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Báez-Grez R, Pino-Rios R. Exploring the Nature of Chemical Bonding between Noble Gases and Hypercoordinate Group 13 Compounds: Beyond Boron. J Phys Chem A 2024; 128:4950-4955. [PMID: 38864772 DOI: 10.1021/acs.jpca.4c00685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
In this article, we systematically study the stability and chemical bond nature of EH4Ng+ compounds (E = Al-Tl; Ng = He-Rn) at the CCSD(T) and ωB97XD levels of theory. Thermochemical calculations obtained by exploring different dissociation pathways show that these compounds could be stable at low temperatures. In addition, studied compounds have a strong E-Ng bond, which has been characterized using different methodologies such as quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO) theory, and natural energy decomposition analysis (NEDA). Results indicate that the nature of the chemical bond is predominantly covalent, especially in the case those including the heavier gases (Ar-Rn), occurring through a charge transfer from the noble gas to the group 13 element. However, the electrostatic contribution is also important in the stabilization of this bond. This study extends the universe of group 13 molecules containing noble gas bonds beyond boron and other elements from the second period.
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Affiliation(s)
- Rodrigo Báez-Grez
- Facultad de Ciencias, Universidad Arturo Prat., Casilla 121, Iquique 1100000, Chile
| | - Ricardo Pino-Rios
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile
- Centro de Investigación Medicina de Altura - CEIMA, Universidad Arturo Prat, Casilla 121, Iquique 1100000, Chile
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2
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Sigmund LM, S SS, Albers A, Erdmann P, Paton RS, Greb L. Predicting Lewis Acidity: Machine Learning the Fluoride Ion Affinity of p-Block-Atom-Based Molecules. Angew Chem Int Ed Engl 2024; 63:e202401084. [PMID: 38452299 DOI: 10.1002/anie.202401084] [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: 01/19/2024] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
"How strong is this Lewis acid?" is a question researchers often approach by calculating its fluoride ion affinity (FIA) with quantum chemistry. Here, we present FIA49k, an extensive FIA dataset with 48,986 data points calculated at the RI-DSD-BLYP-D3(BJ)/def2-QZVPP//PBEh-3c level of theory, including 13 different p-block atoms as the fluoride accepting site. The FIA49k dataset was used to train FIA-GNN, two message-passing graph neural networks, which predict gas and solution phase FIA values of molecules excluded from training with a mean absolute error of 14 kJ mol-1 (r2=0.93) from the SMILES string of the Lewis acid as the only input. The level of accuracy is notable, given the wide energetic range of 750 kJ mol-1 spanned by FIA49k. The model's value was demonstrated with four case studies, including predictions for molecules extracted from the Cambridge Structural Database and by reproducing results from catalysis research available in the literature. Weaknesses of the model are evaluated and interpreted chemically. FIA-GNN and the FIA49k dataset can be reached via a free web app (www.grebgroup.de/fia-gnn).
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Affiliation(s)
- Lukas M Sigmund
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Shree Sowndarya S
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Andreas Albers
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Philipp Erdmann
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
| | - Robert S Paton
- Department of Chemistry, Colorado State University, 1301 Center Avenue, Fort Collins, CO, 80523, USA
| | - Lutz Greb
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany
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Vásquez-Espinal A, Pino-Rios R. Strong carbon - noble gas covalent bond and fluxionality in hypercoordinate compounds. Phys Chem Chem Phys 2023; 25:27468-27474. [PMID: 37800185 DOI: 10.1039/d3cp03576j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Thermodynamic, kinetic, and chemical bonding analysis at the coupled cluster level has been carried out for a series of hypercoordinated carbon compounds with formula CH4Ng2+ (Ng = He-Rn). Results show that these compounds could be stable at room temperature and Born-Oppenheimer molecular dynamics simulations (BOMD) in conjunction with activation energies indicate high kinetic stability. In addition, all chemical bonding descriptors agree with a strong C-Ng covalent bond and a bonding pattern similar to that of CH5+. Finally, BOMD simulations showed that these compounds are fluxional, with a continuous formation/breaking of H-H and C-H bonds. To the best of the authors' knowledge, these results represent the first series of fluxional compounds possessing a covalent bond between a main group element and a noble gas atom.
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Affiliation(s)
- Alejandro Vásquez-Espinal
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat. Casilla 121, Iquique 1100000, Chile.
| | - Ricardo Pino-Rios
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat. Casilla 121, Iquique 1100000, Chile.
- Instituto de Estudios de la Salud, Universidad Arturo Prat, Iquique, 1100000, Chile
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Nunzi F, Pannacci G, Tarantelli F, Belpassi L, Cappelletti D, Falcinelli S, Pirani F. Leading Interaction Components in the Structure and Reactivity of Noble Gases Compounds. Molecules 2020; 25:molecules25102367. [PMID: 32443725 PMCID: PMC7287633 DOI: 10.3390/molecules25102367] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/12/2022] Open
Abstract
The nature, strength, range and role of the bonds in adducts of noble gas atoms with both neutral and ionic partners have been investigated by exploiting a fine-tuned integrated phenomenological–theoretical approach. The identification of the leading interaction components in the noble gases adducts and their modeling allows the encompassing of the transitions from pure noncovalent to covalent bound aggregates and to rationalize the anomalous behavior (deviations from noncovalent type interaction) pointed out in peculiar cases. Selected adducts affected by a weak chemical bond, as those promoting the formation of the intermolecular halogen bond, are also properly rationalized. The behavior of noble gas atoms excited in their long-life metastable states, showing a strongly enhanced reactivity, has been also enclosed in the present investigation.
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Affiliation(s)
- Francesca Nunzi
- Dipartimento di Chimica, Biologia e Biotecnologie, via Elce di Sotto 8, I-06123 Perugia, Italy; (G.P.); (F.T.); (D.C.)
- Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta” (CNR-SCITEC), via Elce di Sotto, I-06123 Perugia, Italy;
- Correspondence: (F.N.); (F.P.)
| | - Giacomo Pannacci
- Dipartimento di Chimica, Biologia e Biotecnologie, via Elce di Sotto 8, I-06123 Perugia, Italy; (G.P.); (F.T.); (D.C.)
| | - Francesco Tarantelli
- Dipartimento di Chimica, Biologia e Biotecnologie, via Elce di Sotto 8, I-06123 Perugia, Italy; (G.P.); (F.T.); (D.C.)
- Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta” (CNR-SCITEC), via Elce di Sotto, I-06123 Perugia, Italy;
| | - Leonardo Belpassi
- Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta” (CNR-SCITEC), via Elce di Sotto, I-06123 Perugia, Italy;
| | - David Cappelletti
- Dipartimento di Chimica, Biologia e Biotecnologie, via Elce di Sotto 8, I-06123 Perugia, Italy; (G.P.); (F.T.); (D.C.)
| | - Stefano Falcinelli
- Dipartimento di Ingegneria Civile ed Ambientale, Università degli Studi di Perugia, via G. Duranti 93, 06215 Perugia, Italy;
| | - Fernando Pirani
- Dipartimento di Chimica, Biologia e Biotecnologie, via Elce di Sotto 8, I-06123 Perugia, Italy; (G.P.); (F.T.); (D.C.)
- Istituto CNR di Scienze e Tecnologie Chimiche “Giulio Natta” (CNR-SCITEC), via Elce di Sotto, I-06123 Perugia, Italy;
- Correspondence: (F.N.); (F.P.)
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Cesario D, Nunzi F, Belpassi L, Pirani F, Ronca E, Tarantelli F. Chemical Bond Mechanism for Helium Revealed by Electronic Excitation. J Phys Chem A 2019; 123:6572-6577. [PMID: 31274318 DOI: 10.1021/acs.jpca.9b05351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Helium chemistry is notoriously very impervious. It is therefore certainly no surprise that, for example, beryllium and helium atoms, in their ground state, do not bind. Full configuration-interaction calculations show that the same turns out to be true, save for a long-range shallow attraction, for the Be+ + He system. However, quite astonishingly, when one electron is re-added to Be+ in an excited 2pπ or 3s orbital (Be 1P or 1S), a bound adduct with He is formed, at an interatomic separation as short as 1.5 Å. Understanding why this happens reveals an unsuspected chemical mechanism that stabilizes helium compounds at the molecular level.
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Affiliation(s)
- Diego Cesario
- Dipartimento di Chimica, Biologia e Biotecnologie , Università di Perugia , Via Elce di Sotto 8 , 06123 Perugia , Italy
| | - Francesca Nunzi
- Dipartimento di Chimica, Biologia e Biotecnologie , Università di Perugia , Via Elce di Sotto 8 , 06123 Perugia , Italy.,Istituto di Scienze e Tecnologie Molecolari del CNR (CNR-ISTM) , Via Elce di Sotto 8 , 06123 Perugia , Italy
| | - Leonardo Belpassi
- Istituto di Scienze e Tecnologie Molecolari del CNR (CNR-ISTM) , Via Elce di Sotto 8 , 06123 Perugia , Italy
| | - Fernando Pirani
- Dipartimento di Chimica, Biologia e Biotecnologie , Università di Perugia , Via Elce di Sotto 8 , 06123 Perugia , Italy.,Istituto di Scienze e Tecnologie Molecolari del CNR (CNR-ISTM) , Via Elce di Sotto 8 , 06123 Perugia , Italy
| | - Enrico Ronca
- Max-Planck-Institut für Struktur und Dynamik der Materie , Luruper Chaussee 149 , 22761 Hamburg , Germany
| | - Francesco Tarantelli
- Dipartimento di Chimica, Biologia e Biotecnologie , Università di Perugia , Via Elce di Sotto 8 , 06123 Perugia , Italy.,Istituto di Scienze e Tecnologie Molecolari del CNR (CNR-ISTM) , Via Elce di Sotto 8 , 06123 Perugia , Italy
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Reddy GN, Parida R, Jena P, Jana M, Giri S. Superhalogens as Building Blocks of Super Lewis Acids. Chemphyschem 2019; 20:1607-1612. [PMID: 30989750 DOI: 10.1002/cphc.201900267] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 04/12/2019] [Indexed: 11/07/2022]
Abstract
Lewis acids play an important role in synthetic chemistry. Using first-principle calculations on some newly designed molecules containing boron and organic heterocyclic superhalogen ligands, we show that the acid strength depends on the charge of the central atom as well as on the ligands attached to it. In particular, the strength of the Lewis acid increases with increasing electron withdrawing power of the ligand. With this insight, we highlight the importance of superhalogen-based ligands in the design of strong Lewis acids. Calculated fluoride ion affinity (FIA) values of B[C2 BNO(CN)3 ]3 and B[C2 BNS(CN)3 ]3 show that these are super Lewis acids.
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Affiliation(s)
- G Naaresh Reddy
- Department of Chemistry, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Rakesh Parida
- Department of Chemistry, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Puru Jena
- Department of Physics, Virginia Commonwealth Unoiversity, Richmond, VA, USA
| | - Madhurima Jana
- Department of Chemistry, National Institute of Technology Rourkela, Odisha, 769008, India
| | - Santanab Giri
- School of Applied Sciences and Humanities Haldia Institute of Technology, ICARE Complex, West Bengal, 721657, India
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8
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Greb L. Lewis Superacids: Classifications, Candidates, and Applications. Chemistry 2018; 24:17881-17896. [DOI: 10.1002/chem.201802698] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Lutz Greb
- Anorganisch-Chemisches InstitutUniversität Heidelberg Im Neuenheimer Feld 270 Germany
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Pastorczak E, Corminboeuf C. Perspective: Found in translation: Quantum chemical tools for grasping non-covalent interactions. J Chem Phys 2018; 146:120901. [PMID: 28388098 DOI: 10.1063/1.4978951] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Today's quantum chemistry methods are extremely powerful but rely upon complex quantities such as the massively multidimensional wavefunction or even the simpler electron density. Consequently, chemical insight and a chemist's intuition are often lost in this complexity leaving the results obtained difficult to rationalize. To handle this overabundance of information, computational chemists have developed tools and methodologies that assist in composing a more intuitive picture that permits better understanding of the intricacies of chemical behavior. In particular, the fundamental comprehension of phenomena governed by non-covalent interactions is not easily achieved in terms of either the total wavefunction or the total electron density, but can be accomplished using more informative quantities. This perspective provides an overview of these tools and methods that have been specifically developed or used to analyze, identify, quantify, and visualize non-covalent interactions. These include the quantitative energy decomposition analysis schemes and the more qualitative class of approaches such as the Non-covalent Interaction index, the Density Overlap Region Indicator, or quantum theory of atoms in molecules. Aside from the enhanced knowledge gained from these schemes, their strengths, limitations, as well as a roadmap for expanding their capabilities are emphasized.
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Affiliation(s)
- Ewa Pastorczak
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Clémence Corminboeuf
- Laboratory for Computational Molecular Design, Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Jana G, Pan S, Merino G, Chattaraj PK. MNgCCH (M = Cu, Ag, Au; Ng = Xe, Rn): The First Set of Compounds with M–Ng–C Bonding Motif. J Phys Chem A 2017; 121:6491-6499. [DOI: 10.1021/acs.jpca.7b04993] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gourhari Jana
- Department
of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, 721302 Kharagpur, India
| | - Sudip Pan
- Department
of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, 721302 Kharagpur, India
- Departamento
de Física Aplicada, Centro de Investigación y de Estudios
Avanzados, Unidad Mérida. Km 6 Antigua Carretera a Progreso.
Apdo. Postal 73, Cordemex, 97310, Mérida, Yucatan, México
| | - Gabriel Merino
- Departamento
de Física Aplicada, Centro de Investigación y de Estudios
Avanzados, Unidad Mérida. Km 6 Antigua Carretera a Progreso.
Apdo. Postal 73, Cordemex, 97310, Mérida, Yucatan, México
| | - Pratim K. Chattaraj
- Department
of Chemistry and Centre for Theoretical Studies Indian Institute of Technology Kharagpur, 721302 Kharagpur, India
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Jana G, Saha R, Pan S, Kumar A, Merino G, Chattaraj PK. Noble Gas Binding Ability of Metal-Bipyridine Monocationic Complexes (Metal=Cu, Ag, Au): A Computational Study. ChemistrySelect 2016. [DOI: 10.1002/slct.201601245] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Gourhari Jana
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology Kharagpur; Kharagpur- 721302 India
| | - Ranajit Saha
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology Kharagpur; Kharagpur- 721302 India
| | - Sudip Pan
- Departamento de Física Aplicada; Centro de Investigación y de Estudios Avanzados Unidad Mérida km; 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex 97310 Mérida, Yuc. México
| | - Anand Kumar
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology Kharagpur; Kharagpur- 721302 India
| | - Gabriel Merino
- Departamento de Física Aplicada; Centro de Investigación y de Estudios Avanzados Unidad Mérida km; 6 Antigua carretera a Progreso. Apdo. Postal 73, Cordemex 97310 Mérida, Yuc. México
| | - Pratim K. Chattaraj
- Department of Chemistry and Centre for Theoretical Studies; Indian Institute of Technology Kharagpur; Kharagpur- 721302 India
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