Modeling the secondary structures of the peptaibols antiamoebin I and zervamicin II modified with D-amino acids and proline analogues.

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：:Recently, the massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed. The present study aimed to determine whether the MP-CAFEE method is useful for drug discovery research. In the drug discovery process, it is important for computational chemists t...

journal_title：Journal of molecular modeling

authors： Ohno K,Mitsui T,Tanida Y,Matsuura A,Fujitani H,Niimi T,Orita M

更新日期：2011-02-01 00:00:00

abstract：:The interaction between tetramethylcucurbit[6]uril (host) and 5,5'-dimethyl-2,2'-bipyridyl hydrochloride (guest) was studied by 1H NMR, X-ray crystallography, electronic absorption spectroscopy, fluorescence emission spectra and quantum chemistry calculations. This experimental-computational study that indicated the h...

journal_title：Journal of molecular modeling

authors： Cong H,Zhao YJ,Xue SF,Tao Z,Zhu QJ

更新日期：2007-12-01 00:00:00

abstract：:The potential energy surfaces in gas phase and in aqueous solution for the nitration of benzene, chlorobenzene, and phenol have been elucidated with density functional theory at the M06-2X/6-311G(d,p) level combined with the polarizable continuum solvent model (PCM). Three reaction intermediates have been identified a...

journal_title：Journal of molecular modeling

authors： Liljenberg M,Stenlid JH,Brinck T

更新日期：2017-12-18 00:00:00

abstract：:The impact of a variety of modern computational methods on the structure of biologically relevant zinc complexes is studied. Different density functionals and a Hartree-Fock-based method, scalar-relativistic effects, and basis set integration grid choices, among others, are assessed for set of high-resolution crystall...

journal_title：Journal of molecular modeling

authors： Savasci G,Borges-Martínez M,Berger RJF,Ochsenfeld C,Mera-Adasme R

更新日期：2019-08-09 00:00:00

abstract：:Human gonadotropin hormone receptor, a G-protein coupled receptor, is the target of many medications used in fertility disorders. Obtaining more structural information about the receptor could be useful in many studies related to drug design. In this study, the structure of human gonadotropin receptor was subjected to...

journal_title：Journal of molecular modeling

authors： Sakhteman A,Khoddami M,Negahdaripour M,Mehdizadeh A,Tatar M,Ghasemi Y

更新日期：2016-09-01 00:00:00

abstract：:To date, no suitable vaccine or specific antiviral drug is available to treat Chikungunya viral (CHIKV) fever. Hence, it is essential to identify drug candidates that could potentially impede CHIKV infection. Here, we present the development of a homology model of nsP2 protein based on the crystal structure of the nsP...

journal_title：Journal of molecular modeling

authors： Singh KhD,Kirubakaran P,Nagarajan S,Sakkiah S,Muthusamy K,Velmurgan D,Jeyakanthan J

更新日期：2012-01-01 00:00:00

abstract：:Bacterial cytidylate kinase or cytidine monophosphate kinase (CMP kinase) catalyses the phosphoryl transfer from ATP to CMP and dCMP, resulting in the formation nucleoside diphosphates. In eukaryotes, CMP/UMP kinase catalyses the conversion of UMP and CMP to, respectively, UDP and CDP with high efficiency. This work d...

journal_title：Journal of molecular modeling

authors： Caceres RA,Macedo Timmers LF,Vivan AL,Schneider CZ,Basso LA,De Azevedo WF Jr,Santos DS

更新日期：2008-05-01 00:00:00

abstract：:In this work, the poly(ethylene oxide) bulk as one example has been iteratively heated and cooled back using MD simulations to examine the effects of thermal history on the resulting Tg. It is demonstrated that, after the system is equilibrated once at the high temperatures, the simulated Tg does not exhibit a systema...

journal_title：Journal of molecular modeling

authors： Wu C

更新日期：2017-08-22 00:00:00

abstract：:Aluminum enriched 1, 1-diamino-2, 2-dinitroethylene (Al-FOX-7) crystal, as a new high energy density material (HEDM), was designed and investigated using grand canonical monte carlo (GCMC), NVT+NPT-molecular dynamics (MD) and GGA-PBE-density functional theory (DFT) methods. The results show that, Al atoms break out H-...

journal_title：Journal of molecular modeling

authors： Bian L,Shu Y,Xu J,Wang L

更新日期：2013-01-01 00:00:00

abstract：:The Schiff base compound, 2-[(4-Fluorophenylimino)methyl]-3,5-dimethoxyphenol, has been synthesized and characterized by IR, electronic spectroscopy, and X-ray single-crystal determination. Molecular geometry from X-ray experiment of the title compound in the ground state have been compared using the Hartree-Fock (HF)...

journal_title：Journal of molecular modeling

authors： Tanak H,Ağar A,Yavuz M

更新日期：2010-03-01 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：:Ab initio calculations have been performed using the complete basis set model (CBS-QB3) to study the reaction mechanism of butane radical (C(4)H(9)•) with oxygen (O(2)). On the calculated potential energy surface, the addition of O(2) to C(4)H(9)• forms three intermediates barrierlessly, which can undergo subsequent i...

journal_title：Journal of molecular modeling

authors： Du HC,Gong XD

更新日期：2012-05-01 00:00:00

abstract：:By the use of ellipsoidal coordinates, the two-center Coulomb and hybrid integrals over complete orthonormal sets of Ψα-ETO exponential type orbitals arising in ab initio calculations of molecules are evaluated, where α = 1,0, -1, -2, ...,. These integrals are expressed through the auxiliary functions Q(ns)(q) and G(-...

journal_title：Journal of molecular modeling

authors： Guseinov II,Sahin E

更新日期：2011-04-01 00:00:00

abstract：:Here, we report a structure-based virtual screening of the ZINC database (containing about five million compounds) by computational docking and the analysis of docking energy calculations followed by in vitro screening against H. pylori urease enzyme. One of the compounds selected showed urease inhibition in the low m...

journal_title：Journal of molecular modeling

authors： Azizian H,Nabati F,Sharifi A,Siavoshi F,Mahdavi M,Amanlou M

更新日期：2012-07-01 00:00:00

abstract：:A high-throughput screen against Aurora A kinase revealed several promising submicromolar pyrimidine-aniline leads. The bioactive conformation found by docking these leads into the Aurora A ATP-binding site had a semicircular shape. Macrocycle formation was proposed to achieve novelty and selectivity via ring-closing ...

journal_title：Journal of molecular modeling

authors： Poulsen A,William A,Blanchard S,Nagaraj H,Williams M,Wang H,Lee A,Sun E,Teo EL,Tan E,Goh KC,Dymock B

更新日期：2013-01-01 00:00:00

abstract：:Ionic liquids (ILs) have been extensively studied and are considered green solvents capable of replacing traditional organic solvents. In this study, seven 1,2,3-triazolium derivative ILs have been synthesized. In order to study the effect of the cation nature on the ILs cytotoxicity, their structures were first ident...

journal_title：Journal of molecular modeling

authors： Glanzmann N,Carmo AML,Antinarelli LMR,Coimbra ES,Costa LAS,da Silva AD

更新日期：2018-06-14 00:00:00

abstract：:There is evidence that Tetracyclines are potentially useful drugs to treat prion disease, the fatal neurodegenerative disease in which cellular prion proteins change in conformation to become a disease-specific species (PrP(Sc)). Based on an in vitro anti-fibrillogenesis test, and using the peptide PrP106-126 in the p...

journal_title：Journal of molecular modeling

authors： Cosentino U,Pitea D,Moro G,Saracino GA,Caria P,Varì RM,Colombo L,Forloni G,Tagliavini F,Salmona M

更新日期：2008-10-01 00:00:00

abstract：:The fractional derivative concept to treat non-isothermal solid state thermal decomposition was employed in this work. Simulated data were compared with the exact solutions for the method validation. Calculated fractional kinetics data for four heating rates were initially considered and the Kissinger-Akahira-Sunose (...

journal_title：Journal of molecular modeling

authors： Carvalho FS,Braga JP,Marques MBF,Sebastião RCO

更新日期：2020-06-10 00:00:00

abstract：:Abnormal expression of cyclin-dependent kinase 2 (CDK2)/cyclin-E is detected in colorectal, ovarian, breast and prostate cancers. The study of CDK2 with a bound inhibitor revealed CDK2 as a potential therapeutic target for several proliferative diseases. Several highly selective inhibitors of CDK2 are currently underg...

journal_title：Journal of molecular modeling

authors： Pasha FA,Neaz MM

更新日期：2013-02-01 00:00:00

abstract：:Artificial neural networks (ANNs) have been successfully trained to model and predict the acidity constants (pK(a)) of 128 various phenols with diverse chemical structures using a quantitative structure-activity relationship. An ANN with 6-14-1 architecture was generated using six molecular descriptors that appear in ...

journal_title：Journal of molecular modeling

authors： Habibi-Yangjeh A,Danandeh-Jenagharad M,Nooshyar M

更新日期：2006-02-01 00:00:00

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 substituted effect on excited-state intramolecular proton transfer (ESIPT) of o-LHBDI derivatives (4R-o-LHBDI) was investigated by DFT and TD-DFT methods. The structures of 4R-o-LHBDI (R: OH, NH2, CN, NO2, CF3) were fully optimized, and the H-bond distances, bond angles, and infrared spectra of the atoms involved ...

journal_title：Journal of molecular modeling

authors： Ni M,Su S,Fang H

更新日期：2020-04-23 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：:The mechanism of the cycloaddition reaction CH3M≡MCH3 (M=C, Si, Ge) with C2H4 has been studied at the CCSD(T)/6-311++G(d,p)//MP2/6-311++G(d,p) level. Vibrational analysis and intrinsic reaction coordinate (IRC), calculated at the same level, have been applied to validate the connection of the stationary points. The br...

journal_title：Journal of molecular modeling

authors： Huo S,Li X,Zeng Y,Zheng S,Meng L

更新日期：2013-09-01 00:00:00

abstract：:Orvinols are potent analgesics that target opioid receptors. However, their analgesic mechanism remains unclear and no significant preference for subtype opioid receptor has been achieved. In order to find new orvinols that target the kappa-receptor, comparative 3D-QSAR studies were performed on 26 orvinol analogs usi...

journal_title：Journal of molecular modeling

authors： Li W,Tang Y,Xie Q,Sheng W,Qiu ZB

更新日期：2006-09-01 00:00:00

abstract：:The pathway and ab initio direct kinetics of the decomposition 5-aminotetrazole (5-ATZ) to HN(3) and NH(2)CN was investigated. Reactant, products and transition state were optimized with MP2 and B3LYP methods using 6-311G** and aug-cc-pVDZ basis sets. The intrinsic reaction coordinate curve of the reaction was calcula...

journal_title：Journal of molecular modeling

authors： Zhang JG,Feng LN,Zhang SW,Zhang TL,Zheng HH

更新日期：2008-05-01 00:00:00

abstract：:The dopamine (DAT), serotontin (SERT) and noradrenalin (NET) transporters are molecular targets for different classes of psychotropic drugs. The crystal structure of Aquifex aeolicus LeuT(Aa) was used as a template for molecular modeling of DAT, SERT and NET, and two putative drug binding sites (pocket 1 and 2) in eac...

journal_title：Journal of molecular modeling

authors： Ravna AW,Sylte I,Dahl SG

更新日期：2009-10-01 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