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Journal of Molecular Modeling

Igo T Lima, Leonardo Sousa, Renato da S Freitas, Luiz Antonio Ribeiro Junior, Rafael Timóteo de Sousa Júnior, Demétrio A da Silva Filho
We systematically investigate, at density functional theory level, the electronic properties of a set of ten carotenoid molecules with different conjugation length. Ground state geometries were fully optimized using both B3LYP and its long-range corrected version, i.e., the CAM-B3LYP functional. The time-dependent DFT approach (TD-DFT) was also performed for the calculation of the excited states of the optimized geometries and the results were compared to the experimental ones, when available. Our findings indicate a dependence of the transition vertical energies, oscillator strengths, and transition dipole moments on the extension of conjugation, as expected...
November 17, 2017: Journal of Molecular Modeling
Houari Brahim, Boumediene Haddad, Sefia Brahim, Abdelkrim Guendouzi
The electronic structures and spectroscopic properties of two complexes [M(pic)3] (M = Ir, Rh) containing picolinate as bidentate ligands have been calculated by means density functional theory (DFT) and time-dependent DFT/TD-DFT using three hybrid functionals B3LYP, PBE0 and mPW1PW91. The PBE0 and mPW1PW91 functionals, which have the same HF exchange fraction (25%), give similar results and do not differ drastically from B3LYP results. Calculated geometric parameters of the complexes are in good agreement with the available experimental data...
November 17, 2017: Journal of Molecular Modeling
Julian Cruz-Borbolla, Esteban Garcia-Ochoa, Jayanthi Narayanan, Pablo Maldonado-Rivas, Thangarasu Pandiyan, José M Vásquez-Pérez
The capacity of 2,6-bis[((2-pyridylmethyl)oxy)methyl)]pyridine (BPMMP) to inhibit the corrosion of mild carbon steel in HCl was analyzed. In a polarization study, both the cathodic and anodic currents were appreciably decreased in the presence of BPMMP, suggesting that this ligand is effective at inhibiting corrosion at the metal surface. This conclusion is consistent with the results of impedance analysis, where only one time constant corresponding to one depressed capacitive loop was detected, and the diameter of the impedance plot was directly related to the concentration of BPMMP...
November 15, 2017: Journal of Molecular Modeling
Ayyavoo Kalpana, Lakshminarayanan Akilandeswari
The cation-π interaction can be envisaged as a lewis acid base interaction, and it is in line with Pearson's acid base concept. The critical examination of interactions between the π-acids (alkali metal cations - Li(+), Na(+) and alkaline earth metal cations Mg(2+), Ca(2+)) on one face and tripodal Cr(CO)3 moiety on the other π face of substituted arenes demonstrates the role of cation and substitutents in manipulating the interactions between them. The interaction of the two π acids on both faces of arene is not expectedly additive, rather it shows either depreciation of interaction energy revealing the competition of acids toward the base or enhancement of interaction energy denoting a cooperative effect...
November 15, 2017: Journal of Molecular Modeling
Wei-Peng Lai, Tao Yu, Ying-Zhe Liu, Yi-Ding Ma, Peng Lian, Zhong-Xue Ge, Jian Lv
In order to discover more potential high energy compounds, five computer-aided design methods were founded, and 20 high energetic compounds based on the 1,2,3,4-tetrazine-1,3-dioxide frame were designed. The first step of computer-aided design methods was to design new frame M. Three combination rules were invented, they were simple double-points rule, complicated double-points rule, and complicated multi-points rule. The second step of computer-aided design methods was to design 1,2,3,4-tetrazine 1,3-dioxides derivants by connecting M to 1,2,3,4-tetrazine-1,3-dioxides...
November 9, 2017: Journal of Molecular Modeling
Ján Škoviera, Ivan Černušák, Florent Louis, Pavel Neogrády
Correlated ab initio methods [CASPT2 and R-CCSD(T)] in conjunction with the ANO-RCC basis sets in large contraction were used to calculate potential energy curves (PECs) of the ground and excited electronic states of CsH(+) (doublets and quartets) with the inclusion of the scalar relativistic effects and spin-orbit interaction. The ground X(2)Σ(+) state is a rather fragile van der Waals molecular ion. The binding energy of this X(2)Σ(+) state provided by both computational methods is estimated to be 0.02-0...
November 9, 2017: Journal of Molecular Modeling
S Calvo-Losada, J J Quirante
The regioselectivity of the dinuclear-Cu(I)-catalyzed version of the Huisgen reaction, abbreviated in this paper to Cu2AAC, was analyzed using quantum topological methods in order to study how the electronic charge distribution evolved along different reaction paths. Electronic densities were computed at the LC-wPBE/6-311++G(2d,2p)//LC-wPBE/6-311++G(d,p) level. The presence of two copper ions in the catalyst was found to lead to an electrophilic site in the external alkyne carbon that, in a generalized Sharpless-type mechanism, undergoes an initial donor-acceptor interaction with the azide molecule, but with an inverted electrophile-nucleophile pattern when compared with the corresponding mononuclear process (CuAAC)...
November 9, 2017: Journal of Molecular Modeling
Tomasz Sierański
Extremely extensive calculations of potential energy surfaces for the parallel-displaced configuration of pyridine dimer systems have been carried out using a dispersion-corrected density functional. Instead of focusing on stationary geometries these calculations provide much deeper insight into the "landscape" of the interaction energies of the particular systems-one can learn how the pyridine dimer stability changes along with various geometrical parameters. Other calculations such as natural bond orbital and energy decomposition have also been applied...
November 9, 2017: Journal of Molecular Modeling
Runtian Chu, Xueying Zhang, Lingpeng Meng, Yanli Zeng
For inorganic benzenes C3N3X3 and B3O3X3 (X = H, F, CN), the positive electrostatic potentials (π-hole) were discovered above and below the inorganic benzene ring center. Then, the π-hole interactions between the inorganic benzenes and NCH have been designed and investigated by MP2/aug-cc-pVDZ calculations. In this paper, the termolecular complexes B3O3X3···NCH···NCH, C3N3X3···NCH···NCH (X = H, F, CN) were also designed to illustrate the enhancing effects of the H···N hydrogen bond on the π-hole interactions...
November 8, 2017: Journal of Molecular Modeling
Nguyen Ngoc Ha, Ngo Tuan Cuong, Hoang Van Hung, Ha Manh Hung, Vu Quoc Trung
The conductive properties of polypyrrole chains doped with ClO4(-) or MoO4(2-) anions and the existence of polarons and bipolarons in these doped polypyrrole chains were investigated by performing computational calculations based on density functional theory (DFT). Doping with these anions was found to decrease the band gap of the polypyrrole. Theoretical calculations revealed that changing the type of oxidative agent applied does not affect the conversion of polypyrrole into a conducting polymer, but the conductivity of the doped polypyrrole does depend on the ratio of oxidant to polypyrrole...
November 8, 2017: Journal of Molecular Modeling
Yao Shu, Yong Yi, Jichuan Huo, Ning Liu, Ke Wang, Yingying Lu, Xiaochuan Wang, Zongkai Wu, Yuanjie Shu, Shaowen Zhang
The glass transition temperature (T g) and density of poly-(phthalazinone ether sulfone ketone) (PPESK A) were estimated by molecular dynamic (MD) simulation. A novel poly-(phthalazinone ether sulfone ketone) (PPESK B) was constructed by introducing nitrol and amini energetic groups into PPESK A, and T g and density were also simulated for PPESK B. The estimated T g values of PPESK A were very close to experimental results, while for PPESK B three estimated values differed by < 5 K. The interactions between explosives and polymer binders of polymer bonded explosives (PBXs) were simulated by MD...
November 7, 2017: Journal of Molecular Modeling
V S Anithaa, S Vijayakumar, M Sudha, R Shankar
The interaction of diketo and keto-enol form of thymine and uracil tautomers with acridine (Acr), phenazine (Phen), benzo[c]cinnoline (Ben), 1,10-phenanthroline (1,10-Phe), and 4,7-phenenthroline (4,7-Phe) intercalating drug molecules was studied using density functional theory at B3LYP/6-311++G** and M05-2×/6-311++G** levels of theory. From the interaction energy, it is found that keto-enol form tautomers have stronger interaction with intercalators than diketone form tautomers. On complex formation of thymine and uracil tautomers with benzo[c]cinnoline the drug molecules have high interaction energy values of -20...
November 6, 2017: Journal of Molecular Modeling
Mohammad Hadi Ghatee, Mohammad Mehdi Koleini
We used density functional theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulation to investigate the adsorption and bond formation of hydronium ion (H3O(+)) onto a [Formula: see text] calcite surface. For surface coverage of 25% to 100%, the nature of H3O(+) interaction was explored through electron density and energetics in the context of bond critical points. The adsorbate-adsorbent structure was studied by simulation of pair correlation function. The results revealed that dissociation into water molecule(s) and proton(s) complements H3O(+) ion(s) adsorbtion...
November 6, 2017: Journal of Molecular Modeling
M Salazar-Villanueva, A Bautista Hernandez, J Flores Mendez, A A Peláez Cid, S Valdez
DFT calculations were carried out in order to determine the electronic and structural properties of pentagonal Al n (I h and D 5d symmetries), Al n -CO, and Al n -NO clusters, where n = 7, 13, 19, 43, or 55 atoms. As n was increased, the bare clusters were found to exhibit a transition in electronic behavior (from semiconductor to conductor) at n = 43 atoms. Clusters with a bound CO or NO molecule also showed this behavior, although their HOMO-LUMO energy gaps were smaller than those for the corresponding bare clusters...
November 6, 2017: Journal of Molecular Modeling
Fahimeh Mehralian, Yaghoub Tadi Beni
Molecular dynamics simulations are conducted to investigate the buckling characteristics of functionalized carbon nanotubes (f-CNTs) under axial compression at various temperatures. The influences of functionalization, content of functional groups, chirality and diameter, as well as temperature on buckling response of pristine and functionalized CNTs are investigated. It is found that the buckling capacity of CNTs deteriorates drastically by functionalization, though the increase in the content of functional groups slightly enhances their stability...
November 4, 2017: Journal of Molecular Modeling
Jiacheng Yi, Hua Fang
The original version of this article unfortunately contained a mistake in Table 3. This correct Table 3 is given below.
November 3, 2017: Journal of Molecular Modeling
Ria Sinha Roy, Avijit Mondal, Prasanta K Nandi
The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below.
November 2017: Journal of Molecular Modeling
Jindřich Fanfrlík, Wiktor Zierkiewicz, Petr Švec, Zdeňka Růžičková, Jan Řezáč, Mariusz Michalczyk, Aleš Růžička, Danuta Michalska, Pavel Hobza
This paper presents a study of pnictogen bonding in a series of pyrazine•PnX5 (Pn = P, As, Sb and X = F, Cl, Br) complexes. The whole series was studied computationally. Moreover, the pyrazine complexes with PCl5 and SbCl5 were prepared and characterized experimentally. It was found that the Pn-N distances are only slightly elongated when compared to the sum of covalent radii. The conformation of PnX5 changed considerably upon the complex formation, which resulted in a significant change of the dipole moment of the PnX5 fragment and a considerably more positive σ-hole on the pnictogen atom...
October 30, 2017: Journal of Molecular Modeling
Ondřej Kroutil, Milan Předota, Martin Kabeláč
Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with water were described using charges scaled according to the electronic continuum correction approach with rescaling of nonbonded parameters (ECCR), and those descriptions of anion interactions were found to agree well with relevant AIMD and experimental results...
October 28, 2017: Journal of Molecular Modeling
Houshang Najafi, Saeed Changizi-Ashtiyani, Meysam Najafi
The antioxidant properties of omega-3 were investigated via experimental in vivo and theoretical methods. For experimental evaluation, oxidative stress was induced by 30 min bilateral renal ischemia and 24 h of reperfusion in male Sprague Dawley rats. The oxidative stress was evaluated through measuring malondialdehyde (MDA) and ferric reducing/antioxidant power (FRAP) levels in renal tissue. In theoretical methods, the reaction enthalpies of antioxidant mechanisms of omega-3 were calculated and the effects of NHMe, OMe, OH, Cl, and Me substituents on its antioxidant activity were investigated...
October 28, 2017: Journal of Molecular Modeling
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