Computational dissection of allosteric inhibition of the SH2 domain of Bcr-Abl kinase by the monobody inhibitor AS25.

abstract：:We present a critical discussion related to the recent definition of the intrinsic reactivity index, IRI, (Tetrahedron Lett. 2013, 54, 339-342; Tetrahedron 2013, 69, 4247-4258) formulated to describe both, electrophilicity (charge acceptance) and nucleophilicity (charge donation) reactivities. We here stress that such...

journal_title：Journal of molecular modeling

authors： Chamorro E,Melin J

更新日期：2015-03-01 00:00:00

abstract：:We report the parameterization of AM1 for the elements palladium and silver. The basis sets for both metals contain one set each of s-, p- and d-orbitals. AM1 parameters are now available for H, C, N, O and F (which use the original AM1 parameters), Al, Si, P, S, Cl, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Br, Zr, Mo, Pd, ...

journal_title：Journal of molecular modeling

authors： Kayi H,Clark T

更新日期：2011-10-01 00:00:00

abstract：:The aqueous solvation of Th and Np in the IV oxidation state was examined using cluster models generated by Monte Carlo simulations and density functional theory embedded within the COSMO continuum model to approximate the effect of bulk water. Our results suggest that the coordination number (CN) for both Th(IV) and ...

journal_title：Journal of molecular modeling

authors： Amador DH,Sambrano JR,Gargano R,de Macedo LG

更新日期：2017-03-01 00:00:00

abstract：:Fine-tuning of magnetic states via an understanding of spin injection on the edge of graphene nanoribbons should allow for greater flexibility of the design of graphene-based spintronics. On the basis of calculations, we predict that coupling constants of the exchange interaction in the series of nitroxide-functionali...

journal_title：Journal of molecular modeling

authors： Morozov V,Tretyakov E

更新日期：2019-02-09 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：:CO2 reduction has attracted extensive attentions for its wide applications in chemical engineering and green chemistry. As one of major commercial catalysts, Cu have been widely studied considering its low price and high catalytic efficiency. However, previous studies were mostly focused on the Cu(111) surface, while ...

journal_title：Journal of molecular modeling

authors： Wang R,Zhu B,Zhang G,Gao Y

更新日期：2020-07-09 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：:Quantum chemical calculations are performed to study the interplay between halogen⋯nitrogen and halogen⋯carbene interactions in NCX⋯NCX⋯CH2 complexes, where X = F, Cl, Br and I. Molecular geometries and interaction energies of dyads and triads are investigated at the MP2/aug-cc-pVTZ level of theory. It is found that t...

journal_title：Journal of molecular modeling

authors： Esrafili MD,Mohammdain-Sabet F,Esmailpour P

更新日期：2013-11-01 00:00:00

abstract：:The present study analyzed binding of Cu(2+) to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches in...

journal_title：Journal of molecular modeling

authors： Czyżnikowska Z,Brasuń J

更新日期：2012-04-01 00:00:00

abstract：:The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain p...

journal_title：Journal of molecular modeling

authors： Ahmad F,Shabaz Z,Azam SS

更新日期：2020-08-03 00:00:00

abstract：:Molecular simulations were carried out to study the sodium dodecyl sulfate (SDS) surfactant with the interleukin 8 (IL8) protein as a model to investigate the influence of amphiphilic molecules on proteins. Simulations for an SDS micelle with an IL8 protein show that both aggregates, which were initially separated, ev...

journal_title：Journal of molecular modeling

authors： Dominguez H

更新日期：2017-07-01 00:00:00

abstract：:The geometric and electronic structure of tetracyanoethylene (TCNE)-aniline (donor-acceptor type) complex has been investigated in gas phase using ab initio and time dependent density functional theory calculations. Both the above calculations predict a composed structure for the complex, in which the interacting site...

journal_title：Journal of molecular modeling

authors： Manna T,Bhattacharya S

更新日期：2009-08-01 00:00:00

abstract：:Molecular-dynamics simulations have been used to study the diffusion of a short single model carbonic chain on the graphite (001) surface. The calculated diffusion coefficient (D) first increases, then decreases with increasing chain length (N). This abnormal behavior is similar to polymer lateral diffusion at the sol...

journal_title：Journal of molecular modeling

authors： Yang H,Lu ZY,Li ZS,Sun CC

更新日期：2006-03-01 00:00:00

abstract：:The mechanism of the thermal rearrangement of substituted N-acyl-2,2-dimethylaziridines 1 has been studied using quantum chemistry methods. Geometries of reactants, transition states and products have been optimized at the B3LYP/6-311++G(2d,2p) level. Relative energies for various stationary points have been determine...

journal_title：Journal of molecular modeling

authors： Arfaoui Y,Efrit ML,Besbes N

更新日期：2013-10-01 00:00:00

abstract：:A mechanical molecular rotation model for liquid crystal (LC) systems is employed to evaluate phase transition temperature of fluorinated phenylbicyclohexane isomeric LC compounds. Results show that when a fluorine atom is substituted along the molecular long axis, an LC molecule acquires high rotational speed and its...

journal_title：Journal of molecular modeling

authors： Ma H,Li ZX,Shi DH,Liu YF

更新日期：2008-11-01 00:00:00

abstract：:Corynebacterium pseudotuberculosis is a facultatively intracellular Gram-positive bacterium that causes caseous lymphadenitis, principally in sheep and goats, though sometimes in other species of animals, leading to considerable economic losses. This pathogen has a TCS known as PhoPR, which consists of a sensory histi...

journal_title：Journal of molecular modeling

authors： Moraes G,Azevedo V,Costa M,Miyoshi A,Silva A,da Silva V,de Oliveira D,Teixeira MF,Lameira J,Alves CN

更新日期：2012-03-01 00:00:00

abstract：:Nowadays, scientists are trying to develop low-cost fullerene free acceptors for small organic photovoltaic cells in order to overcome the limitations of fullerene derivatives. Current research work deals with theoretical study on three non-fullerene acceptors based on indaceno, dithiophene core, and thiophene bridge ...

journal_title：Journal of molecular modeling

authors： Ajmal M,Ali U,Javed A,Tariq A,Arif Z,Iqbal J,Shoaib M,Ahmed T

更新日期：2019-09-11 00:00:00

abstract：:The detailed decomposition mechanism of nitroglycerin (NG) in the gas phase was studied by examining reaction pathways using density functional theory (DFT) and canonical variational transition state theory combined with a small-curvature tunneling correction (CVT/SCT). The mechanism of NG autocatalytic decomposition ...

journal_title：Journal of molecular modeling

authors： Pei L,Dong K,Tang Y,Zhang B,Yu C,Li W

更新日期：2017-08-21 00:00:00

abstract：:Zeolites are a group of microporous aluminosilicate frameworks with numerous applications in, for example, catalysis and ion-exchange and sorption processes. One of the most important tools for analyzing the properties of zeolite structures is vibrational spectroscopy. However, the complexity of these structures often...

journal_title：Journal of molecular modeling

authors： Mikuła A,Król M,Koleżyński A

更新日期：2015-10-01 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：:In this article, we explore, both theoretically and experimentally, the general reactivity of alkyl hydrogeno-phenylphosphinates with alcohols. We show that alcohol molecules act exclusively as nucleophilic species, and add to alkyl hydrogeno-phenylphosphinates, leading to pentacoordinated intermediates. These interme...

journal_title：Journal of molecular modeling

authors： Javierre G,Fortrie R,Jean M,Moraleda D,Naubron JV,Fotiadu F

更新日期：2017-05-01 00:00:00

abstract：:Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and t...

journal_title：Journal of molecular modeling

authors： Zhang J,Wang Z,Zhu Z

更新日期：2013-12-01 00:00:00

abstract：:In this work, the molecular modeling method was performed to study adsorption interaction between PAMAM molecules of different generations and silicic acid molecules, and the inhibition effect on silica scale were discussed. The results show that adsorption energies of PAMAM molecule of generation 1.0 with amine-termi...

journal_title：Journal of molecular modeling

authors： Chen C,Bai N,Zhang Y,Jiao L,Xia M,Chen G

更新日期：2017-01-01 00:00:00

abstract：:The increase of multidrug-resistant strains of bacteria to known classes of antibiotics present a severe challenge for modern medicine. The most promising strategy to combat pathogenic bacteria is to discover new drug targets. In this regard, aminoacyl-tRNA synthetases are particularly well suited to develop novel dru...

journal_title：Journal of molecular modeling

authors： Hoffmann M,Torchala M

更新日期：2009-06-01 00:00:00

abstract：:Isothiocyanates (ITC) are well-known chemopreventive agents extracted from vegetables. This activity results from the activation of human oxidoreductase. In this letter, the uncompetitive activatory mechanism of ITC was investigated using docking and molecular dynamics simulations. This indicates that NAD(P)H:quinone ...

journal_title：Journal of molecular modeling

authors： Mazur P,Magdziarz T,Bak A,Chilmonczyk Z,Kasprzycka-Guttman T,Misiewicz-Krzemińska I,Skupińska K,Polanski J

更新日期：2010-07-01 00:00:00

abstract：:The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between ...

journal_title：Journal of molecular modeling

authors： Stojanović SD,Zarić BL,Zarić SD

更新日期：2010-11-01 00:00:00

abstract：:The UV absorption spectra of ten N,N'-bisarylmalonamides have been recorded in the range 200-400 nm in a set of selected solvents. The solute-solvent interactions have been analyzed on the basis of the linear solvation energy relationship (LSER) concept proposed by Kamlet and Taft. The effects of substituents on the a...

journal_title：Journal of molecular modeling

authors： Arsovski VM,Božić BĐ,Mirković JM,Vitnik VD,Vitnik ZJ,Fabian WM,Petrović SD,Mijin DZ

更新日期：2014-08-01 00:00:00

abstract：:Nitrogen-rich heterocycles and their nitro derivatives are one of the important classes of energetic materials. In the present study, the computational methods have been applied to determine the thermodynamic and detonation properties of nitro derivatives of BN indole molecule. Structure optimization and electronic en...

journal_title：Journal of molecular modeling

authors： Gupta S,Singh HJ

更新日期：2020-03-24 00:00:00

abstract：:Studies of the interaction between phenol and intrinsic graphene, as well as phenol and aluminum doped graphene layer are performed using first principles total energy calculations within the periodic density functional theory. A 4x4 periodic structure is used to explore the adsorption of a phenol molecule on the intr...

journal_title：Journal of molecular modeling

authors： Hernández JM,Anota EC,de la Cruz MT,Melchor MG,Cocoletzi GH

更新日期：2012-08-01 00:00:00

abstract：:A theoretical study of a series of five glucose based glycolipid crown ethers and their complexes with Na(+) and K(+) was performed using the density functional theory with B3LYP/6-31 G* to obtain the optimized geometrical structures and electronic properties. The local nucleophilicity of the five molecules was invest...

journal_title：Journal of molecular modeling

authors： Nguan H,Ahmadi S,Hashim R

更新日期：2012-12-01 00:00:00