301
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Tranchant I, Vera L, Czarny B, Amoura M, Cassar E, Beau F, Stura EA, Dive V. Halogen bonding controls selectivity of FRET substrate probes for MMP-9. ACTA ACUST UNITED AC 2014; 21:408-13. [PMID: 24583051 DOI: 10.1016/j.chembiol.2014.01.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 01/07/2014] [Accepted: 01/13/2014] [Indexed: 11/18/2022]
Abstract
Matrix metalloproteinases (MMPs) are a large family of zinc-dependent endoproteases that catalyze cleavage of extracellular matrix and nonmatrix proteins. MMPs play a role in tissue remodeling, and their uncontrolled activity is associated with number of diseases, including tumor metastasis. Thus, there is a need to develop methods to monitor MMP activity, and number of probes has been previously described. The key problem many probes encounter is the issue of selectivity, since 23 human MMPs, despite playing different physiological roles, have structurally similar active sites. Here, we introduce the halogen bonding concept into the probe design and show that the probe containing iodine exhibits an unprecedented selectivity for MMP-9. We provide structure-based explanation for the selectivity, confirming that it is due to formation of the halogen bond that supports catalysis, and we highlight the value of exploring halogen bonding in the context of selective probe design.
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Affiliation(s)
- Isabelle Tranchant
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Laura Vera
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Bertrand Czarny
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Mehdi Amoura
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Evelyne Cassar
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Fabrice Beau
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Enrico A Stura
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France
| | - Vincent Dive
- CEA, iBiTec-S, Service d'Ingénierie Moléculaire des Protéines (SIMOPRO), Labex LERMIT, CE-Saclay, 91191 Gif sur Yvette Cedex, France.
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302
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Mu X, Wang Q, Wang LP, Fried SD, Piquemal JP, Dalby KN, Ren P. Modeling organochlorine compounds and the σ-hole effect using a polarizable multipole force field. J Phys Chem B 2014; 118:6456-65. [PMID: 24484473 PMCID: PMC4065202 DOI: 10.1021/jp411671a] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
The charge distribution of halogen
atoms on organochlorine compounds
can be highly anisotropic and even display a so-called σ-hole,
which leads to strong halogen bonds with electron donors. In this
paper, we have systematically investigated a series of chloromethanes
with one to four chloro substituents using a polarizable multipole-based
molecular mechanics model. The atomic multipoles accurately reproduced
the ab initio electrostatic potential around chloromethanes, including
CCl4, which has a prominent σ-hole on the Cl atom.
The van der Waals parameters for Cl were fitted to the experimental
density and heat of vaporization. The calculated hydration free energy,
solvent reaction fields, and interaction energies of several homo-
and heterodimer of chloromethanes are in good agreement with experimental
and ab initio data. This study suggests that sophisticated electrostatic
models, such as polarizable atomic multipoles, are needed for accurate
description of electrostatics in organochlorine compounds and halogen
bonds, although further improvement is necessary for better transferability.
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Affiliation(s)
- Xiaojiao Mu
- Department of Biomedical Engineering, ‡Division of Medicinal Chemistry, College of Pharmacy, The University of Texas at Austin , Texas 78712, United States
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303
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Xu Z, Yang Z, Liu Y, Lu Y, Chen K, Zhu W. Halogen Bond: Its Role beyond Drug–Target Binding Affinity for Drug Discovery and Development. J Chem Inf Model 2014; 54:69-78. [DOI: 10.1021/ci400539q] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhijian Xu
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Zhuo Yang
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yingtao Liu
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Yunxiang Lu
- Department
of Chemistry, East China University of Science and Technology, Shanghai, 200237, China
| | - Kaixian Chen
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Weiliang Zhu
- Drug
Discovery and Design Center, Key Laboratory of Receptor Research,
State Key Laboratory of Drug Research, Shanghai Institute of Materia
Medica, Chinese Academy of Sciences, Shanghai, 201203, China
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304
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Viger-Gravel J, Meyer JE, Korobkov I, Bryce DL. Probing halogen bonds with solid-state NMR spectroscopy: observation and interpretation of J(77Se,31P) coupling in halogen-bonded PSe⋯I motifs. CrystEngComm 2014. [DOI: 10.1039/c4ce00345d] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Intra-halogen bond J couplings measured via NMR spectroscopy and interpreted using natural localized molecular orbitals offer novel insights into this class of non-covalent interaction.
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Affiliation(s)
- Jasmine Viger-Gravel
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| | - Julia E. Meyer
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| | - Ilia Korobkov
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
| | - David L. Bryce
- Department of Chemistry and Center for Catalysis Research and Innovation
- University of Ottawa
- Ottawa, Canada
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305
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Chen JH, Liu YM, Zhang JX, Zhu YY, Tang MS, Ng SW, Yang G. Halogen-involving weak interactions manifested in the crystal structures of silver(i) or gold(i) 4-halogenated-3,5-diphenylpyrazolato trimers. CrystEngComm 2014. [DOI: 10.1039/c4ce00029c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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306
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Kolář M, Hostaš J, Hobza P. The strength and directionality of a halogen bond are co-determined by the magnitude and size of the σ-hole. Phys Chem Chem Phys 2014; 16:9987-96. [DOI: 10.1039/c3cp55188a] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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307
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Singh R, Meena JS, Chang YC, Wu CS, Ko FH. Control of active semiconducting layer packing in organic thin film transistors through synthetic tailoring of dielectric materials. RSC Adv 2014. [DOI: 10.1039/c4ra02077d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
The influence of dielectric material's property on the solid state structure packing of active semiconducting layer in OTFTs has been carefully studied by employing a whole new family of dielectric materials based on the rigid, tetrahedral bulky moleculei.e.adamantane, a smallest cage structure of diamond.
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Affiliation(s)
- Ranjodh Singh
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
| | - Jagan Singh Meena
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
- Department of Electronics Engineering
- National Chiao Tung University
| | - Yu-Cheng Chang
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
| | - Chung-Shu Wu
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
| | - Fu-Hsiang Ko
- Department of Materials Science and Engineering
- National Chiao Tung University
- Hsinchu, Taiwan
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308
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Saha S, Ganguly S, Desiraju GR. Graded IR Filters: Distinguishing Between Single and Multipoint NO2···I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons). Aust J Chem 2014. [DOI: 10.1071/ch14361] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The NO2···I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2···I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2···I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and R and in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.
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309
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Groni S, Maby-Raud T, Fave C, Branca M, Schöllhorn B. Electrochemical controlling and monitoring of halogen bond formation in solution. Chem Commun (Camb) 2014; 50:14616-9. [DOI: 10.1039/c4cc04134h] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclic voltammetry has been used for the first time to probe and to activate non-covalent halogen bonding via redox switching in solution.
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Affiliation(s)
- Sihem Groni
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- 75205 Paris Cedex 13, France
| | - Tanguy Maby-Raud
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- 75205 Paris Cedex 13, France
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- 75205 Paris Cedex 13, France
| | - Mathieu Branca
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- 75205 Paris Cedex 13, France
| | - Bernd Schöllhorn
- Laboratoire d'Electrochimie Moléculaire
- UMR CNRS 7591
- Université Paris Diderot
- 75205 Paris Cedex 13, France
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310
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Jones RH, Knight KS, Marshall WG, Clews J, Darton RJ, Pyatt D, Coles SJ, Horton PN. Colossal thermal expansion and negative thermal expansion in simple halogen bonded complexes. CrystEngComm 2014. [DOI: 10.1039/c3ce41909f] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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311
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Šimák O, Pachl P, Fábry M, Buděšínský M, Jandušík T, Hnízda A, Skleničková R, Petrová M, Veverka V, Řezáčová P, Brynda J, Rosenberg I. Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-nucleotidases. Org Biomol Chem 2014; 12:7971-82. [DOI: 10.1039/c4ob01332h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Conformationally constrained nucleoside phosphonic acids – potent inhibitors of human mitochondrial and cytosolic 5′(3′)-deoxynucleotidases.
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Affiliation(s)
- Ondřej Šimák
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Petr Pachl
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Milan Fábry
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
- 14220 Prague 4, Czech Republic
| | - Miloš Buděšínský
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Tomáš Jandušík
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Department of Chemistry of Natural Compounds
- Institute of Chemical Technology
| | - Aleš Hnízda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Radka Skleničková
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Magdalena Petrová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
| | - Pavlína Řezáčová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Jiří Brynda
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
- Institute of Molecular Genetics
- of Sciences of the Czech Republic
| | - Ivan Rosenberg
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6, Czech Republic
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312
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Bauzá A, Mooibroek TJ, Frontera A. Influence of ring size on the strength of carbon bonding complexes between anions and perfluorocycloalkanes. Phys Chem Chem Phys 2014; 16:19192-7. [DOI: 10.1039/c4cp01983k] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
High level ab initio calculations and Cambridge Structural Database analysis were used to demonstrate the importance of carbon bonding in cyclobutane rings.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares), Spain
| | - Tiddo J. Mooibroek
- School of Chemistry of the University of Bristol
- Cantock's Close
- Bristol, UK
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca (Baleares), Spain
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313
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Abstract
Halogens are atypical elements in biology, but are common as substituents in ligands, including thyroid hormones and inhibitors, which bind specifically to proteins and nucleic acids. The short-range, stabilizing interactions of halogens - now seen as relatively common in biology - conform generally to halogen bonds characterized in small molecule systems and as described by the σ-hole model. The unique properties of biomolecular halogen bonds (BXBs), particularly in their geometric and energetic relationship to classic hydrogen bonds, make them potentially powerful tools for inhibitor design and molecular engineering. This chapter reviews the current research on BXBs, focusing on experimental studies on their structure-energy relationships, how these studies inform the development of computational methods to model BXBs, and considers how BXBs can be applied to the rational design of more effective inhibitors against therapeutic targets and of new biological-based materials.
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Affiliation(s)
- P Shing Ho
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523-1870, USA,
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314
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Hoque MM, Halim MA, Rahman MM, Hossain MI, Khan MW. Synthesis and structural insights of substituted 2-iodoacetanilides and 2-iodoanilines. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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315
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Cotrina EY, Pinto M, Bosch L, Vilà M, Blasi D, Quintana J, Centeno NB, Arsequell G, Planas A, Valencia G. Modulation of the Fibrillogenesis Inhibition Properties of Two Transthyretin Ligands by Halogenation. J Med Chem 2013; 56:9110-21. [DOI: 10.1021/jm401061w] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Ellen Y. Cotrina
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Marta Pinto
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Lluís Bosch
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Marta Vilà
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Daniel Blasi
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Jordi Quintana
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Nuria B. Centeno
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Gemma Arsequell
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Antoni Planas
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
| | - Gregorio Valencia
- Laboratory of Biochemistry, Bioengineering
Department, Institut Químic de Sarrià, Universitat Ramon Llull, ‡Pharmacoinformatics Group, Research
Programme on Biomedical Informatics (GRIB), Department of Experimental
and Health Sciences, Universitat Pompeu Fabra, IMIM (Hospital del Mar Medical Research Institute)-Universitat Pompeu Fabra, §Institut de Química Avançada de Catalunya
(IQAC−CSIC), ⊥Drug Discovery Platform, Parc Científic de Barcelona, Barcelona, Spain
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316
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Vander Zanden CM, Carter M, Ho PS. Determining thermodynamic properties of molecular interactions from single crystal studies. Methods 2013; 64:12-8. [DOI: 10.1016/j.ymeth.2013.07.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Revised: 07/25/2013] [Accepted: 07/30/2013] [Indexed: 12/01/2022] Open
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317
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Tian W, Sun K, Li Q, Li W, Cheng J. Substitution effect of superhalogens in MX3MCN-YF and MX3MCCY-NH3 complexes: Comparison with XMCN-YF and XMCCY-NH3. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.08.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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318
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The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design. Chempluschem 2013; 78:921-931. [DOI: 10.1002/cplu.201300199] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Indexed: 12/19/2022]
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319
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Carter M, Voth AR, Scholfield MR, Rummel B, Sowers LC, Ho PS. Enthalpy–Entropy Compensation in Biomolecular Halogen Bonds Measured in DNA Junctions. Biochemistry 2013; 52:4891-903. [DOI: 10.1021/bi400590h] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Megan Carter
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Andrea Regier Voth
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Matthew R. Scholfield
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Brittany Rummel
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
| | - Lawrence C. Sowers
- Department of Pharmacology and
Toxicology, University of Texas Medical Branch, Galveston, Texas 77555, United States
| | - P. Shing Ho
- Department of Biochemistry and
Molecular Biology, Colorado State University, Fort Collins, Colorado 80523, United States
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320
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Nagels N, Hauchecorne D, Herrebout WA. Exploring the C-X…π halogen bonding motif: an infrared and Raman study of the complexes of CF₃X (X = Cl, Br and I) with the aromatic model compounds benzene and toluene. Molecules 2013; 18:6829-51. [PMID: 23752468 PMCID: PMC6270472 DOI: 10.3390/molecules18066829] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/29/2013] [Accepted: 05/31/2013] [Indexed: 11/16/2022] Open
Abstract
The formation of halogen bonded complexes formed between the trifluorohalomethanes CF₃Cl, CF₃Br and CF₃I and the Lewis bases benzene and toluene at temperatures below 150K was investigated using FTIR and Raman spectroscopy. Experiments using liquid krypton as solvent show that for both CF₃Br and CF₃I substantial fractions of the monomers can be involved in 1:1 complexes. In addition, weak absorptions illustrating the formation of 2:1 complexes between CF₃I and benzene are observed. Using spectra recorded at temperatures between 120 and 140 K, observed information on the relative stability was obtained for all complexes by determining the complexation enthalpies in solution. The resulting values for CF₃Br.benzene, CF₃I.benzene and (CF₃I)₂.benzene are -6.5(3), -7.6(2) and -14.5(9) kJ mol⁻¹. The values for CF₃Br.toluene and CF₃I.toluene are -6.2(5) and -7.4(5) kJ mol⁻¹. The experimental complexation enthalpies are compared with theoretical data obtained by combining results from MP2/aug-cc-pVDZ(-PP) and MP2/aug-cc-pVTZ(-PP) ab initio calculations, from statistical thermodynamical calculations and from Monte Carlo Free Energy Perturbation simulations. The data are also compared with results derived for other C-X···π halogen bonded complexes involving unsaturated Lewis bases such as ethene and ethyne.
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Affiliation(s)
| | | | - Wouter A. Herrebout
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +32-3-265-3373; FAX: +32-3-265-3205
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