1
|
Báez-Grez R, Inostroza D, Vásquez-Espinal A, Islas R, Pino-Rios R. Exploration of the potential energy surface in mixed Zintl clusters applying an automatic Johnson polyhedra generator: the case of arachno E 6M 24- (E = Si, Ge, Sn; M = Sb, Bi). RSC Adv 2023; 13:24499-24504. [PMID: 37588980 PMCID: PMC10426391 DOI: 10.1039/d3ra04308h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 08/08/2023] [Indexed: 08/18/2023] Open
Abstract
A new algorithm called Automatic Johnson Cluster Generator (AJCG) is presented, which, as its name indicates, allows the definition of the desired Johnson polyhedron to subsequently carry out all the possible permutations between the atoms that form this polyhedron. This new algorithm allows the exhaustive study of the structures' potential energy surface (PES). In addition, the AJCG algorithm is helpful for the study of three-dimensional compounds such as boranes or Zintl clusters and their structural derivatives with two or more different atoms. The automatic filling of vertices is particularly useful in mixed compounds because of the possibility of taking into account all possible configurations in the structure. As a test system, we investigated the arachno-type E6M24- (E = Si, Ge, Sn; M = Sb, Bi) structure which has eight vertices and complies with Wade-Mingos rules. Initially, we defined a bipyramidal structure (10 vertices), and filled the vertices with the atoms in all possible configurations. Since the selected system has eight atoms, the two remaining vertices were filled with pseudo atoms to complete the structure. After re-optimizing the initial population generated with AJCG, a large number of isomers with energy below 10 kcal mol-1 are identified. These results show that the most stable isomers possess homonuclear M-M bonds, except Sn6Bi24-. Although the overall putative minima differ at the PBE0-D3 and DLPNO-CCSD(T) levels, they are always competitive minima. In addition to using high-precision methodologies to correctly study relative energies, applying solvent effects in highly charged systems becomes mandatory. The aromatic character of these studied systems was demonstrated qualitatively with two- and three-dimensional mapping and quantitatively by calculating the value of the z-component of the induced magnetic field at the cage center, including scalar and spin-orbit correction for relativistic effects. The compounds studied have a high degree of aromaticity, which allows us to establish that despite structural modifications (i.e., from closo to arachno), the aromaticity is preserved.
Collapse
Affiliation(s)
- Rodrigo Báez-Grez
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello República 275 Santiago Chile 8370146
| | - Diego Inostroza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello República 275 Santiago Chile 8370146
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello República 275 Santiago Chile
| | - Alejandro Vásquez-Espinal
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat Casilla 121 Iquique Chile 1100000
| | - Rafael Islas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello República 275 Santiago Chile 8370146
- Centro de Química Teórica & Computacional (CQT&C), Facultad de Ciencias Exactas, Universidad Andres Bello República 275 Santiago Chile 8370146
| | - Ricardo Pino-Rios
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat Casilla 121 Iquique Chile 1100000
- Instituto de Estudios de la Salud, Universidad Arturo Prat Casilla 121 Iquique Chile 1100000
| |
Collapse
|
2
|
Sinha S, Giri S, Chakraborty A. Exploring an intermolecular Ge/B frustrated Lewis pair from a multicentre Zintl Lewis base. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02961-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
3
|
Sinha S, Jena P, Giri S. Functionalized nona-silicide [Si 9R 3] Zintl clusters: a new class of superhalogens. Phys Chem Chem Phys 2022; 24:21105-21111. [PMID: 36018293 DOI: 10.1039/d2cp02619h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Superatoms, due to their various applications in redox and materials chemistry, have been a major topic of study in cluster science. Superhalogens constitute a special class of superatoms that mimic the chemistry of halogens and serve as building blocks of novel materials such as super and hyper salts, perovskite-based solar cells, solid-state electrolytes, and ferroelectric materials. These applications have led to a constant search for new class of superhalogens. In this study, using density functional theory, we show that recently synthesized [Si9{Si (tBu)2H}3] and [Si9{Si (TMS)3}3] Zintl clusters not only behave like halogens but also when functionalized with suitable ligands exhibit superhalogen characteristics. Frontier molecular orbital (FMO) analyses give insights into the electron-accepting nature of the Zintl clusters. Additional bonding techniques such as energy density at the bond critical point (BCP) and adaptive natural density partitioning (AdNDP) gives complementary information about the nature of bonding in Si9-based Zintl clusters. The potential of these Zintl clusters in the synthesis of new electrolytes in Li-ion batteries is also investigated.
Collapse
Affiliation(s)
- Swapan Sinha
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India. .,Maulana Abul Kalam Azad University of Technology, Haringhata, 741249, India
| | - Puru Jena
- Physics Department, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Santanab Giri
- School of Applied Science and Humanities, Haldia Institute of Technology, Haldia, 721657, India.
| |
Collapse
|
4
|
Alvarez Becerra M, Ortiz Bolaños D, Cuellar J, Yañez O, Mejía SM. Exploring the potential energy surface of nCO2 (n = 1–5) capture by imidazole-and fluorine-based ionic liquids: A DFT study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
5
|
Thimmakondu VS, Sinjari A, Inostroza D, Vairaprakash P, Thirumoorthy K, Roy S, Anoop A, Tiznado W. Why an integrated approach between search algorithms and chemical intuition is necessary? Phys Chem Chem Phys 2022; 24:11680-11686. [PMID: 35506427 DOI: 10.1039/d2cp00315e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Though search algorithms are appropriate tools for identifying low-energy isomers, fixing several constraints seems to be a fundamental prerequisite to successfully running any structural search program. This causes some potential setbacks as far as identifying all possible isomers, close to the lowest-energy isomer, for any elemental composition. The number of explored candidates, the choice of method, basis set, and availability of CPU time needed to analyze the various initial test structures become necessary restrictions in resolving the issues of structural isomerism reasonably. While one could arrive at new structures through chemical intuition, reproducing or achieving those exact same structures requires increasing the number of variables in any given program, which causes further constraints in exploring the potential energy surface in a reasonable amount of time. Thus, it is emphasized here that an integrated approach between search algorithms and chemical intuition is necessary by taking the C12O2Mg2 system as an example. Our initial search through the AUTOMATON program yielded 1450 different geometries. However, through chemical intuition, we found eighteen new geometries within 40.0 kcal mol-1 at the PBE0-D3/def2-TZVP level. These results indirectly emphasize that an integrated approach between search algorithms and chemical intuition is necessary to further our knowledge in chemical space for any given elemental composition.
Collapse
Affiliation(s)
- Venkatesan S Thimmakondu
- Department of Chemistry and Biochemistry, San Diego State University, San Diego, CA 92182-1030, USA.
| | - Aland Sinjari
- School of Mathematics, Biological, Exercise & Physical Sciences, San Diego Miramar College, San Diego, CA, 92126-2910, USA
| | - Diego Inostroza
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Química, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, Santiago, Chile. .,Universidad Andres Bello, Programa de Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Santiago, Chile
| | - Pothiappan Vairaprakash
- Department of Chemistry, School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur 613 401, Tamil Nadu, India
| | - Krishnan Thirumoorthy
- Department of Chemistry, School of Advanced Sciences, Vellore Institute of Technology, Vellore - 632 014, Tamil Nadu, India
| | - Saikat Roy
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, West Bengal, India.
| | - Anakuthil Anoop
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721 302, West Bengal, India.
| | - William Tiznado
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Química, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, Santiago, Chile.
| |
Collapse
|
6
|
Xu YH, Tkachenko NV, Popov IA, Qiao L, Muñoz-Castro A, Boldyrev AI, Sun ZM. Ternary aromatic and anti-aromatic clusters derived from the hypho species [Sn 2Sb 5] 3. Nat Commun 2021; 12:4465. [PMID: 34294702 PMCID: PMC8298489 DOI: 10.1038/s41467-021-24706-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 07/01/2021] [Indexed: 02/06/2023] Open
Abstract
Heterometallic clusters have attracted broad interests in the synthetic chemistry due to their various coordination modes and potential applications in heterogeneous catalysis. Here we report the synthesis, experimental, and theoretical characterizations of four ternary clusters ([M2(CO)6Sn2Sb5]3- (M = Cr, Mo), and [(MSn2Sb5)2]4-, (M = Cu, Ag)) in the process of capturing the hypho- [Sn2Sb5]3- in ethylenediamine (en) solution. We show that the coordination of the binary anion to transition-metal ions or fragments provides additional stabilization due to the formation of locally σ-aromatic units, producing a spherical aromatic shielding region in the cages. While in the case of [Mo2(CO)6Sn2Sb5]3- stabilization arises from locally σ-aromatic three-centre and five-centre two-electron bonds, aromatic islands in [(AgSn2Sb5)2]4- and [(CuSn2Sb5)2]4- render them globally antiaromatic. This work describes the coordination chemistry of the versatile building block [Sn2Sb5]3-, thus providing conceptual advances in the field of metal-metal bonding in clusters.
Collapse
Affiliation(s)
- Yu-He Xu
- grid.216938.70000 0000 9878 7032State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Lab for Rare Earth Materials and Applications, School of Materials Science and Engineering, Nankai University, Tianjin, China
| | - Nikolay V. Tkachenko
- grid.53857.3c0000 0001 2185 8768Department of Chemistry and Biochemistry, Utah State University, Logan, UT USA
| | - Ivan A. Popov
- grid.148313.c0000 0004 0428 3079Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Lei Qiao
- grid.216938.70000 0000 9878 7032State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Lab for Rare Earth Materials and Applications, School of Materials Science and Engineering, Nankai University, Tianjin, China
| | - Alvaro Muñoz-Castro
- grid.441837.d0000 0001 0765 9762Grupo de Química Inorgánicay Materiales Moleculares, Facultad de Ingenieria, Universidad Autonoma de Chile, El Llano Subercaseaux, Santiago, Chile
| | - Alexander I. Boldyrev
- grid.53857.3c0000 0001 2185 8768Department of Chemistry and Biochemistry, Utah State University, Logan, UT USA
| | - Zhong-Ming Sun
- grid.216938.70000 0000 9878 7032State Key Laboratory of Elemento-Organic Chemistry, Tianjin Key Lab for Rare Earth Materials and Applications, School of Materials Science and Engineering, Nankai University, Tianjin, China
| |
Collapse
|
7
|
Cerqueira HBA, Santos JC, Fantuzzi F, Ribeiro FDA, Rocco MLM, Oliveira RR, Rocha AB. Structure, Stability, and Spectroscopic Properties of Small Acetonitrile Cation Clusters. J Phys Chem A 2020; 124:6845-6855. [PMID: 32702984 DOI: 10.1021/acs.jpca.0c03529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ionization and fragmentation pathways induced by ionizing agents are key to understanding the formation of complex molecules in astrophysical environments. Acetonitrile (CH3CN), the simplest organic nitrile, is an important molecule present in the interstellar medium. In this work, DFT and MP2 calculations were performed in order to obtain the low energy structures of the most relevant cations formed from electron-stimulated ion desorption of CH3CN ices. Selected reaction pathways and spectroscopic properties were also calculated. Our results indicate that the most stable acetonitrile cation structure is CH2CNH+ and that hydrogenation can occur successively without isomerization steps until its complete saturation. Moreover, the stability of distinct cluster families formed from the interaction of acetonitrile with small fragments, such as CHn+, C2Hn+, and CHnCNH+, is discussed in terms of their respective binding energies. Some of these molecular clusters are stabilized by hydrogen bonds, leading to species whose infrared features are characterized by a strong redshift of the N-H stretching mode. Finally, the rotational spectra of CH3CN and protonated acetonitrile, CH3CNH+, were simulated using distinct computational protocols based on DFT, MP2, and CCSD(T) considering centrifugal distortion, vibrational-rotational coupling, and vibrational anharmonicity corrections. By adopting an empirical scaling procedure for calculating spectroscopic parameters, we were able to estimate the rotational frequencies of CH3CNH+ with an expected average error below 1 MHz for J values up to 10.
Collapse
Affiliation(s)
- Henrique B A Cerqueira
- Instituto de Quı́mica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Julia C Santos
- Instituto de Quı́mica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Felipe Fantuzzi
- Institut für Anorganische Chemie, Julius-Maximilians-Universität Würzburg, Am Hubland, 97074 Würzburg, Germany.,Institut für Physikalische und Theoretische Chemie, Julius-Maximilians-Universität Würzburg, Emil-Fischer-Straße 42, 97074 Würzburg, Germany
| | | | - Maria Luiza M Rocco
- Instituto de Quı́mica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Ricardo R Oliveira
- Instituto de Quı́mica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| | - Alexandre B Rocha
- Instituto de Quı́mica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ 21941-909, Brazil
| |
Collapse
|
8
|
Yañez O, Inostroza D, Usuga-Acevedo B, Vásquez-Espinal A, Pino-Rios R, Tabilo-Sepulveda M, Garza J, Barroso J, Merino G, Tiznado W. Evaluation of restricted probabilistic cellular automata on the exploration of the potential energy surface of Be6B11−. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2548-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
9
|
Pino-Rios R, Vásquez-Espinal A, Yañez O, Tiznado W. Searching for double σ- and π-aromaticity in borazine derivatives. RSC Adv 2020; 10:29705-29711. [PMID: 35518239 PMCID: PMC9056176 DOI: 10.1039/d0ra05939k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 07/31/2020] [Indexed: 11/25/2022] Open
Abstract
Inspired by the double-aromatic (σ and π) C6H3+, C6I62+, and C6(SePh)62+ ring-shaped compounds, herein we theoretically study their borazine derivative analogues. The systems studied are the cation and dications with formulas B3N3H3+, B3N3Br62+, B3N3I62+, B3N3(SeH)62+, and B3N3(TeH)62+. Our DFT calculations indicate that the ring-shaped planar structures of B3N3H3+, B3N3I62+, and B3N3(TeH)62+ are more stable in the singlet state, while those of B3N3Br62+ and B3N3(SeH)62+ prefer the triplet state. Besides, exploration of the potential energy surface shows that the ring-shaped structure is the putative global minimum only for B3N3I62+. According to chemical bonding analysis, B3N3H3+, B3N3I62+, and B3N3(TeH)62+ have σ and π delocalized bonds. The number of delocalized σ/π electrons is 2/6 for the first, and 10/6 for the second and third, similar to what their carbon analogs exhibit. Finally, the analysis of the magnetically induced current density allows B3N3H3+, B3N3I62+, and B3N3(TeH)62+ to be classified as strongly σ aromatic, and poorly π aromatic compounds. Evolutionary algorithms, Born–Oppenheimer molecular dynamics and the magnetic criteria of aromaticity have been used to evaluate the stability and σ–π aromaticity of borazine derivatives in order to expand the family of double aromatics systems.![]()
Collapse
Affiliation(s)
- Ricardo Pino-Rios
- Laboratorio de Química Teórica
- Facultad de Química y Biología
- Universidad de Santiago de Chile (USACH)
- Santiago
- Chile
| | - Alejandro Vásquez-Espinal
- Computational and Theoretical Chemistry Group
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
| | - Osvaldo Yañez
- Computational and Theoretical Chemistry Group
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
| | - William Tiznado
- Computational and Theoretical Chemistry Group
- Departamento de Ciencias Químicas
- Facultad de Ciencias Exactas
- Universidad Andres Bello
- Santiago
| |
Collapse
|