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Salazar-Lozas H, Guevara-Vela JM, Pendás ÁM, Francisco E, Rocha-Rinza T. Partition of the electronic energy of the PM7 method via the interacting quantum atoms approach. Phys Chem Chem Phys 2022; 24:19521-19530. [PMID: 35938407 DOI: 10.1039/d2cp02013k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Partitions of the electronic energy such as that provided by the Interacting Quantum Atoms (IQA) approach have given valuable insights for numerous chemical systems and processes. Unfortunately, this kind of analysis may involve the integration of scalar fields over very irregular volumes, a condition which leads to a large and often prohibitive computational effort. These circumstances have limited the use of these energy partitions to systems comprising a few tens of atoms at most. On the other hand, semiempirical methods have proved useful in the study of systems of several thousands of atoms. Therefore, the goal of this work is to carry out partitions of the semiempirical method PM7 in compliance with the IQA approach. For this purpose, we computed one- and two-atomic energetic contributions whose sum equals the PM7 electronic energy. We illustrate how one might exploit the partition of electronic energies computed via the PM7 method by considering small organic and inorganic molecules and the energetics of individual hydrogen bond interactions within several water clusters which include (H2O)30, (H2O)50 and (H2O)100. We also considered the solvation of the amphiphilic caprylate anion to exemplify how to exploit the energy partition proposed in this paper. Overall, this investigation shows how the approach put forward herein might give further insights of the interactions occurring within complex systems in physical and biological chemistry.
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Affiliation(s)
- Hugo Salazar-Lozas
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán C.P. 04510, Ciudad de México, Mexico.
| | | | - Ángel Martín Pendás
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Claveria 8, 33006, Oviedo, Spain
| | - Evelio Francisco
- Departamento de Química Física y Analítica, Universidad de Oviedo, Julián Claveria 8, 33006, Oviedo, Spain
| | - Tomás Rocha-Rinza
- Instituto de Química, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, Alcaldía Coyoacán C.P. 04510, Ciudad de México, Mexico.
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2
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Piña MDLN, Burguera S, Buils J, Crespí MÀ, Morales JE, Pons J, Bauzá A, Frontera A. Substituent effects in π-hole regium bonding interactions between Au(p-X-Py)2 complexes and Lewis bases: an ab initio study. Chemphyschem 2022; 23:e202200010. [PMID: 35191571 DOI: 10.1002/cphc.202200010] [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: 01/06/2022] [Revised: 02/09/2022] [Indexed: 11/10/2022]
Abstract
For the first time, long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated. The Au(I) atom is coordinated to two para -substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide some experimental support to the existence of regium π-hole bonding in [Au(Py) 2 ] + derivatives.
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Affiliation(s)
| | | | - Jordi Buils
- Universitat de les Illes Balears, Chemistry, SPAIN
| | | | | | - Jordi Pons
- Universitat de les Illes Balears, Chemistry, SPAIN
| | | | - Antonio Frontera
- Universitat Illes Balears, Chemistry, Crta de Valldemossa km 7.5, 07122, Palma de Mallorca, SPAIN
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Iribarren I, Sánchez‐Sanz G, Elguero J, Alkorta I, Trujillo C. Reactivity of Coinage Metal Hydrides for the Production of H 2 Molecules. ChemistryOpen 2021; 10:724-730. [PMID: 34319005 PMCID: PMC8340072 DOI: 10.1002/open.202100108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/30/2021] [Indexed: 12/03/2022] Open
Abstract
The formation of molecular hydrogen as well as the possibility of using coinage metal hydrides as a prospective complex to produce hydrogen was presented in this work. Therefore, the reactions involving the interaction between two coinage metal hydrides, MH (M=Cu, Ag and Au, homo and heterodimers), were studied. The free energy profiles corresponding to aforementioned complexation were analysed by means of ab initio methods of quantum chemistry. The characteristics of these intermediates, final complexes and the electron density properties of the established interactions were discussed.
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Affiliation(s)
- Iñigo Iribarren
- Trinity Biomedical Sciences InstituteSchool of ChemistryThe University of DublinTrinity CollegeDublin 2Ireland
| | - Goar Sánchez‐Sanz
- Irish Centre of High-End ComputingGrand Canal QuayDublin 2 (Ireland)& School of ChemistryUniversity College Dublin BelfieldDublin 4Ireland
| | - José Elguero
- Instituto de Química Médica IQM-CSICJuan de la Cierva, 328006MadridSpain
| | - Ibon Alkorta
- Instituto de Química Médica IQM-CSICJuan de la Cierva, 328006MadridSpain
| | - Cristina Trujillo
- Trinity Biomedical Sciences InstituteSchool of ChemistryThe University of DublinTrinity CollegeDublin 2Ireland
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Iribarren I, Sánchez-Sanz G, Alkorta I, Elguero J, Trujillo C. Evaluation of Electron Density Shifts in Noncovalent Interactions. J Phys Chem A 2021; 125:4741-4749. [PMID: 34061527 PMCID: PMC8279648 DOI: 10.1021/acs.jpca.1c00830] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/26/2021] [Indexed: 12/12/2022]
Abstract
In the present paper, we report the quantitative evaluation of the electron density shift (EDS) maps within different complexes. Values associated with the total EDS maps exhibited good correlation with different quantities such as interaction energies, Eint, intermolecular distances, bond critical points, and LMOEDA energy decomposition terms. Besides, EDS maps at different cutoffs were also evaluated and related with the interaction energies values. Finally, EDS maps and their corresponding values are found to correlate with Eint within systems with cooperative effects. To our knowledge, this is the first time that the EDS has been quanitatively evaluated.
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Affiliation(s)
- Iñigo Iribarren
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
| | - Goar Sánchez-Sanz
- Irish
Centre For High-End Computing, 7 Floor, The Tower, Grand Canal Quay, Dublin 2 D02 HP83, Ireland
| | - Ibon Alkorta
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - José Elguero
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva, 3, 28006 Madrid, Spain
| | - Cristina Trujillo
- Trinity
Biomedical Sciences Institute, School of Chemistry, The University of Dublin, Trinity College, Dublin, Dublin 2, Ireland
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Zhao Q. σ-Hole and σ-lump interactions between gold clusters Au n (n = 2-8) and benzene. J Mol Model 2021; 27:132. [PMID: 33893891 DOI: 10.1007/s00894-021-04756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/18/2021] [Indexed: 10/21/2022]
Abstract
In this study, the non-covalent interactions between gold cluster and benzene have been evaluated at the PBE0-D3/def2-TZVP level of theory. Gold clusters Aun (n = 2-8) were used as σ-hole and σ-lump donors, and benzene was the corresponding electron-donating and -accepting molecule. The molecular electrostatic potential of Au clusters was analyzed, and the optimized structures and interaction energies of the Aun (n = 2-8) Bz complexes with σ-hole or σ-lump interaction were studied. Strong σ-hole and relative weak σ-lump interactions exist between Au cluster and benzene. With the help of atoms-in-molecules analysis and plotting of non-covalent interaction map, the interaction zones of the complexes were found out. The nature of these interactions was revealed through energy decomposition analysis by using the symmetry-adapted perturbation theory. σ-Hole interactions are dominated by electrostatic interaction, while σ-lump interactions are mainly driven by dispersion. This study can enrich the knowledge of interaction between Au cluster and π-systems and design of new materials based on coinage metal of σ-hole and σ-lump interactions.
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Affiliation(s)
- Qiang Zhao
- Department of Chemical Engineering, Zibo Vocational Institute, Zibo, 255314, Shandong Province, People's Republic of China.
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Zierkiewicz W, Michalczyk M, Scheiner S. Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons. Molecules 2021; 26:molecules26061740. [PMID: 33804617 PMCID: PMC8003638 DOI: 10.3390/molecules26061740] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 03/16/2021] [Accepted: 03/17/2021] [Indexed: 01/21/2023] Open
Abstract
Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.
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Affiliation(s)
- Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
- Correspondence: (W.Z.); (M.M.)
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University Logan, Logan, UT 84322-0300, USA;
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Non-Covalent Interactions of the Lewis Acids Cu–X, Ag–X, and Au–X (X = F and Cl) with Nine Simple Lewis Bases B: A Systematic Investigation of Coinage–Metal Bonds by Ab Initio Calculations. INORGANICS 2021. [DOI: 10.3390/inorganics9020013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The equilibrium geometry and two measures (the equilibrium dissociation energy in the complete basis set limit, De(CBS) and the intermolecular stretching force constant kσ) of the strength of the non-covalent interaction of each of six Lewis acids M–X (M = Cu, Ag, Au) with each of nine simple Lewis bases B (B = N2, CO, HCCH, CH2CH2, H2S, PH3, HCN, H2O, and NH3) have been calculated at the CCSD(T)/aug-cc-pVTZ level of theory in a systematic investigation of the coinage–metal bond. Unlike the corresponding series of hydrogen-bonded B⋯HX and halogen-bonded B⋯XY complexes (and other series involving non-covalent interactions), De is not directly proportional to kσ. Nevertheless, as for the other series, it has been possible to express De in terms of the equation De = cNB.EMX, where NB and EMX are the nucleophilicities of the Lewis bases B and the electrophilicities of the Lewis acids M–X, respectively. The order of the EMX is determined to be EAuF > EAuCl > ECuF > ECuCl > EAgF ≈ EAgCl. A reduced electrophilicity defined as (EMX/σmax) is introduced, where σmax is the maximum positive value of the molecular electrostatic surface potential on the 0.001 e/bohr3 iso-surface. This quantity is, in good approximation, independent of whether F or Cl is attached to M.
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A Computational Study of Metallacycles Formed by Pyrazolate Ligands and the Coinage Metals M = Cu(I), Ag(I) and Au(I): (pzM) n for n = 2, 3, 4, 5 and 6. Comparison with Structures Reported in the Cambridge Crystallographic Data Center (CCDC). Molecules 2020; 25:molecules25215108. [PMID: 33153197 PMCID: PMC7663606 DOI: 10.3390/molecules25215108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/12/2022] Open
Abstract
The structures reported in the Cambridge Structural Database (CSD) for neutral metallacycles formed by coinage metals in their valence (I) (cations) and pyrazolate anions were examined. Depending on the metal, dimers and trimers are the most common but some larger rings have also been reported, although some of the larger structures are not devoid of ambiguity. M06-2x calculations were carried out on simplified structures (without C-substituents on the pyrazolate rings) in order to facilitate a comparison with the reported X-ray structures (geometries and energies). The problems of stability of the different ring sizes were also analyzed.
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Alkorta I, Elguero J, Trujillo C, Sánchez-Sanz G. Interaction between Trinuclear Regium Complexes of Pyrazolate and Anions, a Computational Study. Int J Mol Sci 2020; 21:E8036. [PMID: 33126636 PMCID: PMC7663457 DOI: 10.3390/ijms21218036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/22/2020] [Accepted: 10/23/2020] [Indexed: 01/27/2023] Open
Abstract
The geometry, energy and electron density properties of the 1:1, 1:2 and 1:3 complexes between cyclic (Py-M)3 (M = Au, Ag and Cu) and halide ions (F-, Cl- and Br-) were studied using Møller Plesset (MP2) computational methods. Three different configurations were explored. In two of them, the anions interact with the metal atoms in planar and apical dispositions, while in the last configuration, the anions interact with the CH(4) group of the pyrazole. The energetic results for the 1:2 and 1:3 complexes are a combination of the specific strength of the interaction plus a repulsive component due to the charge:charge coulombic term. However, stable minima structures with dissociation barriers for the anions indicate that those complexes are stable and (Py-M)3 can hold up to three anions simultaneously. A search in the CSD confirmed the presence of (Pyrazole-Cu)3 systems with two anions interacting in apical disposition.
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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;
| | - Cristina Trujillo
- Trinity Biomedical Sciences Institute, School of Chemistry, Trinity Dublin College, D02 R590 Dublin 2, Ireland;
| | - Goar Sánchez-Sanz
- Irish Centre of High-End Computing, Grand Canal Quay, Dublin 2, Ireland
- School of Chemistry, University College Dublin, Belfield, D02 HP83 Dublin 4, Ireland
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