Large-scale virtual screening for the identification of new Helicobacter pylori urease inhibitor scaffolds.

abstract：:The treatment of neuropathic pain is very complex and there are few drugs approved for this purpose. Among the studied compounds in the literature, sigma-1 receptor antagonists have shown to be promising. In order to develop QSAR studies applied to the compounds of 1-arylpyrazole derivatives, multivariate analyses hav...

journal_title：Journal of molecular modeling

authors： Oliveira AA,Lipinski CF,Pereira EB,Honorio KM,Oliveira PR,Weber KC,Romero RAF,de Sousa AG,da Silva ABF

更新日期：2017-10-02 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：:A 3D QSAR analysis has been performed on a series of 67 benzodiazepine analogues reported as gamma-secretase inhibitors using molecular field analysis (MFA), with G/PLS to predict steric and electrostatic molecular field interaction for the activity. The MFA study was carried out using a training set of 54 compounds. ...

journal_title：Journal of molecular modeling

authors： Sammi T,Silakari O,Ravikumar M

更新日期：2009-04-01 00:00:00

abstract：:The geometrical structure and electronic properties of bis(10-hydroxybenzo[h]quinolinato)beryllium (Bebq2) molecule and its dimer both in the neutral and in the positively and negatively charged states were studied using quantum-chemical calculations. It is found that the excess charge in the charged systems is locali...

journal_title：Journal of molecular modeling

authors： Safonov AA,Bagaturyants AA

更新日期：2014-08-01 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：: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：:We have examined the effects of substituents on the computed electrostatic potentials V(S)(r) and average local ionization energies I(S)(r) on the surfaces of model carbon nanotubes of the types (5,5), (6,1) and (6,0). For the (5,5) and the (6,1), the effects upon both V(S)(r) and I(S)(r) of substituting a hydroxyl gr...

journal_title：Journal of molecular modeling

authors： Politzer P,Murray JS,Lane P,Concha MC,Jin P,Peralta-Inga Z

更新日期：2005-09-01 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 nitrogen doping and phenyl substitution effects on the geometries, molecular stacking character, electronic, and charge transport properties of tetrabenzoheptacene (TTBH) have been investigated by means of density functional theory (DFT) calculation and incoherent charge hopping model. Our results indicate that th...

journal_title：Journal of molecular modeling

authors： Guan L,Wang W,Shao R,Liu F,Yin S

更新日期：2015-05-01 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：:Dirithromycin is a macrolide antibiotic derived from erythromycin A. Dirithromycin is synthesized by the condensation of 9(S)-erythromycylamine with 2-(2-methoxyethoxy)-acetaldehyde. To gain insight into the synthesis, the condensation mechanism has been analyzed computationally by the AM1 method in the gas phase. Fir...

journal_title：Journal of molecular modeling

authors： Duran D,Aviyente V,Baysal C

更新日期：2004-04-01 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：:Defects in the nanoscale are common in the 2D materials irrespective of the fabricated method. Material performance gets significantly affected due to the presence of defects in 2D materials. In the present study, electronic and mechanical properties of 2D-hexagonal boron nitride (hBN) are investigated. At the electro...

journal_title：Journal of molecular modeling

authors： Sagar TC,Chinthapenta V

更新日期：2020-07-03 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 ladder-type polyheterofluorenes were investigated theoretically by using density functional theory (DFT) to reveal their optical and electronic properties for applications in organic optoelectronic devices. The incorporation of heteroatoms (B, Si, Ge, N, P, O, and S) into the ladder-type highly fused polyfluorene ...

journal_title：Journal of molecular modeling

authors： Zheng C,Tao Y,Cao JZ,Chen RF,Zhao P,Wu XJ,Huang W

更新日期：2012-11-01 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：:Tuberculosis still remains one of the most deadly infectious diseases. The emergence of drug resistant strains has fuelled the quest for novel drugs and drug targets for its successful treatment. Thymidine monophosphate kinase (TMPK) lies at the point where the salvage and de novo synthetic pathways meet in nucleotide...

journal_title：Journal of molecular modeling

authors： Kumar M,Sharma S,Srinivasan A,Singh TP,Kaur P

更新日期：2011-05-01 00:00:00

abstract：:The average pull-out force and interaction energy of polyethylene (PE) cross-linked functionalized carbon nanotubes (cfCNTs) embedded in polymer matrices (PE-cfCNTs@polymers) was studied using molecular dynamics (MD) simulations. Accordingly, the pull-out process of PE-cfCNTs from inside polymer matrices, i.e., Aramid...

journal_title：Journal of molecular modeling

authors： Haghighi S,Ansari R,Ajori S

更新日期：2019-03-29 00:00:00

abstract：:B3LYP, PBE, M06-2X, B2PLYP, BN2PLYP-D, ωB97X-D, and MP2 levels of theory, in combination with the 6-311++G(d,p) and cc-pVTZ basis sets were comprehensively assessed for their ability to reproduce experimental FOX-7 structural and detonation data. ωB97X-D/cc-pVTZ, B3LYP/cc-pVTZ, and M06-2X/cc-pVTZ provided highly accur...

journal_title：Journal of molecular modeling

authors： Jeong K,Jeon Y,Kwon S

更新日期：2017-09-01 00:00:00

abstract：:A novel mechanism for switching a molecular junction based on a proton transfer reaction triggered by an external electrostatic field is proposed. As a specific example to demonstrate the feasibility of the mechanism, the tautomers [2,5-(4-hydroxypyridine)] and {2,5-[4(1H)-pyridone]} are considered. Employing a combin...

journal_title：Journal of molecular modeling

authors： Hofmeister C,Härtle R,Rubio-Pons O,Coto PB,Sobolewski AL,Thoss M

更新日期：2014-04-01 00:00:00

abstract：:Multicenter overlap integrals appearing in the evaluation of multicenter-multielectron integrals of central and noncentral interaction potentials are calculated using complete orthonormal sets of psi(alpha)-ETOs (alpha=1, 0, -1, -2,...). The final results are expressed in terms of two-center overlap integrals between ...

journal_title：Journal of molecular modeling

authors： Guseinov I,Aydin R,Mamedov B

更新日期：2003-10-01 00:00:00

abstract：:Mechanical properties of graphene- and carbon nanotube-reinforced Araldite LY 5052/Aradur HY 5052 epoxy resins were investigated by molecular dynamics simulations. The COMPASS II force field was implemented in the simulations. Mechanical properties of the reinforced araldite/aradur resin epoxy system with CNT reveal t...

journal_title：Journal of molecular modeling

authors： Faragi S,Hamedani A,Alahyarizadeh G,Minuchehr A,Aghaie M,Arab B

更新日期：2019-06-15 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：:Low temperature oxidation of CO to CO2 is an important process for the environment. Similarly adsorption of CO from the releasing sources is also of major concern today. Whereas the potential of gold and silver clusters is well proven for the catalysis of the above mentioned reaction, the potential of aluminum (Al) cl...

journal_title：Journal of molecular modeling

authors： Samanta B,Sengupta T,Pal S

更新日期：2018-12-06 00:00:00

abstract：:The removal of AsH3 from synthesis gas is crucial to prevent methanol synthesis catalyst from poisoning. In this work, Ti-, Mn-, Fe-, Co-, Ni-, Cu-, and Ag-doped graphene were proposed and their adsorption capabilities for AsH3 and CO were investigated by DFT method. The optimized structures, adsorption energies, elec...

journal_title：Journal of molecular modeling

authors： Li Y,Sun X,Zhou L,Ning P,Tang L

更新日期：2019-05-04 00:00:00

abstract：:The mechanism and origin of selectivity for [3 + 2]-cycloaddition (32CA) reactions between thioketone and carbohydrate-derived nitrones in THF were investigated by using the density functional theory (DFT) at the M06-2X/6-311+G(d,p)//M06-2X/6-31+G(d,p) level of theory combined with the solvation SMD model. The calcula...

journal_title：Journal of molecular modeling

authors： Yang J,Zhang Y,Yang Y,Xue Y

更新日期：2019-07-02 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：:In this work, we investigate the ground- and excited-state structures as well as the optical properties of a series of five formazanate dyes using state-of-the-art density-based and wavefunction-based methods. The present work is the first to evaluate the properties of formazanate-BF2 dyes with wavefunction-correlated...

journal_title：Journal of molecular modeling

authors： Laurent AD,Otten E,Le Guennic B,Jacquemin D

更新日期：2016-11-01 00:00:00

abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...

journal_title：Journal of molecular modeling

authors： Ortega E,Bernède JC,Ramírez AMR,Louarn G,Díaz FR,Cattin L,Del Valle MA

更新日期：2019-02-27 00:00:00

abstract：:In this work a molecular modeling study was carried out based on a series of organotin(IV) derivatives which were complexed with ONO-Donor type Schiff base ligands to build up a statistical data pool for researchers. For this purpose, various properties of the selected complexes such as energies, band gaps, chemical r...

journal_title：Journal of molecular modeling

authors： Şirikci G,Ancın NA,Öztaş SG

更新日期：2015-09-01 00:00:00