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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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2
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Estimation of resonance assisted hydrogen bond (RAHB) energies using properties of ring critical points in some dihydrogen-bonded complexes. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Alikhani ME. Beryllium bonding: insights from the σ- and π-hole analysis. J Mol Model 2020; 26:94. [PMID: 32248314 DOI: 10.1007/s00894-020-4348-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/09/2020] [Indexed: 12/19/2022]
Abstract
Beryllium bonding is actually a subclass of secondary bonding. Similar to the case of halogen bonding, the σ- and π-holes on the Be atom of the monomers give in zeroth approximation the direction of electrophilic attack favorable to the formation of beryllium bonds. The nature of beryllium bonding is purely electrostatic so that the symmetry-adapted perturbation theory energy decomposition perfectly explains the relevance of the polarization and dispersion contribution on the formation of the beryllium bond.
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Affiliation(s)
- M Esmaïl Alikhani
- Sorbonne Université, CNRS, UMR 8233, MONARIS, Case Courrier 49, 4 Place Jussieu, F-75005, Paris, France.
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4
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Martín-Fernández C, Montero-Campillo MM, Alkorta I, Elguero J. Weak interactions and cooperativity effects on disiloxane: a look at the building block of silicones. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1433337] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
| | | | - Ibon Alkorta
- Instituto de Química Médica, CSIC, Madrid, Spain
| | - José Elguero
- Instituto de Química Médica, CSIC, Madrid, Spain
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5
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Density functional theory study on the dihydrogen bond cooperativity in the growth behavior of dimethyl sulfoxide clusters. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2017.11.062] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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6
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The σ and π Holes. The Halogen and Tetrel Bondings: Their Nature, Importance and Chemical, Biological and Medicinal Implications. ChemistrySelect 2017. [DOI: 10.1002/slct.201701676] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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7
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Affiliation(s)
- Marta Marín-Luna
- Instituto de Química Médica (CSIC), C/Juan de la Cierva, 3, 28006-Madrid, Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), C/Juan de la Cierva, 3, 28006-Madrid, Spain
| | - José Elguero
- Instituto de Química Médica (CSIC), C/Juan de la Cierva, 3, 28006-Madrid, Spain
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8
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Albrecht L, Boyd RJ, Mó O, Yáñez M. Changing Weak Halogen Bonds into Strong Ones through Cooperativity with Beryllium Bonds. J Phys Chem A 2014; 118:4205-13. [DOI: 10.1021/jp503229u] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Laura Albrecht
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Russell J. Boyd
- Department
of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4R2
| | - Otilia Mó
- Departamento
de Quı́mica, Facultad de Ciencias, Módulo
13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Manuel Yáñez
- Departamento
de Quı́mica, Facultad de Ciencias, Módulo
13, Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
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9
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Abstract
Positive cooperativity is found in beryllium bonded complexes similar to that described for hydrogen bonded systems.
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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
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC
- 28049 Madrid, Spain
| | - Otilia Mó
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- Campus de Excelencia UAM-CSIC
- 28049 Madrid, Spain
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10
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Vijaya Pandiyan B, Kolandaivel P, Deepa P. A theoretical perspective of the nature of hydrogen-bond types – the atoms in molecules approach. Mol Phys 2013. [DOI: 10.1080/00268976.2013.850544] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
| | - P. Kolandaivel
- Department of Physics, Bharathiar University, Coimbatore, India
| | - P. Deepa
- Department of Computational Chemistry, Institute of Organic Chemistry and Biochemistry of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
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11
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A B3LYP and MP2 theoretical investigation on the cooperativity effect between the XH⋯HM (X=F, Cl, Br; M=Li, Na, K) dihydrogen-bonding and HM⋯π interactions involving C6H6. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Resonance assisted hydrogen bonds in open-chain and cyclic structures of malonaldehyde enol: A theoretical study. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.069] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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A B3LYP and MP2(full) theoretical investigation into the cooperativity effect between dihydrogen-bonding and H–M∙∙∙π (M = Li, Na, K) interactions among HF, MH with the π-electron donor C2H2, C2H4 or C6H6. J Mol Model 2013; 19:3153-63. [DOI: 10.1007/s00894-013-1840-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2012] [Accepted: 03/25/2013] [Indexed: 10/26/2022]
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14
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Abstract
Ab initio calculations were used to analyze interactions of with 1–4 molecules of NH3at the MP2/6-311++G(d,p) and the B3LYP/6-311++G(d,p) computational levels. In addition to H3B–H⋯H–NH2dihydrogen bond, the H2N–H⋯NH3hydrogen bonds were also predicted in clusters. Negative cooperativity in clusters constructed from mixed H3B–H⋯H–NH2dihydrogen and H2N–H⋯NH3hydrogen bonds are more remarkable. The negative cooperativity increases with size and number of hydrogen bonds in cluster. The B–H stretching frequencies show blue shifts with respect to cluster formation. Greater blue shift in stretching frequencies was predicted for B–H bonds which did not contribute to dihydrogen bonding with NH3molecules. The structures were analyzed with the atoms in molecules (AIM) methodology.
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15
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Modulating weak intramolecular interactions through the formation of beryllium bonds: complexes between squaric acid and BeH2. J Mol Model 2012; 19:2759-66. [PMID: 23053013 DOI: 10.1007/s00894-012-1603-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Accepted: 09/21/2012] [Indexed: 10/27/2022]
Abstract
The electronic structure of the two most stable isomers of squaric acid and their complexes with BeH2 were investigated at the B3LYP/6-311 + G(3df,2p)// B3LYP/6-31 + G(d,p) level of theory. Squaric acid forms rather strong beryllium bonds with BeH2, with binding energies of the order of 60 kJ mol(-1). The preferential sites for BeH2 attachment are the carbonyl oxygen atoms, but the global minima of the potential energy surfaces of both EZ and ZZ isomers are extra-stabilized through the formation of a BeH···HO dihydrogen bond. More importantly, analysis of the electron density of these complexes shows the existence of significant cooperative effects between the beryllium bond and the dihydrogen bond, with both becoming significantly reinforced. The charge transfer involved in the formation of the beryllium bond induces a significant electron density redistribution within the squaric acid subunit, affecting not only the carbonyl group interacting with the BeH2 moiety but significantly increasing the electron delocalization within the four membered ring. Accordingly the intrinsic properties of squaric acid become perturbed, as reflected in its ability to self-associate.
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16
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Li Q, Li R, Liu X, Cheng J, Li W. Ab initiostudy of synergetic effects of two strong interactions of cation–π interaction and lithium bond in M+ ··· phenyl lithium ··· N (M = Li, Na, K; N = H2O and NH3) complex. Mol Phys 2012. [DOI: 10.1080/00268976.2012.655793] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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17
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Zabardasti A, Zare N, Arabpour M. Theoretical study of dihydrogen bonded clusters of water with tetrahydroborate. Struct Chem 2011. [DOI: 10.1007/s11224-011-9747-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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18
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Hydrogen bonding interactions in cysteine–urea complexes: Theoretical studies of structures, properties and topologies. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.08.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Alkorta I, Blanco F, Elguero J. Dihydrogen Bond Cooperativity in Aza-borane Derivatives. J Phys Chem A 2010; 114:8457-62. [DOI: 10.1021/jp1046694] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ibon Alkorta
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain, and Department of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Fernando Blanco
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain, and Department of Chemistry, Trinity College Dublin, Dublin 2, Ireland
| | - Jose Elguero
- Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain, and Department of Chemistry, Trinity College Dublin, Dublin 2, Ireland
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20
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Zabardasti A, Kakanejadi A, Moosavi S, Bigleri Z, Solimannejad M. Anticooperativity in dihydrogen bonded clusters of ammonia and. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.01.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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21
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Blanco F, Alkorta I, Rozas I, Elguero J. Chiral recognition in self-complexes of diketopiperazine derivatives. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1686] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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A theoretical study of three and four proton donors on linear HX···BeH2···HX and bifurcate BeH2···2HX trimolecular dihydrogen-bonded complexes with X = CN and NC. Struct Chem 2009. [DOI: 10.1007/s11224-009-9567-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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23
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Alkorta I, Blanco F, Deyà PM, Elguero J, Estarellas C, Frontera A, Quiñonero D. Cooperativity in multiple unusual weak bonds. Theor Chem Acc 2009. [DOI: 10.1007/s00214-009-0690-1] [Citation(s) in RCA: 196] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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24
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Del Bene JE, Alkorta I, Elguero J. Characterizing Complexes with F−Li+−F Lithium Bonds: Structures, Binding Energies, and Spin−Spin Coupling Constants. J Phys Chem A 2009; 113:8359-65. [DOI: 10.1021/jp9020917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - Ibon Alkorta
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
| | - José Elguero
- Department of Chemistry, Youngstown State University, Youngstown, Ohio 44555, and Instituto de Química Médica, CSIC, Juan de la Cierva, 3, E-28006 Madrid, Spain
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25
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