1
|
Yaghoobi F, Salehzadeh S. Catalysis of the Nitroso-Diels-Alder cycloaddition reaction between CH 3N=O and cis-1,3-butadiene by pnictogen bonding, a theoretical study. J Mol Graph Model 2023; 125:108583. [PMID: 37582304 DOI: 10.1016/j.jmgm.2023.108583] [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: 05/04/2023] [Revised: 07/13/2023] [Accepted: 07/28/2023] [Indexed: 08/17/2023]
Abstract
Density functional theory calculations at the M06-2X/aug-cc-pVTZ level of theory have been used to examine the Nitroso-Diels-Alder (N-D-A) cycloaddition reaction between the CH3N=O and cis-1,3-butadiene in the presence of PO2X (X=F, Cl, OH) as a catalyst. The effect of the above PO2X compounds on the activation energy of the N-D-A reaction, has been studied here. In the first stage, the energies of two different bonding interactions, via P⋯N versus P⋯O binding, between the PO2X and CH3N=O molecules were calculated. The results showed that the largest values of the interaction energy between the above molecules belong to the PO2F, when connects to the nitrogen atom of the CH3N=O. Also, calculations showed that all the above PO2X compounds, decrease the activation energies of N-D-A reaction studied here via both P⋯N and P⋯O interactions. However, the largest effect on activation energies of the reaction belongs to the PO2F catalyst when acts via P⋯N bonding. The activation strain model (ASM) was used to analyze the influence of the PO2X catalyst on the studied reaction. The quantum theory of atoms in molecules (QTAIM) and natural bond orbital (NBO) analysis were performed to understand the nature of forming interactions at the TS structures. The results of this study showed that the PO2X (X=F, Cl, OH) compounds may be suggested as efficient catalysts for N-D-A reactions.
Collapse
Affiliation(s)
- Fereshteh Yaghoobi
- Nahavand Higher Education Complex, Bu-Ali Sina University, Hamedan, Iran.
| | | |
Collapse
|
2
|
Murphy B, Gabbaï FP. Binding, Sensing, And Transporting Anions with Pnictogen Bonds: The Case of Organoantimony Lewis Acids. J Am Chem Soc 2023; 145:19458-19477. [PMID: 37647531 PMCID: PMC10863067 DOI: 10.1021/jacs.3c06991] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Indexed: 09/01/2023]
Abstract
Motivated by the discovery of main group Lewis acids that could compete or possibly outperform the ubiquitous organoboranes, several groups, including ours, have engaged in the chemistry of Lewis acidic organoantimony compounds as new platforms for anion capture, sensing, and transport. Principal to this approach are the intrinsically elevated Lewis acidic properties of antimony, which greatly favor the addition of halide anions to this group 15 element. The introduction of organic substituents to the antimony center and its oxidation from the + III to the + V state provide for tunable Lewis acidity and a breadth of applications in supramolecular chemistry and catalysis. The performances of these antimony-based Lewis acids in the domain of anion sensing in aqueous media illustrate the favorable attributes of antimony as a central element. At the same time, recent advances in anion binding catalysis and anion transport across phospholipid membranes speak to the numerous opportunities that lie ahead in the chemistry of these unique main group compounds.
Collapse
Affiliation(s)
- Brendan
L. Murphy
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843-3255, United States
| | - François P. Gabbaï
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843-3255, United States
| |
Collapse
|
3
|
Das A, Arunan E. Unified classification of non-covalent bonds formed by main group elements: a bridge to chemical bonding. Phys Chem Chem Phys 2023; 25:22583-22594. [PMID: 37435670 DOI: 10.1039/d3cp00370a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
Using correlation plots of binding energy and electron density at the bond critical point, we investigated the nature of intermolecular non-covalent bonds (D-X⋯A, where D = O/S/F/Cl/Br/H, mostly, X = main group elements (except noble gases), A = H2O, NH3, H2S, PH3, HCHO, C2H4, HCN, CO, CH3OH, and CH3OCH3). The binding energies were calculated at the MP2 level of theory, followed by Atoms in Molecules (AIM) analysis of the ab initio wave functions to obtain the electron density at the bond critical point (BCP). For each non-covalent bond, the slopes of the binding energy versus electron density plot have been determined. Based on their slopes, non-covalent bonds are classified as non-covalent bond closed-shell (NCB-C) or non-covalent bond shared-shell (NCB-S). Intriguingly, extrapolating the slopes of the NCB-C and NCB-S cases leads to intramolecular "ionic" and "covalent" bonding regimes, establishing a link between such intermolecular non-covalent and intramolecular chemical bonds. With this new classification, hydrogen bonds and other non-covalent bonds formed by a main-group atom in a covalent molecule are classified as NCB-S. Atoms found in ionic molecules generally form NCB-C type bonds, with the exception of carbon which also forms NCB-C type bonds. Molecules with a tetravalent carbon do behave like ions in ionic molecules such as NaCl and interact with other molecules through NCB-C type bonds. As with the chemical bonds, there are some non-covalent bonds that are intermediate cases.
Collapse
Affiliation(s)
- Arijit Das
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Elangannan Arunan
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
4
|
Maltz L, Gabbaï FP. Analyzing Fluoride Binding by Group 15 Lewis Acids: Pnictogen Bonding in the Pentavalent State. Inorg Chem 2023; 62:13566-13572. [PMID: 37551938 PMCID: PMC10862541 DOI: 10.1021/acs.inorgchem.3c01987] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Indexed: 08/09/2023]
Abstract
We report the results of a computational investigation into fluoride binding by a series of pentavalent pnictogen Lewis acids: pnictogen pentahalides (PnX5), tetraphenyl pnictogeniums (PnPh4+), and triphenyl pnictogen tetrachlorocatecholates (PnPh3Cat). Activation strain and energy decomposition analyses of the Lewis adducts not only clearly delineate the electrostatic and orbital contributions to these acid-base interactions but also highlight the importance of Pauli repulsion and molecular flexibility in determining relative Lewis acidity among the pnictogens.
Collapse
Affiliation(s)
- Logan
T. Maltz
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| | - François P. Gabbaï
- Department of Chemistry, Texas A&M University, College
Station, Texas 77843, United States
| |
Collapse
|
5
|
Oliveira BGD. Why much of Chemistry may be indisputably non-bonded? SEMINA: CIÊNCIAS EXATAS E TECNOLÓGICAS 2023. [DOI: 10.5433/1679-0375.2022v43n2p211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In this compendium, the wide scope of all intermolecular interactions ever known has been revisited, in particular giving emphasis the capability of much of the elements of the periodic table to form non-covalent contacts. Either hydrogen bonds, dihydrogen bonds, halogen bonds, pnictogen bonds, chalcogen bonds, triel bonds, tetrel bonds, regium bonds, spodium bonds or even the aerogen bond interactions may be cited. Obviously that experimental techniques have been used in some works, but it was through the theoretical methods that these interactions were validate, wherein the QTAIM integrations and SAPT energy partitions have been useful in this regard. Therefore, the great goal concerns to elucidate the interaction strength and if the intermolecular system shall be total, partial or non-covalently bonded, wherein this last one encompasses the most majority of the intermolecular interactions what leading to affirm that chemistry is debatably non-bonded.
Collapse
|
6
|
Robinson HT, Haakansson CT, Corkish TR, Watson PD, McKinley AJ, Wild DA. Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes. Chemphyschem 2022; 24:e202200733. [PMID: 36504309 DOI: 10.1002/cphc.202200733] [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: 10/05/2022] [Revised: 12/12/2022] [Accepted: 12/12/2022] [Indexed: 12/14/2022]
Abstract
Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH3 Cl, CH2 Cl2 , CHCl3 , and CCl4 . The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.
Collapse
Affiliation(s)
- Hayden T Robinson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Christian T Haakansson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Timothy R Corkish
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Peter D Watson
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,Department of Chemistry, University of Oxford, South Parks Road, Oxford, United Kingdom, OX1 3QZ
| | - Allan J McKinley
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009
| | - Duncan A Wild
- School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia, 6009.,School of Science, Edith Cowan University, Joondalup, Western Australia, 6027
| |
Collapse
|
7
|
Scheiner S, Michalczyk M, Zierkiewicz W. Involvement of Arsenic Atom of AsF 3 in Five Pnicogen Bonds: Differences between X-ray Structure and Theoretical Models. Molecules 2022; 27:6486. [PMID: 36235021 PMCID: PMC9572024 DOI: 10.3390/molecules27196486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/06/2022] Open
Abstract
Bonding within the AsF3 crystal is analyzed via quantum chemical methods so as to identify and quantify the pnicogen bonds that are present. The structure of a finite crystal segment containing nine molecules is compared with that of a fully optimized cluster of the same size. The geometries are qualitatively different, with a much larger binding energy within the optimized nonamer. Although the total interaction energy of a central unit with the remaining peripheral molecules is comparable for the two structures, the binding of the peripherals with one another is far larger in the optimized cluster. This distinction of much stronger total binding within the optimized cluster is not limited to the nonamer but repeats itself for smaller aggregates as well. The average binding energy of the cluster rises quickly with size, asymptotically approaching a value nearly triple that of the dimer.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
| | - 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
| |
Collapse
|
8
|
López JC, Alkorta I, Macario A, Blanco S. Characterizing the n→π* interaction of pyridine with small ketones: a rotational study of pyridine⋯acetone and pyridine⋯2-butanone. Phys Chem Chem Phys 2022; 24:15484-15493. [PMID: 35713114 DOI: 10.1039/d2cp01611g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Complexes formed by pyridine and small ketones such as acetone and 2-butanone have been generated in a supersonic jet and characterized by broadband Fourier transform microwave spectroscopy combined with high-level theoretical computations. The spectra of the complexes show a quadrupole coupling hyperfine structure due to the presence of a nitrogen atom and the splittings owing to the low barriers of the internal rotation of the methyl groups bonded to the carbonyl group. The corresponding barriers have been determined from the analysis of the spectra. We show in both complexes that pyridine closes a cycle with a ketone carbonyl group through an N⋯CO n→π* tetrel interaction and a C-H⋯O contact. The n→π* tetrel bond involves the pyridine N atom lone pair and the ketone carbonyl group with a geometry approaching the Bürgi-Dunitz trajectory for the nucleophilic attack to a carbonyl group.
Collapse
Affiliation(s)
- Juan Carlos López
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, IU CINQUIMA, Universidad de Valladolid, 47011 Valladolid, Spain.
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva 3, 28006 Madrid, Spain.
| | - Alberto Macario
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, IU CINQUIMA, Universidad de Valladolid, 47011 Valladolid, Spain.
| | - Susana Blanco
- Departamento de Química Física y Química Inorgánica, Facultad de Ciencias, IU CINQUIMA, Universidad de Valladolid, 47011 Valladolid, Spain.
| |
Collapse
|
9
|
Varadwaj A, Varadwaj PR, Marques HM, Yamashita K. The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor. Int J Mol Sci 2022; 23:4674. [PMID: 35563065 PMCID: PMC9099767 DOI: 10.3390/ijms23094674] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/16/2022] [Accepted: 04/18/2022] [Indexed: 12/04/2022] Open
Abstract
A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.
Collapse
Affiliation(s)
- Arpita Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| | - Pradeep R. Varadwaj
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Helder M. Marques
- Molecular Sciences Institute, School of Chemistry, University of the Witwatersrand, Johannesburg 2050, South Africa;
| | - Koichi Yamashita
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo, Tokyo 113-8656, Japan; (A.V.); (K.Y.)
| |
Collapse
|
10
|
Xotlanihua-Flores A, Villaseñor-Granados TO, Colorado-Peralta R, Sánchez-Ruiz SA, Montes-Tolentino P, Flores-Parra A. Tin complexes derived from nitrogen-based 1,3,5-heterocyclohexanes bearing 2-hydroxypropan-1-yl, 2-diphenylphosphitepropan-1-yl and 2-diphenylphosphinepropan-1-yl as pendant N-substituents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
11
|
New 1,3,5-heterocyclohexanes bearing pendant phosphorus groups. Structure and N→P pnicogen interactions. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
12
|
Brzeski J. The influence of tetrel bonds on the acidities of group 14 tetrafluoride - inorganic acid complexes. J Comput Chem 2022; 43:611-618. [PMID: 35147239 DOI: 10.1002/jcc.26822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/21/2022] [Accepted: 01/21/2022] [Indexed: 12/12/2022]
Abstract
Ab initio methods were used to determine the influence of tetrel bond formation on the acidity. The systems composed of inorganic acids and tetrafluorides of 14 group elements have been tested - HA/EF4 , where HA = H2 O, NH3 , HF, HCN, HNC, HCNO, HOCN and E = C, Si, Ge, Sn or Pb. It turns out that the electron density flow involved with formation of tetrel bond to carbon-based systems leads to negligible increase in acidity. In the case of the acceptor compounds based on the remaining 14 group elements however, the effect is much more apparent, as most of those compounds may be considered a Brønsted superacids. The electronic stability of anions formed after the deprotonation of aforementioned complexes has been investigated. Vast majority of the anions were found to exhibit significant electron binding energies.
Collapse
Affiliation(s)
- Jakub Brzeski
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| |
Collapse
|
13
|
Liu Q, Lu Y, Sheng H, Zhang C, Su X, Wang Z, Chen X. Visible‐Light‐Induced Selective Photolysis of Phosphonium Iodide Salts for Monofluoromethylations. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202111006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Qiang Liu
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Yu Lu
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - He Sheng
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Chao‐Shen Zhang
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiao‐Di Su
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Zhi‐Xiang Wang
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| | - Xiang‐Yu Chen
- School of Chemical Sciences University of Chinese Academy of Sciences Beijing 100049 China
| |
Collapse
|
14
|
Liu Q, Lu Y, Sheng H, Zhang CS, Su XD, Wang ZX, Chen XY. Visible-Light-Induced Selective Photolysis of Phosphonium Iodide Salts for Monofluoromethylations. Angew Chem Int Ed Engl 2021; 60:25477-25484. [PMID: 34490742 DOI: 10.1002/anie.202111006] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Indexed: 11/09/2022]
Abstract
The sigma (σ)-hole effect has emerged as a promising tool to construct novel architectures endowed with new properties. A simple yet effective strategy for the generation of monofluoromethyl radicals is a continuing challenge within the synthetic community. Fluoromethylphosphonium salts are easily available, air- and thermally stable, as well as simple-to-handle. Herein, we report the ability of the σ-hole effect to facilitate the visible-light-triggered photolysis of phosphonium iodide salts, a charge-transfer complex, selectively giving fluoromethyl radicals. The usefulness and versatility of this new protocol are demonstrated through the mono-, di-, and trifluoromethylation of a variety of alkenes.
Collapse
Affiliation(s)
- Qiang Liu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Lu
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Sheng
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao-Shen Zhang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Di Su
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Xiang Wang
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiang-Yu Chen
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
15
|
Liu N, Li Q. Group 12 Carbonates and their Binary Complexes with Nitrogen Bases and FH 2 Z Molecules (Z=P, As, Sb): Synergism in Forming Ternary Complexes. Chemphyschem 2021; 22:1698-1705. [PMID: 34106509 DOI: 10.1002/cphc.202100348] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 06/03/2021] [Indexed: 11/10/2022]
Abstract
MCO3 (M=Zn, Cd, Hg) forms a spodium bond with nitrogen-containing bases (HCN, NHCH2 , NH3 ) and a pnicogen bond with FH2 Z (Z=P, As, Sb). The spodium bond is very strong with the interaction energy ranging from -31 kcal/mol to -56 kcal/mol. Both NHCH2 and NH3 have an equal electrostatic potential on the N atom, but the corresponding interaction energy is differentiated by 1.5-4 kcal/mol due to the existence of spodium and hydrogen bonds in the complex with NHCH2 as the electron donor. The spodium bond is weakest in the HCN complex, which is not consistent with the change of the binding distance. The spodium bond becomes stronger in the CdCO3 <ZnCO3 <HgCO3 sequence although the positive electrostatic potential on the Hg atom is smallest. This is because the electrostatic interaction is dominant in the spodium-bonded complexes of CdCO3 and ZnCO3 but the polarization interaction in that of HgCO3 . The pnicogen bond is much weaker than the spodium bond and the former has a larger enhancement than the latter in the FH2 Z⋅⋅⋅OCO2 M⋅⋅⋅N-base ternary complexes.
Collapse
Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, P. R. China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, P. R. China
| |
Collapse
|
16
|
Ullah Z, Kim K, Venkanna A, Kim HS, Kim MI, Kim MH. Plausible Pnicogen Bonding of epi-Cinchonidine as a Chiral Scaffold in Catalysis. Front Chem 2021; 9:669515. [PMID: 34295874 PMCID: PMC8290064 DOI: 10.3389/fchem.2021.669515] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 06/10/2021] [Indexed: 12/11/2022] Open
Abstract
As a non-covalent interaction of a chiral scaffold in catalysis, pnicogen bonding of epi-cinchonidine (epi-CD), a cinchona alkaloid, was simulated to consider whether the interaction can have the potential controlling enantiotopic face like hydrogen bonding. Among five reactive functional groups in epi-CD, two stable complexes of the hydroxyl group (X-epi-CD1) at C17 and of the quinoline ring (X-epi-CD2) at N16 with pnictide family analytes [X = substituted phosphine (PX), i.e., F, Br, Cl, CF3, CN, HO, NO2, and CH3, and pnictide family analytes, i.e., PBr3, BiI3, SbI3, and AsI3] were predicted with intermolecular interaction energies, charge transfer (QMulliken and QNBO), and band gap energies of HOMO-LUMO (Eg) at the B3LYP/6-31G(d,p) level of density functional theory. It was found that the dominant site of pnicogen bonding in epi-CD is the quinoline ring (N16 atom) rather than the hydroxyl group (O36 atom). In addition, the UV-Vis spectra of the complex were calculated by time-dependent density functional theory (TD-DFT) at the B3LYP/6-31+G(d,p) level and compared with experimental measurements. Through these calculations, two intermolecular interactions (H-bond vs. pnicogen bond) of epi-CD were compared.
Collapse
Affiliation(s)
- Zakir Ullah
- Department of Pharmacy, College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon, South Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Kang Kim
- Department of Pharmacy, College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon, South Korea
| | - Arramshetti Venkanna
- Department of Pharmacy, College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon, South Korea
| | - Hye Su Kim
- Department of BioNano Technology, Gachon University, Seongnam, South Korea
| | - Moon Il Kim
- Department of BioNano Technology, Gachon University, Seongnam, South Korea
| | - Mi-Hyun Kim
- Department of Pharmacy, College of Pharmacy, Gachon Institute of Pharmaceutical Science, Gachon University, Incheon, South Korea
| |
Collapse
|
17
|
Jabłoński M. Study of Beryllium, Magnesium, and Spodium Bonds to Carbenes and Carbodiphosphoranes. Molecules 2021; 26:2275. [PMID: 33920004 PMCID: PMC8071025 DOI: 10.3390/molecules26082275] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 04/09/2021] [Accepted: 04/11/2021] [Indexed: 11/17/2022] Open
Abstract
The aim of this article is to present results of theoretical study on the properties of C⋯M bonds, where C is either a carbene or carbodiphosphorane carbon atom and M is an acidic center of MX2 (M = Be, Mg, Zn). Due to the rarity of theoretical data regarding the C⋯Zn bond (i.e., the zinc bond), the main focus is placed on comparing the characteristics of this interaction with C⋯Be (beryllium bond) and C⋯Mg (magnesium bond). For this purpose, theoretical studies (ωB97X-D/6-311++G(2df,2p)) have been performed for a large group of dimers formed by MX2 (X = H, F, Cl, Br, Me) and either a carbene ((NH2)2C, imidazol-2-ylidene, imidazolidin-2-ylidene, tetrahydropyrymid-2-ylidene, cyclopropenylidene) or carbodiphosphorane ((PH3)2C, (NH3)2C) molecule. The investigated dimers are characterized by a very strong charge transfer effect from either the carbene or carbodiphosphorane molecule to the MX2 one. This may even be over six times as strong as in the water dimer. According to the QTAIM and NCI method, the zinc bond is not very different than the beryllium bond, with both featuring a significant covalent contribution. However, the zinc bond should be definitely stronger if delocalization index is considered.
Collapse
Affiliation(s)
- Mirosław Jabłoński
- Faculty of Chemistry, Nicolaus Copernicus University, 87-100 Toruń, Poland
| |
Collapse
|
18
|
Muñoz-Castro A, Wang G, Ponduru TT, Dias HVR. Synthesis and characterization of N-heterocyclic carbene-MOEt 2 complexes (M = Cu, Ag, Au). Analysis of solvated auxiliary-ligand free [(NHC)M] + species. Phys Chem Chem Phys 2021; 23:1577-1583. [PMID: 33406199 DOI: 10.1039/d0cp05222a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis, characterization and computational analysis of coinage metal-ether complexes supported by N-heterocyclic carbenes (NHC), SIPr and Et2CAAC. The related water adducts are also included. The [(NHC)M]+(M = Cu, Ag, Au) species show the noteworthy ability to bind Et2O and H2O. This interaction towards Et2O and H2O is partly ascribed to a σ-hole bonding with an almost linear disposition, taking advantage of the enhanced σ-hole potential evaluated for such [(NHC)M]+ species. This enhanced ability is larger than those found for non-covalent interactions involving main group species.
Collapse
Affiliation(s)
- Alvaro Muñoz-Castro
- Grupo de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autonoma de Chile, El Llano Subercaseaux 2801, Santiago, Chile.
| | - Guocang Wang
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA.
| | - Tharun Teja Ponduru
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA.
| | - H V Rasika Dias
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, Texas 76019, USA.
| |
Collapse
|
19
|
Prokudina YV, Davydova EI, Virovets A, Stöger B, Peresypkina E, Pomogaeva AV, Timoshkin AY. Structures and Chemical Bonding in Antimony(III) Bromide Complexes with Pyridine. Chemistry 2020; 26:16338-16348. [PMID: 32672367 DOI: 10.1002/chem.202002261] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 07/13/2020] [Indexed: 12/21/2022]
Abstract
Weakly or "partially" bonded molecules are an important link between the chemical and van der Waals interactions. Molecular structures of six new SbBr3 -Py complexes in the solid state have been determined by single-crystal X-ray diffraction analysis. In all complexes all Sb atoms adopt a pseudo-octahedral coordination geometry which is completed by additional Sb⋅⋅⋅Br contacts shorter than the sum of the van der Waals radii, with Br-Sb⋅⋅⋅Br angles close to 180°. To reveal the nature of Sb-Br and Sb-N interactions, the DFT calculations were performed followed by the analysis of the electrostatic potentials, the orbital interactions and the topological analysis. Based on Natural Bond Orbital (NBO) analysis, the Sb-Br interactions range from the covalent bonds to the pnictogen bonds. A simple structural parameter, non-covalence criterion (NCC) is defined as a ratio of the atom-atom distance to the linear combination of sums of covalent and van der Waals radii. NCC correlates with E(2) values for Sb-N, Sb-Cl and Sb-Br bonds, and appears to be useful criterion for a preliminary evaluation of the bonding situation.
Collapse
Affiliation(s)
- Yana V Prokudina
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| | - Elena I Davydova
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| | - Alexander Virovets
- University of Regensburg, Universitaetsstr. 31, 93053, Regensburg, Germany
| | - Berthold Stöger
- X-Ray Center, TU Wien, Getreidemarkt, 9, 1060, Vienna, Austria
| | | | - Anna V Pomogaeva
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| | - Alexey Y Timoshkin
- Institute of Chemistry, Saint Petersburg State University, Universitetskaya emb. 7/9, 199034, St. Petersburg, Russia
| |
Collapse
|
20
|
Sruthi PK, Chandra S, Ramanathan N, Sundararajan K. Unusual blue to red shifting of C-H stretching frequency of CHCl 3 in co-operatively P⋯Cl phosphorus bonded POCl 3-CHCl 3 heterodimers at low temperature inert matrixes. J Chem Phys 2020; 153:174305. [PMID: 33167652 DOI: 10.1063/5.0031162] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heterodimers of POCl3-CHCl3 were generated in Ne, Ar, and Kr matrixes at low temperatures and were studied using infrared spectroscopy. The remarkable role of co-operative pentavalent phosphorus bonding in the stabilization of the structure dictated by hydrogen bonding is deciphered. The complete potential energy surface of the heterodimer was scanned by ab initio and density functional theory computational methodologies. The hydrogen bond between the phosphoryl oxygen of POCl3 and C-H group of CHCl3 in heterodimers induces a blue-shift in the C-H stretching frequency within the Ne matrix. However, in Ar and Kr matrixes, the C-H stretching frequency is exceptionally red-shifted in stark contrast with Ne. The plausibility of the Fermi resonance by the C-H stretching vibrational mode with higher order modes in the heterodimers has been eliminated as a possible cause within Ar and Kr matrixes by isotopic substitution (CDCl3) experiments. To evaluate the influence of matrixes as a possible cause of red-shift, self-consistent Iso-density polarized continuum reaction field model was applied. This conveyed the important role of the dielectric matrixes in inducing the fascinating vibrational shift from blue (Ne) to red (Ar and Kr) due to the matrix specific transmutation of the POCl3-CHCl3 structure. The heterodimer produced in the Ne matrix possesses a cyclic structure stabilized by hydrogen bonding with co-operative phosphorus bonding, while in Ar and Kr the generation of an acyclic open structure stabilized solely by hydrogen bonding is promoted. Compelling justification regarding the dispersion force based influence of matrix environments in addition to the well-known dielectric influence is presented.
Collapse
Affiliation(s)
- P K Sruthi
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - Swaroop Chandra
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - N Ramanathan
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| | - K Sundararajan
- Homi Bhabha National Institute, Materials Chemistry and Metal Fuel Cycle Group, Indira Gandhi Centre for Atomic Research, Kalpakkam 603102, India
| |
Collapse
|
21
|
Affiliation(s)
- Martin Breugst
- Department für Chemie Universität zu Köln Greinstraße 4 50939 Köln Germany
| | - Jonas J. Koenig
- Department für Chemie Universität zu Köln Greinstraße 4 50939 Köln Germany
| |
Collapse
|
22
|
Puzzarini C, Spada L, Alessandrini S, Barone V. The challenge of non-covalent interactions: theory meets experiment for reconciling accuracy and interpretation. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:343002. [PMID: 32203942 DOI: 10.1088/1361-648x/ab8253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 03/23/2020] [Indexed: 06/10/2023]
Abstract
In the past decade, many gas-phase spectroscopic investigations have focused on the understanding of the nature of weak interactions in model systems. Despite the fact that non-covalent interactions play a key role in several biological and technological processes, their characterization and interpretation are still far from being satisfactory. In this connection, integrated experimental and computational investigations can play an invaluable role. Indeed, a number of different issues relevant to unraveling the properties of bulk or solvated systems can be addressed from experimental investigations on molecular complexes. Focusing on the interaction of biological model systems with solvent molecules (e.g., water), since the hydration of the biomolecules controls their structure and mechanism of action, the study of the molecular properties of hydrated systems containing a limited number of water molecules (microsolvation) is the basis for understanding the solvation process and how structure and reactivity vary from gas phase to solution. Although hydrogen bonding is probably the most widespread interaction in nature, other emerging classes, such as halogen, chalcogen and pnicogen interactions, have attracted much attention because of the role they play in different fields. Their understanding requires, first of all, the characterization of the directionality, strength, and nature of such interactions as well as a comprehensive analysis of their competition with other non-covalent bonds. In this review, it is shown how state-of-the-art quantum-chemical computations combined with rotational spectroscopy allow for fully characterizing intermolecular interactions taking place in molecular complexes from both structural and energetic points of view. The transition from bi-molecular complex to microsolvation and then to condensed phase is shortly addressed.
Collapse
Affiliation(s)
- Cristina Puzzarini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
| | - Lorenzo Spada
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Silvia Alessandrini
- Dipartimento di Chimica 'Giacomo Ciamician', Via F. Selmi 2, I-40126 Bologna, Italy
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| |
Collapse
|
23
|
Investigation of the hydrogen, halogen and pnicogen dimers by means of molecular face calculated by ab initio method. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2568-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
24
|
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.
Collapse
|
25
|
Azofra LM, Elguero J, Alkorta I. A Conceptual DFT Study of Phosphonate Dimers: Dianions Supported by H-Bonds. J Phys Chem A 2020; 124:2207-2214. [DOI: 10.1021/acs.jpca.9b10681] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Luis Miguel Azofra
- CIDIA-FEAM (Unidad Asociada al Consejo Superior de Investigaciones Científicas, CSIC, avalada por el Instituto de Ciencia de Materiales de Sevilla, Universidad de Sevilla), Instituto de Estudios Ambientales y Recursos Naturales (i-UNAT), Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
- Departamento de Química, Universidad de Las Palmas de Gran Canaria (ULPGC), Campus de Tafira, 35017, Las Palmas de Gran Canaria, Spain
| | - José Elguero
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (IQM-CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| |
Collapse
|
26
|
Dutta J, Sahoo DK, Jena S, Tulsiyan KD, Biswal HS. Non-covalent interactions with inverted carbon: a carbo-hydrogen bond or a new type of hydrogen bond? Phys Chem Chem Phys 2020; 22:8988-8997. [DOI: 10.1039/d0cp00330a] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Crystal structure analysis and quantum chemical calculations enabled us to discover a new non-covalent interaction, coined as carbo-hydrogen bond (CH-bond).
Collapse
Affiliation(s)
- Juhi Dutta
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Dipak Kumar Sahoo
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Subhrakant Jena
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Kiran Devi Tulsiyan
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| | - Himansu S. Biswal
- National Institute of Science Education and Research (NISER) PO-Bhimpur-Padanpur
- Bhubaneswar
- India
- Homi Bhaba National Institute
- Training School Complex Anushakti Nagar
| |
Collapse
|
27
|
|
28
|
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: 1.2] [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.
Collapse
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
| |
Collapse
|
29
|
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]
|
30
|
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: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
31
|
Synergistic and antagonistic interplay between tetrel bond and pnicogen bond in complexes involving ring compounds. J Mol Model 2019; 25:351. [DOI: 10.1007/s00894-019-4206-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/11/2019] [Indexed: 10/25/2022]
|
32
|
|
33
|
Del Bene JE, Alkorta I, Elguero J. N …C and S …S Interactions in Complexes, Molecules, and Transition Structures HN(CH)SX:SCO, for X = F, Cl, NC, CCH, H, and CN. Molecules 2019; 24:E3232. [PMID: 31491953 PMCID: PMC6767182 DOI: 10.3390/molecules24183232] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 08/29/2019] [Accepted: 09/01/2019] [Indexed: 01/04/2023] Open
Abstract
Ab initio Møller-Plesset perturbation theory (MP2)/aug'-cc-pVTZ calculations have been carried out in search of complexes, molecules, and transition structures on HN(CH)SX:SCO potential energy surfaces for X = F, Cl, NC, CCH, H, and CN. Equilibrium complexes on these surfaces have C1 symmetry, but these have binding energies that are no more than 0.5 kJ·mol-1 greater than the corresponding Cs complexes which are vibrationally averaged equilibrium complexes. The binding energies of these span a narrow range and are independent of the N-C distance across the tetrel bond, but they exhibit a second-order dependence on the S-S distance across the chalcogen bond. Charge-transfer interactions stabilize all of these complexes. Only the potential energy surfaces HN(CH)SF:SCO and HN(CH)SCl:SCO have bound molecules that have short covalent N-C bonds and significantly shorter S…S chalcogen bonds compared to the complexes. Equation-of-motion coupled cluster singles and doubles (EOM-CCSD) spin-spin coupling constants 1tJ(N-C) for the HN(CH)SX:SCO complexes are small and exhibit no dependence on the N-C distance, while 1cJ(S-S) exhibit a second-order dependence on the S-S distance, increasing as the S-S distance decreases. Coupling constants 1tJ(N-C) and 1cJ(S-S) as a function of the N-C and S-S distances, respectively, in HN(CH)SF:SCO and HN(CH)SCl:SCO increase in the transition structures and then decrease in the molecules. These changes reflect the changing nature of the N…C and S…S bonds in these two systems.
Collapse
Affiliation(s)
- Janet E Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, OH 44555, USA.
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain.
| | - José Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, E-28006 Madrid, Spain
| |
Collapse
|
34
|
Del Bene JE, Alkorta I, Elguero J. Exploring N C tetrel and O S chalcogen bonds in HN(CH)SX:OCS systems, for X = F, NC, Cl, CN, CCH, and H. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.05.044] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
35
|
Chi Z, Yan T, Li Q, Scheiner S. Violation of Electrostatic Rules: Shifting the Balance between Pnicogen Bonds and Lone Pair−π Interactions Tuned by Substituents. J Phys Chem A 2019; 123:7288-7295. [DOI: 10.1021/acs.jpca.9b06864] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Zongqing Chi
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People’s Republic of China
| | - Tong Yan
- 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
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United States
| |
Collapse
|
36
|
Juanes M, Saragi RT, Caminati W, Lesarri A. The Hydrogen Bond and Beyond: Perspectives for Rotational Investigations of Non‐Covalent Interactions. Chemistry 2019; 25:11402-11411. [DOI: 10.1002/chem.201901113] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Revised: 04/15/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Marcos Juanes
- Departamento de Química Física y Química Inorgánica—IU CINQUIMAFacultad de CienciasUniversidad de Valladolid 47011 Valladolid Spain
| | - Rizalina T. Saragi
- Departamento de Química Física y Química Inorgánica—IU CINQUIMAFacultad de CienciasUniversidad de Valladolid 47011 Valladolid Spain
| | - Walther Caminati
- Dipartimento di Chimica “G. Ciamician”Università di Bologna Via Selmi 2 40126 Bologna Italy
| | - Alberto Lesarri
- Departamento de Química Física y Química Inorgánica—IU CINQUIMAFacultad de CienciasUniversidad de Valladolid 47011 Valladolid Spain
| |
Collapse
|
37
|
|
38
|
Ibrahim MAA, Telb EMZ. A Computational Investigation of Unconventional Lone‐Pair Hole Interactions of Group V–VIII Elements. ChemistrySelect 2019. [DOI: 10.1002/slct.201900603] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry LaboratoryChemistry DepartmentFaculty of ScienceMinia University Minia 61519 Egypt
| | - Ebtisam M. Z. Telb
- Computational Chemistry LaboratoryChemistry DepartmentFaculty of ScienceMinia University Minia 61519 Egypt
| |
Collapse
|
39
|
Ghafari Nikoo Jooneghani S, Gholipour A. Mutual cooperation of π-π stacking and pnicogen bond interactions of substituted monomeric Lawesson’s reagent and pyridine rings: Theoretical insight into Pyr||X-PhPS2⊥pyr complexes. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
40
|
Dual Geometry Schemes in Tetrel Bonds: Complexes between TF₄ (T = Si, Ge, Sn) and Pyridine Derivatives. Molecules 2019; 24:molecules24020376. [PMID: 30669688 PMCID: PMC6359171 DOI: 10.3390/molecules24020376] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
When an N-base approaches the tetrel atom of TF4 (T = Si, Ge, Sn) the latter molecule deforms from a tetrahedral structure in the monomer to a trigonal bipyramid. The base can situate itself at either an axial or equatorial position, leading to two different equilibrium geometries. The interaction energies are considerably larger for the equatorial structures, up around 50 kcal/mol, which also have a shorter R(T··N) separation. On the other hand, the energy needed to deform the tetrahedral monomer into the equatorial structure is much higher than the equivalent deformation energy in the axial dimer. When these two opposite trends are combined, it is the axial geometry which is somewhat more stable than the equatorial, yielding binding energies in the 8–34 kcal/mol range. There is a clear trend of increasing interaction energy as the tetrel atom grows larger: Si < Ge < Sn, a pattern which is accentuated for the binding energies.
Collapse
|
41
|
Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions. Molecules 2019; 24:molecules24020227. [PMID: 30634503 PMCID: PMC6358819 DOI: 10.3390/molecules24020227] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/05/2019] [Accepted: 01/05/2019] [Indexed: 11/22/2022] Open
Abstract
Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl− was thus compared to that of HCOO−, HSO4−, and H2PO4− with a wide variety of bidentate receptors. A pair of SnFH2 groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as appendages. The ordering of the binding energetics follows the HCO2− > Cl− > H2PO4− > HSO4− general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor.
Collapse
|
42
|
Theoretical and conceptual DFT study of pnicogen- and halogen-bonded complexes of PH 2X---BrCl. J Mol Model 2019; 25:28. [PMID: 30612194 DOI: 10.1007/s00894-018-3905-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 12/12/2018] [Indexed: 10/27/2022]
Abstract
The pnicogen and halogen bonding interactions in the PH2X---BrCl(X = H, F, OH, OCH3 and CH3) complexes have been studied at the MP2/aug-cc-pVTZ level. Analysis of interaction energies shows that the pnicogen-bonded structures are less stable than the corresponding halogen-bonded structures. The pnicogen and halogen bonds were also studied by conceptual DFT reactivity indices. Noncovalent interaction (NCI) and SAPT analysis reveals that the dispersion interactions dominate the pnicogen-bonded complexes of PH2X---BrCl in nature, while the halogen-bonded complexes are dominantly electrostatic energy. Graphical abstract It is found that the local softness s+ or s-on the basic center P of PH2X is related to the interaction energies (ΔECP) of halogen- or pnicogen-bonded complexes.
Collapse
|
43
|
Sruthi PK, Sarkar S, Ramanathan N, Sundararajan K. Elusive hypervalent phosphorus⋯π interactions: evidence for paradigm transformation from hydrogen to phosphorus bonding at low temperatures. Phys Chem Chem Phys 2019; 21:12250-12264. [DOI: 10.1039/c9cp01925a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A paradigm transformation from hydrogen to phosphorus bonding is found to depend on the proton affinity of the interacting π-systems.
Collapse
Affiliation(s)
- P. K. Sruthi
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| | - Shubhra Sarkar
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| | - N. Ramanathan
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| | - K. Sundararajan
- Materials Chemistry and Metal Fuel Cycle Group
- Homi Bhabha National Institute
- Indira Gandhi Centre for Atomic Research
- Kalpakkam-603 102
- India
| |
Collapse
|
44
|
Ibrahim MAA, Safy MEA. A new insight for chalcogen bonding based on Point-of-Charge approach. PHOSPHORUS SULFUR 2018. [DOI: 10.1080/10426507.2018.1528255] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mohamed E. A. Safy
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| |
Collapse
|
45
|
Unravelling syn- and anti- orientation in the regioselectivity of carbonyl groups of 5-fluorouracil an anticancer drug toward proton donors. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.09.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
46
|
Solel E, Kozuch S. On the Power of Geometry over Tetrel Bonds. Molecules 2018; 23:molecules23112742. [PMID: 30352983 PMCID: PMC6278272 DOI: 10.3390/molecules23112742] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 12/03/2022] Open
Abstract
Tetrel bonds are noncovalent interactions formed by tetrel atoms (as σ-hole carriers) with a Lewis base. Here, we present a computational and molecular orbital study on the effect of the geometry of the substituents around the tetrel atom on the σ-hole and on the binding strengths. We show that changing the angles between substituents can dramatically increase bond strength. In addition, our findings suggest that the established Sn > Ge > Si order of binding strength can be changed in sufficiently distorted molecules due to the enhancement of the charge transfer component, making silicon the strongest tetrel donor.
Collapse
Affiliation(s)
- Ephrath Solel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| | - Sebastian Kozuch
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva 841051, Israel.
| |
Collapse
|
47
|
Li W, Spada L, Tasinato N, Rampino S, Evangelisti L, Gualandi A, Cozzi PG, Melandri S, Barone V, Puzzarini C. Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions. Angew Chem Int Ed Engl 2018; 57:13853-13857. [DOI: 10.1002/anie.201807751] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 08/20/2018] [Indexed: 01/29/2023]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Sergio Rampino
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| |
Collapse
|
48
|
Abstract
A theoretical study of the substituent and solvent effects on the reaction of phosphines with CO2 has been carried out by means of Møller-Plesset (MP2) computational level calculations and continuum polarizable method (PCM) solvent models. Three stationary points along the reaction coordinate have been characterized, a pre-transition state (TS) assembly in which a pnicogen bond or tetrel bond is established between the phosphine and the CO2 molecule, followed by a transition state, and leading finally to the adduct in which the P–C bond has been formed. The solvent effects on the stability and geometry of the stationary points are different. Thus, the pnicogen bonded complexes are destabilized as the dielectric constant of the solvent increases while the opposite happens within the adducts with the P–C bond and the TSs trend. A combination of the substituents and solvents can be used to control the most stable minimum.
Collapse
|
49
|
Wang C, Danovich D, Shaik S, Wu W, Mo Y. Attraction between electrophilic caps: A counterintuitive case of noncovalent interactions. J Comput Chem 2018; 40:1015-1022. [DOI: 10.1002/jcc.25566] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/03/2018] [Accepted: 07/29/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Changwei Wang
- School of Chemistry & Chemical EngineeringShaanxi Normal University Xi'an 710119 China
| | - David Danovich
- Institute of ChemistryThe Hebrew University Jerusalem 91904 Israel
| | - Sason Shaik
- Institute of ChemistryThe Hebrew University Jerusalem 91904 Israel
| | - Wei Wu
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry and State Key Laboratory of Physical Chemistry of Solid Surfaces, College of Chemistry and Chemical EngineeringXiamen University Xiamen 360015 China
| | - Yirong Mo
- Department of ChemistryWestern Michigan University Kalamazoo Michigan 49008
| |
Collapse
|
50
|
Li W, Spada L, Tasinato N, Rampino S, Evangelisti L, Gualandi A, Cozzi PG, Melandri S, Barone V, Puzzarini C. Theory Meets Experiment for Noncovalent Complexes: The Puzzling Case of Pnicogen Interactions. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807751] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Weixing Li
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Lorenzo Spada
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Nicola Tasinato
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Sergio Rampino
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Luca Evangelisti
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Andrea Gualandi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Pier Giorgio Cozzi
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Sonia Melandri
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| | - Vincenzo Barone
- Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy
| | - Cristina Puzzarini
- Dipartimento di Chimica “Giacomo Ciamician”University of Bologna Via Selmi 2 40126 Bologna Italy
| |
Collapse
|