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Amonov A, Scheiner S. Halogen Bonding to the π-Systems of Polycyclic Aromatics. Chemphyschem 2024; 25:e202400482. [PMID: 38923736 DOI: 10.1002/cphc.202400482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/06/2024] [Accepted: 06/26/2024] [Indexed: 06/28/2024]
Abstract
The propensity of the π-electron system lying above a polycyclic aromatic system to engage in a halogen bond is examined by DFT calculations. Prototype Lewis acid CF3I is placed above the planes of benzene, naphthalene, anthracene, phenanthrene, naphthacene, chrysene, triphenyl, pyrene, and coronene. The I atom positions itself some 3.3-3.4 Å above the polycyclic plane, and the associated interaction energy is about 4 kcal/mol. This quantity is a little smaller for benzene, but is roughly equal for the larger polycyclics. The energy only oscillates a little as the Lewis acid slides across the face of the polycyclic, preferring regions of higher π-electron density over minima of the electrostatic potential. The binding is dominated by dispersion which contributes half of the total interaction energy.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy, Institute of Engineering Physics Samarkand State University, University blv. 15, 140104, Samarkand, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah, 84322-0300, USA
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2
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Martín-Fernández C, Elguero J, Alkorta I. Beryllium as a Base: Complexes of Be(CO) 3 with HX (X=F, Cl, Br, CN, NC, CCH, OH). Chemphyschem 2024:e202400608. [PMID: 38950128 DOI: 10.1002/cphc.202400608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/03/2024]
Abstract
Beryllium chemistry is typically governed by its electron deficient character, but in some compounds it can act as a base. In order to understand better the unusual basicity of Be, we have systematically explored the complexes of one such compound, Be(CO)3, towards several hydrogen bond donors HX (X=F, Cl, Br, CN, NC, CCH, OH). For all complexes we find three different minima, two hydrogen bonded minima (to the Be or O atoms), and one weak beryllium bonded minimum. Further characterization of the interactions using a topological analysis of the electron density and Symmetry Adapted Perturbation Theory (SAPT) provide insight into the nature of these interactions. Overall these results highlight the capability of certain beryllium compounds to act as either a weak Lewis acid or, unconventionally, a Lewis base whose basicity towards hydrogen bonding is comparable to that of π systems.
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Affiliation(s)
| | - José Elguero
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006, Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Juan de la Cierva, 3, 28006, Madrid, Spain
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3
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Yashmin F, Mazumder LJ, Sharma PK, Guha AK. Spodium bonding with noble gas atoms. Phys Chem Chem Phys 2024; 26:8115-8124. [PMID: 38410934 DOI: 10.1039/d3cp06184a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
The nature of the bonding between a neutral group 12 member (Zn3, Cd3 and Hg3) ring and a noble gas atom was explored using quantum chemical simulations. Natural bond orbital, quantum theory of atoms in molecules, symmetry-adapted perturbation theory, and molecular electrostatic potential surface analysis were also used to investigate the type of interaction between the noble gas atom and the metal rings (Zn3, Cd3 and Hg3). The Zn3, Cd3 and Hg3 rings are bonded to the noble gas through non-covalent interactions, which was revealed by the non-covalent interaction index. Additionally, energy decomposition analysis reveals that dispersion energy is the key factor in stabilizing these systems.
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Affiliation(s)
- Farnaz Yashmin
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Lakhya J Mazumder
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Pankaz K Sharma
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
| | - Ankur K Guha
- Department of Chemistry, Cotton University, Panbazar, Guwahati, Assam, 781001, India.
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Amonov A, Scheiner S. Heavy pnicogen atoms as electron donors in sigma-hole bonds. Phys Chem Chem Phys 2023; 25:23530-23537. [PMID: 37656119 DOI: 10.1039/d3cp03479h] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
DFT calculations evaluate the strength of σ-hole bonds formed by ZH3 and ZMe3 (Z = N, P, As, Sb) acting as electron donor. Bond types considered include H-bond, halogen, chalcogen, pnicogen, and tetrel bond to perfluorinated Lewis acids FH, FBr, F2Se F3As, F4Ge, respectively, as well as their monofluorinated analogues. All of the Z atoms can engage in bonds of at least moderate strength, varying from 3 to more than 40 kcal mol-1. In most cases, N forms the strongest bonds, but the falloff from P to Sb is quite mild. However, this pattern is not characteristic of all cases, as for example in the halogen bonds, where the heavier Z atoms are comparable to, or even stronger than N. Most of the bonds are strengthened by replacing the three H atoms of ZH3 by methyl groups, better simulating the situation that would be generally encountered. Structural and NMR shielding data ought to facilitate the identification of these bonds within crystals or in solution.
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Affiliation(s)
- Akhtam Amonov
- Department of Optics and Spectroscopy Engineering Physics Institute, Samarkand State University, University blv. 15, Samarkand 140104, Uzbekistan
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Utah 84322-0300, USA.
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Mazumder LJ, Guha AK. Three-membered beryllium ring, Be 3: not just a hydrogen bond acceptor. Phys Chem Chem Phys 2023; 25:20947-20950. [PMID: 37496445 DOI: 10.1039/d3cp01979a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Quantum chemical calculations predict that the three-membered beryllium ring, Be3 is not just a hydrogen bond acceptor. It is a bond breaker. Calculations reveal that the global minimum geometry of Be3HX (X = F, Cl, OH, CN) features a linear geometry with complete cleavage of the H-X bond along with linearization of the Be3 unit. The linear geometry is radical stabilized Be trimer, R-Be-Be-Be-R. Thus, the present study clearly reveals that the Be3 ring has more to offer than just showing hydrogen bond accepting ability.
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Affiliation(s)
- Lakhya J Mazumder
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam-781001, India.
| | - Ankur K Guha
- Advanced Computational Chemistry Centre, Cotton University, Panbazar, Guwahati, Assam-781001, India.
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6
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Mazumder LJ, Sharma R, Yashmin F, Sharma PK. Beryllium bonding with noble gas atoms. J Comput Chem 2023; 44:644-655. [PMID: 36394306 DOI: 10.1002/jcc.27028] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/25/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022]
Abstract
Quantum chemical calculations were carried out to investigate the nature of the bonding between a neutral Be3 ring and noble gas atom. Electronic structure calculation for these complexes was carried out at different computational levels in association with natural bond orbital, quantum theory of atoms in molecules, electron localization function, symmetry adapted perturbation theory, and molecular electrostatic potential surface analysis of Be3 complexes. The Be atoms in the Be3 moiety are chemically bonded to one another, with the BeBe bond dissociation energy being ~125 kJ mol-1 . The Be3 ring interacts with the noble gases through non-covalent interactions. The binding energies of the noble gas atoms with the Be3 ring increases with increase in their atomic number. The non-covalent interaction index, density overlap region indicator and independent gradient model analyses reveal the presence of non-covalent inter-fragment interactions in the complexes. Energy decomposition analysis reveals that dispersion plays the major role towards stabilizing these systems.
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Affiliation(s)
| | - Rohan Sharma
- Department of Chemistry, Cotton University, Guwahati, Assam, India
| | - Farnaz Yashmin
- Department of Chemistry, Cotton University, Guwahati, Assam, India
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Salazar-Lozas H, Guevara-Vela JM, Pendás ÁM, Francisco E, Rocha-Rinza T. Partition of the electronic energy of the PM7 method via the interacting quantum atoms approach. Phys Chem Chem Phys 2022; 24:19521-19530. [PMID: 35938407 DOI: 10.1039/d2cp02013k] [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
Partitions of the electronic energy such as that provided by the Interacting Quantum Atoms (IQA) approach have given valuable insights for numerous chemical systems and processes. Unfortunately, this kind of analysis may involve the integration of scalar fields over very irregular volumes, a condition which leads to a large and often prohibitive computational effort. These circumstances have limited the use of these energy partitions to systems comprising a few tens of atoms at most. On the other hand, semiempirical methods have proved useful in the study of systems of several thousands of atoms. Therefore, the goal of this work is to carry out partitions of the semiempirical method PM7 in compliance with the IQA approach. For this purpose, we computed one- and two-atomic energetic contributions whose sum equals the PM7 electronic energy. We illustrate how one might exploit the partition of electronic energies computed via the PM7 method by considering small organic and inorganic molecules and the energetics of individual hydrogen bond interactions within several water clusters which include (H2O)30, (H2O)50 and (H2O)100. We also considered the solvation of the amphiphilic caprylate anion to exemplify how to exploit the energy partition proposed in this paper. Overall, this investigation shows how the approach put forward herein might give further insights of the interactions occurring within complex systems in physical and biological chemistry.
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Affiliation(s)
- Hugo Salazar-Lozas
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán C.P. 04510, Ciudad de México, Mexico.
| | | | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Claveria 8, 33006, Oviedo, Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Claveria 8, 33006, Oviedo, Spain
| | - Tomás Rocha-Rinza
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán C.P. 04510, Ciudad de México, Mexico.
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8
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Neutral all metal aromatic half-sandwich complexes between alkaline earth and transition metals: an ab initio exploration. Struct Chem 2021. [DOI: 10.1007/s11224-021-01807-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Vos E, Corral I, Montero-Campillo MM, Mó O, Elguero J, Alkorta I, Yáñez M. Spontaneous bond dissociation cascades induced by Be n clusters (n = 2,4). Phys Chem Chem Phys 2021; 23:6448-6454. [PMID: 33720220 DOI: 10.1039/d0cp06009g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
High-level single and multireference ab initio calculations show that the Be4 cluster behaves as a very efficient Lewis acid when interacting with conventional Lewis bases such as ammonia, water or hydrogen fluoride, to the point that the corresponding acid-base interaction triggers a sequential dissociation of all the bonds of the Lewis base. Notably, this behavior is already found for the simplest beryllium cluster, the Be2 dimer. However, whereas for Be2 the first dissociation process involves a low activation barrier which is above the reactants, for Be4 all the bond dissociation processes involve barriers below the entrance channel leading to a cascade of successive exothermic processes, which end up spontaneously in a global minimum in which the bonding patterns of both the base and the Lewis acid are completely destroyed. Indeed, the global minimum, in all cases, is stabilized by three-center Be-H-Be bonds and covalent interactions between the Be atoms and the basic center of the base, which replace the initial metallic bond stabilizing the Be4 cluster. As a consequence, in the global minimum the basic atoms (N, O and F) behave as hyper-coordinated centers. Also importantly, the Be4 cluster and its complexes present RHF-UHF instabilities (not reported before for Be4), which require the use of multireference methods to correctly describe them.
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Affiliation(s)
- Eva Vos
- Departamento de Química (Módulo 13, Facultad de Ciencias) and Institute of Advanced Chemical Sciences (IadChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049-Madrid, Spain.
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10
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Scheiner S. Comparison of Bifurcated Halogen with Hydrogen Bonds. Molecules 2021; 26:molecules26020350. [PMID: 33445461 PMCID: PMC7827642 DOI: 10.3390/molecules26020350] [Citation(s) in RCA: 10] [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: 12/28/2020] [Revised: 01/08/2021] [Accepted: 01/09/2021] [Indexed: 01/30/2023] Open
Abstract
Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH3 and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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11
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Abstract
An algorithm for the efficient computation of molecular electrostatic potential is reported. It is based on the partition/expansion of density into (pseudo) atomic fragments with the method of Deformed Atoms in Molecules, which allows to compute the potential as a sum of atomic contributions. These contributions are expressed as a series of irregular spherical harmonics times effective multipole moments and inverse multipole moments, including short-range terms. The problem is split into two steps. The first one consists of the partition/expansion of density accompanied by the computation of multipole moments, and its cost depends on the size of the basis set used in the computation of electron density within the Linear Combination of Atomic Orbitals framework. The second one is the actual computation of the electrostatic potential from the quantities calculated in the first step, and its cost depends on the number of computation points. For a precision in the electrostatic potential of six decimal figures, the algorithm leads to a dramatic reduction of the computation time with respect to the calculation from electron density matrix and integrals involving basis set functions.
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Sánchez-Sanz G, Trujillo C, Alkorta I, Elguero J. Understanding Regium Bonds and their Competition with Hydrogen Bonds in Au 2 :HX Complexes. Chemphyschem 2019; 20:1572-1580. [PMID: 30974036 DOI: 10.1002/cphc.201900354] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Indexed: 01/08/2023]
Abstract
A theoretical study of the regium and hydrogen bonds (RB and HB, respectively) in Au2 :HX complexes has been carried out by means of CCSD(T) calculations. The theoretical study shows as overall outcome that in all cases the complexes exhibiting RB are more stable that those with HB. The binding energies for RB complexes range between -24 and -180 kJ ⋅ mol-1, whereas those of the HB complexes are between -6 and -19 kJ ⋅ mol-1 . DFT-SAPT also indicated that HB complexes are governed by electrostatics, but RB complexes present larger contribution of the induction term to the total attractive forces. 197 Au chemical shifts have been calculated using the relativistic ZORA Hamiltonian.
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Affiliation(s)
- 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 Dublin, 152-160 Pearse St., Dublin, 2, Ireland
| | - 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
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Grabowski SJ. A-H…σ Hydrogen Bonds: Dihydrogen and Cycloalkanes as Proton Acceptors. Chemphyschem 2019; 20:565-574. [PMID: 30645024 DOI: 10.1002/cphc.201900045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Indexed: 11/11/2022]
Abstract
ωB97XD/aug-cc-pVTZ calculations were performed for complexes of dihydrogen, cyclopropane, cyclobutane and cyclopentane, with simple proton donating species such as hydrogen fluoride, hydrogen chloride, water, hydrogen cyanide and acetylene. Numerous dependencies between geometrical, energetic and topological parameters of complexes considered were found, since various theoretical approaches were applied: Quantum Theory of 'Atoms in Molecules' (QTAIM), Natural Bond Orbital (NBO) method and energy decomposition analysis (EDA). It was confirmed that complexes of dihydrogen and cyclopropane are linked through the A-H…σ interactions that may be classified as hydrogen bonds. In the case of complexes of cyclobutane such hydrogen bonds are rather weak. Other type and also weak A-H…C hydrogen bonds are formed for complexes with cyclopentane.
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Affiliation(s)
- Sławomir J Grabowski
- Faculty of Chemistry, University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072, 20080, Donostia, Spain.,IKERBASQUE, Basque Foundation for Science, 48011, Bilbao, Spain
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Alkorta I, Montero-Campillo MM, Elguero J, Yáñez M, Mó O. Complexes between neutral oxyacid beryllium salts and dihydrogen: a possible way for hydrogen storage? Dalton Trans 2018; 47:12516-12520. [DOI: 10.1039/c8dt01679h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Very stable 1 : 1 and 1 : 2 complexes between oxyacid beryllium salts and H2 are found.
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Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica
- IQM-CSIC
- 28006 Madrid
- Spain
| | | | - José Elguero
- Instituto de Química Médica
- IQM-CSIC
- 28006 Madrid
- Spain
| | - Manuel Yáñez
- Dep. de Química
- Módulo 13
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC
| | - Otilia Mó
- Dep. de Química
- Módulo 13
- Facultad de Ciencias
- Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC
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