A mixed basis with off-center Gaussian functions for the calculation of the potential energy surfaces for π-stacking interactions: dimers of benzene and planar C₆.

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：:Contact sites between amino acids characterize important structural features of a protein. We investigated characteristics of contact sites in a representative set of proteins and their relations between protein class or topology. For this purpose, we used a non-redundant set of 5872 protein domains, identically categ...

journal_title：Journal of molecular modeling

authors： Wozniak PP,Kotulska M

更新日期：2014-11-01 00:00:00

abstract：:White spot disease caused by the white spot syndrome virus (WSSV) incurs a huge loss to the shrimp farming industry. Since no effective therapeutic measures are available, early detection and prevention of the disease are indispensable. Towards this goal, we previously identified a 12-mer phage displayed peptide (desi...

journal_title：Journal of molecular modeling

authors： Jamalpure S,Panditrao G,Kulabhusan PK,Hameed ASS,Paknikar KM,Joshi M,Rajwade JM

更新日期：2020-09-10 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：: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：:This paper investigates the thermodynamics of gas-phase CO(2) cascade uptake-reactions in the form of carbonate or monomethylcarbonate anions in the host cavity of various dinuclear octa-azacryptates of m-CH(2)C(6)H(4)CH(2) and 2,5-furano-spaced hosts, L (1) and L (2) cryptands, using density functional theory (DFT). ...

journal_title：Journal of molecular modeling

authors： El-Hendawy MM,English NJ,Mooney DA

更新日期：2011-12-01 00:00:00

abstract：:In this study, the complete orthonormal sets of phi(alpha)-momentum space orbitals (where alpha = 1, 0, -1, -2, ...) obtained from the psi(alpha)-ETO in coordinate representation (I.I. Guseinov, J. Mol. Model., 9 (2003) 135) are reduced to the complete orthonormal sets of hyperspherical harmonics (HSH) by means of a F...

journal_title：Journal of molecular modeling

authors： Guseinov II

更新日期：2006-09-01 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：: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 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：:The structure of a two-dimensional film formed by adsorbed polymer chains was studied by means of Monte Carlo simulations. The polymer chains were represented by linear sequences of lattice beads and positions of these beads were restricted to vertices of a two-dimensional square lattice. Two different Monte Carlo met...

journal_title：Journal of molecular modeling

authors： Pawłowska M,Sikorski A

更新日期：2013-10-01 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：: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：:This theoretical study presents a comparative analysis of the molecular properties of heterocyclic (C2H4O...HF and C2H5...HF) and homocyclic (C3H6...HF) hydrogen-bonded complexes. Initially, the equilibrium geometries of these complexes were analyzed in detail at the B3LYP/6-311++G(d,p) level of theory. Subsequently, ...

journal_title：Journal of molecular modeling

authors： Oliveira BG,Araújo RC,Carvalho AB,Ramos MN

更新日期：2009-02-01 00:00:00

abstract：:Nitriles are important chemical species in organic transformations, material chemistry, and environmental sciences. Nitriles are used as cyanating reagents in many organic reactions, where the C-CN bond dissociation has an important role. The reactivity of nitriles can be better understood by studying the bond dissoci...

journal_title：Journal of molecular modeling

authors： Kosar N,Ayub K,Gilani MA,Mahmood T

更新日期：2019-01-28 00:00:00

abstract：:B-C binary monolayers and fullerenes (borafullerenes) have received considerable attention in recent years. Inspired by the newly reported B4C3 semiconducting boron carbide monolayer isovalent to graphene (Tian et al., Nanoscale, 2019, 11, 11099), we predict herein at density functional theory level a new class of bor...

journal_title：Journal of molecular modeling

authors： Yan M,Tian XX,Pei L,Ma YY,Zan WY,Mu YW,Li SD

更新日期：2020-07-07 00:00:00

abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

journal_title：Journal of molecular modeling

authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

更新日期：2011-07-01 00:00:00

abstract：:The capture of N3-chains and N5-rings on the outer surface of C60 was studied using density functional calculations. For the neutral N5-ring, it was found that a N5-ring trapped by a C60 cage becomes more stable than an isolated N5-ring radical, and a C60-N5 compound with a C-N bond at an exohedral position of C60 is ...

journal_title：Journal of molecular modeling

authors： Liang Y,Gao X,Li N,Zhang X

更新日期：2015-10-01 00:00:00

abstract：:Solar-assisted water splitting using photoelectrochemical cells (PECs) is one of the promising ways for the production of hydrogen to store renewable energy. Semiconducting materials are used as a key factor which controls the overall energy conversion efficiency in PECs. However, finding new semiconductors with appro...

journal_title：Journal of molecular modeling

authors： Uğur Ş,Akbudak S,Kushwaha AK,Bayrak G

更新日期：2020-05-15 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：:The internal rotation in ammonia borane (AB) was studied on the basis of natural orbitals for chemical valence (NOCV) and eigenvectors for Pauli repulsion (NOPR). We found that the total hyperconjugation stabilization (ca. 5 kcal mol(-1)), based on the charge transfer from the occupied σ (B-H) orbitals into the empty ...

journal_title：Journal of molecular modeling

authors： Parafiniuk M,Mitoraj MP

更新日期：2014-06-01 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：:This work focuses on the role of the dynamic hydrogen bonds (HB) formed in an aqueous solution of aspirin using molecular dynamics simulation. The statistics reveal the existence of internal HB that inhibit the rotational movements of the acetyl and the carboxylic acid groups, forcing the molecule to adopt a closed co...

journal_title：Journal of molecular modeling

authors： Donnamaria MC,de Xammar Oro JR

更新日期：2011-10-01 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：:Colorectal cancer, which is considered one of the leading causes of mortality worldwide, develops through the formation of benign polyps on the inner colon or rectum wall. Truncations in adenomatous polyposis coli (APC) gene lead to the spread of the disease in the entire colon region when combined with the guanine nu...

journal_title：Journal of molecular modeling

authors： Jadav SS,Macalino SJY,Alluri R

更新日期：2020-07-16 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

abstract：:Cyclin-dependent kinases (Cdks) play important roles in the regulation of the cell cycle. Their inhibitors have entered clinical trials to treat cancer. Very recently, Davis et al. (Nat Struct Biol 9:745-749, 2002) have found a ligand NU6102, which has a high affinity with cyclin-dependent kinase 2 (K(i) = 6 nM) but a...

journal_title：Journal of molecular modeling

authors： Jiang Y,Zou J,Gui C

更新日期：2005-11-01 00:00:00

abstract：:The performances of quantum chemistry methods (i.e., DFT and ab initio) in calculating the structural and vibrational properties of phosphates and phosphorylated compounds have been evaluated. Diethyl-phosphate, phosphonic acid, dihydrogen phosphate anion, phosphoric acid dimer and protonated glycylphosphotyrosine dip...

journal_title：Journal of molecular modeling

authors： Sharma A,Ohanessian G,Clavaguéra C

更新日期：2014-09-01 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：:The p38-mitogen-activated protein kinases (p38-MAPKs) belong to a family of serine-threonine kinases activated by pro-inflammatory or stressful stimuli that are known to be involved in several diseases. Their biological importance, related to the release of inflammatory pro-cytokines such as tumor necrosis factor-alph...

journal_title：Journal of molecular modeling

authors： Romeiro NC,Albuquerque MG,de Alencastro RB,Ravi M,Hopfinger AJ

更新日期：2006-09-01 00:00:00