hess, DKH) segmented all-electron Gaussian basis sets of valence triple zeta quality plus polarization functions (TZP) for the lanthanides were developed. As some atomic and molecular properties depend on a good description of the electrons far from the nuclei, these basis sets are augmented with diffuse functions, giving rise to the augmented TZP (ATZP) and ATZP-DKH basis sets. At the DKH level of theory, the B3LYP hybrid functional in conjunction with the TZP-DKH basis set were used to calculate the atomic charges and valence orbital populations of the lanthanide and oxygen atoms, the bond lengths, and the equilibrium dissociation energies of lanthanide monoxides...
January 15, 2019: Journal of Molecular Modeling
Danyil Huraskin, Anselm H C Horn
Alzheimer's disease is characterized by the aggregation of Amyloid-β (Aβ) peptide into oligomers, fibrils and plaques. Many factors influencing this process as well as the stability of the various Aβ aggregates are known to date, and include the concentration and type of metal ions. Most experimental and theoretical studies have concentrated on heavy metal ions, like Fe2+ , Zn2+ , or Cu2+ , while the smaller alkali ions Li+ , Na+ , and K+ have not gained much attention notwithstanding their role and ubiquity in physiological environments...
January 12, 2019: Journal of Molecular Modeling
Chunmei Zheng, Tianyi Wang, Fengyun Wang, Xuedong Gong, Mingzhu Xia
To continue our previous work, the structure and some properties of a new series of 1,2,3,4-tetrazine 1,3-dioxides annulated with an imidazole ring or oxazole ring were studied in this paper. Four imidazolo-v-tetrazine 1,3-dioxides (ITDOs) I1-I4 and eight oxazolo-v-tetrazine 1,3-dioxides (OTDOs) O1-O8 were designed. We employed the density functional theory (DFT) in B3LYP/6-311++G(d,p) to study their geometrical structures and the homodesmotic reaction method to calculate the enthalpies of formation. Detonation properties and stabilities were also studied...
January 10, 2019: Journal of Molecular Modeling
Sergey V Panteleev, Artëm E Masunov, Subith S Vasu
Fossil fuel oxy-combustion is an emergent technology where habitual nitrogen diluent is replaced by high pressure (supercritical) carbon dioxide. The supercritical state of CO2 increases the efficiency of the energy conversion and the absence of nitrogen from the reaction mixture reduces pollution by NOx . However, the effects of a supercritical environment on elementary reactions kinetics are not well understood at present. We used boxed molecular dynamics simulations at the QM/MM theory level to predict the kinetics of dissociation/recombination reaction HCO•  + [M] ↔ H•  + CO + [M], an important elementary step in many combustion processes...
January 10, 2019: Journal of Molecular Modeling
Rogério J Costa, Elton A S Castro, José R S Politi, Ricardo Gargano, João B L Martins
The search for renewable raw materials less harmful to the environment, such as methanol, ethanol, 1-propanol, and 1-butanol has become attractive. These products are obtained more rapidly and efficiently by specific solid catalysts, mainly the zeolites. The Brønsted acid sites distributed over the sinusoidal and the straight channels are important for the alcohol dehydration reaction that produces widely used chemicals. Therefore, the ONIOM method was used to study methanol, ethanol, propanol, and butanol adsorption in H-ZSM-5 zeolite...
January 9, 2019: Journal of Molecular Modeling
Brian J Levandowski, Trevor A Hamlin, Hannah J Eckvahl, F Matthias Bickelhaupt, K N Houk
Quantum chemical calculations were used to investigate the Diels-Alder reactivities for a series of cycloalkenediones with tetrazine. We find that the reactivity trend of cycloalkenediones toward tetrazine is opposite to cycloalkenes. The electrostatic interactions between the cycloalkenediones and tetrazine become more stabilizing as the ring size of the cycloalkenediones increases, resulting in lower activation energies. The origin of the more favorable electrostatic interactions and the accelerated reactivities of larger cycloalkenediones result from a stabilizing CH/π interaction that is not present in the reaction of the 4-membered cycloalkenedione...
January 9, 2019: Journal of Molecular Modeling
Sergey V Gudkovskikh, Mikhail V Kirov
This work is devoted to the study of the mechanical properties of hexagonal ice Ih and gas hydrate frameworks sI, sII and sH, taking into account the disorder in the positions of the hydrogen atoms (protons). The article emphasizes the critical role of the elastic energy for the evaluation of the relative energy of the proton configurations. The calculations are performed with the help of the TINKER package using the AMOEBA polarizable force field. The elastic constants, elastic modulus, and anisotropy indices are calculated...
January 8, 2019: Journal of Molecular Modeling
Linyuan Wang, Kai Zhong, Jie Ma, Jian Liu, Hua Xu
Plastic bonded explosive (PBX) is a typical composite material used widely in the defense industry and in aerospace engineering. The mechanical behavior of PBX is an important factor to be considered in its formulation design, but the initial mechanical response is not well understood due to the complexities of atomic interactions in a multi-component system. We applied a hybrid force field to investigate the initial mechanical response of cyclotrimethylenetrinitramine(RDX)-based PBX, by molecular dynamics...
January 7, 2019: Journal of Molecular Modeling
Chan Zou, Chunbo Wang
The reactions between arsenic and nitrogen oxides (N2 O, NO2 , and NO) were investigated using density functional theory. The geometries of the reactants, intermediates, transition states, and products in each reaction were optimized. Frequency analysis was applied to verify those geometries, and the authenticity of each transition state was checked using intrinsic reaction coordinate analysis (IRC). The single point energy of each stationary point was calculated at the B2PLYP level, and kinetic analysis was conducted to explore each reaction mechanism in more detail...
January 7, 2019: Journal of Molecular Modeling
Wiktoria Jedwabny, Edyta Dyguda-Kazimierowicz
Halogenated ligands are nowadays commonly designed in order to increase their potency against protein targets. Although novel computational methods of evaluating the affinity of such halogenated inhibitors have emerged, they still lack the sufficient accuracy, which is especially noticeable in the case of empirical scoring functions, being the method of choice in the drug design process. Here, we evaluated a series of halogenated inhibitors of phosphodiesterase type 5 with ab initio methods, revealing the physical nature of ligand binding and determining the components of interaction energy that are essential for proper inhibitor ranking...
January 7, 2019: Journal of Molecular Modeling
Aiqin Hao, Haibo Xue, Jianfeng Jia
The geometries, stabilities, and magnetic properties of Co2 Bn (n = 1-10) clusters were systematically investigated by performing spin-polarized density functional theory calculations. We found that doping Bn clusters with Co significantly changed their structures. Co2 B2 and Co2 B5 had planar and quasi-planar structures, while Co2 B3 and Co2 B7 had bipyramidal structures. Co2 B10 had a tubular structure. In analyses of the dissociation energies and the second-order differences in total energy of the clusters, Co2 B3 and Co2 B7 were identified as magic-number (i...
January 6, 2019: Journal of Molecular Modeling
Junyong Wu, Hua Yan, Aiguo Zhong, Hao Chen, Yanxian Jin, Guoliang Dai
The pnicogen and halogen bonding interactions in the PH2 X---BrCl(X = H, F, OH, OCH3 and CH3 ) complexes have been studied at the MP2/aug-cc-pVTZ level. Analysis of interaction energies shows that the pnicogen-bonded structures are less stable than the corresponding halogen-bonded structures. The pnicogen and halogen bonds were also studied by conceptual DFT reactivity indices. Noncovalent interaction (NCI) and SAPT analysis reveals that the dispersion interactions dominate the pnicogen-bonded complexes of PH2 X---BrCl in nature, while the halogen-bonded complexes are dominantly electrostatic energy...
January 6, 2019: Journal of Molecular Modeling
Butong Li, Mengchun Zhou, Ju Peng, Lulin Li, Yinli Guo
A series of derivatives of pyridine were designed through substituting hydrogen atoms by nitro groups systematically. By using the density functional theory at B3PW91/6-311++G(d,p)//MP2/311++G(d,p) level, heats of formation, bond orders, and bond dissociation energies were calculated to explore the thermodynamic stabilities of title molecules. Furthermore, the regularity of stability was explained based on the electronic population. Our results indicated that title molecules had enough stability to exist. To evaluate the potential usage as a high-energy-density molecule, the detonation pressure and detonation velocity were explored by using the semi-empirical Kamlet-Jacobs equation and excellent detonation character was confirmed...
January 5, 2019: Journal of Molecular Modeling
Natalia Pino, Diana López, Juan F Espinal
Furfural is a valuable oxygenated compound derived from the thermal decomposition of biomass, and is one of the major problems of bio-oil upgrading. Due to its high reactivity, this compound requires further upgrading to more stable products such as furfuryl alcohol, 2-methylfuran (MF), furan, 2-methyltetrahydrofuran, and tetrahydrofuran. The thermochemical data and kinetic analysis of the reactions involved in the conversion of furfural were investigated by molecular modeling to guide experimental investigations in the process of designing efficient catalysts that allows the control of the reaction pathways in specific directions, towards the production of fuel precursors or chemicals...
January 5, 2019: Journal of Molecular Modeling
Dawid Faron, Piotr Skurski, Iwona Anusiewicz
The existence and stabilities of various neutral metal oxides of formula MON and MON2 (M = Fe, Co, Ni; N = Li, Na) and their corresponding cations MON+ and MON2 + are predicted using density functional theory (B3LYP) with the 6-311 + G(d) basis set. Ab initio calculations carried out at the CCSD(T)/6-311 + G(3df) level of theory reveal that the ionization potentials (IPs) of the oxides MO decrease by ca. 3-5 eV upon functionalization with N to give either MON or MON2 . The influences of the chemical constitution and local spin magnetic moment (on the transition metal atom) of the oxide or cation on its IP are presented and discussed...
January 5, 2019: Journal of Molecular Modeling
Peng Lian, Song Chen, Yao-Xuan Zhang, Chao Kang, Xin-Chen Fan, Wei-Peng Lai
The B3PW91/6-31G** theoretical method was carried out to optimize the structure of 12 polynitro imidazo [4,5-e] oxadiazolo [3,4-b] pyrazine compounds (two structural type). The influence of nitro groups on the structure, oxygen balance, density, heat of formation, detonation performances, and charge were investigated. The results showed that the oxygen balance, density, heat of formation, detonation velocity, detonation pressure, and detonation heat increased with different relationships when the number of nitro groups increased...
January 5, 2019: Journal of Molecular Modeling
Ting Cao, Xiangfei Ji, Jinpeng Wu, Shiju Zhang, Xiaofeng Yang
Although simulation boxes used in molecular dynamics are normally chosen to be cubic or rectangular, two other cell shapes that are very familiar to crystallographers-the truncated octahedron and the rhombic dodecahedron-could also be used because they are also space-filling cells. Due to their spherical nature, these boxes have been intentionally applied in simulations of biomolecular solutions and liquid structures. Indeed, due to the advantages of running many molecular dynamic codes in parallel, simulations based on these non-rectangular boxes have been growing in popularity in recent years...
January 4, 2019: Journal of Molecular Modeling
Deepika Chauhan, Pulkit A Srivastava, Vidushi Agnihotri, Ragothaman M Yennamalli, Richa Priyadarshini
Arsenic prevalence in the environment impelled many organisms to develop resistance over the course of evolution. Tolerance to arsenic, either as the pentavalent [As(V)] form or the trivalent form [As(III)], by bacteria has been well studied in prokaryotes, and the mechanism of action is well defined. However, in the rod-shaped arsenic tolerant Deinococcus indicus DR1, the key enzyme, arsenate reductase (ArsC) has not been well studied. ArsC of D. indicus belongs to the Grx-linked prokaryotic arsenate reductase family...
January 4, 2019: Journal of Molecular Modeling
Indu Kumari, Navjot Kaur, Shuchi Gupta, Neetu Goel
Oxidation of ethene and benzene by chromium oxide (CrO3 ) supported on silica (SiO2 ) was investigated by employing hybrid quantum mechanics/molecular mechanics (QM/MM) model calculations. Various mechanistic possibilities, such as C-H or C=C bond activation of hydrocarbons, were investigated in detail for the reaction of ethene and benzene with CrO3 grafted on a silica surface. While activation of the C-H bond leads to the formation of alcohol, epoxide is obtained via C=C bond activation. The complete reaction routes for the formation of each product were traced and found to be exothermic...
January 4, 2019: Journal of Molecular Modeling
Nan Yan, Suhong Huo, Xiaoyan Li, Yanli Zeng, Lingpeng Meng
As a kind of intermolecular noncovalent interaction, chalcogen bonding plays a critical role in the fields of chemistry and biology. In this paper, S⋅⋅⋅S chalcogen bonds in three groups of complexes, F2 P(S)N⋅⋅⋅SX2 , F2 PNS⋅⋅⋅SX2 , and F2 PSN⋅⋅⋅SX2 (X = F, Cl, Br, OH, CH3 , NH2 ), were investigated at the MP2/aug-cc-pVTZ level of theory. The calculated results show that the formation of S⋅⋅⋅S chalcogen bond is in the manner of attraction between the positive molecular electrostatic potential (VS,max ) of chalcogen bond donator and the negative VS,min of chalcogen bond acceptor...
January 4, 2019: Journal of Molecular Modeling
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