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Ravi Sankar A, Arunachalam S, Gnanasekaran R. A computational study to determine the role of σ-hole in Br/OH substituted nido-carborane and its binding capabilities. J Mol Graph Model 2024; 127:108680. [PMID: 38039786 DOI: 10.1016/j.jmgm.2023.108680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 11/19/2023] [Indexed: 12/03/2023]
Abstract
A detailed investigation of the σ-hole on the halogen atom present in the nido-heteroboranes is made by employing quantum mechanical methods. The bromide and the hydroxyl groups are incorporated in the exo-substituents of the nido-boranes. The potential of the bromide σ-hole was compared to that of electrostatic potential of hydroxyl group counterpart. The presence of a carbon atom vertex, in a different position of a system, influences the σ-hole and hence its binding abilities. Bromide substituted nido-carboranes have less potential and hence weaker binding ability compared to their closo-counterparts. Binding affinity with aliphatic is found to be more compared to that of aromatic system. The presence of solvent dampened the electrostatic interactions. Apart from the neutral system, the binding capabilities of charged nido-heteroboranes were also studied. The results of this study will be further useful for several applications viz., crystal engineering, drug designing (Pharmaceuticals), medicine, material science, energy storage devices, etc.
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Keller W, Hofmann M, Wadepohl H, Enders M, Fanfrlík J, Hnyk D. Chlorinated polyhedral selenaboranes revisited by joint experimental/computational efforts: the formation of closo-1-SeB 9Cl 9 and the crystal structure of closo-SeB 11Cl 11. Dalton Trans 2023; 52:16886-16893. [PMID: 37916993 DOI: 10.1039/d3dt02987e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
The recent success in the formation of chlorinated telluraboranes and the reactivities of pnictogenaboranes prompted us to re-examine the vacuum co-pyrolysis of B2Cl4 with Se2Cl2 at various molar ratios and temperatures in order to search for the generation of other polyhedral selenaboranes than closo-SeB5Cl5 (1a) and closo-SeB11Cl11 (1b), the latter being observed earlier. Interestingly, a new compound with the elemental composition SeB9Cl9 (2) was detected, this time by high- and low-resolution mass spectrometry. Further characterization by 1- and 2-D 11B-NMR spectroscopy suggests that 2 should adopt a closed bicapped square-antiprismatic geometry with selenium at the apical position. Moreover, vacuum sublimation gave suitable crystals of 1b, which were subjected to single-crystal X-ray structure determination. Crystallographic data analysis confirmed that 1b, consistent with its 26 skeletal electron count, adopts a distorted icosahedral structure close to the symmetry of C5v. Computations at the DFT-D3 level have revealed that 33% of the total computed binding motifs in the grown 1b crystals are due to the very strong chalcogen bonding. Moreover, SAPT decomposition has shown that the bonding motifs in the crystals are stabilized mainly by dispersion and electrostatic terms. Homodecoupling and high resolution 11B NMR and 77Se NMR experiments have resolved both coupling constants 1J(11B11B) and 1J(77Se11B) as well as the 77Se chemical shift of 1a and 1b, which are in reasonable agreement with the corresponding computed values. The computed 11B chemical shifts of 2 were determined by the well-established DFT/GIAO/NMR structural tool based on its B3LYP/6-311+G** internal coordinates. They agree well with the experimental values and provide a good representation of the molecular structure of 2 in solution. The extraordinary downfield 11B NMR chemical shift of B(10) in 2 has been ascribed to the intensive paramagnetic contribution to the shielding tensor in this bicapped square-antiprismatic motif. Calculations of the synproportionation free energies of smaller (n - 1) closo-selenaboranes with larger-sized (n + 1) ones support the extraordinary stability of octahedral, bicapped square-antiprismatic and icosahedral closo motifs in the SeBnCln family (n = 4-12).
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Affiliation(s)
- Willi Keller
- Institut für Chemie, Universität Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany.
| | - Matthias Hofmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Hubert Wadepohl
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Markus Enders
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic.
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Keller W, Hofmann M, Sárosi MB, Fanfrlík J, Hnyk D. Reactivity of Perhalogenated Octahedral Phospha- and Arsaboranes toward THF: A Joint Experimental/Computational Study. Inorg Chem 2022; 61:16565-16572. [PMID: 36229410 DOI: 10.1021/acs.inorgchem.2c00971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions of the perhalogenated polyhedral pnictogenaboranes closo-1,2-Pn2B4Hal4 (Pn = P, As; Hal = Cl, Br) with Lewis bases are presently being studied with a focus on rationalizing the sites of nucleophilic attacks on clusters bearing σ-holes. These σ-holes are localized both on pnictogens and, for Hal = Br, on bromine atoms, as revealed by electrostatic potential (ESP) and intrinsic bond orbital (IBO) analyses. Surprisingly, the attack of the cyclic ether THF on closo-1,2-Pn2B4Br4 does not occur on the site with the largest positive partial charge, centered in the middle of the pnictogen-pnictogen vector. Instead, presumably promoted by the positivated bromine substituents, THF inserts into the boron-bromine bonds of the negatively charged boron atoms opposite to the pnictogen atoms to form 4-(4-bromobut-1-oxy)-closo-1,2-Pn2B4Br3 (1-PB and 1-AsB) and 4,6-(4-bromobut-1-oxy)2-closo-1,2-Pn2B4Br2 (2-PB and 2-AsB). 11B and 31P chemical shift computations at various levels support the assignments of the signals, which reflect the correctness of the molecular geometries in solutions. The Lewis-acidic perchlorinated analogues closo-1,2-P2B4Cl4, closo-1,2-As2B4Cl4, and the mixed closo-1,2-AsPB4Cl4 bear negative charges. These negative charges are revealed by the Vs,max values when computing the electrostatic potentials both on the boron and the chlorine atoms. Due to this negative charge, the analogues do not react with THF unless they are heated above 66 °C, where they slowly decompose to borate esters B(OR)3 without the formation of concrete intermediates. The evaluation of 31P NMR data of 1-PB has allowed the experimental determination of the coupling constant 1J(31P(1), 31P(2)) = |143| Hz in a closo-diphosphaborane for the first time, which agrees well with the computed value of -178 Hz. The pioneering joint experimental vs computational interpretation of 31P NMR spectra in the area of boron cluster chemistry was decisive for the structural characterization of 1-PB and 2-PB.
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Affiliation(s)
- Willi Keller
- Institut für Chemie, Universität Hohenheim, Garbenstrasse 30, 70599 Stuttgart, Germany
| | - Matthias Hofmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Menyhárt-Botond Sárosi
- Wilhelm-Ostwald-Institut für Physikalische und Theoretische Chemie, Universität Leipzig, Linnéstrasse 2, 04103 Leipzig, Germany
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
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Bakardjiev M, Holub J, Bavol D, Vrána J, Samsonov MA, Růžička A, Růžičková Z, Fanfrlík J, Hnyk D. Thiaborane Icosahedral Barrier Increased by the Functionalization of all Terminal Hydrogens in closo-1-SB 11H 11. Inorg Chem 2021; 60:8428-8431. [PMID: 34101456 DOI: 10.1021/acs.inorgchem.1c00796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrophilic substitution of icosahedral closo-1-SB11H11 with methyl iodide has resulted in two B-functionalized thiaboranes, 7,12-I2-2,3,4,5,6,8,9,10,11-(CH3)9-1-closo-SB11 and 7,8,12-I3-2,3,4,5,6,9,10,11-(CH3)8-closo-1-SB11, with the former being significantly predominant. These two icosahedral thiaboranes are the first cases of polysubstituted polyhedral boron clusters with another vertex that differs from B and C. Such polyfunctionalizations have increased the earlier observed thiaborane icosahedral barrier, not exhibiting any reactivity toward bases, unlike the parent thiaborane. The search for methylation pathways has revealed that the complete B11-methylation is impossible, like in the case of decaborane(14), where this seems to be a result of the positively charged upper parts of these two molecules.
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Affiliation(s)
- Mario Bakardjiev
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Dmytro Bavol
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
| | - Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Maksim A Samsonov
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 573, 532 10 Pardubice, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, 166 10 Praha 6, Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry, Czech Academy of Sciences, 250 68 Husinec-Řež, Czech Republic
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Murphy N, McCarthy E, Dwyer R, Farràs P. Boron clusters as breast cancer therapeutics. J Inorg Biochem 2021; 218:111412. [PMID: 33773323 DOI: 10.1016/j.jinorgbio.2021.111412] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/21/2021] [Accepted: 02/24/2021] [Indexed: 12/16/2022]
Abstract
Since the foundation of small molecule-based therapeutics over 100 years ago, their design has been dominated by organic based components. This has also been apparent in anti-cancer therapeutics in a broad range of strategies; from the older DNA chelating drugs, to the more recent molecular-targeted therapies. The main challenges facing current treatments; multidrug resistance and low therapeutic index, can potentially be alleviated by the incorporation of boron clusters. While retaining the versatility of their organic counterparts, these compounds offer a unique set of molecular interactions, which are a useful tool in targeted therapies and can improve many organic formulations with their incorporation. This review will discuss the potential of boron clusters in medicine while focusing on their activity in the breast cancer setting.
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Affiliation(s)
- Neville Murphy
- School of Chemistry, Ryan Institute, National University of Ireland, Galway H91CF50, Ireland; CÚRAM, the SFI Research Centre for Medical Devices, National University of Ireland, Galway H91W2TY, Ireland
| | - Elan McCarthy
- Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland
| | - Róisín Dwyer
- Lambe Institute for Translational Research, National University of Ireland, Galway, Ireland; CÚRAM, the SFI Research Centre for Medical Devices, National University of Ireland, Galway H91W2TY, Ireland
| | - Pau Farràs
- School of Chemistry, Ryan Institute, National University of Ireland, Galway H91CF50, Ireland; CÚRAM, the SFI Research Centre for Medical Devices, National University of Ireland, Galway H91W2TY, Ireland.
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Beau M, Lee S, Kim S, Han WS, Jeannin O, Fourmigué M, Aubert E, Espinosa E, Jeon IR. Strong σ-Hole Activation on Icosahedral Carborane Derivatives for a Directional Halide Recognition. Angew Chem Int Ed Engl 2021; 60:366-370. [PMID: 32926491 DOI: 10.1002/anie.202010462] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Indexed: 12/14/2022]
Abstract
Crystal engineering based on σ-hole interactions is an emerging approach for realization of new materials with higher complexity. Neutral inorganic clusters derived from 1,2-dicarba-closo-dodecaborane, substituted with -SeMe, -TeMe, and -I moieties on both skeletal carbon vertices are experimentally demonstrated herein as outstanding chalcogen- and halogen-bond donors. In particular, these new molecules strongly interact with halide anions in the solid-state. The halide ions are coordinated by one or two donor groups (μ1 - and μ2 -coordinations), to stabilize a discrete monomer or dimer motifs to 1D supramolecular zig-zag chains. Crucially, the observed chalcogen bond and halogen bond interactions feature remarkably short distances and high directionality. Electrostatic potential calculations further demonstrate the efficiency of the carborane derivatives, with Vs,max being similar or even superior to that of reference organic halogen-bond donors, such as iodopentafluorobenzene.
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Affiliation(s)
- Maxime Beau
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), Campus de Beaulieu, 35000, Rennes, France
| | - Sunhee Lee
- Department of Chemistry, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Sooyeon Kim
- Department of Chemistry, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Won-Sik Han
- Department of Chemistry, Seoul Women's University, Seoul, 01797, Republic of Korea
| | - Olivier Jeannin
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), Campus de Beaulieu, 35000, Rennes, France
| | - Marc Fourmigué
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), Campus de Beaulieu, 35000, Rennes, France
| | - Emmanuel Aubert
- Laboratoire CRM2, UMR CNRS 7036, Institut Jean Barriol, Université de Lorraine, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
| | - Enrique Espinosa
- Laboratoire CRM2, UMR CNRS 7036, Institut Jean Barriol, Université de Lorraine, BP 70239, 54506, Vandoeuvre-lès-Nancy, France
| | - Ie-Rang Jeon
- Univ Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes), Campus de Beaulieu, 35000, Rennes, France
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7
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Beau M, Lee S, Kim S, Han W, Jeannin O, Fourmigué M, Aubert E, Espinosa E, Jeon I. Strong
σ
‐Hole Activation on Icosahedral Carborane Derivatives for a Directional Halide Recognition. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Maxime Beau
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) Campus de Beaulieu 35000 Rennes France
| | - Sunhee Lee
- Department of Chemistry Seoul Women's University Seoul 01797 Republic of Korea
| | - Sooyeon Kim
- Department of Chemistry Seoul Women's University Seoul 01797 Republic of Korea
| | - Won‐Sik Han
- Department of Chemistry Seoul Women's University Seoul 01797 Republic of Korea
| | - Olivier Jeannin
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) Campus de Beaulieu 35000 Rennes France
| | - Marc Fourmigué
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) Campus de Beaulieu 35000 Rennes France
| | - Emmanuel Aubert
- Laboratoire CRM2 UMR CNRS 7036 Institut Jean Barriol Université de Lorraine BP 70239, 54506 Vandoeuvre-lès-Nancy France
| | - Enrique Espinosa
- Laboratoire CRM2 UMR CNRS 7036 Institut Jean Barriol Université de Lorraine BP 70239, 54506 Vandoeuvre-lès-Nancy France
| | - Ie‐Rang Jeon
- Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes) Campus de Beaulieu 35000 Rennes France
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8
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Fojt L, Grüner B, Šícha V, Nekvinda J, Vespalec R, Fojta M. Electrochemistry of icosahedral cobalt bis(dicarbollide) ions and their carbon and boron substituted derivatives in aqueous phosphate buffers. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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Shiekh BA, Kaur D, Kaur R. Probing non-covalent interactions of phosphine and arsine derivatives: an energy decomposition analysis using localized molecular orbitals. Struct Chem 2019. [DOI: 10.1007/s11224-019-01328-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
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12
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Unravelling the Importance of H bonds, σ–hole and π–hole-Directed Intermolecular Interactions in Nature. J Indian Inst Sci 2019. [DOI: 10.1007/s41745-019-00144-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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13
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Vrána J, Holub J, Růžičková Z, Fanfrlík J, Hnyk D, Růžička A. Investigation of Thiaborane closo- nido Conversion Pathways Promoted by N-Heterocyclic Carbenes. Inorg Chem 2019; 58:2471-2482. [PMID: 30729783 DOI: 10.1021/acs.inorgchem.8b03037] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 12-X- closo-SB11H10 (X = H or I) thiaboranes react with one or two molar equivalents of various N-heterocyclic carbenes (NHCs) to give the deprotonated 12-vertex species of [12-X-SB11H9·NHC]-[NHC-H]+composition as kinetic products. The use of one molar equivalent of a sterically more hindered NHC reactant leads to the formation of 12-X-SB11H10·NHC adducts with a heavily distorted cage and the nido electron count. Further reaction of 12-I-SB11H10·NHC to deboronated 12-X-SB10H9·NHC proceeds in acetone to complete the closo- nido reaction pathway under the thermodynamic control. The structures of all compounds have been investigated by NMR spectroscopy and diffraction techniques. The results are supported by theoretical methods.
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Affiliation(s)
- Jan Vrána
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry , Czech Academy of Sciences , 250 68 Řež , Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry , Czech Academy of Sciences , Flemingovo náměstí 542/2 , 166 10 Praha 6 , Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry , Czech Academy of Sciences , 250 68 Řež , Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology , University of Pardubice , Studentská 573 , 532 10 Pardubice , Czech Republic
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14
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Effect of external electric field on C–X ··· π halogen bonds. J Mol Model 2019; 25:57. [DOI: 10.1007/s00894-019-3938-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 01/24/2019] [Indexed: 01/20/2023]
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15
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Abstract
Noncovalent interactions in the single crystal of 3,6-Cl2-closo-1,2-P2B10H8 and in the crystal of closo-1,7-P2B10Cl10•toluene were analyzed by means of quantum chemical computations. The crystal packing in the second crystal was dominated by numerous B-Cl···Cl-B dihalogen and strong B-P···π pnictogen bonds, the latter of which were characterized by a small length of 3.08 Å and a large interaction energy value, exceeding −10 kcal mol−1.
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16
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Kříž K, Fanfrlík J, Lepšík M. Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations. Chemphyschem 2018; 19:2540-2548. [PMID: 30003638 DOI: 10.1002/cphc.201800409] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Indexed: 11/10/2022]
Abstract
A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the Protein Data Bank (PDB). We have found that a large fraction (23 %) of complexes with a S/Se-containing ligand feature close S/Se⋅⋅⋅O/N/S contacts. Eleven non-redundant representative potential S/Se⋅⋅⋅O chalcogen-bond motifs were selected and truncated to model systems and seven more model systems were prepared by S-to-Se substitution. These systems were then subjected to analysis by quantum chemical (QM) methods-electrostatic potential, geometry optimisation or interaction energy calculations, including solvent effects. The QM calculations indicate that chalcogen bonding does indeed play a dominant role in stabilising some of the interaction motifs studied. We thus advocate further exploration of chalcogen bonding with the aim of potential future use in structure-based drug design.
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Affiliation(s)
- Kristian Kříž
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic.,Department of Physical and Macromolecular Chemistry Faculty of Science, Charles University, Hlavova 8, 128 40, Praha 2, Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the, Czech Academy of Sciences, Flemingovo nám. 2, 16610, Prague 6, Czech Republic
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17
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Ababsa S, Zouchoune B. Electronic Structure and Relative Stabilities of 10- and 12-Vertex. Closoand Nido-Heteroborane Clusters of Ga, Ge, and As Elements. J STRUCT CHEM+ 2018. [DOI: 10.1134/s002247661802004x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Mahmudov KT, Kopylovich MN, Guedes da Silva MFC, Pombeiro AJL. Chalcogen bonding in synthesis, catalysis and design of materials. Dalton Trans 2018; 46:10121-10138. [PMID: 28686248 DOI: 10.1039/c7dt01685a] [Citation(s) in RCA: 274] [Impact Index Per Article: 45.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Chalcogen bonding is a type of noncovalent interaction in which a covalently bonded chalcogen atom (O, S, Se or Te) acts as an electrophilic species towards a nucleophilic (negative) region(s) in another or in the same molecule. In general, this interaction is strengthened by the presence of an electron-withdrawing group on the electron-acceptor chalcogen atom and upon moving down in the periodic table of elements, from O to Te. Following a short discussion of the phenomenon of chalcogen bonding, this Perspective presents some demonstrative experimental observations in which this bonding is crucial for synthetic transformations, crystal engineering, catalysis and design of materials as synthons/tectons.
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Affiliation(s)
- Kamran T Mahmudov
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal. and Department of Chemistry, Baku State University, Z. Xalilov Str. 23, Az 1148 Baku, Azerbaijan and Organic Chemistry Department, RUDN University, 6 Miklukho-Maklaya str., Moscow 117198, Russian Federation
| | - Maximilian N Kopylovich
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - M Fátima C Guedes da Silva
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
| | - Armando J L Pombeiro
- Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.
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Melichar P, Hnyk D, Fanfrlík J. A systematic examination of classical and multi-center bonding in heteroborane clusters. Phys Chem Chem Phys 2018; 20:4666-4675. [DOI: 10.1039/c7cp07422k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A systematic revision of bonding types on a broad series of heteroboranes covering closo, nido, arachno and hypho architectures with incorporated tetrel, pnictogen or chalcogen heterovertices.
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Affiliation(s)
- Petr Melichar
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i
- 250 68 Husinec-Řež
- Czech Republic
| | - Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
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Oliveira V, Cremer D, Kraka E. The Many Facets of Chalcogen Bonding: Described by Vibrational Spectroscopy. J Phys Chem A 2017; 121:6845-6862. [PMID: 28782954 DOI: 10.1021/acs.jpca.7b06479] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
A diverse set of 100 chalcogen-bonded complexes comprising neutral, cationic, anionic, divalent, and double bonded chalcogens has been investigated using ωB97X-D/aug-cc-pVTZ to determine geometries, binding energies, electron and energy density distributions, difference density distributions, vibrational frequencies, local stretching force constants, and associated bond strength orders. The accuracy of ωB97X-D was accessed by CCSD(T)/aug-cc-pVTZ calculations of a subset of 12 complexes and by the CCSD(T)/aug-cc-pVTZ //ωB97X-D binding energies of 95 complexes. Most of the weak chalcogen bonds can be rationalized on the basis of electrostatic contributions, but as the bond becomes stronger, covalent contributions can assume a primary role in the strength and geometry of the complexes. Covalency in chalcogen bonds involves the charge transfer from a lone pair orbital of a Lewis base into the σ* orbital of a divalent chalcogen or a π* orbital of a double bonded chalcogen. We describe for the first time a symmetric chalcogen-bonded homodimer stabilized by a charge transfer from a lone pair orbital into a π* orbital. New polymeric materials based on chalcogen bonds should take advantage of the extra stabilization granted by multiple chalcogen bonds, as is shown for 1,2,5-telluradiazole dimers.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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Štíbr B, Holub J, Bakardjiev M, Lane PD, McKee ML, Wann DA, Hnyk D. Unusual Cage Rearrangements in 10-Vertex nido-5,6-Dicarbaborane Derivatives: An Interplay between Theory and Experiment. Inorg Chem 2017; 56:852-860. [PMID: 28004918 DOI: 10.1021/acs.inorgchem.6b02320] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction between selected X-nido-5,6-C2B8H11 compounds (where X = Cl, Br, I) and "Proton Sponge" [PS; 1,8-bis(dimethylamino)naphthalene], followed by acidification, results in extensive rearrangement of all cage vertices. Specifically, deprotonation of 7-X-5,6-C2B8H11 compounds with one equivalent of PS in hexane or CH2Cl2 at ambient temperature led to a 7 → 10 halogen rearrangement, forming a series of PSH+[10-X-5,6-C2B8H10]- salts. Reprotonation using concentrated H2SO4 in CH2Cl2 generates a series of neutral carbaboranes 10-X-5,6-C2B8H11, with the overall 7 → 10 conversion being 75%, 95%, and 100% for X = Cl, Br, and I, respectively. Under similar conditions, 4-Cl-5,6-C2B8H11 gave ∼66% conversion to 3-Cl-5,6-C2B8H11. Since these rearrangements could not be rationalized using the B-vertex swing mechanism, new cage rearrangement mechanisms, which are substantiated using DFT calculations, have been proposed. Experimental 11B NMR chemical shifts are well reproduced by the computations; as expected δ(11B) for B(10) atoms in derivatives with X = Br and I are heavily affected by spin-orbit coupling.
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Affiliation(s)
- Bohumil Štíbr
- Institute of Inorganic Chemistry of the ASCR, v.v.i. , CZ-250 68 Husinec-Řež, Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry of the ASCR, v.v.i. , CZ-250 68 Husinec-Řež, Czech Republic
| | - Mario Bakardjiev
- Institute of Inorganic Chemistry of the ASCR, v.v.i. , CZ-250 68 Husinec-Řež, Czech Republic
| | - Paul D Lane
- Department of Chemistry, University of York , Heslington, York, U.K. YO10 5DD
| | - Michael L McKee
- Department of Chemistry and Biochemistry, Auburn University , Auburn, Alabama 36849, United States
| | - Derek A Wann
- Department of Chemistry, University of York , Heslington, York, U.K. YO10 5DD
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the ASCR, v.v.i. , CZ-250 68 Husinec-Řež, Czech Republic
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Fanfrlík J, Pecina A, Řezáč J, Sedlak R, Hnyk D, Lepšík M, Hobza P. B–H⋯π: a nonclassical hydrogen bond or dispersion contact? Phys Chem Chem Phys 2017; 19:18194-18200. [DOI: 10.1039/c7cp02762a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Quantum mechanical calculations disprove the attractive electrostatic nature of B–H⋯π motif and define it as dispersion-driven contact.
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Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Adam Pecina
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Robert Sedlak
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry of the Czech Academy of Sciences
- v.v.i., 250 68 Husinec-Řež
- Czech Republic
| | - Martin Lepšík
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences
- 166 10 Prague 6
- Czech Republic
- Regional Center of Advanced Technologies and Materials
- Department of Physical Chemistry
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Fanfrlík J, Holub J, Růžičková Z, Řezáč J, Lane PD, Wann DA, Hnyk D, Růžička A, Hobza P. Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes. Chemphyschem 2016; 17:3373-3376. [DOI: 10.1002/cphc.201600848] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/01/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Jindřich Fanfrlík
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic v.v.i.; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Josef Holub
- Institute of Inorganic Chemistry; Academy of Sciences of the Czech Republic v.v.i.; 250 68 Řež u Prahy Czech Republic
| | - Zdeňka Růžičková
- University of Pardubice; Studentská 573 Pardubice Czech Republic
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic v.v.i.; Flemingovo nám. 2 16610 Prague 6 Czech Republic
| | - Paul D. Lane
- Department of Chemistry; University of York, Heslington; York YO10 5DD UK
- School of Engineering and Physical Sciences; Heriot-Watt University, Riccarton; Edinburgh EH14 4AS UK
| | - Derek A. Wann
- Department of Chemistry; University of York, Heslington; York YO10 5DD UK
| | - Drahomír Hnyk
- Institute of Inorganic Chemistry; Academy of Sciences of the Czech Republic v.v.i.; 250 68 Řež u Prahy Czech Republic
| | - Aleš Růžička
- University of Pardubice; Studentská 573 Pardubice Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic v.v.i.; Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Center of Advanced Technologies and Materials; Department of Physical Chemistry; Palacký University; 77146 Olomouc Czech Republic
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Zierkiewicz W, Fanfrlík J, Hobza P, Michalska D, Zeegers-Huyskens T. Ab initio and DFT studies of the interaction between carbonyl and thiocarbonyl groups: the role of S···O chalcogen bonds. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1972-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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26
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Tang Q, Li Q. Enhancing effect of metal coordination interaction on pnicogen bonding. J Mol Model 2016; 22:64. [DOI: 10.1007/s00894-016-2929-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Accepted: 02/04/2016] [Indexed: 10/22/2022]
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Affiliation(s)
- Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Federal Republic of Germany
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacky University, 771 46 Olomouc, Czech Republic
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Fanfrlík J, Hnyk D. Chalcogens act as inner and outer heteroatoms in borane cages with possible consequences for σ-hole interactions. CrystEngComm 2016. [DOI: 10.1039/c6ce01861k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Wei Y, Li Q, Li W, Cheng J, McDowell SAC. Influence of the protonation of pyridine nitrogen on pnicogen bonding: competition and cooperativity. Phys Chem Chem Phys 2016; 18:11348-56. [PMID: 27055488 DOI: 10.1039/c6cp00551a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio MP2/aug-cc-pVTZ calculations were performed to investigate the pnicogen-bonded complexes of PyZX2 (Py = pyridine, Z = P and As, X = H and F) and their protonated analogues.
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Affiliation(s)
- Yuanxin Wei
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Wenzuo Li
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Jianbo Cheng
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- People's Republic of China
| | - Sean A. C. McDowell
- Department of Biological and Chemical Sciences
- The University of the West Indies
- Cave Hill Campus
- Barbados
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LIU YANZHI, YUAN KUN, YUAN ZHAO, ZHU YUANCHENG, ZHAO XIANG. Theoretical exploration of pnicogen bond noncovalent interactions in HCHO⋯PH2X (X=CH3, H, C6H5, F, Cl, Br, and NO2) complexes. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0933-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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31
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Lo R, Fanfrlík J, Lepšík M, Hobza P. The properties of substituted 3D-aromatic neutral carboranes: the potential for σ-hole bonding. Phys Chem Chem Phys 2015. [PMID: 26213995 DOI: 10.1039/c5cp03617h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The calculated properties of substituted carboranes such as dipole moment, polarisability, the magnitude of the σ-hole and the desolvation free energy are compared with these properties in comparable aromatic and cyclic aliphatic organic compounds. Dispersion and charge transfer energies are similar. However, the predicted strength of the halogen bonds with the same electron donor (based on the magnitude of the σ-hole) is larger for neutral C-vertex halogen-substituted carboranes than for their organic counterparts. Furthermore, the desolvation penalties of substituted carboranes are smaller than those of the corresponding organic compounds, which should further strengthen the halogen bonds of the former in the solvent. It is predicted that substituted carboranes have the potential to form stronger halogen bonds than comparable aromatic hydrocarbons, which will be even more pronounced in the medium. This theoretical study thus lays ground for the rational engineering of halogen bonding in inorganic crystals as well as in biomolecular complexes.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry (IOCB) and Gilead Sciences and IOCB Research Center, Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic.
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