DFT analysis of the interaction between Hg2+ and monodentate neutral ligands using NBO, EDA, and QTAIM.

abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,Kieninger M,Ventura ON

更新日期：2017-12-05 00:00:00

abstract：:The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, repr...

journal_title：Journal of molecular modeling

authors： Perdih A,Bren U,Solmajer T

更新日期：2009-08-01 00:00:00

abstract：:The electron transport of the 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate (S-FNPPB-o) molecule assembled in two Au (111) electrodes, was studied using two approaches: in the first approximate approach an electric field was applied to the pure molecule attached to two thiolate ends fi...

journal_title：Journal of molecular modeling

authors： Serrato-Villegas L,Gallo M,Delgado-Ríos M,Romero MT,Glossman-Mitnik D

更新日期：2012-02-01 00:00:00

abstract：:Density functional theory investigations at the DFT-B3LYP/6-311++G** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH3, 4-R-F, 4-R-NO2) in the selected solvent (acetone, acetonitrile...

journal_title：Journal of molecular modeling

authors： Shiroudi A,Safaei Z,Kazeminejad Z,Repo E,Pourshamsian K

更新日期：2020-02-13 00:00:00

abstract：:The double-histone fold is a rare protein fold in which two consecutive regions characterized by the typical structure of histones assemble together, thus giving a histone pseudodimer. Previously, this fold was found in a few prokaryotic histones and in the regulatory region of guanine-nucleotide exchange factors of t...

journal_title：Journal of molecular modeling

authors： Greco C,Sacco E,Vanoni M,De Gioia L

更新日期：2005-12-01 00:00:00

abstract：:The crystal structure of the human cystatin C (hCC) dimer revealed that a stable twofold-symmetric dimer was formed via 3D domain swapping. Domain swapping with the need for near-complete unfolding has been proposed as a possible route for amyloid fibril initiation. Thus, the interesting interactions that occur betwee...

journal_title：Journal of molecular modeling

authors： He J,Xu L,Zhang S,Guan J,Shen M,Li H,Song Y

更新日期：2013-02-01 00:00:00

abstract：:A theoretical study of the chemisorption and dissociation pathways of water on the Al₁₃ cluster was performed using the hybrid density functional B3LYP method with the 6-311+G(d, p) basis set. The activation energies, reaction enthalpies, and Gibbs free energy of activation for the reaction were determined. Calculatio...

journal_title：Journal of molecular modeling

authors： Zhao JY,Zhao FQ,Gao HX,Ju XH

更新日期：2013-04-01 00:00:00

abstract：:The effects of substituting nitrogen atoms on the stability of novel singlet (s) and triplet (t) forms of germylenes (1-20) are compared and contrasted, at B3LYP/AUG-cc-pVTZ level of theory. Every one of the 40 new divalents scrutinized appears as a minimum on its energy surface, for showing no negative force constant...

journal_title：Journal of molecular modeling

authors： Abedini N,Kassaee MZ

更新日期：2020-10-31 00:00:00

abstract：:The functionalization of pristine and Stone-Wales defected BC3 nanosheets with a pyrene molecule was investigated using density functional theory. Frontier molecular analysis shows that the main interaction is π-π stacking, releasing energies in the range of 143.6 to 169.1 kJ mol(-1). We predicted that after the funct...

journal_title：Journal of molecular modeling

authors： Peyghan AA,Noei M,Bagheri Z

更新日期：2014-12-01 00:00:00

abstract：:We report results of numerical simulations of complex fluids, using a combination of discrete-particle methods. Our molecular modeling repertoire comprises three simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD), and the fluid particle model (FPM). This type of model can depict multi-...

journal_title：Journal of molecular modeling

authors： Dzwinel W,Yuen DA,Boryczko K

更新日期：2002-01-01 00:00:00

abstract：:Tetrachlorodibenzodioxin (TCDD) is one of the most famous dioxin families that is hazardous to humans and the environment. Designing cheap and novel catalysts for its detecting and removing is an essential need for the environment. In this work, DFT + VdW is used to investigate the potentiality of proposed catalysts i...

journal_title：Journal of molecular modeling

authors： Behjatmanesh-Ardakani R,Heydari A

更新日期：2020-06-03 00:00:00

abstract：:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...

journal_title：Journal of molecular modeling

authors： Swart M,van der Wijst T,Fonseca Guerra C,Bickelhaupt FM

更新日期：2007-12-01 00:00:00

abstract：:This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...

journal_title：Journal of molecular modeling

authors： Esrafili MD,Vakili M,Solimannejad M

更新日期：2014-02-01 00:00:00

abstract：:Hydrogenoxalate (charge -1) and oxalate (charge -2) anions and their solvated forms were studied by various computational techniques. Ab initio quantum chemical calculations in gas phase, in implicit solvent and microsolvated (up to 32 water molecules) environment were performed in order to explore a potential energy ...

journal_title：Journal of molecular modeling

authors： Kroutil O,Minofar B,Kabeláč M

更新日期：2016-09-01 00:00:00

abstract：:The nature and strength of intermolecular Se⋯N interaction between selenium-containing compounds HSeX (X = CH3, NH2, CF3, OCH3, CN, OH, NO2, Cl, F), and NH3 have been investigated at the MP2/aug-cc-pVDZ level. The Se⋯N interaction is found to be dependent on the substituent groups, which greatly affect the positive el...

journal_title：Journal of molecular modeling

authors： Zhou F,Liu R,Tang J,Li P,Cui Y,Zhang H

更新日期：2016-01-01 00:00:00

abstract：:The interactions between chemosensors, donor-π-acceptor (D-π-A) dipolar organoboron derivatives, and different (CN⁻, F⁻, Cl⁻, and Br⁻) anions have been theoretically investigated using DFT approaches. Theoretical investigations have been performed to explore the optical, electronic, charge transport, and stability pro...

journal_title：Journal of molecular modeling

authors： Jin R,Tang S,Luo D

更新日期：2014-03-01 00:00:00

abstract：:It is well-established that many covalently-bonded atoms of Groups IV-VII have directionally-specific regions of positive electrostatic potential (σ-holes) through which they can interact with negative sites. In the case of Group VII, this is called "halogen bonding." We have studied two series of molecules: the F3MX ...

journal_title：Journal of molecular modeling

authors： Bundhun A,Ramasami P,Murray JS,Politzer P

更新日期：2013-07-01 00:00:00

abstract：:HP1γ, a non-histone chromatin protein, has elicited significant attention because of its role in gene silencing, elongation, splicing, DNA repair, cell growth, differentiation, and many other cancer-associated processes, including therapy resistance. These characteristics make it an ideal target for developing small d...

journal_title：Journal of molecular modeling

authors： Velez G,Lin M,Christensen T,Faubion WA,Lomberk G,Urrutia R

更新日期：2016-01-01 00:00:00

abstract：:We present an ab initio based molecular mechanics model for prominent additives used in lubricants to moderate oil-steel interfaces. The force field is created for zinc dialkyldithiophosphate and calcium sulfonate charge neutral ligand-ion-ligand complexes and benchmarked to the widely spread generalized amber force f...

journal_title：Journal of molecular modeling

authors： Ectors P,Zahn D

更新日期：2019-03-25 00:00:00

abstract：:The nuclear magnetic shieldings of Si, Ge, and Sn in MH(4-n) Y(n) (M = Si, Ge, Sn; Y = F, Cl, Br, I and n = 1-4) molecular systems are highly influenced by the substitution of one or more hydrogens by heavy-halogen atoms. We applied the linear response elimination of small components (LRESC) formalism to calculate tho...

journal_title：Journal of molecular modeling

authors： Maldonado AF,Aucar GA,Melo JI

更新日期：2014-09-01 00:00:00

abstract：:The mechanism of C-H bond activation of ethane was catalyzed by palladium halide cations (PdX+ (X = F, Cl, Br, H, and CH3)), which was investigated using density functional theory (DFT) at B3LYP level. The reaction mechanism was taken into account in triplet and singlet spin state potential energy surfaces. For PdF+, ...

journal_title：Journal of molecular modeling

authors： Nie YX,Zhang XX,Yuan YN,Lu F,Geng ZY

更新日期：2020-04-03 00:00:00

abstract：:Theoretical investigation of Pt(0)-olefin organometallic complexes containing tertiary phosphine ligands was focused on the strength of platinum-olefin electronic interaction. DFT theoretical study of electronic effects in a substantial number of ethylene derivatives was evaluated in terms of the Pt-olefin binding ene...

journal_title：Journal of molecular modeling

authors： Karhánek D,Kacer P,Kuzma M,Splíchalová J,Cervený L

更新日期：2007-09-01 00:00:00

abstract：:Since the three-dimensional structure of the NMDA receptor has not been determined experimentally, indirect computer-assisted molecular modeling techniques appear to be of great usefulness in the characterization of the common pharmacophore of all NMDA receptor noncompetitive antagonists, despite their structural diff...

journal_title：Journal of molecular modeling

authors： Elhallaoui M,Laguerre M,Carpy A,Ouazzani FC

更新日期：2002-02-01 00:00:00

abstract：:We examine a short way to reach an exceptional point that corresponds to a coalescence of two resonance energies. The application concerns the photodissociation of the Na2 molecule exposed to a laser field. In this case, the resonances can be correlated with the field-free vibrational states of the diatomic species. T...

journal_title：Journal of molecular modeling

authors： Lefebvre R,Atabek O

更新日期：2013-05-01 00:00:00

abstract：:The ternary complexes ML∙∙∙PyZX2∙∙∙NH3 (ML = CuCl, CuCN, AgCN, and AuCN; Z = P, As, and Sb; X = H and F) have been investigated with quantum chemical calculations. The results showed that the existence of coordination interaction has a prominent enhancing effect on the strength of pnicogen bonding. Even in ML∙∙∙PySbH2...

journal_title：Journal of molecular modeling

authors： Tang Q,Li Q

更新日期：2016-03-01 00:00:00

abstract：:Ab initio and molecular simulation methods were used in calculations of the neutral individual betulin molecule, and molecular simulations were used to optimize the betulin molecule immersed in various amounts of water. Individual betulin was optimized in different force fields to find the one exhibiting best agreemen...

journal_title：Journal of molecular modeling

authors： Pospíšil M,Kovář P,Vácha R,Svoboda M

更新日期：2012-01-01 00:00:00

abstract：:Thermotropic polyurethanes with mesogenic groups in side chains were prepared from two diisocyanates and four diols with stoichiometric ratios of reactive isocyanate (NCO) and hydroxy (OH) groups. Their thermal behavior was determined by differential scanning calorimetry. The effect of structure modifications of the d...

journal_title：Journal of molecular modeling

authors： Repáková J,Capková P,Studenovský M,Ilavský M

更新日期：2004-08-01 00:00:00

abstract：:Density functional theory (DFT) has been applied to understand the influence of various linkages on the energetic properties and stability of the polynitro-biphenyl compounds. Structures were optimized using the B3PW91/6-31G(d,p) level, and the heats of formation (HOFs) were computed by employing the selected isodesmi...

journal_title：Journal of molecular modeling

authors： Nirwan A,Devi A,Ghule VD

更新日期：2019-09-15 00:00:00

abstract：:ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since stru...

journal_title：Journal of molecular modeling

authors： Hsu HJ,Fischer WB

更新日期：2012-02-01 00:00:00

abstract：:Molecular-dynamics (MD) simulations of urea crystals of different shapes (cubic, rectangular prismatic, and sheet) have been performed using our previously published force field for urea. This force field has been validated by calculating values for the cohesive energy, sublimation temperature, and melting point from ...

journal_title：Journal of molecular modeling

authors： Özpınar GA,Beierlein FR,Peukert W,Zahn D,Clark T

更新日期：2012-08-01 00:00:00