DFT study on tautomerism and natural bond orbital analysis of 4-substituted 1,2,4-triazole and its derivatives: solvation and substituent effects.

abstract：:Complexes F2XO∙∙∙HCN (X = C and Si) have been studied by quantum chemical calculations at the MP2/aug-cc-pVTZ level to investigate the competition between π-hole interaction and hydrogen bond. F2XO has a dual role of a Lewis acid and base with the π-hole on the X atom and the O atom to participate in the π-hole intera...

journal_title：Journal of molecular modeling

authors： Guo X,Cao L,Li Q,Li W,Cheng J

更新日期：2014-11-01 00:00:00

abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...

journal_title：Journal of molecular modeling

authors： Ravna AW,Sylte I,Dahl SG

更新日期：2009-10-01 00:00:00

abstract：:Metallo-β-lactamases (MβLs) can hydrolyze and deactivate lactam-containing antibiotics, which are the major mechanism to cause drug resistance in the treatment of bacterial infections. This has become a global concern due to the lack of clinically approved inhibitors so far. SMB-1 from Serratia marcescents is a novel ...

journal_title：Journal of molecular modeling

authors： Mu X,Xu D

更新日期：2020-03-07 00:00:00

abstract：:The generation of the highly reactive ylide in thiamin diphosphate catalysis is analyzed in terms of the nucleophilicity of key atoms, by means of density functional calculations at X3LYP/6-31++G(d,p) level of theory. The Fukui functions of all tautomeric/ionization forms are calculated in order to assess their reacti...

journal_title：Journal of molecular modeling

authors： Jaña GA,Delgado EJ

更新日期：2013-09-01 00:00:00

abstract：:Hydrogen dissociative chemisorption and desorption on small lowest energy Ni(n) clusters up to n=13 as a function of H coverage was studied using density functional theory. H adsorption on the clusters was found to be preferentially at edge sites followed by 3-fold hollow sites and on-top sites. The minimum energy pat...

journal_title：Journal of molecular modeling

authors： Zhou C,Yao S,Zhang Q,Wu J,Yang M,Forrey RC,Cheng H

更新日期：2011-09-01 00:00:00

abstract：:Matrix metalloproteinase-8 (MMP-8) is the key mediator in initiating type I collagen degradation and is associated with rheumatoid arthritis. In the present study, a pharmacophore hypothesis was developed based on selective non zinc binding inhibitors of MMP-8. The pharmacophore hypothesis was refined manually and val...

journal_title：Journal of molecular modeling

authors： Kalva S,Vinod D,Saleena LM

更新日期：2014-05-01 00:00:00

abstract：:In order to introduce effectively the external electric fields into the explosive systems, the change trends of the strengths of trigger linkages, nitro group charges, and explosive sensitivities of 1,4-dinitroimidazole-N-oxide (1,4-DNIO) were investigated in the external electric fields at the B3LYP/6-311++G(2d,p) an...

journal_title：Journal of molecular modeling

authors： Wang BG,Ren FD,Wang Y

更新日期：2019-11-28 00:00:00

abstract：:There is evidence that Tetracyclines are potentially useful drugs to treat prion disease, the fatal neurodegenerative disease in which cellular prion proteins change in conformation to become a disease-specific species (PrP(Sc)). Based on an in vitro anti-fibrillogenesis test, and using the peptide PrP106-126 in the p...

journal_title：Journal of molecular modeling

authors： Cosentino U,Pitea D,Moro G,Saracino GA,Caria P,Varì RM,Colombo L,Forloni G,Tagliavini F,Salmona M

更新日期：2008-10-01 00:00:00

abstract：:Very recently, an unprecedented novel monometallic cluster of fullerenes entrapping a yttrium cyanide (YCN) cluster inside a popular C82 cage YCN@Cs(6)-C82 was synthesized and characterized. Inspired by this investigation, four non-IPR YCN@C1(17459)-C76, YCN@C2v(19138)-C76, YCN@C2(17646)-C76, and YCN@C1(17894)-C76 (1,...

journal_title：Journal of molecular modeling

authors： Gao FW,Xu HL,Su ZM

更新日期：2016-08-01 00:00:00

abstract：:Proteins in the gas phase present an extreme (and unrealistic) challenge for self-consistent-field iteration schemes because their ionized groups are very strong electron donors or acceptors, depending on their formal charge. This means that gas-phase proteins have a very small band gap but that their frontier orbital...

journal_title：Journal of molecular modeling

authors： Wick CR,Hennemann M,Stewart JJ,Clark T

更新日期：2014-03-01 00:00:00

abstract：:Thermodynamic integration (TI) molecular dynamics (MD) simulations for the binding of a pair of a reference ("ref") ligand and an analogous ("analog") ligand to either tagged (with six extra residues at the N-terminus) or untagged p38 kinase proteins were carried out in order to probe how the binding affinity is influ...

journal_title：Journal of molecular modeling

authors： Sun YC,Hsu WC,Hsu CJ,Chang CM,Cheng KH

更新日期：2015-11-01 00:00:00

abstract：:49Ti chemical shifts for a total of 20 titanium complexes are reported, and several levels of theory are evaluated in order to identify a reliable approach for the calculation of titanium NMR data. The popular B3LYP/6-31G(d)//B3LYP/6-31G(d) proves to give very good agreement with experimental data over a range from 1,...

journal_title：Journal of molecular modeling

authors： Koch R,Bruhn T

更新日期：2006-07-01 00:00:00

abstract：:Hepatic fibrosis is a common complication of the infection by the parasite, Clonorchis sinensis. There is a high incidence of this disease in the Asian countries with an increased risk of conversion to cancer. A secretory phospholipase A(2) (PLA(2)) enzyme from the parasite is implicated in the pathology. This is an a...

journal_title：Journal of molecular modeling

authors： Hariprasad G,Kaur P,Srinivasan A,Singh TP,Kumar M

更新日期：2012-07-01 00:00:00

abstract：:Recent experiments have confirmed the importance of nuclear quantum effects even in large biomolecules at physiological temperature. Here we describe how the path integral formalism can be used to describe rigorously the nuclear quantum effects on equilibrium and kinetic properties of molecules. Specifically, we expla...

journal_title：Journal of molecular modeling

authors： Zimmermann T,Vaníček J

更新日期：2010-11-01 00:00:00

abstract：:Cation-π interactions are known to be one of the strongest noncovalent forces in the gas phase, but they rarely occur in a fully solvated environment. The present work used two different ab initio molecular dynamics-based approaches to describe the correlation between the strength of the cation-π interactions and the ...

journal_title：Journal of molecular modeling

authors： Larrucea J

更新日期：2012-09-01 00:00:00

abstract：:The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The pref...

journal_title：Journal of molecular modeling

authors： Bekri L,Zouaoui-Rabah M,Springborg M,Rahal MS

更新日期：2018-10-10 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：:Six nitramines (N1-6) were designed with all possible arrangements of N-NO2 groups on a cyclic skeleton and structural optimization was performed using the density functional theory (DFT). We observed that all nitramines have high positive heats of formation proportionate to the number of N-NO2 groups in their molecul...

journal_title：Journal of molecular modeling

authors： Devi A,Deswal S,Dharavath S,Ghule VD

更新日期：2015-11-01 00:00:00

abstract：:In this work, a computational framework is proposed by utilizing molecular dynamics simulation to explore the existing relation between molecular structure and ionic conductivity of the electrolyte system [LiPF6+(EC+DMC 1:1)] consisting of a mixture of cyclic ethylene carbonate (EC) and acyclic dimethyl carbonate (DMC...

journal_title：Journal of molecular modeling

authors： Haghkhah H,Ghalami Choobar B,Amjad-Iranagh S

更新日期：2020-08-01 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：:In this work we present the results of a study of the X-ray structure of 2-[(2,4-dimethoxyphenyl)amino]-1,3-thiazolidin-4-one. Using the FTIR spectra in solid state and results of ab initio calculations we explain the issue of the tautomerism of this molecule. The compound is shown to exist as the 2-amino tautomer rat...

journal_title：Journal of molecular modeling

authors： Nowaczyk A,Kowiel M,Gzella A,Fijałkowski L,Horishny V,Lesyk R

更新日期：2014-08-01 00:00:00

abstract：:In this work, the poly(ethylene oxide) bulk as one example has been iteratively heated and cooled back using MD simulations to examine the effects of thermal history on the resulting Tg. It is demonstrated that, after the system is equilibrated once at the high temperatures, the simulated Tg does not exhibit a systema...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2017-08-22 00:00:00

abstract：:The structures of the 4,4',4″-tris(N,N-phenyl-3-methylphenylamino)triphenylamine (m-MTDATA) molecule and its dimer in their neutral and positively charged forms were studied by performing quantum-chemical calculations at the Hartree-Fock (HF) and density functional theory (DFT) levels of theory using several exchange-...

journal_title：Journal of molecular modeling

authors： Safonov A,Rykova E,Bagaturyants A

更新日期：2018-11-28 00:00:00

abstract：:Iridium (III) 2-phenylpyridine (ppy) complexes with two suitable monodentate L ligands [Ir(ppy)₂(L)₂]⁺ (ppy = 2-phenylpyridine, py = pyridine, L = 4-pyCN 1, 4-pyCHO 2, 4-pyCl 3, py 4, 4-pyNH₂ 5) were studied by density functional theory (DFT) and time-dependent DFT methods. The influences of ligands L on the electroni...

journal_title：Journal of molecular modeling

authors： Zhang TT,Qi XX,Jia J,Wu HS

更新日期：2012-10-01 00:00:00

abstract：:The ability to accurately predict the oxidation and reduction potentials of molecules is very useful in various fields and applications. Quantum mechanical calculations can be used to access this information, yet sometimes the usefulness of these calculations can be limited because of the computational requirements fo...

journal_title：Journal of molecular modeling

authors： Méndez-Hernández DD,Tarakeshwar P,Gust D,Moore TA,Moore AL,Mujica V

更新日期：2013-07-01 00:00:00

abstract：:Various kinetic studies of the addition of hydrogen halides to alkenes were carried out in the 1930s, 1940s, and 1970s. Since then, there have been theoretical analyses of several aspects of alkene reactivity and regioselectivity during hydrohalogenation. A few works have studied the influence of the hydrogen halide w...

journal_title：Journal of molecular modeling

authors： Firme CL

更新日期：2019-04-25 00:00:00

abstract：:BsoBI is a type II restriction endonuclease belonging to the EcoRI family. There is only one previously published X-ray structure for this endonuclease: it shows a homodimer of BsoBI completely encircling DNA in a tunnel. In this work, molecular dynamics simulations were employed to elucidate possible ways in which DN...

journal_title：Journal of molecular modeling

authors： Štěpán J,Kabelka I,Koča J,Kulhánek P

更新日期：2017-12-20 00:00:00

abstract：:Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C(4)H(9)•) with oxygen (O(2)). On the calculated potential energy surface, the addition of O(2) to C(4)H(9)• forms three intermediates barrierlessly, which can undergo subsequent i...

journal_title：Journal of molecular modeling

authors： Du HC,Gong XD

更新日期：2012-05-01 00:00:00

abstract：:The CO and O2 adsorption as well as CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd, Ag) are studied by density functional calculations. Our results show that CO and O2 are adsorbed more stably on AuPd dimers than on AuAg dimers with corresponding charge state. O2 is favorable to be adsorbed on Pd at...

journal_title：Journal of molecular modeling

authors： Chen X,Lu RF,Kan EJ,Liu YZ,Xiao CY,Deng KM

更新日期：2014-06-01 00:00:00

abstract：:The aquatic leech, Theromyzon tessulatum, secretes a proteinaceous cocoon with extraordinary physical properties (e.g., proteolytic, thermal resiliency). The deduced amino acid sequence of a major protein (Tcp-Theromyzon cocoon protein) from the T. tessulatum cocoon wall has been used to model the endogenous structure...

journal_title：Journal of molecular modeling

authors： Mason TA,McIlroy PJ,Shain DH

更新日期：2006-09-01 00:00:00