当前位置： SCI文献检索 > JOURNAL OF MOLECULAR MODELING期刊下所有文献 > Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine.

Halogen bond tunability I: the effects of aromatic fluorine substitution on the strengths of halogen-bonding interactions involving chlorine, bromine, and iodine.

Abstract：

:In the past several years, halogen bonds have been shown to be relevant in crystal engineering and biomedical applications. One of the reasons for the utility of these types of noncovalent interactions in the development of, for example, pharmaceutical ligands is that their strengths and geometric properties are very tunable. That is, substitution of atoms or chemical groups in the vicinity of a halogen can have a very strong effect on the strength of the halogen bond. In this study we investigate halogen-bonding interactions involving aromatically-bound halogens (Cl, Br, and I) and a carbonyl oxygen. The properties of these halogen bonds are modulated by substitution of aromatic hydrogens with fluorines, which are very electronegative. It is found that these types of substitutions have dramatic effects on the strengths of the halogen bonds, leading to interactions that can be up to 100% stronger. Very good correlations are obtained between the interaction energies and the magnitudes of the positive electrostatic potentials (σ-holes) on the halogens. Interestingly, it is seen that the substitution of fluorines in systems containing smaller halogens results in electrostatic potentials resembling those of systems with larger halogens, with correspondingly stronger interaction energies. It is also shown that aromatic fluorine substitutions affect the optimal geometries of the halogen-bonded complexes, often as the result of secondary interactions.

journal_name

J Mol Model

journal_title

Journal of molecular modeling

authors

Riley KE,Murray JS,Fanfrlík J,Rezáč J,Solá RJ,Concha MC,Ramos FM,Politzer P

doi

10.1007/s00894-011-1015-6

subject

Has Abstract

pub_date

2011-12-01 00:00:00

pages

3309-18

issue

12

eissn

1610-2940

issn

0948-5023

journal_volume

17

pub_type

杂志文章

相关文献

JOURNAL OF MOLECULAR MODELING文献大全
  • Trends in σ-hole strengths and interactions of F3MX molecules (M = C, Si, Ge and X = F, Cl, Br, I).

    abstract：:It is well-established that many covalently-bonded atoms of Groups IV-VII have directionally-specific regions of positive electrostatic potential (σ-holes) through which they can interact with negative sites. In the case of Group VII, this is called "halogen bonding." We have studied two series of molecules: the F3MX ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1571-4

    authors： Bundhun A,Ramasami P,Murray JS,Politzer P

    更新日期：2013-07-01 00:00:00

  • A three-dimensional model of the human transglutaminase 1: insights into the understanding of lamellar ichthyosis.

    abstract：:The stratum corneum, the outer layer of the epidermis, serves as a protective barrier to isolate the skin from the external environment. Keratinocyte transglutaminase 1 (TGase 1) catalyzes amide crosslinking between glutamine and lysine residues on precursor proteins forming the impermeable layers of the epidermal cel...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-006-0144-9

    authors： Boeshans KM,Mueser TC,Ahvazi B

    更新日期：2007-01-01 00:00:00

  • Theoretical studies on metal porphyrin halides: geometrical parameters and nonlinear optical responses.

    abstract：:The geometrical parameters and static electric properties of several metal porphyrin halides, including Fe(III) porphine chloride (FePCl), Fe(III) porphine bromide (FePBr), Fe(III) tetraphenylporphine chloride (FeTPPCl), aluminum phthalocyanine chloride (AlPcCl), gallium(III) phthalocyanine chloride (GaPcCl), and mang...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0556-4

    authors： Asghari-Khiavi M,Safinejad F

    更新日期：2010-03-01 00:00:00

  • Syn- and anti-conformations of 5'-deoxy- and 5'-O-methyl-uridine 2',3'-cyclic monophosphate.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0019-5

    authors： Grabarkiewicz T,Hoffmann M

    更新日期：2006-01-01 00:00:00

  • Stability of rolled-up GaAs nanotubes.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3371-3

    authors： Silva JCF,Dos Santos JD,Taft CA,Martins JBL,Longo E

    更新日期：2017-07-01 00:00:00

  • Adsorption into the MFI zeolite of aromatic molecule of biological relevance. Investigations by Monte Carlo simulations.

    abstract：:Adsorption of paracresol and water into the silicalite-1 (MFI) zeolite has been investigated using canonical and grand-canonical Monte Carlo simulations. The most stable sites of adsorption of paracresol are found to be located at the channel intersections. Grand-canonical simulations have shown that at low loading, w...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0417-6

    authors： Boulet P,Narasimhan L,Berg'e-Lefranc D,Kuchta B,Schäf O,Denoyel R

    更新日期：2009-06-01 00:00:00

  • Predicting the efficiencies of 2-mercaptobenzothiazole collectors used as chelating agents in flotation processes: a density-functional study.

    abstract：:In recent years, several new chelating reagents have been synthesized and tested for their collecting power in sulfide and non-sulfide minerals flotation. Many researchers have indicated that chelating reagents have the advantage of offering better selectivity and specificity as flotation collectors. Therefore, densit...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-005-0092-9

    authors： Yekeler H,Yekeler M

    更新日期：2006-09-01 00:00:00

  • Pi-pi stacking tackled with density functional theory.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-007-0239-y

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

    更新日期：2007-12-01 00:00:00

  • The mechanism and kinetics of decomposition of 5-aminotetrazole.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-008-0290-3

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

    更新日期：2008-05-01 00:00:00

  • Periodic DFT modeling and vibrational analysis of silver(I) cyanide complexes of thioureas.

    abstract：:The structures of non-ionic [Ag(Tu)(CN)] (1) and ionic [Ag(Dmtu)2]+[Ag(CN)2]- (2) and [Ag(Imt)2]+[Ag(CN)2]- (3) silver(I) complexes, where Tu = thiourea, Dmtu = N,N'-dimethylthiourea and Imt = imidazoline-2-thione), were modeled by periodic DFT/PAW-PBE calculations; results were in good agreement with experiments. The...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-019-3970-2

    authors： Ahmad S,Georgieva I,Hanif M,Monim-Ul-Mehboob M,Munir S,Sohail A,Isab AA

    更新日期：2019-03-08 00:00:00

  • Distinct interactions between the human adrenergic beta(2) receptor and Galpha(s)--an in silico study.

    abstract：:The aim of this study was to perform an in silico analysis of the interaction of the human beta(2) adrenergic receptor with Galpha(s). In a first step, a systematic surface-interaction-scan between the inactive or active human beta(2) adrenergic receptor and Galpha(s) was performed in order to gain knowledge about ene...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0646-3

    authors： Strasser A,Wittmann HJ

    更新日期：2010-08-01 00:00:00

  • Study of the betulin molecule in a water environment; ab initio and molecular simulation calculations.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1055-y

    authors： Pospíšil M,Kovář P,Vácha R,Svoboda M

    更新日期：2012-01-01 00:00:00

  • Reaction mechanisms of DNT with hydroxyl radicals for advanced oxidation processes-a DFT study.

    abstract：:In advanced oxidation processes (AOPs), the detailed degradation mechanisms of a typical explosive of 2,4-dinitrotoluene (DNT) can be investigated by the density function theory (DFT) method at the SMD/M062X/6-311+G(d) level. Several possible degradation routes for DNT were explored in the current study. The results s...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3277-0

    authors： Zhou Y,Yang Z,Yang H,Zhang C,Liu X

    更新日期：2017-04-01 00:00:00

  • Racemization and transesterification of alkyl hydrogeno-phenylphosphinates.

    abstract：:In this article, we explore, both theoretically and experimentally, the general reactivity of alkyl hydrogeno-phenylphosphinates with alcohols. We show that alcohol molecules act exclusively as nucleophilic species, and add to alkyl hydrogeno-phenylphosphinates, leading to pentacoordinated intermediates. These interme...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3343-7

    authors： Javierre G,Fortrie R,Jean M,Moraleda D,Naubron JV,Fotiadu F

    更新日期：2017-05-01 00:00:00

  • Adsorption and dissociation of sulfur-based toxic gas molecules on silicene nanoribbons: a quest for high-performance gas sensors and catalysts.

    abstract：:The adsorption behavior of sulfur-based toxic gases (H2S and SO2) on armchair silicene nanoribbons (ASiNRs) was investigated using first-principles density functional theory (DFT). Being a zero band gap material, application of bulk silicene is limited in nanoelectronics, despite its high carrier mobility. By restrict...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3631-x

    authors： Walia GK,Randhawa DKK

    更新日期：2018-03-16 00:00:00

  • Simulation of homology models for the extracellular domains (ECD) of ErbB3, ErbB4 and the ErbB2-ErbB3 complex in their active conformations.

    abstract：:Epidermal growth factor receptors (EGFR) are associated with a number of biological processes and are becoming increasingly recognized as important therapeutic targets against cancer. In this work, we provide models based on homology for the extracellular domains (ECD) of ErbB3 and ErbB4 in their active conformations,...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1613-y

    authors： Franco-Gonzalez JF,Ramos J,Cruz VL,Martínez-Salazar J

    更新日期：2013-02-01 00:00:00

  • dockYard--a repository to assist modeling of protein-protein docking.

    abstract：:In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0758-9

    authors： Mitra P,Pal D

    更新日期：2011-03-01 00:00:00

  • Theoretical insights into thermal cyclophanediene to dihydropyrene electrocyclic reactions; a comparative study of Woodward Hoffmann allowed and forbidden reactions.

    abstract：:The thermally allowed electrocyclic reaction syn-cyclophanediene (CPD) to dihydropyrene (DHP) was compared with the disallowed thermal electrocyclic reaction in anti CPD through density functional theory (DFT) calculations at the B3LYP/6-31 + G(d) level. Moreover, the results were also compared with the electrocycliza...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-016-2948-6

    authors： Saima B,Khan A,Nisa RU,Mahmood T,Ayub K

    更新日期：2016-04-01 00:00:00

  • Structure-based design of nitrogen-linked macrocyclic kinase inhibitors leading to the clinical candidate SB1317/TG02, a potent inhibitor of cyclin dependant kinases (CDKs), Janus kinase 2 (JAK2), and Fms-like tyrosine kinase-3 (FLT3).

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1528-7

    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

  • Supramolecular synthon pattern in solid clioquinol and cloxiquine (APIs of antibacterial, antifungal, antiaging and antituberculosis drugs) studied by ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR and DFT/QTAIM.

    abstract：:The quinolinol derivatives clioquinol (5-chloro-7-iodo-8-quinolinol, Quinoform) and cloxiquine (5-chloro-8-quinolinol) were studied experimentally in the solid state via ³⁵Cl NQR, ¹H-¹⁷O and ¹H-¹⁴N NQDR spectroscopies, and theoretically by density functional theory (DFT). The supramolecular synthon pattern of O-H···N ...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0876-4

    authors： Latosińska JN,Latosińska M,Tomczak MA,Seliger J,Zagar V

    更新日期：2011-07-01 00:00:00

  • Mechanism and regioselectivity of electrophilic aromatic nitration in solution: the validity of the transition state approach.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-017-3561-z

    authors： Liljenberg M,Stenlid JH,Brinck T

    更新日期：2017-12-18 00:00:00

  • Molecular dynamics and QM/MM-based 3D interaction analyses of cyclin-E inhibitors.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-012-1620-z

    authors： Pasha FA,Neaz MM

    更新日期：2013-02-01 00:00:00

  • The effect of cross linking density on the mechanical properties and structure of the epoxy polymers: molecular dynamics simulation.

    abstract：:Recently, great attention has been focused on using epoxy polymers in different fields such as aerospace, automotive, biotechnology, and electronics, owing to their superior properties. In this study, the classical molecular dynamics (MD) was used to simulate the cross linking of diglycidyl ether of bisphenol-A (DGEBA...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-1906-9

    authors： Shokuhfar A,Arab B

    更新日期：2013-09-01 00:00:00

  • Theoretical investigations into the intermolecular hydrogen-bonding interactions of N-(hydroxymethyl)acetamide dimers.

    abstract：:The structures of the N-(hydroxymethyl)acetamide (model molecule of ceramide) dimers have been fully optimized at B3LYP/6-311++G** level. The intermolecular hydrogen bonding interaction energies have been calculated using the B3LYP/6-311++G**, B3LYP/6-311++G(2df,2p), MP2(full)/6-311++G** and MP2(full)/6-311++G(2df,2p)...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-018-3672-1

    authors： Tang HF,Zhong H,Zhang LL,Gong MX,Song SQ,Tian QP

    更新日期：2018-05-31 00:00:00

  • Studies on filarial GST as a target for antifilarial drug development-in silico and in vitro inhibition of filarial GST by substituted 1,4-naphthoquinones.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0952-9

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

    更新日期：2011-10-01 00:00:00

  • Use of molecular modeling, docking, and 3D-QSAR studies for the determination of the binding mode of benzofuran-3-yl-(indol-3-yl)maleimides as GSK-3beta inhibitors.

    abstract：:Molecular modeling and docking studies along with three-dimensional quantitative structure relationships (3D-QSAR) studies have been used to determine the correct binding mode of glycogen synthase kinase 3beta (GSK-3beta) inhibitors. The approaches of comparative molecular field analysis (CoMFA) and comparative molecu...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-009-0498-x

    authors： Kim KH,Gaisina I,Gallier F,Holzle D,Blond SY,Mesecar A,Kozikowski AP

    更新日期：2009-12-01 00:00:00

  • A density functional theory study on oxygen reduction reaction on nitrogen-doped graphene.

    abstract：:Nitrogen (N)-doped carbons reportedly exhibit good electrocatalytic activity for the oxygen reduction reaction (ORR) of fuel cells. This work provides theoretical insights into the ORR mechanism of N-doped graphene by using density functional theory calculations. All possible reaction pathways were investigated, and t...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-013-2047-x

    authors： Zhang J,Wang Z,Zhu Z

    更新日期：2013-12-01 00:00:00

  • Ab initio study of electron transport in 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate.

    abstract：:The electron transport of the 4-(3-nitro-4-tetrafluorophenylthiolate-ethynyl, phenylethynyl) benzenethiolate (S-FNPPB-o) molecule assembled in two Au (111) electrodes, was studied using two approaches: in the first approximate approach an electric field was applied to the pure molecule attached to two thiolate ends fi...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-011-1106-4

    authors： Serrato-Villegas L,Gallo M,Delgado-Ríos M,Romero MT,Glossman-Mitnik D

    更新日期：2012-02-01 00:00:00

  • Computational simulations of structural role of the active-site W374C mutation of acetyl-coenzyme-A carboxylase: multi-drug resistance mechanism.

    abstract：:Herbicides targeting grass plastidic acetyl-CoA carboxylase (ACCase, EC 6.4.1.2) are selectively effective against graminicides. The intensive worldwide use of this herbicide family has selected for resistance genes in a number of grass weed species. Recently, the active-site W374C mutation was found to confer multi-d...

    journal_title：Journal of molecular modeling

    pub_type： 杂志文章

    doi：10.1007/s00894-010-0742-4

    authors： Zhu XL,Yang WC,Yu NX,Yang SG,Yang GF

    更新日期：2011-03-01 00:00:00

  • Trapping N5 rings and N3 chains on the outer surface of fullerene C60: a theoretical study.

    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

    pub_type： 杂志文章

    doi：10.1007/s00894-015-2811-1

    authors： Liang Y,Gao X,Li N,Zhang X

    更新日期：2015-10-01 00:00:00