1
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Sutradhar D, Sarmah A, Hobza P, Chandra AK. Strong Be-N Interaction Induced Complementary Chemical Tuning to Design a Dual-gated Single Molecule Junction. Chemistry 2023; 29:e202301473. [PMID: 37401206 DOI: 10.1002/chem.202301473] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/23/2023] [Accepted: 06/29/2023] [Indexed: 07/05/2023]
Abstract
The interaction between pyridines and the π-hole of BeH2 leads to the formation of strong beryllium-bonded complexes. Theoretical investigations demonstrate that the Be-N bonding interaction can effectively regulate the electronic current through a molecular junction. The electronic conductance exhibits distinct switching behavior depending on the substituent groups at the para position of pyridine, highlighting the role of Be-N interaction as a potent chemical gate in the proposed device. The complexes exhibit short intermolecular distances ranging from 1.724 to 1.752 Å, emphasizing their strong binding. Detailed analysis of electronic rearrangements and geometric perturbations upon complex formation provides insights into the underlying reasons for the formation of such strong Be-N bonds, with bond strengths varying from -116.25 to -92.96 kJ/mol. Moreover, the influence of chemical substituents on the local electronic transmission of the beryllium-bonded complex offers valuable insights for the implementation of a secondary chemical gate in single-molecule devices. This study paves the way for the development of chemically gateable, functional single-molecule transistors, advancing the design and fabrication of multifunctional single-molecule devices in the nanoscale regime.
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Affiliation(s)
- Dipankar Sutradhar
- School of Advanced Sciences and Languages, VIT Bhopal University, Bhopal, 466114, India
| | - Amrit Sarmah
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
- Regional Centre for Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu, 1192/12, 771 46, Olomouc, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, CZ-16610, Prague 6, Czech Republic
| | - Asit K Chandra
- Department of Chemistry, North-Eastern Hill University, Shillong, 793022, India
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2
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Yáñez M, Ortíz-Chi F, Merino G, Alkorta I. Dismantlement of ammonia upon interaction with Be n (n ≤ 10) clusters. J Comput Chem 2023; 44:159-167. [PMID: 35297069 PMCID: PMC10078787 DOI: 10.1002/jcc.26843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 12/31/2022]
Abstract
The interaction of ammonia with Ben (n < 1-10) clusters has been investigated by density functional theory and ab initio calculations. The main conclusion is that, regardless of the size of the Be cluster, neither the structure of ammonia nor that of the Be clusters are preserved due to a systematic dissociation of its NH bonds and a spontaneous H-shift toward the available Be atoms. This H migration not only leads to rather stable BeH bonds, but dramatically enhances the strength of the BeN bonds as well. Accordingly, the maximum stability is found for the interaction with the beryllium trimer, leading to a complex with three NBe and three BeH bonds. Another maximum in stability, although lower than that reached for n = 3, is found for the Be heptamer, since from n = 6, a new NBe bond is formed, so that complexes from n = 6 to n = 10 are characterized by the formation of a NBe4 moiety, whose stability reaches a maximum at n = 7. The bonding characteristics of the different species formed are analyzed by means of AIM, NBO, ELF and AdNDP approaches.
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Affiliation(s)
- Manuel Yáñez
- Departamento de Química, Módulo 13, Facultad de Ciencias and Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid, Spain
| | - Filiberto Ortíz-Chi
- CONACYT-Universidad Juárez Autónoma de Tabasco, Centro de Investigación de Ciencia y Tecnología Aplicada de Tabasco, Cunduacán, Tabasco, Mexico
| | - Gabriel Merino
- Centro Investigación & Estudios Avanzados, Unidad Mérida, Dept. Física Aplicada, Merida, Mexico
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC), Madrid, Spain
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3
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Wu Q, Yang S, Li Q. Triel Bond Formed by Malondialdehyde and Its Influence on the Intramolecular H-Bond and Proton Transfer. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186091. [PMID: 36144822 PMCID: PMC9505241 DOI: 10.3390/molecules27186091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/19/2022]
Abstract
Malondialdehyde (MDA) engages in a triel bond (TrB) with TrX3 (Tr = B and Al; X = H, F, Cl, and Br) in three modes, in which the hydroxyl O, carbonyl O, and central carbon atoms of MDA act as the electron donors, respectively. A H···X secondary interaction coexists with the TrB in the former two types of complexes. The carbonyl O forms a stronger TrB than the hydroxyl O, and both of them are better electron donors than the central carbon atom. The TrB formed by the hydroxyl O enhances the intramolecular H-bond in MDA and thus promotes proton transfer in MDA-BX3 (X = Cl and Br) and MDA-AlX3 (X = halogen), while a weakening H-bond and the inhibition of proton transfer are caused by the TrB formed by the carbonyl O. The TrB formed by the central carbon atom imposes little influence on the H-bond. The BH2 substitution on the central C-H bond can also realise the proton transfer in the triel-bonded complexes between the hydroxyl O and TrH3 (Tr = B and Al).
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4
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Yang Q, Wu Q, Zhang X, Yang X, Li Q. Hydrogen and halogen bonds formed by MCO 3 (M = Zn, Cd) and their enhancement by a spodium bond. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Qingqing Yang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Qiaozhuo Wu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Xiaolong Zhang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Xin Yang
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
| | - Qingzhong Li
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai, People’s Republic of China
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5
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Liu N, Wu Q, Li Q, Scheiner S. Promotion of TH 3 (T = Si and Ge) group transfer within a tetrel bond by a cation-π interaction. Phys Chem Chem Phys 2022; 24:1113-1119. [PMID: 34927648 DOI: 10.1039/d1cp05323j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The possibility of the transfer of the TH3 group across a tetrel bond is considered by ab initio calculations. The TB is constructed by pairing PhTH3 (Ph = phenyl; T = Si and Ge) with bases NH3, NHCH2, and the C3N2H4 carbene. The TH3 moves toward the base but only by a small amount in these dimers. However, when a Be2+ or Mg2+ dication is placed above the phenyl ring, the tetrel bond strength is greatly magnified reaching up to nearly 100 kcal mol-1. This dication also induces a much higher degree of transfer which can be best categorized as half-transfer for the two N-bases and a near complete transfer for the carbene.
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Affiliation(s)
- Na Liu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
| | - Qiaozhuo Wu
- 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, UT 84322-0300, USA.
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Wu Q, Xie X, Li Q, Scheiner S. Enhancement of tetrel bond involving tetrazole-TtR 3 (Tt = C, Si; R = H, F). Promotion of SiR 3 transfer by a triel bond. Phys Chem Chem Phys 2022; 24:25895-25903. [DOI: 10.1039/d2cp04194d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The combination of a CR3 (R = H, F) with a tetrazole can result in a moderate carbon bond, which can be further strengthened by a triel bond. On the other hand, SiR3 group is half transferred between the two N atoms in these conditions.
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Affiliation(s)
- Qiaozhuo Wu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, P. R. China
| | - Xiaoying Xie
- 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
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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7
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Liu N, Xie X, Li Q, Scheiner S. Enhancement of the Tetrel Bond by the Effects of Substituents, Cooperativity, and Electric Field: Transition from Noncovalent to Covalent Bond. Chemphyschem 2021; 22:2305-2312. [PMID: 34436816 DOI: 10.1002/cphc.202100612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Indexed: 12/14/2022]
Abstract
The T⋅⋅⋅N tetrel bond (TB) formed between TX3 OH (T=C, Si, Ge; X=H, F) and the Lewis base N≡CM (M=H, Li, Na) is studied by ab initio calculations at the MP2/aug-cc-pVTZ level. Complexes involving TH3 OH contain a conventional TB with interaction energy less than 10 kcal/mol. This bond is substantially strengthened, approaching 35 kcal/mol and covalent character, when fluorosubstituted TF3 OH is combined with NCLi or NCNa. Along with this enhanced binding comes a near equalization of the TB T⋅⋅⋅N and the internal T-O bond lengths, and the associated structure acquires a trigonal bipyramidal shape, despite a high internal deformation energy. This structural transformation becomes more complete, and the TB is further strengthened upon adding an electron acceptor BeCl2 to the Lewis acid and a base to the NCM unit. This same TB strengthening can be accomplished also by imposition of an external electric field.
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Affiliation(s)
- Na Liu
- Laboratory of Theoretical and Computational Chemistry and, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Xiaoying Xie
- Laboratory of Theoretical and Computational Chemistry and, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and, School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA
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8
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Clustering of Electron Deficient B‐ and Be‐Containing Analogues: In the Fight for Tetracoordination, Beryllium Takes the Lead. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100737] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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9
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Grabowski SJ. The coordination of beryllium and magnesium centres in half-sandwich and sandwich compounds. J Organomet Chem 2021. [DOI: 10.1016/j.jorganchem.2021.121906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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10
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Classification of So-Called Non-Covalent Interactions Based on VSEPR Model. Molecules 2021; 26:molecules26164939. [PMID: 34443526 PMCID: PMC8399763 DOI: 10.3390/molecules26164939] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 11/20/2022] Open
Abstract
The variety of interactions have been analyzed in numerous studies. They are often compared with the hydrogen bond that is crucial in numerous chemical and biological processes. One can mention such interactions as the halogen bond, pnicogen bond, and others that may be classified as σ-hole bonds. However, not only σ-holes may act as Lewis acid centers. Numerous species are characterized by the occurrence of π-holes, which also may play a role of the electron acceptor. The situation is complicated since numerous interactions, such as the pnicogen bond or the chalcogen bond, for example, may be classified as a σ-hole bond or π-hole bond; it ultimately depends on the configuration at the Lewis acid centre. The disadvantage of classifications of interactions is also connected with their names, derived from the names of groups such as halogen and tetrel bonds or from single elements such as hydrogen and carbon bonds. The chaos is aggravated by the properties of elements. For example, a hydrogen atom can act as the Lewis acid or as the Lewis base site if it is positively or negatively charged, respectively. Hence names of the corresponding interactions occur in literature, namely hydrogen bonds and hydride bonds. There are other numerous disadvantages connected with classifications and names of interactions; these are discussed in this study. Several studies show that the majority of interactions are ruled by the same mechanisms related to the electron charge shifts, and that the occurrence of numerous interactions leads to specific changes in geometries of interacting species. These changes follow the rules of the valence-shell electron-pair repulsion model (VSEPR). That is why the simple classification of interactions based on VSEPR is proposed here. This classification is still open since numerous processes and interactions not discussed in this study may be included within it.
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11
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Lamsabhi AM, Mó O, Yáñez M. Perturbating Intramolecular Hydrogen Bonds through Substituent Effects or Non-Covalent Interactions. Molecules 2021; 26:3556. [PMID: 34200912 PMCID: PMC8230504 DOI: 10.3390/molecules26123556] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/07/2021] [Accepted: 06/08/2021] [Indexed: 12/02/2022] Open
Abstract
An analysis of the effects induced by F, Cl, and Br-substituents at the α-position of both, the hydroxyl or the amino group for a series of amino-alcohols, HOCH2(CH2)nCH2NH2 (n = 0-5) on the strength and characteristics of their OH···N or NH···O intramolecular hydrogen bonds (IMHBs) was carried out through the use of high-level G4 ab initio calculations. For the parent unsubstituted amino-alcohols, it is found that the strength of the OH···N IMHB goes through a maximum for n = 2, as revealed by the use of appropriate isodesmic reactions, natural bond orbital (NBO) analysis and atoms in molecules (AIM), and non-covalent interaction (NCI) procedures. The corresponding infrared (IR) spectra also reflect the same trends. When the α-position to the hydroxyl group is substituted by halogen atoms, the OH···N IMHB significantly reinforces following the trend H < F < Cl < Br. Conversely, when the substitution takes place at the α-position with respect to the amino group, the result is a weakening of the OH···N IMHB. A totally different scenario is found when the amino-alcohols HOCH2(CH2)nCH2NH2 (n = 0-3) interact with BeF2. Although the presence of the beryllium derivative dramatically increases the strength of the IMHBs, the possibility for the beryllium atom to interact simultaneously with the O and the N atoms of the amino-alcohol leads to the global minimum of the potential energy surface, with the result that the IMHBs are replaced by two beryllium bonds.
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Affiliation(s)
- Al Mokhtar Lamsabhi
- 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;
| | | | - Manuel Yáñez
- 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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12
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Alkorta I, Elguero J, Del Bene JE. Perturbing the O-H …O Hydrogen Bond in 1-oxo-3-hydroxy-2-propene. Molecules 2021; 26:3086. [PMID: 34064185 PMCID: PMC8196739 DOI: 10.3390/molecules26113086] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/06/2021] [Accepted: 05/12/2021] [Indexed: 11/16/2022] Open
Abstract
Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to identify and characterize equilibrium structures and transition structures on the 1-oxo-3-hydroxy-2-propene: Lewis acid potential energy surfaces, with the acids LiH, LiF, BeH2, and BeF2. Two equilibrium structures, one with the acid interacting with the C=O group and the other with the interaction occurring at the O-H group, exist on all surfaces. These structures are separated by transition structures that present the barriers to the interconversion of the two equilibrium structures. The structures with the acid interacting at the C=O group have the greater binding energies. Since the barriers to convert the structures with interaction occurring at the O-H group are small, only the isomers with interaction occurring at the C=O group could be experimentally observed, even at low temperatures. Charge-transfer energies were computed for equilibrium structures, and EOM-CCSD spin-spin coupling constants 2hJ(O-O), 1hJ(H-O), and 1J(O-H) were computed for equilibrium and transition structures. These coupling constants exhibit a second-order dependence on the corresponding distances, with very high correlation coefficients.
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Affiliation(s)
- 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;
| | - Janet E. Del Bene
- Department of Chemistry, Youngstown State University, Youngstown, OH 44555, USA
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13
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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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14
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Liu Y, Yu T, Lai W, Ma Y, Ge Z, Yang FL, Liang PY, Long Y, Zhou PP, Yang Z. High-energetic and low-sensitive 1,3,5-triamino 2,4,6-trinitrobenzene (TATB) crystal: first principles investigation and Hirshfeld surface analysis. NEW J CHEM 2021. [DOI: 10.1039/d1nj00170a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The N–H⋯O hydrogen bonding between neighboring TATB molecules within a planar layer cooperates with π⋯π interaction between two adjacent molecules from two adjacent layers in the TATB crystal.
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Affiliation(s)
- Yingzhe Liu
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Tao Yu
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Weipeng Lai
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Yiding Ma
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Zhongxue Ge
- State Key Laboratory of Fluorine & Nitrogen Chemicals
- Xi’an Modern Chemistry Research Institute
- Xi’an
- P. R. China
| | - Fang-Ling Yang
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Peng-Yu Liang
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Yu Long
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Pan-Pan Zhou
- College of Chemistry and Chemical Engineering
- Key Laboratory of Special Function Materials and Structure Design of Ministry of Education
- Advanced Catalysis Center
- Lanzhou University
- Lanzhou
| | - Zhaoyong Yang
- Key Laboratory of Biotechnology of Antibiotics
- Ministry of Health, Institute of Medicinal Biotechnology
- Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College(PUMC)
- Beijing 100050
- China
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15
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Molecular Hydrogen as a Lewis Base in Hydrogen Bonds and Other Interactions. Molecules 2020; 25:molecules25143294. [PMID: 32698483 PMCID: PMC7397284 DOI: 10.3390/molecules25143294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 07/14/2020] [Accepted: 07/17/2020] [Indexed: 11/23/2022] Open
Abstract
The second-order Møller–Plesset perturbation theory calculations with the aug-cc-pVTZ basis set were performed for complexes of molecular hydrogen. These complexes are connected by various types of interactions, the hydrogen bonds and halogen bonds are most often represented in the sample of species analysed; most interactions can be classified as σ-hole and π-hole bonds. Different theoretical approaches were applied to describe these interactions: Quantum Theory of ‘Atoms in Molecules’, Natural Bond Orbital method, or the decomposition of the energy of interaction. The energetic, geometrical, and topological parameters are analysed and spectroscopic properties are discussed. The stretching frequency of the H-H bond of molecular hydrogen involved in intermolecular interactions is considered as a parameter expressing the strength of interaction.
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16
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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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17
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Abstract
In this review, we provide a consistent description of noncovalent interactions, covering most groups of the Periodic Table. Different types of bonds are discussed using their trivial names. Moreover, the new name “Spodium bonds” is proposed for group 12 since noncovalent interactions involving this group of elements as electron acceptors have not yet been named. Excluding hydrogen bonds, the following noncovalent interactions will be discussed: alkali, alkaline earth, regium, spodium, triel, tetrel, pnictogen, chalcogen, halogen, and aerogen, which almost covers the Periodic Table entirely. Other interactions, such as orthogonal interactions and π-π stacking, will also be considered. Research and applications of σ-hole and π-hole interactions involving the p-block element is growing exponentially. The important applications include supramolecular chemistry, crystal engineering, catalysis, enzymatic chemistry molecular machines, membrane ion transport, etc. Despite the fact that this review is not intended to be comprehensive, a number of representative works for each type of interaction is provided. The possibility of modeling the dissociation energies of the complexes using different models (HSAB, ECW, Alkorta-Legon) was analyzed. Finally, the extension of Cahn-Ingold-Prelog priority rules to noncovalent is proposed.
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18
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Grabowski SJ. Triel bond and coordination of triel centres – Comparison with hydrogen bond interaction. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213171] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Hou M, Zhu Y, Li Q, Scheiner S. Tuning the Competition between Hydrogen and Tetrel Bonds by a Magnesium Bond. Chemphyschem 2020; 21:212-219. [DOI: 10.1002/cphc.201901076] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 12/04/2019] [Indexed: 01/28/2023]
Affiliation(s)
- Mingchang Hou
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Yifan Zhu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical EngineeringYantai University Yantai 264005 China
| | - Steve Scheiner
- Department of Chemistry and BiochemistryUtah State University Logan UT 84322-0300 USA
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20
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Yang J, Yu Q, Yang FL, Lu K, Yan CX, Dou W, Yang L, Zhou PP. Competition and cooperativity of hydrogen-bonding and tetrel-bonding interactions involving triethylene diamine (DABCO), H2O and CO2in air. NEW J CHEM 2020. [DOI: 10.1039/c9nj06036g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triethylene diamine (DABCO) can interact with H2O and CO2in air to form dimeric and trimeric complexesviahydrogen bond, tetrel bond as well as van der Waals interactions.
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Affiliation(s)
- Jianming Yang
- Xi’an Modern Chemistry Research Institute
- Xi’an 710065
- P. R. China
| | - Qinwei Yu
- Xi’an Modern Chemistry Research Institute
- Xi’an 710065
- P. R. China
| | - Fang-Ling Yang
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Ka Lu
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Chao-Xian Yan
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Wei Dou
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Lizi Yang
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
| | - Pan-Pan Zhou
- Key Laboratory of Nonferrous Metal Chemistry and Resources Utilization of Gansu Province
- College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou
- P. R. China
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21
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Ferrer M, Montero-Campillo MM, Mó O, Yáñez M, Alkorta I, Elguero J. Bonding between electron-deficient atoms: strong Lewis-acid character preserved in X–Y–X (X = B, Al; Y = Be, Mg) bridges. NEW J CHEM 2020. [DOI: 10.1039/d0nj01803a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Beryllium bis(diazaborolyl) derivatives and their Mg and Al-containing analogues are stable compounds stabilized through covalent bonds between electron-deficient atoms, and behave as good Lewis acids.
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Affiliation(s)
- Maxime Ferrer
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - M. Merced Montero-Campillo
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Otilia Mó
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Manuel Yáñez
- Departamento de Química
- Facultad de Ciencias
- Módulo 13, and Institute of Advanced Chemical Sciences (IadChem). Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
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22
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23
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León I, Lesarri A, Fernández JA. Evaluation of the aggregation process in a mixture of propofol and benzocaine. Phys Chem Chem Phys 2019; 21:3537-3544. [PMID: 30137107 DOI: 10.1039/c8cp04386h] [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
We report on a mass-resolved IR spectrosopic study on propofol-benzocaine aggregates. This is a complex system due to the several conformational isomers that both monomers may adopt and to the combination of functional groups they present, which allow the molecules to interact in many possible ways. However, our results demonstrate that a single conformation is favored for each stoichiometry. In the heterodimer, propofol acts as a proton donor to the ester group of benzocaine, while the whole cluster is stabilized by dispersive forces. These dispersive forces account for an important part of the system's stabilization energy as the calculations suggest. Propofol does not show any affinity for the amino group of benzocaine, even when a second molecule of propofol is introduced. These results demonstrate the difficulty in anticipating the aggregation preferences of even small organic molecules.
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Affiliation(s)
- I León
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country, Barrio Sarriena s/n, 48940 Leioa, Spain.
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24
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25
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Intramolecular magnesium bonds in malonaldehyde-like systems: a critical view of the resonance-assisted phenomena. Theor Chem Acc 2018. [DOI: 10.1007/s00214-018-2274-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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26
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Huran AW, Ben Amor N, Evangelisti S, Hoyau S, Leininger T, Brumas V. The Electronic Structure of Beryllium Chains. J Phys Chem A 2018; 122:5321-5332. [DOI: 10.1021/acs.jpca.7b12187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ahmad W. Huran
- Institut für Physik, Martin-Luther-Universität Halle-Wittenberg, D-06120 Halle (Saale), Germany
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse et CNRS, 118, Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Nadia Ben Amor
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse et CNRS, 118, Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Stefano Evangelisti
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse et CNRS, 118, Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Sophie Hoyau
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse et CNRS, 118, Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Thierry Leininger
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse et CNRS, 118, Route de Narbonne, F-31062 Toulouse Cedex, France
| | - Véronique Brumas
- SIMAD, Université de Toulouse, 118, Route de Narbonne, F-31062 Toulouse Cedex, France
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27
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Grabowski SJ. Coordination of Be and Mg Centres by HCN Ligands - Be…N and Mg…N Interactions. Chemphyschem 2018; 19:1830-1840. [PMID: 29709103 DOI: 10.1002/cphc.201800274] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Indexed: 11/06/2022]
Abstract
ωB97XD/aug-cc-pVTZ calculations were performed for clusters of Z2+ cations (Z=Be and Mg) and HCN molecules (up to six molecules). The clusters of Be(CH3 )2 and Mg(CH3 )2 with HCN species were also calculated to analyse the influence of the Be/Mg-C formally covalent bonds on interactions of Be or Mg centre with ligands. The beryllium and magnesium centres possess different areas of a positive electrostatic potential that depend on a number of HCN ligands in the cluster considered. Numerous correlations between geometrical, energetic and topological parameters of the clusters considered are discussed since various theoretical approaches are applied; Quantum Theory of 'Atoms in Molecules', Natural Bond Orbital method and decomposition of the energy of interaction. The Be/Mg…N interactions classified as beryllium and magnesium bonds possess numerous characteristics which are known for the hydrogen bonds. Different types of coordination of Be and Mg centres analysed here exist also in crystal structures.
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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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28
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Xu HL, Li QZ, Scheiner S. Effect of Magnesium Bond on the Competition Between Hydrogen and Halogen Bonds and the Induction of Proton and Halogen Transfer. Chemphyschem 2018; 19:1456-1464. [PMID: 29544030 DOI: 10.1002/cphc.201800102] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 01/18/2023]
Abstract
HOX (X=Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base-like HCN, NH3 , and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY2 forms a Mg-bond with the O atom of HOX, which grows stronger in the order X=Cl<Br<I<At and Y=F<Cl<Br. When all three molecules are combined, both the Mg and the H/X bonds are cooperatively strengthened to a large degree. Rather than causing a reversal in the HB/XB competition, the Mg-bond acts primarily to amplify the natural preference within the dimer. The Mg-bond induces a certain degree of transfer from O to N of the bridging atom in the H/X bond. Comparison is also made with the effects of a Be-bond.
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Affiliation(s)
- Hui-Li Xu
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Qing-Zhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering, Yantai University, Yantai, 264005, China
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322-0300, USA
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29
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Grabowski SJ. Magnesium Bonds: From Divalent Mg Centres to Trigonal and Tetrahedral Coordination. ChemistrySelect 2018. [DOI: 10.1002/slct.201703137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sławomir J. Grabowski
- Faculty of Chemistry; University of the Basque Country and Donostia International Physics Center (DIPC), P.K. 1072; 20080 San Sebastian Spain
- IKERBASQUE; Basque Foundation for Science; 48011 Bilbao Spain
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30
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Montero-Campillo MM, Alkorta I, Elguero J. Fostering the Basic Instinct of Boron in Boron-Beryllium Interactions. J Phys Chem A 2018. [PMID: 29537845 DOI: 10.1021/acs.jpca.8b01551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A set of complexes L2HB···BeX2 (L = CNH, CO, CS, N2, NH3, NCCH3, PH3, PF3, PMe3, OH2; X = H, F) containing a boron-beryllium bond is described at the M06-2X/6-311+G(3df,2pd)//M062-2X/6-31+G(d) level of theory. In this quite unusual bond, boron acts as a Lewis base and beryllium as a Lewis acid, reaching binding energies up to -283.3 kJ/mol ((H2O)2HB···BeF2). The stabilization of these complexes is possible thanks to the σ-donor role of the L ligands in the L2HB···BeX2 structures and the powerful acceptor nature of beryllium. According to the topology of the density, these B-Be interactions present positive laplacian values and negative energy densities, covering different degrees of electron sharing. ELF calculations allowed measuring the population in the interboundary B-Be region, which varies between 0.20 and 2.05 electrons upon switching from the weakest ((CS)2HB···BeH2) to the strongest complex ((H2O)2HB···BeF2). These B-Be interactions can be considered as beryllium bonds in most cases.
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Affiliation(s)
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3 , 28006 Madrid , Spain
| | - José Elguero
- Instituto de Química Médica (CSIC) , Juan de la Cierva, 3 , 28006 Madrid , Spain
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31
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Brea O, Corral I. Super Strong Be–Be Bonds: Theoretical Insight into the Electronic Structure of Be–Be Complexes with Radical Ligands. J Phys Chem A 2018; 122:2258-2265. [DOI: 10.1021/acs.jpca.7b11758] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Oriana Brea
- Departamento de Química, Facultad
de Ciencias, Módulo 13, and Institute of Advanced
Chemical Sciences (IadChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Inés Corral
- Departamento de Química, Facultad
de Ciencias, Módulo 13, and Institute of Advanced
Chemical Sciences (IadChem), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco, 28049 Madrid, Spain
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32
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Wei Y, Li Q, Scheiner S. The π-Tetrel Bond and its Influence on Hydrogen Bonding and Proton Transfer. Chemphyschem 2018; 19:736-743. [DOI: 10.1002/cphc.201701136] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Revised: 11/27/2017] [Indexed: 12/18/2022]
Affiliation(s)
- Yuanxin Wei
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Qingzhong Li
- Laboratory of Theoretical and Computational Chemistry and School of Chemistry and Chemical Engineering; Yantai University; Yantai 264005 China), Fax: (+86) 535-6902063
| | - Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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33
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Zhao XF, Li JJ, Li HR, Yuan C, Tian X, Li SD, Wu YB, Guo JC, Wang ZX. Viable aromatic BenHn stars enclosing a planar hypercoordinate boron or late transition metal. Phys Chem Chem Phys 2018; 20:7217-7222. [DOI: 10.1039/c7cp06955c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Similar to Bn rings, star-like BenHn rings can serve as the n-electron σ-donors for designing species with planar hypercoordinate atom.
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Affiliation(s)
- Xue-Feng Zhao
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Jia-Jia Li
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Hai-Ru Li
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Caixia Yuan
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Xinxin Tian
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Si-Dian Li
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Yan-Bo Wu
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Jin-Chang Guo
- The Key Lab of Materials for Energy Conversion and Storage of Shanxi Province
- Institute of Molecular Science
- Shanxi University
- Taiyuan
- People's Republic of China
| | - Zhi-Xiang Wang
- College of Chemistry and Chemical Engineering, University of Chinese Academy of Sciences
- Beijing 100049
- People's Republic of China
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34
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Oliveira V, Kraka E. Systematic Coupled Cluster Study of Noncovalent Interactions Involving Halogens, Chalcogens, and Pnicogens. J Phys Chem A 2017; 121:9544-9556. [PMID: 29154546 DOI: 10.1021/acs.jpca.7b10196] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The noncovalent interactions of 32 complexes involving pnicogens, chalcogens, and halogens atoms were investigated at the CCSD(T)/aug-cc-pVTZ level of theory. Two different types of complexes could be distinguished on the basis of geometric parameters, electron difference densities, and the charge transfer mechanisms associated with each type. In the type I conformation, the monomers adopt a skewed orientation allowing charge to be transfer between both monomers, whereas in the type II conformation the monomers adopt a linear arrangement, maximizing charge transfer in only one direction. Type I complexes involving the interaction between pnicogens and chalcogens cannot be unambiguously defined as chalcogen or pnicogen bonds, they are an admixture of both. The charge transfer dependence on the conformation adopted by the complexes described in this work can serve as a novel conformationally driven design concept for materials.
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Affiliation(s)
- Vytor Oliveira
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University , 3215 Daniel Ave, Dallas, Texas 75275-0314, United States
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35
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Bauzá A, Frontera A. On the Importance of π-Hole Beryllium Bonds: Theoretical Study and Biological Implications. Chemistry 2017; 23:5375-5380. [DOI: 10.1002/chem.201700682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Indexed: 01/29/2023]
Affiliation(s)
- Antonio Bauzá
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
| | - Antonio Frontera
- Department of Chemistry; Universitat de les Illes Balears; Crta. de Valldemossa km 7.5 07122 Palma de Mallorca Spain
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36
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Tama R, Mó O, Yáñez M, Montero-Campillo MM. Characterizing magnesium bonds: main features of a non-covalent interaction. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2065-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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37
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Grabowski SJ. Hydrogen bonds, and σ-hole and π-hole bonds – mechanisms protecting doublet and octet electron structures. Phys Chem Chem Phys 2017; 19:29742-29759. [DOI: 10.1039/c7cp06393h] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
For various interactions electron charge shifts try to protect the former doublet or octet electronic structure of the Lewis acid centre.
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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
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38
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Modulating the strength of tetrel bonding through beryllium bonding. J Mol Model 2016; 22:192. [PMID: 27464738 DOI: 10.1007/s00894-016-3060-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 07/03/2016] [Indexed: 01/28/2023]
Abstract
Quantum chemical calculations were performed to investigate the stability of the ternary complexes BeH2···XMH3···NH3 (X = F, Cl, and Br; M = C, Si, and Ge) and the corresponding binary complexes at the atomic level. Our results reveal that the stability of the XMH3···BeH2 complexes is mainly due to both a strong beryllium bond and a weak tetrel-hydride interaction, while the XMH3···NH3 complexes are stabilized by a tetrel bond. The beryllium bond with a halogen atom as the electron donor has many features in common with a beryllium bond with an O or N atom as the electron donor, although they do exhibit some different characteristics. The stability of the XMH3···NH3 complex is dominated by the electrostatic interaction, while the orbital interaction also makes an important contribution. Interestingly, as the identities of the X and M atoms are varied, the strength of the tetrel bond fluctuates in an irregular manner, which can explained by changes in electrostatic potentials and orbital interactions. In the ternary systems, both the beryllium bond and the tetrel bond are enhanced, which is mainly ascribed to increased electrostatic potentials on the corresponding atoms and charge transfer. In particular, when compared to the strengths of the tetrel and beryllium bonds in the binary systems, in the ternary systems the tetrel bond is enhanced to a greater degree than the beryllium bond. Graphical Abstract A tetrel bond can be strengthened greatly by a beryllium bond.
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39
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Brea O, Alkorta I, Mó O, Yáñez M, Elguero J, Corral I. Exergonic and Spontaneous Production of Radicals through Beryllium Bonds. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603690] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Oriana Brea
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC).; C/ Juan de la Cierva, 3 28006 Madrid Spain
| | - Otilia Mó
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
| | - Manuel Yáñez
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
| | - José Elguero
- Instituto de Química Médica (CSIC).; C/ Juan de la Cierva, 3 28006 Madrid Spain
| | - Inés Corral
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
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40
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Brea O, Alkorta I, Mó O, Yáñez M, Elguero J, Corral I. Exergonic and Spontaneous Production of Radicals through Beryllium Bonds. Angew Chem Int Ed Engl 2016; 55:8736-9. [DOI: 10.1002/anie.201603690] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Oriana Brea
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC).; C/ Juan de la Cierva, 3 28006 Madrid Spain
| | - Otilia Mó
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
| | - Manuel Yáñez
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
| | - José Elguero
- Instituto de Química Médica (CSIC).; C/ Juan de la Cierva, 3 28006 Madrid Spain
| | - Inés Corral
- Universidad Autónoma de Madrid; Departamento de Química, Facultad de Ciencias, Módulo 13, Campus de Excelencia UAM-CSIC, Cantoblanco; 28049 Madrid Spain
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41
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Effect of beryllium bonds on the keto–enol tautomerism of formamide derivatives: a subtle basicity–acidity balance. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1902-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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McDowell SA, Fiedler CS. A computational study of beryllium-bonded H 2 Be⋯FNgH/FKrCl (Ng = Ar, Kr) dyads and their intermolecular interactions with the model nucleophiles F − , NH 3 and NCH. COMPUT THEOR CHEM 2016. [DOI: 10.1016/j.comptc.2016.03.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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43
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Marín-Luna M, Alkorta I, Elguero J. Interaction of beryllium derivatives with N-methylated DNA bases: 9-methylguanine and 1-methylcytosine. Tetrahedron 2016. [DOI: 10.1016/j.tet.2016.02.062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Koukaras EN, Sgouros AP, Sigalas MM. Fully Hydrogenated Beryllium Nanoclusters. J Am Chem Soc 2016; 138:3218-27. [PMID: 26906563 DOI: 10.1021/jacs.6b00135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present the ground state and energetically low structures of BenH2n nanoclusters as predicted using density functional theory (DFT) and employing the M06 meta-hybrid exchange-correlation functional. Results using the M06 functional are benchmarked against high accuracy coupled-cluster CCSD(T) and found to be in excellent agreement. For small values of n, the linear or polymeric form is the lowest energy geometry, while for sizes larger, n > 9 ring type and link type structures are the energetically lowest configurations. This trend has also been observed through ab initio molecular dynamics (AIMD) simulations at finite temperatures. In addition to the binding energies of the structures we report on polymerization energies, Be-H bond energies with respect to coordination details, hydrogen desorption energies of saturated and oversaturated species, as well as computed infrared spectra of all the ground state and energetically low lying structures presented. Furthermore, we find that the saturated polymeric forms of the nanoclusters cannot retain molecular hydrogen, in contrast to what is expected when zero point energy corrections are not taken into account.
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Affiliation(s)
- Emmanuel N Koukaras
- Nanotechnology and Advanced Materials Laboratory, Department of Chemical Engineering, University of Patras , 26500 GR Patras, Greece
| | - Aris P Sgouros
- School of Chemical Engineering, National Technical University of Athens (NTUA) , GR-15780 Athens, Greece.,Department of Materials Science, University of Patras , GR-26504 Patras, Greece
| | - Michael M Sigalas
- Department of Materials Science, University of Patras , GR-26504 Patras, Greece
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McDowell SAC, Maynard SJ. A computational study of model hydrogen-, halogen-, beryllium- and magnesium-bonded complexes of aziridine derivatives. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1142128] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Sean A. C. McDowell
- Department of Biological and Chemical Sciences, The University of the West Indies, Bridgetown, Barbados
| | - Satoria J. Maynard
- Department of Biological and Chemical Sciences, The University of the West Indies, Bridgetown, Barbados
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Marín-Luna M, Alkorta I, Elguero J, Mó O, Yáñez M. Fullerene and corannulene derivatives acting as insulators of Cl−and BeH2. Phys Chem Chem Phys 2016; 18:6059-68. [DOI: 10.1039/c5cp08046k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Corannulene and its benzo-derivatives CxH10(x= 20–60) as prototypes of non-planar π-aromatic systems have been studied as insulators of BeH2and Cl−.
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Affiliation(s)
| | - Ibon Alkorta
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
| | - José Elguero
- Instituto de Química Médica (CSIC)
- E-28006 Madrid
- Spain
| | - Otilia Mó
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - Manuel Yáñez
- Departamento de Química
- Módulo 13
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
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Brea O, Mó O, Yáñez M, Alkorta I, Elguero J. Creating σ-Holes through the Formation of Beryllium Bonds. Chemistry 2015. [DOI: 10.1002/chem.201500981] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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48
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McDowell SA, Maynard SJ. A computational study of model beryllium-bonded complexes of oxirane and F-substituted oxiranes with BeX2 (X=H, Cl). Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.04.046] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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49
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Interplay between Beryllium Bonds and Anion-π Interactions in BeR2:C6X6:Y- Complexes (R = H, F and Cl, X = H and F, and Y = Cl and Br). Molecules 2015; 20:9961-76. [PMID: 26035097 PMCID: PMC6272305 DOI: 10.3390/molecules20069961] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/23/2015] [Accepted: 05/26/2015] [Indexed: 01/29/2023] Open
Abstract
A theoretical study of the beryllium bonds in BeR2:C6X6 (R = H, F, Cl and X = H and F) has been carried out by means of MP2/aug′-cc-pVDZ computational methods. In addition, the ternary complexes BeR2:C6X6:Y− (Y = Cl and Br) have been analyzed. Geometric, energetic and electronic aspects of the complexes have been taken into account. All the parameters analyzed provide a clear indication of favorable cooperativity in both interactions observed, beryllium bond and aromatic ring:anion interaction.
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Dual functions of Lewis acid and base of Se in F2C=Se and their interplay in F 2CSe•••NH 3•••HX. J Mol Model 2015; 21:157. [PMID: 26016943 DOI: 10.1007/s00894-015-2701-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/10/2015] [Indexed: 10/23/2022]
Abstract
High-level quantum chemical calculations of the ternary systems F2CSe∙∙∙NH3∙∙∙HX (X=BeH, BH2, OH, CN, OCH3, Cl, and F) and the corresponding binary systems have been carried out in view of geometries, vibrational frequencies, interaction energies, orbital interactions, and electron densities. The molecular electrostatic potentials of F2CSe demonstrate that the Se atom could play a dual role of Lewis acid and base to form a chalcogen bond with NH3 and a hydrogen bond or a covalent interaction with HX, respectively. The chalcogen bond can compete with the hydrogen bond for the complexes involving F2CSe, but the covalent interaction is far stronger than the chalcogen bond. In the ternary complexes, both types of interactions are strengthened by each other, characterized by a shorter binding distance, a larger electron density, and a stronger orbital interaction. The covalent interaction has a greater enhancing effect on the chalcogen bond than the hydrogen bond does, resulting in a prominent shortening of ~0.23 Å distance for the Se∙∙∙N distance in F2CSe∙∙∙NH3∙∙∙BH3. The enhancement of both interactions in the ternary complexes has been understood with the electrostatic potentials and orbital interactions. Graphical Abstract The dual functions of Lewis acid and base of Se in F2CSe are enhanced each other in the ternary complexes.
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