Stability and molecular properties of the boron-nitrogen alternating analogs of azulene and naphthalene: a computational study.

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：:The effect of CO2 and H2O on the behavior of shale gas confined in calcite [104] slit-like nanopore is investigated using molecular dynamics simulation technique. The study is relevant as the advancement of enhance gas recovery (EGR) technologies requires in-depth atomistic understanding of the hydrocarbons, water, ca...

journal_title：Journal of molecular modeling

authors： Berghe G,Kline S,Burket S,Bivens L,Johnson D,Singh R

更新日期：2019-09-02 00:00:00

abstract：:The nature of E-M bonds in CpE-MCp (E = B, Al, Ga; M = Li, Na, K; Cp = η (5)-C5H5) donor-acceptor sandwiches was studied using the atoms in molecules (AIM) theory, electron localization function (ELF), energy decomposition analysis (EDA), and natural bond orbital analysis (NBO) methods. Both topological and orbital an...

journal_title：Journal of molecular modeling

authors： Huo S,Meng D,Zhang X,Meng L,Li X

更新日期：2014-10-01 00:00:00

abstract：:The character of the bridged hydrogen atom (Hb) of B2H6 has become a hot issue in recent years. In this work, the complexes B2H6 · · · NH3, B2H2X4 · · · nNH3 (n = 1, 2) and 2HF · · · B2H2X4 · · · 2NH3 (X = Cl, Br, I) were constructed and studied based on the M06-2X calculations to investigate how to enhance the Hb · ·...

journal_title：Journal of molecular modeling

authors： Gao L,Zhang X,Meng L,Zeng Y

更新日期：2015-09-01 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：:Nitrogen-rich heterocycles and their nitro derivatives are one of the important classes of energetic materials. In the present study, the computational methods have been applied to determine the thermodynamic and detonation properties of nitro derivatives of BN indole molecule. Structure optimization and electronic en...

journal_title：Journal of molecular modeling

authors： Gupta S,Singh HJ

更新日期：2020-03-24 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：:Through comparison with ab initio reference data, we have evaluated the performance of various density functionals for describing pi-pi interactions as a function of the geometry between two stacked benzenes or benzene analogs, between two stacked DNA bases, and between two stacked Watson-Crick pairs. Our main purpose...

journal_title：Journal of molecular modeling

authors： Swart M,van der Wijst T,Fonseca Guerra C,Bickelhaupt FM

更新日期：2007-12-01 00:00:00

abstract：:The density functional theory method using the B3LYP/6-31G(d,p) level of theory was used to perform isoenergetic maps in order to determine the lower energy conformers of four disaccharides constituting alginic acids, which are based on β-D-mannuronic (M) and α-L-guluronic acid (G), called MM, GG, MG, and GM. The pref...

journal_title：Journal of molecular modeling

authors： Bekri L,Zouaoui-Rabah M,Springborg M,Rahal MS

更新日期：2018-10-10 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：:Very recently, an unprecedented novel monometallic cluster of fullerenes entrapping a yttrium cyanide (YCN) cluster inside a popular C82 cage YCN@Cs(6)-C82 was synthesized and characterized. Inspired by this investigation, four non-IPR YCN@C1(17459)-C76, YCN@C2v(19138)-C76, YCN@C2(17646)-C76, and YCN@C1(17894)-C76 (1,...

journal_title：Journal of molecular modeling

authors： Gao FW,Xu HL,Su ZM

更新日期：2016-08-01 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：: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：: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：:The stability, geometry and electronic structure of the title nanoclusters were compared by using density functional theory (DFT) calculations. Their electrical property analysis showed that the relative magnitude of the HOMO-LUMO gaps (eV) that are average values from the calculated results with five different DFT fu...

journal_title：Journal of molecular modeling

authors： Beheshtian J,Bagheri Z,Kamfiroozi M,Ahmadi A

更新日期：2012-06-01 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：:Density functional theory investigations at the DFT-B3LYP/6-311++G** theoretical level employed to determine the tautomerism, substituent effects of 4-substituted 4-amino-5-methyl-2,4-dihydro-3H-1,2,4-triazole-3-thione, and its derivatives (4-R-H, 4-R-CH3, 4-R-F, 4-R-NO2) in the selected solvent (acetone, acetonitrile...

journal_title：Journal of molecular modeling

authors： Shiroudi A,Safaei Z,Kazeminejad Z,Repo E,Pourshamsian K

更新日期：2020-02-13 00:00:00

abstract：:ET(A) subtype selective antagonists constitute a novel and potentially important class of agents for the treatment of pulmonary hypertension, heart failure, and other pathological conditions. In this paper, 60 benzodiazepine derivatives displaying potent activities against ET(A) and ET(B) subtypes of endothelin recept...

journal_title：Journal of molecular modeling

authors： Xia J,Li J,Sun H

更新日期：2012-04-01 00:00:00

abstract：:Effects of substituents on anion binding in different urea based receptors have been examined using density functional (B3LYP/6-311+G**) level of theory. The complexes formed by a variety of substituted urea with a halide anion (fluoride) and an oxy-anion (acetate) have been calculated. The stronger complexes were pre...

journal_title：Journal of molecular modeling

authors： Ghosh A,Jose DA,Das A,Ganguly B

更新日期：2010-09-01 00:00:00

abstract：:The formation of selenium species in some biological processes involves the generation of ionic and radical intermediates such as RSe●, RSe-, RSeO●, and RSeO-, among others. We performed a theoretical study of the possible mechanisms for the reaction of the two simplest Se radicals-the hydroselenyl (HSe●) and seleneni...

journal_title：Journal of molecular modeling

authors： Vega-Teijido MA,Kieninger M,Ventura ON

更新日期：2017-12-05 00:00:00

abstract：:The CO and O2 adsorption as well as CO oxidation on cationic, neutral, and anionic AuM dimers (M = Pd, Ag) are studied by density functional calculations. Our results show that CO and O2 are adsorbed more stably on AuPd dimers than on AuAg dimers with corresponding charge state. O2 is favorable to be adsorbed on Pd at...

journal_title：Journal of molecular modeling

authors： Chen X,Lu RF,Kan EJ,Liu YZ,Xiao CY,Deng KM

更新日期：2014-06-01 00:00:00

abstract：:Quantum chemical calculations of the structures and stabilities of the title series at the CCSD(T) theoretical level are performed. Laplacian, electron density deformation, electron localization function and reduced density gradient analysis are investigated to explore the nature of the interaction. The results show t...

journal_title：Journal of molecular modeling

authors： Li X

更新日期：2012-03-01 00:00:00

abstract：:Detailed density functional theory (DFT) calculations on the structure and harmonic frequencies of model all-trans and all-cis polyenes were undertaken. For the first time, we report on the convergence of selected B3LYP/6-311++G** and BLYP/6-311++G** calculated structural parameters resulting from a systematic increas...

journal_title：Journal of molecular modeling

authors： Kupka T,Buczek A,Broda MA,Stachów M,Tarnowski P

更新日期：2016-05-01 00:00:00

abstract：:The reactivity of the 5-arylidenerhodanine and 5-arylideneisorhodanine derivatives in reactions with dimethyl maleate was computationally studied at the DFT(M06-2X)/6-311+G(d,p) theory level. Eight stereoisomers of the reaction products were considered. The effect of the solvent was taken into account by means of the ...

journal_title：Journal of molecular modeling

authors： Tejchman W,Michalski M,Zborowski KK,Berski S

更新日期：2019-06-14 00:00:00

abstract：:The mechanism of the copper(I)-catalyzed cyclopropanation reaction for methyl diazoacetate with both (Z)- and (E)-but-2-ene stereoisomers has been studied using the 6-311++G(d,p) basis set by means of M06-2X and O3LYP functionals. According to both methods, the rate-limiting step is the formation of a copper-carbene i...

journal_title：Journal of molecular modeling

authors： Angulo B,Herrerías CI,Hormigón Z,Mayoral JA,Salvatella L

更新日期：2018-07-05 00:00:00

abstract：:Prussian Blue is a paradigmatic mixed valence material and a parent compound to a broad family of electronically, optically, and magnetically active materials. Its exact composition varies greatly depending on the preparation route, leading to large variations in its electronic properties. The influence of water molec...

journal_title：Journal of molecular modeling

authors： Wojdeł JC

更新日期：2009-06-01 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：:We use density functional theory-based calculations to study structural, electronic, and magnetic properties of two key reaction intermediates on a hematite, [Formula: see text]-Fe2O3, photoanode during the solar-driven water splitting reaction. Both intermediates contain an oxygen atom bonded to a surface iron atom. ...

journal_title：Journal of molecular modeling

authors： Poaty LT,Ulman K,Seriani N,M'Passi-Mabiala B,Gebauer R

更新日期：2018-09-18 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

abstract：:Two uridine 2',3'-cyclic monophosphate (cUMP) derivatives, 5'-deoxy (DcUMP) and 5'-O-methyl (McUMP), were studied by means of quantum chemical methods. Aqueous solvent effects were estimated based on the isodensity-surface polarized-continuum model (IPCM). Gas phase calculations revealed only slight energy differences...

journal_title：Journal of molecular modeling

authors： Grabarkiewicz T,Hoffmann M

更新日期：2006-01-01 00:00:00