Molecular dipole effects on tuning electron transfer in a porphine-quinone complex: a DFT and TDDFT study.

abstract：:This work presents a theoretical study of gallium arsenide (GaAs) nanotubes obtained from the (100), (110) and (111) crystal planes of zincblende structure in order to evaluate the electronic properties. The DFT/B3LYP/6-31G method was used to predict structures and stabilities. It was found that nanotubes from the (11...

journal_title：Journal of molecular modeling

authors： Silva JCF,Dos Santos JD,Taft CA,Martins JBL,Longo E

更新日期：2017-07-01 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：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...

journal_title：Journal of molecular modeling

authors： da Silva WB,Albernaz AF,Barreto PR,Correa E

更新日期：2017-04-01 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 hydration free energies, structures, and dynamics of open- and closed-shell trivalent lanthanide and actinide metal cations are studied using molecular dynamics simulations (MD) based on a polarizable force field. Parameters for the metal cations are derived from an ab initio bottom-up strategy. MD simulations of ...

journal_title：Journal of molecular modeling

authors： Marjolin A,Gourlaouen C,Clavaguéra C,Ren PY,Piquemal JP,Dognon JP

更新日期：2014-10-01 00:00:00

abstract：:The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (...

journal_title：Journal of molecular modeling

authors： Gupta DC,Bhat IH

更新日期：2013-12-01 00:00:00

abstract：:The halogen bonding interactions between C6F5I and a series of transition metal monohalides trans-[M(X)(2-C5NF4)-(PR3)2] (M = Ni, Pd, Pt; X = F, Cl, Br; R = Me, Cy) have been studied with quantum chemical calculations. Optimized geometries of the halogen bonding complexes indicate that angles C1-I···X are basically li...

journal_title：Journal of molecular modeling

authors： Cheng N,Liu Y,Zhang C,Liu C

更新日期：2013-09-01 00:00:00

abstract：:Nanosecond molecular dynamics using the Ewald summation method have been performed to elucidate the structural and energetic role of the closing base pair in loop-loop RNA duplexes neutralized by Mg2+ counterions in aqueous phases. Mismatches GA, CU and Watson-Crick GC base pairs have been considered for closing the l...

journal_title：Journal of molecular modeling

authors： Golebiowski J,Antonczak S,Fernandez-Carmona J,Condom R,Cabrol-Bass D

更新日期：2004-12-01 00:00:00

abstract：:Membranolytic anticancer peptides (ACPs) are drawing increasing attention as potential future therapeutics against cancer, due to their ability to hinder the development of cellular resistance and their potential to overcome common hurdles of chemotherapy, e.g., side effects and cytotoxicity. In this work, we present ...

journal_title：Journal of molecular modeling

authors： Grisoni F,Neuhaus CS,Hishinuma M,Gabernet G,Hiss JA,Kotera M,Schneider G

更新日期：2019-04-05 00:00:00

abstract：:Meta-hybrid density functional theory calculations using M06-2X/6-31+G(d,p) and M06-2X/6-311+G(d,p) levels of theory have been performed to understand the strength of C-H(…)π interactions of two possible types for benzene-acetylene, 1,3,5-trifluorobenzene-acetylene and coronene-acetylene complexes. Our study reveals t...

journal_title：Journal of molecular modeling

authors： Dinadayalane TC,Paytakov G,Leszczynski J

更新日期：2013-07-01 00:00:00

abstract：:In this work, the low-lying states of several isomers of ScSi n-/0 (n = 4-6) were investigated with the B3LYP functional and CASPT2 method. The ground states of the anionic clusters were predicted to be the singlet states of the trigonal bipyramid ScSi4- (A-ScSi4-), the face-capped trigonal bipyramid ScSi5- (A-ScSi5-)...

journal_title：Journal of molecular modeling

authors： Nguyen MT,Tran QT,Tran VT

更新日期：2017-09-20 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：:Comprehensive molecular dynamics simulations are conducted to identify material modifications which can improve strength and reduce hysteresis losses at the nanointerfaces formed between silica, silane coupling agent (SCA) and styrene-butadiene rubber (SBR), all of which are important ingredients of green tyres. Impro...

journal_title：Journal of molecular modeling

authors： Joseph E,Swaminathan N,Kannan K

更新日期：2020-08-17 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：:CD44 is a cell-surface glycoprotein and receptor for hyaluronan, one of the major components of the tumor extracellular matrix. There is evidence that the interaction between CD44 and hyaluronan promotes breast cancer metastasis. Recently, the molecule F-19848A was shown to inhibit hyaluronan binding to receptor CD44 ...

journal_title：Journal of molecular modeling

authors： Nguyen TT,Tran DP,Pham Dinh Quoc Huy,Hoang Z,Carloni P,Van Pham P,Nguyen C,Li MS

更新日期：2016-07-01 00:00:00

abstract：:4-hydroxybenzoate oligoprenyltransferase of E. coli, encoded in the gene ubiA, is an important key enzyme in the biosynthetic pathway to ubiquinone. It catalyzes the prenylation of 4-hydroxybenzoic acid in position 3 using an oligoprenyl diphosphate as a second substrate. Up to now, no X-ray structure of this oligopre...

journal_title：Journal of molecular modeling

authors： Bräuer L,Brandt W,Wessjohann LA

更新日期：2004-12-01 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：:Understanding the interactions of the cage molecules with a variety of invited molecules is getting very important. But, the hydrogen bonds can also play a crucial role in the interaction phenomenon. In this work, natural population analysis (NPA), chemical shifts, and atom in molecules (AIM) analysis have been used t...

journal_title：Journal of molecular modeling

authors： Gassoumi B,Chaabene M,Ghalla H,Chaabane RB

更新日期：2019-12-13 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：: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

abstract：:In this work, the spectroscopic information, stability and aromaticity of the boron-nitrogen azulene and naphthalene molecules are provided by the use of CC2 (geometry optimization, dipole moment, UV-vis spectrum calculations) and DFT (vibrational spectrum and NMR calculations) methodologies. One isomer of the investi...

journal_title：Journal of molecular modeling

authors： Catão AJ,López-Castillo A

更新日期：2017-04-01 00:00:00

abstract：:The DFT potential energy hypersurfaces of closed-shell nitrogen clusters up to ten atoms are explored via a genetic algorithm (GA). An atom-atom distance threshold parameter, controlled by the user, and an "operator manager" were added to the standard evolutionary procedure. Both B3LYP and PBE exchange-correlation fun...

journal_title：Journal of molecular modeling

authors： Silva MX,Silva FT,Galvão BRL,Braga JP,Belchior JC

更新日期：2018-07-07 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：:In the present work, we applied density functional theory and temperature-dependent Gibbs free energy calculations to wurtzoid structures to explain the sensitivity of ZnO nanocrystals towards chlorine molecules. In agreement with experimental findings, our results revealed that chlorine sensing under ambient conditio...

journal_title：Journal of molecular modeling

authors： Abdulsattar MA

更新日期：2017-04-01 00:00:00

abstract：:Periplasmic binding proteins are the initial receptors for the transport of various substrates over the inner membrane of gram-negative bacteria. The binding proteins are composed of two domains, and the substrate is entrapped between these domains. For several of the binding proteins it has been established that a cl...

journal_title：Journal of molecular modeling

authors： Siuda I,Thøgersen L

更新日期：2013-11-01 00:00:00

abstract：:We have used density-functional theory to investigate the neighboring-group stabilization of iodine, arsenic, and phosphorus-centered oxyanion moieties in species such as deprotonated 2-iodoxybenzoic acid (IBX) and its analogs. The magnitudes of different stabilizing effects and further candidates for analogous stabil...

journal_title：Journal of molecular modeling

authors： O'Hair RA,Williams CM,Clark T

更新日期：2010-03-01 00:00:00

abstract：: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...

journal_title：Journal of molecular modeling

authors： Mehralian F,Tadi Beni Y

更新日期：2017-11-04 00:00:00

abstract：:High-level quantum chemical techniques have been utilized to accurately describe the geometrical parameters, vibrational frequencies and dissociation pathways of the X (2)A″, 1 (2)A', 2 (2)A', 2 (2)A″ states of S(2)Cl; X (1)A', 1 (3)A″, 1 (1)A″, 1 (3)A' states of S(2)Cl(+); X (1)A', 1 (3)A', (1)A″ states of S(2)Cl(-),...

journal_title：Journal of molecular modeling

authors： Czernek J,Zivný O

更新日期：2012-09-01 00:00:00

abstract：:Quantum chemical calculations on the isomerization of 24-methylenecycloartanol are described. An energetically viable mechanism, with a rate-determining protonation step, is proposed. This rearrangement may find applicability in tests for determining if an olive oil has been refined. ...

journal_title：Journal of molecular modeling

authors： Wedler HB,Pemberton RP,Lounnas V,Vriend G,Tantillo DJ,Wang SC

更新日期：2015-05-01 00:00:00

abstract：:A molecular modeling strategy is proposed to describe the temperature (T) dependence of solubility parameter (δ) for the amorphous polymers which exhibit glass-rubber transition behavior. The commercial forcefield "COMPASS" is used to support the atomistic simulations of the polymer. The temperature dependence behavio...

journal_title：Journal of molecular modeling

authors： Chen X,Yuan C,Wong CK,Zhang G

更新日期：2012-06-01 00:00:00