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Bedoya V, Rodríguez V, Rincón L, Zambrano C, Seijas L, Torres FJ. KLD: a program to elucidate the localization of the Fermi and Coulomb holes in molecular systems. J Mol Model 2024; 30:289. [PMID: 39073478 DOI: 10.1007/s00894-024-06070-4] [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: 05/16/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
CONTEXT The electron localization is a concept that allows scientists to better understand the physical and chemical properties of electronic systems. It is associated with the propensity of electron pairs with opposite spins to accumulate as well as with their response to external perturbations. This paper contains a detailed description of the design and implementation of the program KLD, which was primarily developed in our research group to elucidate electron localization in molecular systems by evaluating the information content of electron-pair density functions. KLD employs two information-based functions as a real space measure of the Fermi and Coulomb holes for same-spin electrons and shows a better resolution as compared to other methods (i.e., ELF). Information about the acceleration of the code is also included in the present work, being noticeable the reduction of wall-time calculation and the error calculation between versions. METHODS KLD was designed to be easy to use, extend, and maintain; thus, many principles of modern software development, extensive testing, and package management were adopted. The latest version of the KLD program was created utilizing the Compute Unified Device Architecture (CUDA) version, which allows it to use the computational capacity of NVIDIA Graphics Processing Units (GPUs) for processing purposes. The electron-pair conditional density was calculated from the canonical molecular orbitals obtained at the HF/6-31G(2df,p) level, or alternatively the natural orbitals in the case of explicit correlated wavefunctions computed at the MP2/6-31G(2df,p)//HF/6-31G(2df,p) level.
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Affiliation(s)
- Valeria Bedoya
- Departamento de Ingeniería Química, Grupo de Química Computacional y Teórica (QCT-USFQ), Universidad San Francisco de Quito (USFQ), Diego de Robles S/N y Vía Interoceánica, Quito, 170901, Ecuador
| | - Vladimir Rodríguez
- Departamento de Ingeniería Química, Grupo de Química Computacional y Teórica (QCT-USFQ), Universidad San Francisco de Quito (USFQ), Diego de Robles S/N y Vía Interoceánica, Quito, 170901, Ecuador
- Departamento de Matemática, Universidad San Francisco de Quito (USFQ), Diego de Robles S/N y Vía Interoceánica, Quito, 170901, Ecuador
| | - Luis Rincón
- Departamento de Ingeniería Química, Grupo de Química Computacional y Teórica (QCT-USFQ), Universidad San Francisco de Quito (USFQ), Diego de Robles S/N y Vía Interoceánica, Quito, 170901, Ecuador
| | - Cesar Zambrano
- Departamento de Ingeniería Química, Grupo de Química Computacional y Teórica (QCT-USFQ), Universidad San Francisco de Quito (USFQ), Diego de Robles S/N y Vía Interoceánica, Quito, 170901, Ecuador
| | - Luis Seijas
- Escuela de Ingeniería, Ciencia y Tecnología, Universidad del Rosario, 11171, Bogotá, Colombia
| | - F Javier Torres
- Departamento de Ingeniería Química, Grupo de Química Computacional y Teórica (QCT-USFQ), Universidad San Francisco de Quito (USFQ), Diego de Robles S/N y Vía Interoceánica, Quito, 170901, Ecuador.
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Seijas LE, Almeida R, Rincón L, Zambrano C, Rodríguez V, Merino G, Torres FJ. Revisiting the bonding of the pentagonal-pyramidal C 6H 62+ and C 6(CH 3) 62+ dications. Phys Chem Chem Phys 2023. [PMID: 38018412 DOI: 10.1039/d3cp04247b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
This work delves into the bonding nature of the pentagonal-pyramidal benzene and hexamethylbenzene dications, C6R62+ (R = H and CH3), which contain a hexacoordinate carbon. The study employs a range of methodologies to analyze a series of scalar fields, including electron density, electron localization function, local momentum representation, and the evaluation of the Coulomb hole through information theory-derived functions. The findings unveil that electron density undergoes transfer from the pentagonal ring to the apical group. As a result, the base of the complex accumulates the positive charge. Moreover, an extended electron density domain emerges between the carbon pentagon and the apical carbon atom. This phenomenon is related to the molecular orbitals with a dipolar character aligned with the principal axis of the molecule. The results also indicate an electron density polarization towards the apical carbon, coupled with an exclusion of electron density surrounding both the apical carbon and the lower portion of the pentagonal ring. These provide valuable insights into the complex bonding nature of hexacoordinate carbon and its implications for organic chemistry.
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Affiliation(s)
- Luis E Seijas
- Escuela de Ingeniería Ciencia y Tecnología, Universidad del Rosario, Bogotá 11171, Colombia
| | - Rafael Almeida
- Laboratorio de Procesos Dinámicos en Química, Departamento de Química, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Luis Rincón
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Cesar Zambrano
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Vladimir Rodríguez
- Departamento de Matemática, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
| | - Gabriel Merino
- Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Física Aplicada, Km. 6 Antigua carretera a Progreso Apdo. Postal 73, Cordemex, 97310 Merida, Mexico
| | - F Javier Torres
- Escuela de Ingeniería Ciencia y Tecnología, Universidad del Rosario, Bogotá 11171, Colombia
- Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Ingeniería Química, Universidad San Francisco de Quito, Diego de Robles y Vía Interoceánica, Quito 17-1200-841, Ecuador
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Theoretical Description of R-X⋯NH 3 Halogen Bond Complexes: Effect of the R Group on the Complex Stability and Sigma-Hole Electron Depletion. Molecules 2020; 25:molecules25030530. [PMID: 31991810 PMCID: PMC7037998 DOI: 10.3390/molecules25030530] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 01/14/2020] [Accepted: 01/17/2020] [Indexed: 11/16/2022] Open
Abstract
In the present work, a number of R–X⋯NH3 (X = Cl, Br, and I) halogen bonded systems were theoretical studied by means of DFT calculations performed at the ωB97XD/6-31+G(d,p) level of theory in order to get insights on the effect of the electron-donating or electron-withdrawing character of the different R substituent groups (R = halogen, methyl, partially fluorinated methyl, perfluoro-methyl, ethyl, vinyl, and acetyl) on the stability of the halogen bond. The results indicate that the relative stability of the halogen bond follows the Cl < Br < I trend considering the same R substituent whereas the more electron-withdrawing character of the R substituent the more stable the halogen bond. Refinement of the latter results, performed at the MP2/6-31+G(d,p) level showed that the DFT and the MP2 binding energies correlate remarkably well, suggesting that the Grimme’s type dispersion-corrected functional produces reasonable structural and energetic features of halogen bond systems. DFT results were also observed to agree with more refined calculations performed at the CCSD(T) level. In a further stage, a more thorough analysis of the R–Br⋯NH3 complexes was performed by means of a novel electron localization/delocalization tool, defined in terms of an Information Theory, IT, based quantity obtained from the conditional pair density. For the latter, our in-house developed C++/CUDA program, called KLD (acronym of Kullback–Leibler divergence), was employed. KLD results mapped onto the one-electron density plotted at a 0.04 a.u. isovalue, showed that (i) as expected, the localized electron depletion of the Br sigma-hole is largely affected by the electron-withdrawing character of the R substituent group and (ii) the R–X bond is significantly polarized due to the presence of the NH3 molecule in the complexes. The afore-mentioned constitutes a clear indication of the dominant character of electrostatics on the stabilization of halogen bonds in agreement with a number of studies reported in the main literature. Finally, the cooperative effects on the [Br—CN]n system (n = 1–8) was evaluated at the MP2/6-31+G(d,p) level, where it was observed that an increase of about ~14.2% on the complex stability is obtained when going from n = 2 to n = 8. The latter results were corroborated by the analysis of the changes on the Fermi-hole localization pattern on the halogen bond zones, which suggests an also important contribution of the electron correlation in the stabilization of these systems.
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Rincon L, Javier Torres F, Becerra M, Liu S, Fritsch A, Almeida R. On the separation of the information content of the Fermi and Coulomb holes and their influence on the electronic properties of molecular systems. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Luis Rincon
- Grupo de Química Computacional y Teórica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Dept. de Ingeniería Química, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito, Ecuador
- Departamento de Química, Facultad de Ciencias, Universidad de Los Andes (ULA), Mérida, Venezuela
| | - F. Javier Torres
- Grupo de Química Computacional y Teórica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Dept. de Ingeniería Química, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito, Ecuador
| | - Marcos Becerra
- Grupo de Química Computacional y Teórica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Dept. de Ingeniería Química, Colegio de Ciencias e Ingeniería, Universidad San Francisco de Quito, Quito, Ecuador
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, USA
| | - Alain Fritsch
- Institut des Sciences Molèculaires, Theoretical Chemistry & Modeling Group, Universitè Bordeaux, Talance, France
| | - Rafael Almeida
- Departamento de Química, Facultad de Ciencias, Universidad de Los Andes (ULA), Mérida, Venezuela
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Rincón L, Torres FJ, Almeida R. Is the Pauli exclusion principle the origin of electron localisation? Mol Phys 2017. [DOI: 10.1080/00268976.2017.1363921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Luis Rincón
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Téorica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Colegio Politecnico de Ciencias e Ingeniería, Diego de Robles y Vía Interoceánica, Quito, Ecuador
- Departamento de Qímica, Facultad de Ciencias, Universidad de Los Andes, La Hechicera, Merida, Venezuela
| | - F. Javier Torres
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Téorica (QCT-USFQ) and Instituto de Simulación Computacional (ISC-USFQ), Departamento de Ingeniería Química, Colegio Politecnico de Ciencias e Ingeniería, Diego de Robles y Vía Interoceánica, Quito, Ecuador
| | - Rafael Almeida
- Departamento de Qímica, Facultad de Ciencias, Universidad de Los Andes, La Hechicera, Merida, Venezuela
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Urbina AS, Torres FJ, Rincon L. The electron localization as the information content of the conditional pair density. J Chem Phys 2016; 144:244104. [PMID: 27369494 DOI: 10.1063/1.4954291] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
In the present work, the information gained by an electron for "knowing" about the position of another electron with the same spin is calculated using the Kullback-Leibler divergence (DKL) between the same-spin conditional pair probability density and the marginal probability. DKL is proposed as an electron localization measurement, based on the observation that regions of the space with high information gain can be associated with strong correlated localized electrons. Taking into consideration the scaling of DKL with the number of σ-spin electrons of a system (N(σ)), the quantity χ = (N(σ) - 1) DKLfcut is introduced as a general descriptor that allows the quantification of the electron localization in the space. fcut is defined such that it goes smoothly to zero for negligible densities. χ is computed for a selection of atomic and molecular systems in order to test its capability to determine the region in space where electrons are localized. As a general conclusion, χ is able to explain the electron structure of molecules on the basis of chemical grounds with a high degree of success and to produce a clear differentiation of the localization of electrons that can be traced to the fluctuation in the average number of electrons in these regions.
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Affiliation(s)
- Andres S Urbina
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Química e Ingeniería Química, Diego de Robles y Via Interoceanica, Quito 17-1200-841, Ecuador
| | - F Javier Torres
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Química e Ingeniería Química, Diego de Robles y Via Interoceanica, Quito 17-1200-841, Ecuador
| | - Luis Rincon
- Universidad San Francisco de Quito (USFQ), Grupo de Química Computacional y Teórica (QCT-USFQ), Departamento de Química e Ingeniería Química, Diego de Robles y Via Interoceanica, Quito 17-1200-841, Ecuador
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