Theoretical calculation of polarizability isotope effects.

abstract：:The USFDA has approved pramlintide, commercially named Symlin (sIAPP), as adjunctive therapy for type 2 diabetes (T2D). This analogue of the human amylin peptide (hIAPP) has triple proline substitutions typical of the rat isoform (rIAPP). Recently, it was proposed that pramlintide solubility and aggregation resistance...

journal_title：Journal of molecular modeling

authors： Alves NA,Dias LG,Frigori RB

更新日期：2019-08-19 00:00:00

abstract：:Conjugated organic polymers represent an important class of materials for varied technological applications including in active layers of chemical sensors. In this context, polyaniline (PANI) derivatives are promising candidates, mainly due to their high chemical stability, good processability, versatility of synthesi...

journal_title：Journal of molecular modeling

authors： Mandú LO,Batagin-Neto A

更新日期：2018-06-09 00:00:00

abstract：:We report thermodynamic, geometric, and electronic parameters for the interaction between neutral ligands and the [Hg(H2O)]2+ dication, using the B3LYP/6-311 + G(d,p) approach. Gibbs free energies for the interaction were employed to rank the affinity order of the several neutral ligands. To identify the parameters th...

journal_title：Journal of molecular modeling

authors： da Silva VHM,de Mesquita Carneiro JW,da Costa LM,Ferreira GB

更新日期：2020-05-20 00:00:00

abstract：:The three-dimensional (3D) structure of the substrate binding domain (SBD) of human ubiquitin ligase Siah2 (seven in absentia homolog) was constructed based on the homology modeling approach using the Modeller 9v7 program. The molecular dynamics method was utilized to refine the model and it was further assessed by Pr...

journal_title：Journal of molecular modeling

authors： Anupriya G,Roopa K,Basappa S,Chong YS,Annamalai L

更新日期：2011-12-01 00:00:00

abstract：:The influences of the temperature and the BDNPA/BDNPF (A3) content on the mechanical properties of and the binding energies between hexanitrohexaazaisowurtzitane (HNIW) and cellulose acetate butyrate (CAB)/A3 were studied via molecular dynamics simulations. The morphology of HNIW in acetone was simulated using an atta...

journal_title：Journal of molecular modeling

authors： Lan G,Jin S,Wang D,Li J,Lu Z,Jing B,Li L

更新日期：2018-07-02 00:00:00

abstract：:Using density functional theory (DFT) and molecular dynamics (MD), we studied the interaction of a titanium atom with a half of a C60 fullerene (i.e., C30), formed from the corannulene structure with a pentagonal base. We considered atmospheric pressure and 300 K. We found that the most stable adsorption of the titani...

journal_title：Journal of molecular modeling

authors： Canales M,Ramírez-de-Arellano JM,Magana LF

更新日期：2016-09-01 00:00:00

abstract：:Quantum chemical calculations were performed for LiNH2-HMgX (X=H, F, Cl, Br, CH3, OH, and NH2) complexes to propose a new interaction mechanism between them. This theoretical survey showed that the complexes are stabilized through the combinative interaction of magnesium and lithium bonds. The binding energies are in ...

journal_title：Journal of molecular modeling

authors： Yang X,Li Q,Cheng J,Li W

更新日期：2013-01-01 00:00:00

abstract：:The geometries, relative stabilities of some 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives were calculated with full geometry optimization using AM1 and PM3 in aqueous phase. With the exception of molecules 4, 6 and 7 for all the 4(7) and 5(6) substituted 2-hydroxybenzimidazole derivatives the 3H and ke...

journal_title：Journal of molecular modeling

authors： Oğretir C,Yarligan S,Berber H,Arslan T,Topal S

更新日期：2003-12-01 00:00:00

abstract：:Temperature dependences of the spontaneous polarization and the dielectric constant are calculated near the paraelectric-ferroelectric (cubic-tetragonal) transition in BaTiO3 using our mean field model. By expanding the free energy in terms of the spontaneous polarization (order parameter), expressions for the tempera...

journal_title：Journal of molecular modeling

authors： Yurtseven H,Kiraci A

更新日期：2013-09-01 00:00:00

abstract：:Acene-thiophenes compounds have been used successfully as active materials in thin-film transistors and photodetectors. This work aims at obtaining an adequate theoretical framework to accurately characterize the optical and electronic properties of two such compounds: NaT2 and NaT3. This is done by comparing the resu...

journal_title：Journal of molecular modeling

authors： de Sousa LE,Mamiya AA,Kjelstrup-Hansen J,da Silva Filho DA

更新日期：2017-02-01 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：:Fifteen KSP inhibitors were docked into the receptor and the binding mode was analyzed for the first time. It was considered that in addition to the main binding pocket all the inhibitors merged in, there exists a cooperative minor binding pocket, which could be explored for significantly increased binding affinity. I...

journal_title：Journal of molecular modeling

authors： Jiang C,Chen Y,Wang X,You Q

更新日期：2007-09-01 00:00:00

abstract：:The nuclear magnetic shieldings of Si, Ge, and Sn in MH(4-n) Y(n) (M = Si, Ge, Sn; Y = F, Cl, Br, I and n = 1-4) molecular systems are highly influenced by the substitution of one or more hydrogens by heavy-halogen atoms. We applied the linear response elimination of small components (LRESC) formalism to calculate tho...

journal_title：Journal of molecular modeling

authors： Maldonado AF,Aucar GA,Melo JI

更新日期：2014-09-01 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：:We tested different approaches to including the effect of binding-site water molecules for ligand-binding affinities within the MM/GBSA approach (molecular mechanics combined with generalised Born and surface-area solvation). As a test case, we studied the binding of nine phenol analogues to ferritin. The effect of wa...

journal_title：Journal of molecular modeling

authors： Mikulskis P,Genheden S,Ryde U

更新日期：2014-06-01 00:00:00

abstract：:Ab initio computations are performed to study the structural, elastic, electronic, and vibrational characteristics of the cubic antiperovskite compound PbNCa3 under pressure up to 50 GPa. By using the generalized gradient approximation (GGA), the equilibrium structural parameters, energy band structure, density of sta...

journal_title：Journal of molecular modeling

authors： Ciftci YO,Evecen M,Alp İO

更新日期：2021-01-03 00:00:00

abstract：:The feasibility of electron transport conduction through a guanine base of DNA was investigated and then compared with another component of DNA, i.e., cytosine. A mathematical approach based on the jellium model using non-equilibrium Green's function combined with semi empirical extended Huckel theory was applied usin...

journal_title：Journal of molecular modeling

authors： Vohra R,Sawhney RS

更新日期：2018-11-01 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：:Eleven 1,4-naphthoquinone analogues with different amino substitutions at position 3 of the quinone ring earlier reported for macrofilaricidal activity were selected and screened against purified cytosolic GST isolated from the bovine filarial worm Setaria digitata and IC(50) values were determined. Of the 11 compound...

journal_title：Journal of molecular modeling

authors： Mathew N,Srinivasan L,Karunan T,Ayyanar E,Muthuswamy K

更新日期：2011-10-01 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 the present study, we analyze the interactions of NAD+-dependent deacetylase (Sir2 homolog yeast Hst2) with carba-nicotinamide-adenine-dinucleotide (ADP-HPD). For the Sir2 homolog, a yeast Hst2 docking procedure was applied. The structure of the protein-ADP-HPD complex obtained during the docking procedure was used...

journal_title：Journal of molecular modeling

authors： Czeleń P,Czyżnikowska Ż

更新日期：2016-06-01 00:00:00

abstract：:To improve understanding of the unimolecular decomposition mechanism of 1,2,4-butanetriol trinitrate (BTTN) in the gas phase, density functional theory calculations were performed to determine various decomposition pathways at the B3LYP/6-311G** level. Two main mechanisms for the unimolecular decomposition of BTTN wer...

journal_title：Journal of molecular modeling

authors： Zhu W,Yan Q,Pang A,Chi X,Du X,Xiao H

更新日期：2014-02-01 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：:The formation of silaspiropentane from addition of singlet silacyclopropylidene 1 and silacyclopropylidenoid 8 to ethylene has been investigated separately at the B3LYP, X3LYP, WB97XD, and M05-2X theories using the 6-31+G(d,p) basis set. The silacycloproylidenoid addition follows a stepwise route. In contrast, a conce...

journal_title：Journal of molecular modeling

authors： Yildiz CB,Azizoglu A

更新日期：2016-07-01 00:00:00

abstract：:Density functional theory and its time-dependent extension (DFT, TDDFT) were employed to establish the feasibility of using a series of 4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) in photodynamic therapy. Their absorption electronic spectra, singlet-triplet energy gaps, and spin-orbit matrix elements were co...

journal_title：Journal of molecular modeling

authors： Ponte F,Mazzone G,Russo N,Sicilia E

更新日期：2018-06-29 00:00:00

abstract：:Understanding how temperature affects the electronic transitions of BFO is important for design of BiFeO3 (BFO)-based temperature-sensitive device. Hitherto, however, there have been only very limited reports of the quantitative simulation. Here, we used density functional theory (DFT) and two-dimensional correlation ...

journal_title：Journal of molecular modeling

authors： Bian L,Xu JB,Song MX,Dong FQ,Dong HL,Shi FN,Zhang XY,Duan T

更新日期：2015-04-01 00:00:00

abstract：:The complexes formed between TX3-ZX2 (T = C, Si, Ge; Z = P, As, Sb; X = F, Cl) and NH3 were studied at the MP2/aug-cc-pVTZ(PP) level. For each TX3-ZX2, two types of complex were obtained. For CX3-ZX2, NH3 is inclined to approach the σ-hole on the Z atom, forming a pnicogen bond. For TX3-ZX2 (T = Si and Ge), however, t...

journal_title：Journal of molecular modeling

authors： Li Y,Xu Z

更新日期：2018-08-20 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：:A good understanding of the inhibition mechanism of enzymes exhibiting high levels of similarity is the first step to the discovery of new drugs with selective potential. Examples of such proteins include glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinase 2 (CDK-2). This article reports the mechanism of s...

journal_title：Journal of molecular modeling

authors： Czeleń P

更新日期：2017-08-01 00:00:00

abstract：:Antihistamines are frequently used pharmaceuticals that treat the symptoms of allergic reactions. Loratadine (LOR) is an active component of the second generation of selective antihistaminic pharmaceutical usually known as Claritin. Frequent usage of this type of pharmaceuticals imposes the need for understanding thei...

journal_title：Journal of molecular modeling

authors： Armaković S,Armaković SJ,Abramović BF

更新日期：2016-10-01 00:00:00