Theoretical study of photophysical properties of 1,4-dihydropyrrolo[3,2-b]pyrrole-cored branched molecules with thienylenevinylene arms toward broad absorption spectra for solar cells.

abstract：:Ten functionals were used to assess their capability to compute a local reactivity descriptor coming from the Conceptual Density Functional Theory on a group of iron-based organometallic compounds that have been synthesized by Zohuri, G.H. et al. in 2010; these compounds bear the following substituent groups: H-, O2N-...

journal_title：Journal of molecular modeling

authors： Martínez-Araya JI,Glossman-Mitnik D

更新日期：2018-01-18 00:00:00

abstract：:Three-dimensional pharmacophore models of human adenosine receptor A(₂A) antagonists were developed based on 23 diverse compounds selected from a large number of A(₂A) antagonists. The best pharmacophore model, Hypo1, contained five features: one hydrogen bond donor , three hydrophobic points and one ring aromatic. It...

journal_title：Journal of molecular modeling

authors： Xu Z,Cheng F,Da C,Liu G,Tang Y

更新日期：2010-12-01 00:00:00

abstract：:Adsorption of three heavy metals (Ni, Pd, Cd) onto (10,0) single-walled carbon nanotube (SWCNT) was investigated using density functional theory (DFT). Metals were adsorbed to both inside and outside of SWCNT and their structures and electronic properties [e.g., band structures and density of states (DOS)] were calcul...

journal_title：Journal of molecular modeling

authors： Aghashiri A,Fotooh FK,Hashemian S

更新日期：2019-06-10 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：:Checkpoint kinase 1 (Chk1), a member of the serine/threonine kinase family, is an attractive therapeutic target for anticancer combination therapy. A structure-based modeling approach complemented with shape components was pursued to develop a reliable pharmacophore model for ATP-competitive Chk1 inhibitors. Common ch...

journal_title：Journal of molecular modeling

authors： Chen XM,Lu T,Lu S,Li HF,Yuan HL,Ran T,Liu HC,Chen YD

更新日期：2010-07-01 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：:The pathogen Legionella longbeachae is a causative agent of legionellosis. The antibiotic resistance is the major problem of this modern world. Thus, selective pressure warrants the need for identification of newer drug target. In current study, subtractive proteomics approach screen out SIS (sugar isomerase) domain p...

journal_title：Journal of molecular modeling

authors： Ahmad F,Shabaz Z,Azam SS

更新日期：2020-08-03 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：:Realistic molecular models of one and two-centre catalytic active sites originating from the cleavage of a precursor material known to give rise to an active double metal cyanide catalyst are described. Via periodic density functional calculations the structure of the proposed catalytic sites are shown to be dependent...

journal_title：Journal of molecular modeling

authors： Wojdeł JC,Bromley ST,Illas F,Jansen JC

更新日期：2007-07-01 00:00:00

abstract：:We present the synthesis and structure determination for two thiohydantoin compounds (5-benzylidene-2-sulfanylideneimidazolidin-4-one and 5-cinnamylidene-2-sulfanylideneimidazolidin-4-one), proposed as potential novel fungicides. The exact chemical structure of these molecules has not yet been determined since they ca...

journal_title：Journal of molecular modeling

authors： Kobyłka K,Żuchowski G,Tejchman W,Zborowski KK

更新日期：2019-08-24 00:00:00

abstract：:Nowadays, scientists are trying to develop low-cost fullerene free acceptors for small organic photovoltaic cells in order to overcome the limitations of fullerene derivatives. Current research work deals with theoretical study on three non-fullerene acceptors based on indaceno, dithiophene core, and thiophene bridge ...

journal_title：Journal of molecular modeling

authors： Ajmal M,Ali U,Javed A,Tariq A,Arif Z,Iqbal J,Shoaib M,Ahmed T

更新日期：2019-09-11 00:00:00

abstract：:Beta-lactamase (ampC) in general causes the onset of antibiotic resistance in pathogenic bacteria against the β-lactam antibiotics. Morganella morganii which belongs to the Proteae tribe of the Enterobacteriaceae family is a Gram-negative bacillus. Gram-negative bacteria are the key problematic agents among the human ...

journal_title：Journal of molecular modeling

authors： Alazmi M

更新日期：2020-07-07 00:00:00

abstract：:Aminoglycoside-arginine conjugates (AAC and APAC) are multi-target inhibitors of human immunodeficiency virus type-1 (HIV-1). Here, we predict new conjugates of neomycin with two arginine peptide chains binding at specific sites on neomycin [poly-arginine-neomycin-poly-arginine (PA-Neo-PA)]. The rationale for the desi...

journal_title：Journal of molecular modeling

authors： Berchanski A,Lapidot A

更新日期：2009-03-01 00:00:00

abstract：:The mechanism for the hydroxyl-radical-induced depolymerization of cellulose under alkaline conditions in air was investigated using density functional theory at the B3LYP/6-31+G(d,p) level as well as electron transfer theory. The pathway for the depolymerization of cellulose was obtained theoretically and H abstracti...

journal_title：Journal of molecular modeling

authors： Shao C,Shi K,Hua Q,Zhang L,Dai Y,You W,Liu Y,Li C,Zhang C

更新日期：2018-05-02 00:00:00

abstract：:The equilibrium structures, spectroscopic and thermodynamic parameters [entropy (S), internal energy (E), heat capacity (C p)] of U₂, U₂O, U₂O₂ and U₂O₄ uranium oxide molecules were investigated systematically using density functional theory (DFT). Our computations indicated that the ground electronic state of U₂ is t...

journal_title：Journal of molecular modeling

authors： Li P,Niu WX,Gao T,Wang F,Jia TT,Meng DQ,Li G

更新日期：2013-12-01 00:00:00

abstract：:We have performed a multivariate logistic regression analysis to establish a statistical correlation between the structural properties of water molecules in the binding site of a free protein crystal structure, with the probability of observing the water molecules in the same location in the crystal structure of the l...

journal_title：Journal of molecular modeling

authors： García-Sosa AT,Mancera RL,Dean PM

更新日期：2003-06-01 00:00:00

abstract：:Four clusters of ZnO, O-Zn-SR (-SR = ligand) and doping ZnO structures (with Cr, Cu, Al atoms) were investigated using density functional theory at theB3LYP/Lanl2dz level. The characteristics of Zn(3)O(3) and Zn(4)O(4) structures, which are the units of experimental wurtzite and zinc blende structures, were found to b...

journal_title：Journal of molecular modeling

authors： Wang C,Xu S,Ye L,Lei W,Cui Y

更新日期：2011-05-01 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：:This article analyzes the interplay between X···N and X···X halogen bonds interactions in NCX···NCX···XCH3 complexes, where X=Cl and Br. To better understand the properties of these systems, the corresponding dyads were also studied. These effects are studied theoretically in terms of geometric and energetic features ...

journal_title：Journal of molecular modeling

authors： Esrafili MD,Vakili M,Solimannejad M

更新日期：2014-02-01 00:00:00

abstract：:Numerous studies suggest that two-phase morphology and thick interface are separately beneficial to the viscosity reduction and mechanical property maintainence of the matrix when normal molecular weight polymer (NMWP) is used for modification of ultrahigh molecular weight polyethylene (UHMWPE). Nevertheless, it is ve...

journal_title：Journal of molecular modeling

authors： Gai JG,Zuo Y

更新日期：2012-06-01 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：:The effect of terminal GLY114* deletion on the binding affinity of the PA-IIL lectin toward L: -fucose was investigated. Both experimental (isothermal titration calorimetry) and computational (molecular dynamics simulations) methods have shown that the deletion mutation decreases the L-fucose affinity. It implies that...

journal_title：Journal of molecular modeling

authors： Wimmerová M,Mishra NK,Pokorná M,Koca J

更新日期：2009-06-01 00:00:00

abstract：:A density functional theory investigation of adsorption of monomer, dimer and trimer forms of pyrrole on the outer surface of zigzag (7,0) single-walled carbon nanotube (SWCNT) has been reported. Geometries of the complexes were optimized using the M06-2X functional and the 6-31G(d,p) basis set. Moreover, 6-311G(d,p),...

journal_title：Journal of molecular modeling

authors： Shukla MK,Boddu V,Hill F

更新日期：2014-09-01 00:00:00

abstract：:The title compound, C(6)H(4)N(4)S(2)·C(3)H(7)NO, crystallizes in the monoclinic space group C 2/c with a = 26.673(5), b = 5.397(1), c = 16.522(3) Å, β = 95.49(3)°, Z = 8, R = 0.0461 for 1891 reflections with I > 2σ(I) and 174 parameters (4 restraints). Single pteridine-2,4(1 H,3 H)-dithione and dimethylformamide molec...

journal_title：Journal of molecular modeling

authors： Illán-Cabeza NA,Peña-Ruiz T,Moreno-Carretero MN

更新日期：2012-02-01 00:00:00

abstract：:Models of the hydrogenoxalate (bioxalate, charge -1) and oxalate (charge -2) anions were developed for classical molecular dynamics (CMD) simulations and parametrized against ab initio molecular dynamics (AIMD) data from our previous study (Kroutil et al. (2016) J Mol Model 22:210). The interactions of the anions with...

journal_title：Journal of molecular modeling

authors： Kroutil O,Předota M,Kabeláč M

更新日期：2017-10-28 00:00:00

abstract：:The structural and energetic properties of native and oxidized telomeric complexes were defined by means of molecular dynamic (MD) simulations. As a starting point, the experimental conformation of B-DNA d(GpTpTpApGpGpGpTpTpApGpGpG) oligomer bound to human protein telomeric repeat binding factor 1 (TRF1) was used. The...

journal_title：Journal of molecular modeling

authors： Czeleń P,Cysewski P

更新日期：2013-08-01 00:00:00

abstract：:It is well-known that properties of poly(vinyl alcohol) (PVA) in the pure and solution states depend largely on the hydrogen bonding networks formed. In the context of molecular simulation, such networks are handled through the Coulombic interactions. Therefore, a good set of partial atom charges (PACs) for simulation...

journal_title：Journal of molecular modeling

authors： Noorjahan A,Choi P

更新日期：2015-03-01 00:00:00

abstract：:Density functional theory (DFT) was used to investigate cobalt(0)-catalyzed intramolecular hydroacylation of 4-pentenal. The calculated results indicated the involvement of five possible reaction pathways: the formation of cyclopentanone, cyclobutanone, butylenes, cyclobutane, and cyclopropane, respectively. The forme...

journal_title：Journal of molecular modeling

authors： Meng Q,Wang F,Li M

更新日期：2013-06-01 00:00:00

abstract：:Survivin, the smallest inhibitor of apoptosis protein (IAP), is a valid target for cancer research. It mediates both the apoptosis pathway and the cell cycle and has been proposed to form a complex with the cyclin-dependent kinase protein CDK4. The resulting complex transports CDK4 from the cytosol to the nucleus, whe...

journal_title：Journal of molecular modeling

authors： Selent J,Kaczor AA,Guixà-González R,Carrió P,Pastor M,Obiol-Pardo C

更新日期：2013-04-01 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