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Rahali E, Noori Z, Arfaoui Y, Poater J. Chalcogen Noncovalent Interactions between Diazines and Sulfur Oxides in Supramolecular Circular Chains. Int J Mol Sci 2024; 25:7497. [PMID: 39000604 PMCID: PMC11242197 DOI: 10.3390/ijms25137497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2024] [Revised: 06/30/2024] [Accepted: 07/06/2024] [Indexed: 07/16/2024] Open
Abstract
The noncovalent chalcogen interaction between SO2/SO3 and diazines was studied through a dispersion-corrected DFT Kohn-Sham molecular orbital together with quantitative energy decomposition analyses. For this, supramolecular circular chains of up to 12 molecules were built with the aim of checking the capability of diazine molecules to detect SO2/SO3 compounds within the atmosphere. Trends in the interaction energies with the increasing number of molecules are mainly determined by the Pauli steric repulsion involved in these σ-hole/π-hole interactions. But more importantly, despite the assumed electrostatic nature of the involved interactions, the covalent component also plays a determinant role in its strength in the involved chalcogen bonds. Noticeably, π-hole interactions are supported by the charge transfer from diazines to SO2/SO3 molecules. Interaction energies in these supramolecular complexes are not only determined by the S···N bond lengths but attractive electrostatic and orbital interactions also determine the trends. These results should allow us to establish the fundamental characteristics of chalcogen bonding based on its strength and nature, which is of relevance for the capture of sulfur oxides.
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Affiliation(s)
- Emna Rahali
- Laboratory of Characterizations, Applications and Modeling of Materials (LR18ES08), Department of Chemistry, University of Tunis El Manar, Tunis 1068, Tunisia; (E.R.); (Y.A.)
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
| | - Zahra Noori
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
| | - Youssef Arfaoui
- Laboratory of Characterizations, Applications and Modeling of Materials (LR18ES08), Department of Chemistry, University of Tunis El Manar, Tunis 1068, Tunisia; (E.R.); (Y.A.)
| | - Jordi Poater
- Department de Química Inorgànica i Orgànica & IQTCUB, Universitat de Barcelona, Martí i Franquès 1-11, 08028 Barcelona, Spain;
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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2
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AIEE Active Stilbene Based Fluorescent Sensor with Red-Shifted Emission for Vapor Phase Detection of Nitrobenzene and Moisture Sensing. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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3
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The structure, stability, thermochemistry, and bonding in SO3-(H2O)n (n = 1–7) clusters: a computational analysis. Struct Chem 2022. [DOI: 10.1007/s11224-022-02085-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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4
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Sajid H, Khan S, Ayub K, Amjad Gilani M, Mahmood T, Farooq U, Akhter MS. Ab initio study for superior sensitivity of graphyne nanoflake towards nitrogen halides over ammonia. J Mol Model 2022; 28:161. [PMID: 35597854 DOI: 10.1007/s00894-022-05159-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 05/12/2022] [Indexed: 11/30/2022]
Abstract
Graphyne (GYN) has received immense attention in gas adsorption applications due to its large surface area. The adsorption of toxic ammonia and nitrogen halides gaseous molecules on graphyne has been theoretically studied at ωB97XD/6-31 + G(d, p) level of DFT. The counterpoise corrected interaction energies of NH3, NF3, NCl3, and NBr3 molecules with GYN are - 4.73, - 2.27, - 5.22, and - 7.19 kcal mol-1, respectively. Symmetry-adapted perturbation theory (SAPT0) and noncovalent interaction index (NCI) reveal that the noncovalent interaction between analytes and GYN is dominated by dispersion forces. The significant change in electronic behavior, i.e., energies of HOMO and LUMO orbitals and NBO charge transfer correspond to the pronounced sensitivity of GYN towards considered analytes, especially NBr3. Finally, TD-DFT calculation reveals a decrease in electronic transition energies and shifting of adsorption to a longer wavelength. The recovery time for NX3@GYN is observed in nanoseconds, which is many orders of magnitude smaller than the reported systems. The recovery time is further decreased with increasing temperature, indicating that the GYN benefits from a short recovery time as a chemical sensor.
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Affiliation(s)
- Hasnain Sajid
- School of Science and Technology, Nottingham Trent University, Clifton Lane, Nottingham, NG11 8NS, UK
| | - Sidra Khan
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Mazhar Amjad Gilani
- Department of Chemistry, COMSATS University Islamabad, Lahore Campus, Lahore, Pakistan
| | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan. .,Department of Chemistry, College of Science, University of Bahrain, P. O. Box 32038, Zallaq, Bahrain.
| | - Umar Farooq
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad, 22060, Pakistan
| | - Mohammed Salim Akhter
- Department of Chemistry, College of Science, University of Bahrain, P. O. Box 32038, Zallaq, Bahrain
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5
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Effect of water molecule in the structure, stability, and electronic properties of sulfur trioxide clusters: a computational analysis. MONATSHEFTE FUR CHEMIE 2022. [DOI: 10.1007/s00706-022-02909-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Bhattarai S, Sutradhar D, Huyskens TZ, Chandra AK. Nature and Strength of the π‐Hole Chalcogen Bonded Complexes between Substituted Pyridines and SO
3
Molecule. ChemistrySelect 2021. [DOI: 10.1002/slct.202101981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Sumitra Bhattarai
- Department of Chemistry North-Eastern Hill University Shillong 793022 India
| | | | | | - Asit K. Chandra
- Department of Chemistry North-Eastern Hill University Shillong 793022 India
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7
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Wang X, Li Y, Wang H, Ni Y, Wang H. Which triel bond is stronger? TrHX⋯H2Y versus TrH2X⋯H2Y (Tr = Ga, In; X = F, Cl, Br, I; Y = O, S). Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02790-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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8
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Asif M, Sajid H, Ullah F, Khan S, Ayub K, Amjad Gilani M, Arshad M, Salim Akhter M, Mahmood T. Quantum chemical study on sensing of NH3, NF3, NCl3 and NBr3 by using cyclic tetrapyrrole. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113221] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Mehta N, Fellowes T, White JM, Goerigk L. CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions? J Chem Theory Comput 2021; 17:2783-2806. [PMID: 33881869 DOI: 10.1021/acs.jctc.1c00006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.
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Affiliation(s)
- Nisha Mehta
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Thomas Fellowes
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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10
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Effective adsorption of A-series chemical warfare agents on graphdiyne nanoflake: a DFT study. J Mol Model 2021; 27:117. [PMID: 33796926 DOI: 10.1007/s00894-021-04730-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/14/2021] [Indexed: 10/21/2022]
Abstract
Chemical warfare agents (CWAs) are highly poisonous and their presence may cause diverse effects not only on living organisms but also on environment. Therefore, their detection and removal in a short time span is very important. In this regard, here the utility of graphdiyne (GDY) nanoflake is studied theoretically as an electrochemical sensor material for the hazardous CWAs including A-230, A-232, and A-234. Herein, we explain the phenomenon of adsorption of A-series CWAs on GDY nanoflake within the density functional theory (DFT) framework. The characterisation of adsorption is based on optimised geometries, BSSE-corrected energies, SAPT0, RDG, FMO, CHELPG charge transfer, QTAIM and UV-Vis analyses. The calculated counterpoise adsorption energies for reported complexes range from - 13.70 to - 17.19 kcal mol-1. These adsorption energies show that analytes are physiosorbed onto GDY which usually takes place through noncovalent interactions. The noncovalent adsorption of CWAs on GDY is also attributed by the SAPT0, RDG and QTAIM analyses. These properties also reveal that dispersion factors dominate in the complexes among many noncovalent components (exchange, induction, electrostatic, steric and repulsion). In order to estimate the sensitivity of GDY, the %sensitivity and average energy gap variations are quantitatively measured by energies of HOMO and LUMO orbitals. In terms of adsorption affinity of GDY, UV-Vis analysis, CHELPG charge transfer and DOS analyses depict an appreciable response towards these toxic CWAs. Graphical abstract.
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11
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Abstract
The heavier chalcogen atoms S, Se, and Te can each participate in a range of different noncovalent interactions. They can serve as both proton donor and acceptor in H-bonds. Each atom can also act as electron acceptor in a chalcogen bond.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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12
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Khan S, Sajid H, Ayub K, Mahmood T. Sensing of toxic Lewisite (L
1
, L
2
, and L
3
) molecules by graphdiyne nanoflake using density functional theory calculations and quantum theory of atoms in molecule analysis. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4181] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Sidra Khan
- Department of Chemistry COMSATS University Islamabad‐Abbottabad Campus Abbottabad Pakistan
| | - Hasnain Sajid
- Department of Chemistry COMSATS University Islamabad‐Abbottabad Campus Abbottabad Pakistan
| | - Khurshid Ayub
- Department of Chemistry COMSATS University Islamabad‐Abbottabad Campus Abbottabad Pakistan
| | - Tariq Mahmood
- Department of Chemistry COMSATS University Islamabad‐Abbottabad Campus Abbottabad Pakistan
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13
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High sensitivity of graphdiyne nanoflake toward detection of phosgene, thiophosgene and phosogenoxime; a first-principles study. J Mol Graph Model 2020; 100:107658. [DOI: 10.1016/j.jmgm.2020.107658] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 11/24/2022]
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14
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Local Vibrational Mode Analysis of π–Hole Interactions between Aryl Donors and Small Molecule Acceptors. CRYSTALS 2020. [DOI: 10.3390/cryst10070556] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
11 aryl–lone pair and three aryl–anion π –hole interactions are investigated, along with the argon–benzene dimer and water dimer as reference compounds, utilizing the local vibrational mode theory, originally introduced by Konkoli and Cremer, to quantify the strength of the π –hole interaction in terms of a new local vibrational mode stretching force constant between the two engaged monomers, which can be conveniently used to compare different π –hole systems. Several factors have emerged which influence strength of the π –hole interactions, including aryl substituent effects, the chemical nature of atoms composing the aryl rings/ π –hole acceptors, and secondary bonding interactions between donors/acceptors. Substituent effects indirectly affect the π –hole interaction strength, where electronegative aryl-substituents moderately increase π –hole interaction strength. N-aryl members significantly increase π –hole interaction strength, and anion acceptors bind more strongly with the π –hole compared to charge neutral acceptors (lone–pair donors). Secondary bonding interactions between the acceptor and the atoms in the aryl ring can increase π –hole interaction strength, while hydrogen bonding between the π –hole acceptor/donor can significantly increase or decrease strength of the π –hole interaction depending on the directionality of hydrogen bond donation. Work is in progress expanding this research on aryl π –hole interactions to a large number of systems, including halides, CO, and OCH3− as acceptors, in order to derive a general design protocol for new members of this interesting class of compounds.
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15
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Regium Bonds between Silver(I) Pyrazolates Dinuclear Complexes and Lewis Bases (N2, OH2, NCH, SH2, NH3, PH3, CO and CNH). CRYSTALS 2020. [DOI: 10.3390/cryst10020137] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A theoretical study and Cambridge Structural Database (CSD) search of dinuclear Ag(I) pyrazolates interactions with Lewis bases were carried out and the effect of the substituents and ligands on the structure and on the aromaticity were analyzed. A relationship between the intramolecular Ag–Ag distance and stability was found in the unsubstituted system, which indicates a destabilization at longer distances compensated by ligands upon complexation. It was also observed that the asymmetrical interaction with phosphines as ligands increases the Ag–Ag distance. This increase is dramatically higher when two simultaneous PH3 ligands are taken into account. The calculated 109Ag chemical shielding shows variation up to 1200 ppm due to the complexation. Calculations showed that six-membered rings possessed non-aromatic character while pyrazole rings do not change their aromatic character significantly upon complexation.
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16
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Mikherdov AS, Katkova SA, Novikov AS, Efremova MM, Reutskaya EY, Kinzhalov MA. (Isocyano group)⋯lone pair interactions involving coordinated isocyanides: experimental, theoretical and CSD studies. CrystEngComm 2020. [DOI: 10.1039/c9ce01741k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both carbon and nitrogen centers in the coordinated isocyano group are capable of acting as a π-hole donor toward lone pairs.
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Affiliation(s)
| | | | | | - Mariia M. Efremova
- Saint Petersburg State University
- 199034 Saint Petersburg
- Russian Federation
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17
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Previtali V, Sánchez-Sanz G, Trujillo C. Theoretical Investigation of Cyano-Chalcogen Dimers and Their Importance in Molecular Recognition. Chemphyschem 2019; 20:3186-3194. [PMID: 31608563 DOI: 10.1002/cphc.201900899] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 10/07/2019] [Indexed: 11/10/2022]
Abstract
In this manuscript the different noncovalent interactions established between (HYCN)2 dimers (Y=S, Se and Te) have been studied at the MP2 and CCSD(T) level of theory. Several homodimers have been taken into account, highlighting the capacity of these compounds to act both as electron donor and acceptor. The main properties studied were geometries, binding energy (Eb ), and molecular electrostatic potential (MEP). Given the wide application of chalcogen bonds, and more specifically of cyano-chalcogen moieties in molecular recognition, natural bond orbital (NBO), "atoms-in-molecules" (AIM), and electron density shift (EDS) analysis were also used to analyse the different noncovalent interactions upon complexation. The presence of hydrogen, chalcogen and dipole-dipole interactions was confirmed and their implications on molecular recognition were analysed.
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Affiliation(s)
- Viola Previtali
- Center for Nanomedicine & Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby, DK, Denmark
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland & School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Cristina Trujillo
- School of Chemistry Trinity Biomedical Sciences Institute, Trinity College Dublini, 152-160 Pearse Street, Dublin 2, Ireland
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18
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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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19
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Enhancing effects of π-hole tetrel bonds on the σ-hole interactions in complexes involving F2TO (T = Si, Ge, Sn). Struct Chem 2019. [DOI: 10.1007/s11224-018-1274-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Cooperative Effects in Weak Interactions: Enhancement of Tetrel Bonds by Intramolecular Hydrogen Bonds. Molecules 2019; 24:molecules24020308. [PMID: 30654469 PMCID: PMC6359400 DOI: 10.3390/molecules24020308] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 01/08/2019] [Accepted: 01/09/2019] [Indexed: 12/02/2022] Open
Abstract
A series of silyl and germanium complexes containing halogen atoms (fluorine and chlorine atoms) and exhibiting tetrel bonds with Lewis bases were analyzed by means of Møller-Plesset computational theory. Binding energies of germanium derivatives were more negative than silicon ones. Amongst the different Lewis bases utilized, ammonia produced the strongest tetrel bonded complexes in both Ge and Si cases, and substitution of the F atom by Cl led to stronger complexes with an ethylene backbone. However, with phenyl backbones, the fluorosilyl complexes were shown to be less stable than the chlorosilyl ones, but the opposite occurred for halogermanium complexes. In all the cases studied, the presence of a hydroxyl group enhanced the tetrel bond. That effect becomes more remarkable when an intramolecular hydrogen bond between the halogen and the hydrogen atom of the hydroxyl group takes places.
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21
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Gogoi A, Nashre-ul-Islam SM, Frontera A, Bhattacharyya MK. Supramolecular association in Cu(II) and Co(II) coordination complexes of 3,5-dimethylpyrazole: Experimental and theoretical studies. Inorganica Chim Acta 2019. [DOI: 10.1016/j.ica.2018.09.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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Ams MR, Trapp N, Schwab A, Milić JV, Diederich F. Chalcogen Bonding "2S-2N Squares" versus Competing Interactions: Exploring the Recognition Properties of Sulfur. Chemistry 2018; 25:323-333. [PMID: 30600860 DOI: 10.1002/chem.201804261] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Indexed: 12/25/2022]
Abstract
Chalcogen bonding (CB) is the focus of increased attention for its applications in medicinal chemistry, materials science, and crystal engineering. However, the origin of sulfur's recognition properties remains controversial, and experimental evidence for supporting theories is still emerging. Here, a comprehensive evaluation of sulfur CB interactions is presented by investigating 2,1,3-benzothiadiazole X-ray crystallographic structures gathered from the Cambridge Structure Database (CSD), Protein Data Bank (PDB), and own laboratory findings. Through the systematic analysis of substituent effects on a subset library of over thirty benzothiadiazole derivatives, the competing interactions have been categorized into four main classes, namely 2S-2N CB square, halogen bonding (XB), S⋅⋅⋅S, and hydrogen-bonding (HB). A geometric model is employed to characterize the 2S-2N CB square motifs and discuss the role of electrostatic, dipole, and orbital contributions toward the interaction.
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Affiliation(s)
- Mark R Ams
- Department of Chemistry, Allegheny College, Meadville, PA, 16335, USA
| | - Nils Trapp
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | - Anatol Schwab
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | - Jovana V Milić
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
| | - François Diederich
- Laboratory of Organic Chemistry, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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23
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Michalczyk M, Zierkiewicz W, Scheiner S. Triel-Bonded Complexes between TrR3
(Tr=B, Al, Ga; R=H, F, Cl, Br, CH3
) and Pyrazine. Chemphyschem 2018; 19:3122-3133. [DOI: 10.1002/cphc.201800774] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Indexed: 01/20/2023]
Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University Logan; Utah 84322-0300 United States
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24
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Comparison between Tetrel Bonded Complexes Stabilized by σ and π Hole Interactions. Molecules 2018; 23:molecules23061416. [PMID: 29891824 PMCID: PMC6100375 DOI: 10.3390/molecules23061416] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 06/08/2018] [Accepted: 06/09/2018] [Indexed: 01/22/2023] Open
Abstract
The σ-hole tetrel bonds formed by a tetravalent molecule are compared with those involving a π-hole above the tetrel atom in a trivalent bonding situation. The former are modeled by TH₄, TH₃F, and TH₂F₂ (T = Si, Ge, Sn) and the latter by TH₂=CH₂, THF=CH₂, and TF₂=CH₂, all paired with NH₃ as Lewis base. The latter π-bonded complexes are considerably more strongly bound, despite the near equivalence of the σ and π-hole intensities. The larger binding energies of the π-dimers are attributed to greater electrostatic attraction and orbital interaction. Each progressive replacement of H by F increases the strength of the tetrel bond, whether σ or π. The magnitudes of the maxima of the molecular electrostatic potential in the two types of systems are not good indicators of either the interaction energy or even the full Coulombic energy. The geometry of the Lewis acid is significantly distorted by the formation of the dimer, more so in the case of the σ-bonded complexes, and this deformation intensifies the σ and π holes.
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25
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Mikherdov AS, Kinzhalov MA, Novikov AS, Boyarskiy VP, Boyarskaya IA, Avdontceva MS, Kukushkin VY. Ligation-Enhanced π-Hole···π Interactions Involving Isocyanides: Effect of π-Hole···π Noncovalent Bonding on Conformational Stabilization of Acyclic Diaminocarbene Ligands. Inorg Chem 2018; 57:6722-6733. [PMID: 29792332 DOI: 10.1021/acs.inorgchem.8b01027] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The reaction of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with the aminoazoles [1 H-imidazol-2-amine (1), 4 H-1,2,4-triazol-3-amine (2), 1 H-tetrazol-5-amine (3), 1 H-benzimidazol-2-amine (4), 1-alkyl-1 H-benzimidazol-2-amines, where alkyl = Me (5), Et (6)] in a 2:1 ratio in the presence of a base in CHCl3 at RT proceeds regioselectively and leads to the binuclear diaminocarbene complexes [(ClPdCNXyl)2{μ-C(N-azolyl)N(Xyl)C═NXyl}] (7-12; 73-91%). Compounds 7-12 were characterized by C, H, N elemental analyses, high-resolution ESI+-MS, Fourier transform infrared spectroscopy, 1D (1H, 13C) and 2D (1H,1H-COSY, 1H,1H-NOESY, 1H,13C-HSQC, 1H,13C-HMBC) NMR spectroscopies, and X-ray diffraction (XRDn). Inspection of the XRDn data and results of the Hirshfeld surface analysis suggest the presence in all six structures of intramolecular π-holeisocyanide···πarene interactions between the electrophilic C atom of the isocyanide moiety and the neighboring arene ring. These interactions also result in distortion of the Pd-C≡N-Xyl fragment from the linearity. Results of density functional theory calculations [M06/MWB28 (Pd) and 6-31G* (other atoms) level of theory] for model structures of 7-9 followed by the topological analysis of the electron density distribution within the framework of Bader's theory (QTAIM method) reveal the presence of these weak interactions also in a CHCl3 solution, and their calculated strength is 1.9-2.2 kcal/mol. The natural bond orbital analysis of 7-9 revealed that π(C-C)Xyl → π*(C-N)isocyanide charge transfer (CT) takes place along with the intramolecular π-holeisocyanide···πarene interactions. The observed π(C-C)Xyl → π*(C-N)isocyanide CT is due to ligation of the isocyanide to the metal center, whereas in the cases of the uncomplexed p-CNC6H4NC and CNXyl species, the effects of CT are negligible. Available CCDC data were processed from the perspective of isocyanide-involving π-hole···π interactions, disclosed the role of metal coordination in the π-hole donor ability of isocyanides, and verified the π-holeisocyanide···πarene interaction effect on the stabilization of the in-conformation in metal-bound acyclic diaminocarbenes.
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Affiliation(s)
- Alexander S Mikherdov
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
| | - Mikhail A Kinzhalov
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
| | - Alexander S Novikov
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
| | - Vadim P Boyarskiy
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
| | - Irina A Boyarskaya
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
| | - Margarita S Avdontceva
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
| | - Vadim Yu Kukushkin
- Saint Petersburg State University , 7/9 Universitetskaya Nab ., Saint Petersburg , 199034 , Russian Federation
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Bauzá A, Frontera A. Chalcogen 'like-like' Interactions Involving Trisulphide and Triselenide Compounds: A Combined CSD and Ab Initio Study. Molecules 2018; 23:molecules23030699. [PMID: 29562728 PMCID: PMC6017106 DOI: 10.3390/molecules23030699] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 11/30/2022] Open
Abstract
In this manuscript, we combined a search in the Cambridge Structural Database (CSD) and ab initio calculations (RI-MP2/def2-TZVPD level of theory) to analyze the ability of trisulphide and triselenide moieties to establish chalcogen ‘like-like’ interactions. A preliminary CSD inspection revealed two predominant structural patterns, depending on the anti or syn conformation adopted by the substituents of the S3/Se3 bridge, leading to bifurcated or double chalcogen bonding interactions, respectively. In order to analyze these two relevant structural motifs we have used a series of S and Se derivatives Ch3X2 (Ch = S and Se and X = H, F, CN, and CF3) which act as both electron donor (using the lone pairs) and acceptor (using the σ-holes) entities. Besides, we have carried out “atoms in molecules” (AIM) and natural bonding orbital (NBO) analyses to further describe and characterize the chalcogen bonding interactions described herein. As far as we know, chalcogen···chalcogen interactions involving trichalconides (S3/Se3) have not been previously described in literature a may be of great importance in the preparation and characterization of new solids based on this subclass of σ-hole bonding.
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Affiliation(s)
- Antonio Bauzá
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
| | - Antonio Frontera
- Department of Chemistry, Universitat de les Illes Balears, Crta de Valldemossa km 7.5, 07122 Palma de Mallorca (Baleares), Spain.
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Venkataramanan NS, Suvitha A. Nature of bonding and cooperativity in linear DMSO clusters: A DFT, AIM and NCI analysis. J Mol Graph Model 2018. [PMID: 29524753 DOI: 10.1016/j.jmgm.2018.02.010] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
This study aims to cast light on the nature of interactions and cooperativity that exists in linear dimethyl sulfoxide (DMSO) clusters using dispersion corrected density functional theory. In the linear DMSO, DMSO molecules in the middle of the clusters are bound strongly than at the terminal. The plot of the total binding energy of the clusters vs the cluster size and mean polarizabilities vs cluster size shows an excellent linearity demonstrating the presence of cooperativity effect. The computed incremental binding energy of the clusters remains nearly constant, implying that DMSO addition at the terminal site can happen to form an infinite chain. In the linear clusters, two σ-hole at the terminal DMSO molecules were found and the value on it was found to increase with the increase in cluster size. The quantum theory of atoms in molecules topography shows the existence of hydrogen and SO⋯S type in linear tetramer and larger clusters. In the dimer and trimer SO⋯OS type of interaction exists. In 2D non-covalent interactions plot, additional peaks in the regions which contribute to the stabilization of the clusters were observed and it splits in the trimer and intensifies in the larger clusters. In the trimer and larger clusters in addition to the blue patches due to hydrogen bonds, additional, light blue patches were seen between the hydrogen atom of the methyl groups and the sulphur atom of the nearby DMSO molecule. Thus, in addition to the strong H-bonds, strong electrostatic interactions between the sulphur atom and methyl hydrogens exists in the linear clusters.
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Affiliation(s)
| | - Ambigapathy Suvitha
- Department of Chemistry, School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Thanjavur, 613 401, India
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28
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Zierkiewicz W, Michalczyk M, Scheiner S. Aerogen bonds formed between AeOF 2 (Ae = Kr, Xe) and diazines: comparisons between σ-hole and π-hole complexes. Phys Chem Chem Phys 2018; 20:4676-4687. [PMID: 29345698 DOI: 10.1039/c7cp08048d] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interaction between KrOF2 or XeOF2 and the 1,2, 1,3, and 1,4 diazines is characterized chiefly by a Kr/XeN aerogen bond, as deduced from ab initio calculations. The most stable dimers take advantage of the σ-hole on the aerogen atom, wherein the two molecules lie in the same plane. The interaction is quite strong, as much as 18 kcal mol-1. A second class of dimer geometry utilizes the π-hole above the aerogen atom in an approximate perpendicular arrangement of the two monomers; these structures are not as strongly bound: 6-8 kcal mol-1. Both sorts of dimers contain auxiliary CHF H-bonds which contribute to their stability, but even with their removal, the aerogen bond energy remains as high as 14 kcal mol-1. The nature and strength of each specific interaction is confirmed and quantified by AIM, NCI, NBO, and electron density shift patterns. There is not a great deal of sensitivity to the identity of either the aerogen atom or the position of the two N atoms in the diazine.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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Frontera A, Bauzá A. Concurrent aerogen bonding and lone pair/anion-π interactions in the stability of organoxenon derivatives: a combined CSD and ab initio study. Phys Chem Chem Phys 2018; 19:30063-30068. [PMID: 29095452 DOI: 10.1039/c7cp06685f] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
In this manuscript the ability of organoxenon fluorides to establish concurrent π-hole aerogen bonding and lone pair/anion-π interactions has been studied at the RI-MP2/def2-TZVP level of theory. The presence of both an aromatic system (benzene, trifluorobenzene and pentafluorobenzene) and a xenon atom makes these molecules suitable for simultaneously establishing both interactions. In this regard, we have used CH3CN, NH3, O(CH3)2, Cl-, CN- and BF4- as neutral and charged electron donors, respectively. Moreover, the NBO analysis showed that orbital effects contribute to the global stabilization of the complexes studied. Furthermore, we have used Bader's theory of "atoms in molecules" to analyse and characterize the noncovalent interactions described herein from a charge-density perspective. Finally, several examples retrieved from the CSD are also included, highlighting the impact of these interactions in the solid state chemistry of Xe.
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Affiliation(s)
- Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain.
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30
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Buralli GJ, Duarte DJR, Peruchena NM, Alkorta I. Simultaneous Occurrence of Quadruple Lewis Acid-Base Interactions between Selenium Atoms in Selenocarbonyl Dimers. Chemphyschem 2017; 18:3498-3503. [DOI: 10.1002/cphc.201700682] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/25/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Gabriel J. Buralli
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física; Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Avenida Libertad 5460 3400 Corrientes Argentina
- IQUIBA-NEA (UNNE-CONICET); Avenida Libertad 5460 3400 Corrientes Argentina
| | - Darío J. R. Duarte
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física; Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Avenida Libertad 5460 3400 Corrientes Argentina
- IQUIBA-NEA (UNNE-CONICET); Avenida Libertad 5460 3400 Corrientes Argentina
| | - Nélida M. Peruchena
- Laboratorio de Estructura Molecular y Propiedades, Área de Química Física; Departamento de Química, Facultad de Ciencias Exactas y Naturales y Agrimensura; Universidad Nacional del Nordeste; Avenida Libertad 5460 3400 Corrientes Argentina
- IQUIBA-NEA (UNNE-CONICET); Avenida Libertad 5460 3400 Corrientes Argentina
| | - Ibon Alkorta
- Instituto de Química Médica, CSIC; Juan de la Cierva, 3 28006 Madrid Spain
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31
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Echeverría J. Frustrated Lewis Trios and Long-Range Hole Interactions: A Combined Structural and Theoretical Study of LB−AX3
⋅⋅⋅LB and LB⋅⋅⋅AX3
⋅⋅⋅LB (A=B, Al, Ga, In) Systems. Chemphyschem 2017; 18:2864-2872. [DOI: 10.1002/cphc.201700856] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Indexed: 11/11/2022]
Affiliation(s)
- Jorge Echeverría
- Departament de Química Inorgànica i Orgànica and Institut de Química Teòrica i Computacional IQTC-UB; Universitat de Barcelona; Martí i Franquès 1-11 08028 Barcelona Spain
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Bauzá A, Seth SK, Frontera A. Molecular electrostatic potential and “atoms-in-molecules” analyses of the interplay between π-hole and lone pair···π/X-H···π/metal···π interactions. J Comput Chem 2017; 39:458-463. [DOI: 10.1002/jcc.24869] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 06/08/2017] [Accepted: 06/11/2017] [Indexed: 01/19/2023]
Affiliation(s)
- Antonio Bauzá
- Department of Chemistry; Universitat de les Illes Balears, Crta de Valldemossa km 7.5; Palma de Mallorca Baleares 07122 Spain
| | - Saikat Kumar Seth
- Department of Chemistry; Universitat de les Illes Balears, Crta de Valldemossa km 7.5; Palma de Mallorca Baleares 07122 Spain
- Department of Physics; Jadavpur University; Kolkata 700032 India
| | - Antonio Frontera
- Department of Chemistry; Universitat de les Illes Balears, Crta de Valldemossa km 7.5; Palma de Mallorca Baleares 07122 Spain
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33
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Bauzá A, Frontera A. On the Importance of Nonbonding Donor-Acceptor Interactions Involving PO2.Radicals: An ab Initio Study. Chemphyschem 2017; 18:2191-2196. [DOI: 10.1002/cphc.201700399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 05/24/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Antonio Bauzá
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Baleares Spain
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34
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Zhao Q. Theoretical study of noncovalent interactions in XCN···YO2H (X = F, Cl, Br, I; Y = P, As, Sb) complexes. J Mol Model 2017; 23:188. [DOI: 10.1007/s00894-017-3358-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 04/24/2017] [Indexed: 10/19/2022]
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35
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Wang Y, Li X, Zeng Y, Meng L, Zhang X. Theoretical insights into the π-hole interactions in the complexes containing triphosphorus hydride (P 3H 3) and its derivatives. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2017; 73:195-202. [PMID: 28362282 DOI: 10.1107/s2052520616019223] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 12/02/2016] [Indexed: 06/07/2023]
Abstract
The π-hole of triphosphorus hydride (P3H3) and its derivatives Z3X3 (Z = P, As; X = H, F, Cl, Br) was discovered and analyzed. MP2/aug-cc-pVDZ calculations were performed on the π-hole interactions in the HCN...Z3X3 complexes and the mutual influence between π-hole interactions and the hydrogen bond in the HCN...HCN...Z3X3 and HCN...Z3X3...HCN complexes studied. The π-hole interaction belongs to the typical closed-shell noncovalent interaction. The linear relationship was found between the most positive electrostatic potential of the π-hole (VS,max) and the interaction energy. Moreover, the VS,max of the π-hole was also found to be linearly correlated to the electrostatic energy term, indicating the important contribution of the electrostatic energy term to the π-hole interaction. There is positive cooperativity between the π-hole interaction and the hydrogen bond in the termolecular complexes. The π-hole interaction has a greater influence on the hydrogen bond than vice versa. The mutual enhancing effect between the π-hole interaction and the hydrogen bond in the HCN...HCN...Z3X3 complexes is greater than that in the HCN...Z3X3...HCN complexes.
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Affiliation(s)
- Yuehong Wang
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Xiaoyan Li
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Yanli Zeng
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Lingpeng Meng
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
| | - Xueying Zhang
- College of Chemistry and Material Sciences, Key Laboratory of Inorganic Nano-materials of Hebei Province, Hebei Normal University, Shijiazhuang, Hebei 050024, People's Republic of China
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Bauzá A, Frontera A. On the Importance of π-Hole Beryllium Bonds: Theoretical Study and Biological Implications. Chemistry 2017; 23:5375-5380. [DOI: 10.1002/chem.201700682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Antonio Bauzá
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Antonio Frontera
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
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Bauzá A, Frontera A. Competition between lone pair-π, halogen-π and triel bonding interactions involving BX3 (X = F, Cl, Br and I) compounds: an ab initio study. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2068-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Bauzá A, García-Llinás X, Frontera A. Charge-assisted triel bonding interactions in solid state chemistry: A combined computational and crystallographic study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.11.010] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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39
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Mikherdov AS, Kinzhalov MA, Novikov AS, Boyarskiy VP, Boyarskaya IA, Dar'in DV, Starova GL, Kukushkin VY. Difference in Energy between Two Distinct Types of Chalcogen Bonds Drives Regioisomerization of Binuclear (Diaminocarbene)Pd II Complexes. J Am Chem Soc 2016; 138:14129-14137. [PMID: 27700082 DOI: 10.1021/jacs.6b09133] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The reaction of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with various 1,3-thiazol- and 1,3,4-thiadiazol-2-amines in chloroform gives a mixture of two regioisomeric binuclear diaminocarbene complexes. For 1,3-thiazol-2-amines the isomeric ratio depends on the reaction conditions and kinetically (KRs) or thermodynamically (TRs) controlled regioisomers were obtained at room temperature and on heating, respectively. In CHCl3 solutions, the isomers are subject to reversible isomerization accompanied by the cleavage of Pd-N and C-N bonds in the carbene fragment XylNCN(R)Xyl. Results of DFT calculations followed by the topological analysis of the electron density distribution within the formalism of Bader's theory (AIM method) reveal that in CHCl3 solution the relative stability of the regioisomers (ΔGexp = 1.2 kcal/mol; ΔGcalcd = 3.2 kcal/mol) is determined by the energy difference between two types of the intramolecular chalcogen bonds, viz. S···Cl in KRs (2.8-3.0 kcal/mol) and S···N in TRs (4.6-5.3 kcal/mol). In the case of the 1,3,4-thiadiazol-2-amines, the regioisomers are formed in approximately equal amounts and, accordingly, the energy difference between these species is only 0.1 kcal/mol in terms of ΔGexp (ΔGcalcd = 2.1 kcal/mol). The regioisomers were characterized by elemental analyses (C, H, N), HRESI+-MS and FTIR, 1D (1H, 13C{1H}) and 2D (1H,1H-COSY, 1H,1H-NOESY, 1H,13C-HSQC, 1H,13C-HMBC) NMR spectroscopies, and structures of six complexes (three KRs and three TRs) were elucidated by single-crystal X-ray diffraction.
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Affiliation(s)
- Alexander S Mikherdov
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Mikhail A Kinzhalov
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Alexander S Novikov
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Vadim P Boyarskiy
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Irina A Boyarskaya
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Dmitry V Dar'in
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Galina L Starova
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
| | - Vadim Yu Kukushkin
- Saint Petersburg State University , 7/9 Universitetskaya Nab., Saint Petersburg, 199034, Russian Federation
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40
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Bauzá A, Frontera A. On the Versatility of BH 2 X (X=F, Cl, Br, and I) Compounds as Halogen-, Hydrogen-, and Triel-Bond Donors: An Ab Initio Study. Chemphyschem 2016; 17:3181-3186. [PMID: 27428897 DOI: 10.1002/cphc.201600683] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Indexed: 11/08/2022]
Abstract
In this manuscript, the ability of BH2 X compounds (X=F, Cl, Br, and I) to establish halogen-, hydrogen-, and triel-bonding interactions was studied at the RI-MP2/aug-cc-pVQZ level of theory. Several homodimers were taken into account, highlighting the versatility of these compounds to act as both electron donors and electron acceptors. Natural bond orbital analysis showed that orbital effects were important contributors to the global stabilization of the σ- and π-hole bonded complexes studied. Finally, some X-ray solid-state structures retrieved from the Cambridge structural database were described to demonstrate the importance of these interactions involving boron derivatives in the solid state.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain
| | - Antonio Frontera
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122, Palma de Mallorca, Baleares, Spain.
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Abstract
In this manuscript we combine high level ab initio calculations (RI-MP2/aug-cc-pVTZ) and the analysis of several crystal structures to demonstrate the existence of π-hole aerogen bonding interactions in Xe(iv) compounds. The ability of XeF4 and Xe(OMe)4 to interact with electron rich molecules is rationalized using several computational tools, including molecular electrostatic potential surfaces, energetic and geometric features of the complexes and "atoms in molecules" (AIM) and Natural Bond Orbital (NBO) analyses. We have found support for the π-hole interaction involving the xenon atom from the solid state architecture of several X-ray structures retrieved from the crystal structural depot. Particularly, π-hole aerogen bonding interactions are quite common in the solid state of Xe(IV) compounds.
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Affiliation(s)
- Antonio Bauzá
- Departament de Química, Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma de Mallorca, Baleares, Spain.
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Bhasi P, Nhlabatsi ZP, Sitha S. Expanding the applicability of electrostatic potentials to the realm of transition states. Phys Chem Chem Phys 2016; 18:13002-9. [PMID: 27108668 DOI: 10.1039/c6cp01506a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Central to any reaction mechanism study, and sometimes a challenging job, is tracing a transition state in a reaction path. For the first time, electrostatic potentials (ESP) of the reactants were used as guiding tactics to predict whether there is a possibility of any transition state in a reaction surface. The main motive behind this strategy is to see whether the directionality nature of the transition state has something to do with the anisotropic natures of the ESP with their embedded directionalities. Strategically, some atmospherically important, but simple, reactions have been chosen for this study, which heretofore were believed to be barrierless. By carefully analysing the ESP maps of the reactants, regions of possible interactions were located. Using the bilinear interpolation of the 2D grids of the ESP surfaces, search co-ordinates were fine-tuned for a local gradient based approach for the search of a transition state. Out of the three reactions studied in this work, we were able to successfully locate transition states, for the first time, in two cases and the third one still proved to be barrierless. This gives a clear indication that though ESP maps can qualitatively predict the possibility of a transition state; it is not always true that there should definitely be a transition state, as some of the reaction surfaces may genuinely be barrierless. But, nevertheless this strategy definitely has credential to be tested for many more reactions, either new or already established, and may be applied to create the initial search co-ordinates for any well-established transition state search method. Moreover, we have observed that the analysis of the ESP maps of the reactants were very much useful in explaining the nature of interactions existing in those observed transition states and we hope the same can also be extended to any transition state in an electrostatically driven reaction potential energy surface.
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Affiliation(s)
- Priya Bhasi
- Department of Chemistry, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, 2006, South Africa.
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43
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The mutual influence between π-hole pnicogen bonds and σ-hole halogen bonds in complexes of PO2Cl and XCN/C6H6 (X = F, Cl, Br). Struct Chem 2016. [DOI: 10.1007/s11224-016-0762-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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44
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Bauzá A, Frontera A. Theoretical study on σ- and π-hole carbon⋯carbon bonding interactions: implications in CFC chemistry. Phys Chem Chem Phys 2016; 18:32155-32159. [DOI: 10.1039/c6cp06449c] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this manuscript the ability of CO2 and several CFCs to establish noncovalent carbon⋯carbon interactions with atmospheric gases CO, ethene and ethyne has been studied at the RI-MP2/def2-TZVPD level of theory.
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Affiliation(s)
- Antonio Bauzá
- Department of Chemistry Universitat de les Illes Balears
- 07122 Palma
- Spain
| | - Antonio Frontera
- Department of Chemistry Universitat de les Illes Balears
- 07122 Palma
- Spain
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45
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Quiñonero D, Bauzá A, Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Weak interactions within nitryl halide heterodimers. NEW J CHEM 2016. [DOI: 10.1039/c6nj01334a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Nitryl halides (XNO2, X = F, Cl, Br and I) are versatile molecules that exhibit several types of interactions within XNO2:YNO2 heterodimers mainly governed by dispersion.
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Affiliation(s)
- David Quiñonero
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma de Mallorca
- Spain
| | | | - Cristina Trujillo
- School of Chemistry
- Trinity Biomedical Sciences Institute
- Trinity College Dublin
- Dublin 2
- Ireland
| | - Ibon Alkorta
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica
- CSIC
- E-28006 Madrid
- Spain
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46
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Banerjee S, Bauzá A, Frontera A, Saha A. Exploration of unconventional π–hole and C–H⋯H–C types of supramolecular interactions in a trinuclear Cd(ii) and a heteronuclear Cd(ii)–Ni(ii) complex and experimental evidence for preferential site selection of the ligand by 3d and 4d metal ions. RSC Adv 2016. [DOI: 10.1039/c6ra04428j] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
We report the synthesis of a trinuclear cadmium(ii) (1) and a di(phenoxido)-bridged dinuclear cadmium(ii)–nickel(ii) (2) complex derived from a bicompartmental (N2O4) Schiff base ligand.
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Affiliation(s)
- Saikat Banerjee
- Department of Chemistry
- Jadavpur University
- Kolkata-700032, India
| | - Antonio Bauzá
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares), Spain
| | - Antonio Frontera
- Departament de Química
- Universitat de les Illes Balears
- 07122 Palma (Baleares), Spain
| | - Amrita Saha
- Department of Chemistry
- Jadavpur University
- Kolkata-700032, India
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47
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Nziko VDPN, Scheiner S. Comparison of π-hole tetrel bonding with σ-hole halogen bonds in complexes of XCN (X = F, Cl, Br, I) and NH3. Phys Chem Chem Phys 2016; 18:3581-90. [DOI: 10.1039/c5cp07545a] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In addition to the standard halogen bond formed when NH3approaches XCN (X = F, Cl, Br, I) along its molecular axis, a perpendicular approach is also possible, toward a π-hole that is present above the X–C bond.
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Affiliation(s)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry
- Utah State University
- Logan
- USA
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48
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Trujillo C, Sánchez-Sanz G. A Study of π-π Stacking Interactions and Aromaticity in Polycyclic Aromatic Hydrocarbon/Nucleobase Complexes. Chemphyschem 2015; 17:395-405. [PMID: 26663678 DOI: 10.1002/cphc.201501019] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 12/05/2015] [Indexed: 11/10/2022]
Abstract
We analysed the interactions and aromaticity electron-density delocalisation observed in π-π complexes between the phenalenyl radical and acenaphthylene, and the DNA and RNA nucleobases (adenine, guanine, cytosine, thymine and uracil). Interaction energies are obtained at the M06-2X/6-311++G(2df,p) computational level for gas phase and PCM-water conditions. For both the phenalenyl radical and acenaphthylene, the complexes formed with guanine are the most stable ones. Atoms in molecules and natural bond orbital results reveal weak π-π interactions between both interacting moieties, characterized by bond critical points between C⋅⋅⋅C and C⋅⋅⋅N atoms. Nucleus independent chemical shifts (NICS) indicate the retention of the aromatic character of the monomers in the outer region of the complex. The fluctuation indexes reveal a loss of electron delocalisation upon complexation for all cases except guanine complexes. Nevertheless, the interface region shows large negative NICS values, which is not associated with an increase of the aromaticity or electron-density delocalisation, but with magnetic couplings of both molecules, leading to an unrealistic description of the aromatic behaviour in that region.
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Affiliation(s)
- Cristina Trujillo
- School of Chemistry, Trinity Biomedical Sciences, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland.
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Bauzá A, Frontera A, Mooibroek TJ. 1,1,2,2-Tetracyanocyclopropane (TCCP) as supramolecular synthon. Phys Chem Chem Phys 2015; 18:1693-8. [PMID: 26674457 DOI: 10.1039/c5cp06350g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The 1,1,2,2-tetracyanocyclopropane (TCCP) unit presents a synthetically accessible and versatile synthon that can interact with lone-pair or π-electrons by 'non-covalent carbon bonding'. Complexes of TCCP with common small molecules, anions, aromatics like fullerenes, amino acids and nucleobases were computed at the DFT BP86-D3/def2-TZVP level of theory. Binding energies vary between about -10 kcal mol(-1) for neutral guests and -15 to -50 kcal mol(-1) for anionic species. This is comparable to strong and very strong hydrogen bonding respectively. Thus, in addition to synthons that contain polarized hydrogen or halogen atoms, TCCP presents a new supramolecular synthon that awaits experimental exploitation.
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Affiliation(s)
- Antonio Bauzá
- Department of Chemistry Universitat de les Illes Balears, Crta. de Valldemossa km 7.5, 07122 Palma (Baleares), Spain.
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50
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Bauzá A, Frontera A. Theoretical Study on the Dual Behavior of XeO3and XeF4toward Aromatic Rings: Lone Pair-π versus Aerogen-π Interactions. Chemphyschem 2015; 16:3625-30. [DOI: 10.1002/cphc.201500757] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Indexed: 01/18/2023]
Affiliation(s)
- Antonio Bauzá
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca, Baleares Spain
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca, Baleares Spain
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