Abstract：
:The present study deals with the decomposition of CF(3)OCF(2)O radical formed from a hydrofluoroether, CF(3)OCHF(2) (HFE-125), in the atmosphere. The study is performed using ab initio quantum mechanical methods. Two plausible pathways of decomposition of the titled species have been considered, one involving C-O bond scission and the other occurring via F atom elimination. The geometries of the reactant, products and transition states involved in the decomposition pathways are optimized and characterized at DFT (B3LYP) level of theory using 6-311G(d,p) basis set. Single point energy calculations have been performed at G2M(CC,MP2) level of theory. Out of the two prominent decomposition channels considered, the C-O bond scission is found to be dominant involving a barrier height of 15.3 kcal mol(-1) whereas the F-elimination path proceeds with a barrier of 26.1 kcal mol(-1). The thermal rate constants for the above two decomposition pathways are evaluated using canonical transition state theory (CTST) and these are found to be 1.78 × 10(6) s(-1) and 2.83 × 10(-7) s(-1) for C-O bond scission and F-elimination respectively at 298 K and 1 atm pressure. Transition states are searched on the potential energy surfaces involved during the decomposition channels and each of the transition states is characterized. The existence of transition states on the corresponding potential energy surface is ascertained by performing intrinsic reaction coordinate (IRC) calculation.
journal_name
J Mol Modeljournal_title
Journal of molecular modelingauthors
Singh HJ,Mishra BKdoi
10.1007/s00894-010-0735-3subject
Has Abstractpub_date
2011-03-01 00:00:00pages
415-22issue
3eissn
1610-2940issn
0948-5023journal_volume
17pub_type
杂志文章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
pub_type： 杂志文章
doi：10.1007/s00894-011-1310-2
更新日期：2012-07-01 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
pub_type： 杂志文章
doi：10.1007/s00894-016-2969-1
更新日期：2016-05-01 00:00:00
abstract：:Selective A(2B) receptor antagonists and agonists may play a role in important pathologies such as gastrointestinal, neurological (i.e., Alzheimer disease and dementia) and hypersensitive disorders (i.e., asthma), diabetes, atherosclerosis, restenosis and cancer. Hence, it is regarded as a good target for the developm...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1427-y
更新日期：2012-09-01 00:00:00
abstract：:Recently, both lithium (Li) salts and Li electrides formed by one Li atom interacting with ligand complexes, have been widely investigated. An interesting question emerges: is the configuration of one Li atom interacting with ligand complexes a Li salt or electride? In the present work, four configurations n-Li-PNA (n...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-014-2560-6
更新日期：2015-02-01 00:00:00
abstract：:The binding behavior of coinage metal anions with some electron-deficient arenes has been investigated by MP2 calculations, and the character of interactions in these complexes has been examined by NBO analysis. The results indicate that coinage metal anions can interact with electron-deficient arenes to form anion-π,...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-015-2584-6
更新日期：2015-03-01 00:00:00
abstract：:The interaction of a model Lys flanked α-helical peptides K2-X24-K2, (X = A,I,L,L+A,V) with lipid bilayers composed of dimyristoylphosphatidylcholine (DMPC) and dipalmitoylphosphatidylcholine (DPPC) both, in a gel and in a liquid-crystalline state, has been studied by molecular dynamics simulations. It has been shown ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-012-1550-9
更新日期：2013-11-01 00:00:00
abstract：:The addition of C2 to HCN is of relevant interest in astrochemistry. We studied the pathways of this addition to produce CCCN and estimated its reaction rate using the Master Equation in the circumstellar environment. From the results of this study, it was possible to show that a different pathway in the Surface Poten...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3305-0
更新日期：2017-04-01 00:00:00
abstract：:Studying the electrochemical characteristics is an important step for determining interactions between molecules and the chemical environment. Moreover, the electrochemical evaluation of dyes is highly needed to establish the behavior of electro-active chemical species inside dye-sensitized solar cells (DSSCs). Four c...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-019-3955-1
更新日期：2019-02-27 00:00:00
abstract：:Although there are a multitude of aromaticity indexes, only a few have a widespread usage. All famous aromaticity indexes are limited: HOMA and FLU are reference-dependent; ELF is π-bond-dependent; PDI is structurally dependent and NICS is ring size dependent. These limitations stimulate the continuous search for bett...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-017-3433-6
更新日期：2017-09-01 00:00:00
abstract：:The structural, elastic and electronic properties of lutatium-pnictides (LuN, LuP, LuAs, LuSb, and LuBi) were analyzed by using full-potential linearized augmented plane wave within generalized gradient approximation in the stable rock-salt structure (B1 phase) with space group Fm-3m and high-pressure CsCl structure (...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-2021-7
更新日期：2013-12-01 00:00:00
abstract：:The original version of this article unfortunately contained a mistake. Schemes I and II were missing. These important components are given below. ...
journal_title：Journal of molecular modeling
pub_type： 已发布勘误
doi：10.1007/s00894-017-3466-x
更新日期：2017-11-01 00:00:00
abstract：:In this study, the newly synthesized non-centrosymmetric, 4-dimethylamino-3'-isothiocyanatochalcone (PKA) compound was presented. This compound belongs to the chalcone group, and its main purpose is to be used in biomedical imaging as a fluorescence dye. For this reason, the linear and nonlinear properties in solvents...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2990-4
更新日期：2016-06-01 00:00:00
abstract：:The increasing incidence of bacterial resistance to most available antibiotics has underlined the urgent need for the discovery of novel efficacious antibacterial agents. The biosynthesis of bacterial peptidoglycan, where the MurD enzyme is involved in the intracellular phase of UDP-MurNAc-pentapeptide formation, repr...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-009-0455-8
更新日期：2009-08-01 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
pub_type： 杂志文章
doi：10.1007/s00894-005-0263-8
更新日期：2005-11-01 00:00:00
abstract：:The cold shock protein from the hyperthermophile Thermotoga maritima (Tm-Csp) exhibits significantly higher thermostability than its homologue from the thermophile Bacillus caldolyticus (Bc-Csp). Experimental studies have shown that the electrostatic interactions unique to Tm-Csp are responsible for improving its ther...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-2958-4
更新日期：2016-04-01 00:00:00
abstract：:Defects in the nanoscale are common in the 2D materials irrespective of the fabricated method. Material performance gets significantly affected due to the presence of defects in 2D materials. In the present study, electronic and mechanical properties of 2D-hexagonal boron nitride (hBN) are investigated. At the electro...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-020-04452-y
更新日期：2020-07-03 00:00:00
abstract：:The optical properties of polymer/solvent systems composed by the polymers P3HT and PolyeraActivInk N2200 under the present of chloroform as solvent are experimentally and theoretically investigated using UV-Vis spectroscopy, molecular dynamics (MD), and density functional theory (DFT) calculations. The study is focus...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-016-3196-5
更新日期：2017-02-01 00:00:00
abstract：:The biological toxicity of uranyl ion (UO (2) (2+) ) lies in interacting with proteins and disrupting their native functions. The structural and functional consequences of UO (2) (2+) interacting with cytochrome b (5) (cyt b (5)), a small membrane heme protein, and its heme axial ligand His39Ser variant, cyt b (5) H39...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1097-1
更新日期：2012-03-01 00:00:00
abstract：:ORF 3a of human severe acute respiratory syndrome corona virus (SARS-CoV) has been identified as a 274 amino acid membrane protein. When expressed in Xenopus oocytes the protein forms channels. Based on bioinformatics approaches the topology has been identified to include three transmembrane domains (TMDs). Since stru...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-011-1092-6
更新日期：2012-02-01 00:00:00
abstract：:The applicability of the newly developed PM6 method for modeling proteins is investigated. In order to allow the geometries of such large systems to be optimized rapidly, three modifications were made to the conventional semiempirical procedure: the matrix algebra method for solving the self-consistent field (SCF) equ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-008-0420-y
更新日期：2009-07-01 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
pub_type： 杂志文章
doi：10.1007/s00894-005-0050-6
更新日期：2006-02-01 00:00:00
abstract：:The geometric and electronic structures, absorption spectra, transporting properties, chemical reactivity indices and electrostatic potentials of the planar three-coordinate organoboron compounds 1-2 and twisted reference compound Mes(3)B, have been investigated by employing density functional theory (DFT) and concept...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-013-1845-5
更新日期：2013-08-01 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
pub_type： 杂志文章
doi：10.1007/s00894-018-3727-3
更新日期：2018-06-29 00:00:00
abstract：:The distinguishing property of Sm protein associations is very high stability. In order to understand this property, we analyzed the interfaces and compared the properties of Sm protein interfaces with those of a test set, the Binding Interface Database (BID). The comparison revealed that the main differences between ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-010-0787-4
更新日期：2010-11-01 00:00:00
abstract：:To determine the kinase inhibitory potential of natural products that could be utilized in lung cancer therapy in the near future, a pharmacophore-based activity profiling protocol using parallel pharmacophore-based virtual screening of ZINC-a natural product database-was employed. The work presented here is based on ...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3849-7
更新日期：2018-10-20 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
pub_type： 杂志文章
doi：10.1007/s00894-006-0106-2
更新日期：2006-09-01 00:00:00
abstract：:The aquatic leech, Theromyzon tessulatum, secretes a proteinaceous cocoon with extraordinary physical properties (e.g., proteolytic, thermal resiliency). The deduced amino acid sequence of a major protein (Tcp-Theromyzon cocoon protein) from the T. tessulatum cocoon wall has been used to model the endogenous structure...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-006-0107-1
更新日期：2006-09-01 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
pub_type： 杂志文章
doi：10.1007/s00894-020-04656-2
更新日期：2021-01-03 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
pub_type： 杂志文章
doi：10.1007/s00894-015-2652-y
更新日期：2015-05-01 00:00:00
abstract：:Multi-tetrazole derivatives with conjugated structures were designed and investigated in this study. Using quantum chemistry methods, the crystal structures, electrostatic potentials (ESPs), multicenter bond orders, HOMO-LUMO energy gaps, and detonation properties of the derivatives were calculated. As expected, these...
journal_title：Journal of molecular modeling
pub_type： 杂志文章
doi：10.1007/s00894-018-3710-z
更新日期：2018-06-23 00:00:00
