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Rojas-González FE, Castillo-Quevedo C, Rodríguez-Kessler PL, Jimenez-Halla JOC, Vásquez-Espinal A, Eithiraj RD, Cortez-Valadez M, Cabellos JL. Exploration of Free Energy Surface of the Au 10 Nanocluster at Finite Temperature. Molecules 2024; 29:3374. [PMID: 39064952 PMCID: PMC11279810 DOI: 10.3390/molecules29143374] [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: 05/26/2024] [Revised: 07/08/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
The first step in comprehending the properties of Au10 clusters is understanding the lowest energy structure at low and high temperatures. Functional materials operate at finite temperatures; however, energy computations employing density functional theory (DFT) methodology are typically carried out at zero temperature, leaving many properties unexplored. This study explored the potential and free energy surface of the neutral Au10 nanocluster at a finite temperature, employing a genetic algorithm coupled with DFT and nanothermodynamics. Furthermore, we computed the thermal population and infrared Boltzmann spectrum at a finite temperature and compared it with the validated experimental data. Moreover, we performed the chemical bonding analysis using the quantum theory of atoms in molecules (QTAIM) approach and the adaptive natural density partitioning method (AdNDP) to shed light on the bonding of Au atoms in the low-energy structures. In the calculations, we take into consideration the relativistic effects through the zero-order regular approximation (ZORA), the dispersion through Grimme's dispersion with Becke-Johnson damping (D3BJ), and we employed nanothermodynamics to consider temperature contributions. Small Au clusters prefer the planar shape, and the transition from 2D to 3D could take place at atomic clusters consisting of ten atoms, which could be affected by temperature, relativistic effects, and dispersion. We analyzed the energetic ordering of structures calculated using DFT with ZORA and single-point energy calculation employing the DLPNO-CCSD(T) methodology. Our findings indicate that the planar lowest energy structure computed with DFT is not the lowest energy structure computed at the DLPN0-CCSD(T) level of theory. The computed thermal population indicates that the 2D elongated hexagon configuration strongly dominates at a temperature range of 50-800 K. Based on the thermal population, at a temperature of 100 K, the computed IR Boltzmann spectrum agrees with the experimental IR spectrum. The chemical bonding analysis on the lowest energy structure indicates that the cluster bond is due only to the electrons of the 6 s orbital, and the Au d orbitals do not participate in the bonding of this system.
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Affiliation(s)
| | - César Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Carretera Federal No. 23, km. 191, Colotlán 46200, Jalisco, Mexico;
| | | | - José Oscar Carlos Jimenez-Halla
- Departamento de Química, División de Ciencias Exactas y Naturales, Universidad de Guanajuato, Noria Alta s/n, Guanajuato 36050, Guanajuato, Mexico;
| | - Alejandro Vásquez-Espinal
- Química y Farmacia, Facultad de Ciencias de la Salud, Universidad Arturo Prat. Casilla 121, Iquique 1100000, Chile;
| | | | - Manuel Cortez-Valadez
- CONAHCYT-Departamento de Investigación en Física, Universidad de Sonora, Apdo. Postal 5-88, Hermosillo 83190, Sonora, Mexico;
| | - José Luis Cabellos
- Coordinación de Investigación y Desarrollo Tecnológico, Universidad Politécnica de Tapachula, Carretera Tapachula a Puerto Madero km. 24, Tapachula 30830, Chiapas, Mexico
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Napiórkowska E, Szeleszczuk Ł, Milcarz K, Pisklak DM. Density Functional Theory and Density Functional Tight Binding Studies of Thiamine Hydrochloride Hydrates. Molecules 2023; 28:7497. [PMID: 38005219 PMCID: PMC10673443 DOI: 10.3390/molecules28227497] [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: 10/13/2023] [Revised: 11/01/2023] [Accepted: 11/07/2023] [Indexed: 11/26/2023] Open
Abstract
Thiamine hydrochloride (THCL), also known as vitamin B1, is an active pharmaceutical ingredient (API), present on the list of essential medicines developed by the WHO, which proves its importance for public health. THCL is highly hygroscopic and can occur in the form of hydrates with varying degrees of hydration, depending on the air humidity. Although experimental characterization of the THCL hydrates has been described in the literature, the questions raised in previously published works suggest that additional research and in-depth analysis of THCL dehydration behavior are still needed. Therefore, the main aim of this study was to characterize, by means of quantum chemical calculations, the behavior of thiamine hydrates and explain the previously obtained results, including changes in the NMR spectra, at the molecular level. To achieve this goal, a series of DFT (CASTEP) and DFTB (DFTB+) calculations under periodic boundary conditions have been performed, including molecular dynamics simulations and GIPAW NMR calculations. The obtained results explain the differences in the relative stability of the studied forms and changes in the spectra observed for the samples of various degrees of hydration. This work highlights the application of periodic DFT calculations in the analysis of various solid forms of APIs.
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Affiliation(s)
- Ewa Napiórkowska
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
- Doctoral School, Medical University of Warsaw, Żwirki i Wigury 81 Str., 02-093 Warsaw, Poland
| | - Łukasz Szeleszczuk
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
| | - Katarzyna Milcarz
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
| | - Dariusz Maciej Pisklak
- Department of Organic and Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1 Str., 02-093 Warsaw, Poland
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Li F, Quan D, Zhang X, Li X, Esimbek J. Quantum mechanical modeling of interstellar molecules on cosmic dusts: H2O, NH3, and CO2. Front Chem 2022; 10:1040703. [DOI: 10.3389/fchem.2022.1040703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/20/2022] [Indexed: 11/12/2022] Open
Abstract
Since the first detection of CH molecule in interstellar medium (ISM), more than 270 molecules have been identified in various astronomical sources in ISM. These molecules include big complex ones, such as fullerene (C60) and polycyclic aromatic hydrocarbons (PAHs), which are the main components of carbonaceous dust. Dust surface chemistry plays an important role in explaining the formation of interstellar molecules. However, many of the dust surface chemical parameters, such as the adsorption energies, are still of uncertainty. Here we present a study of the adsorption of water (H2O), ammonia (NH3), and carbon dioxide (CO2) on graphene-like substrate within the framework of density functional theory (DFT). We used Gaussian 16 software and adopted the corrected generalized gradient approximation (GGA) with the Perdew–Burke–Ernzerhof (PBE) functions. We determined the optimal accretion position of the studied molecules on the graphene-like surface and calculated the adsorption energies. Furthermore, according to the density of states and molecular orbitals of the adsorbed states, we analyzed the charge transfer between the molecules and the graphene-like surface. These results can provide more accurate parameters for calculating the chemical reaction rates on the dust surface, thus contributing to the understanding of dust-surface reactions in ISM.
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Mendoza-Wilson AM, Balandrán-Quintana RR, Valdés-Covarrubias MÁ, Cabellos JL. Potential of quercetin in combination with antioxidants of different polarity incorporated in oil-in-water nanoemulsions to control enzymatic browning of apples. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132372] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Buelna-García CE, Castillo-Quevedo C, Quiroz-Castillo JM, Paredes-Sotelo E, Cortez-Valadez M, Martin-del-Campo-Solis MF, López-Luke T, Utrilla-Vázquez M, Mendoza-Wilson AM, Rodríguez-Kessler PL, Vazquez-Espinal A, Pan S, de Leon-Flores A, Mis-May JR, Rodríguez-Domínguez AR, Martínez-Guajardo G, Cabellos JL. Relative Populations and IR Spectra of Cu38 Cluster at Finite Temperature Based on DFT and Statistical Thermodynamics Calculations. Front Chem 2022; 10:841964. [PMID: 35300385 PMCID: PMC8921525 DOI: 10.3389/fchem.2022.841964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The relative populations of Cu38 isomers depend to a great extent on the temperature. Density functional theory and nanothermodynamics can be combined to compute the geometrical optimization of isomers and their spectroscopic properties in an approximate manner. In this article, we investigate entropy-driven isomer distributions of Cu38 clusters and the effect of temperature on their IR spectra. An extensive, systematic global search is performed on the potential and free energy surfaces of Cu38 using a two-stage strategy to identify the lowest-energy structure and its low-energy neighbors. The effects of temperature on the populations and IR spectra are considered via Boltzmann factors. The computed IR spectrum of each isomer is multiplied by its corresponding Boltzmann weight at finite temperature. Then, they are summed together to produce a final temperature-dependent, Boltzmann-weighted spectrum. Our results show that the disordered structure dominates at high temperatures and the overall Boltzmann-weighted spectrum is composed of a mixture of spectra from several individual isomers.
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Affiliation(s)
- Carlos Emiliano Buelna-García
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
- Organización Científica y Tecnológica del Desierto, Hermosillo, Mexico
| | - Cesar Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, Mexico
| | | | - Edgar Paredes-Sotelo
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
| | - Manuel Cortez-Valadez
- CONACYT-Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Mexico
| | | | - Tzarara López-Luke
- Instituto de Investigación en Metalurgia y Materiales, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Mexico
| | | | | | - Peter L. Rodríguez-Kessler
- Laboratorio de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autonoma de Chile, Santiago, Chile
| | - Alejandro Vazquez-Espinal
- Comput. Theor. Chem. Group Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | - Sudip Pan
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Aned de Leon-Flores
- Departamento de Ciencias Químico Biologicas, Universidad de Sonora, Hermosillo, Mexico
| | | | | | - Gerardo Martínez-Guajardo
- Unidad Académica de Ciencias Químicas, Área de Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
- *Correspondence: Gerardo Martinez-Guajardo, ; Jose Luis Cabellos,
| | - Jose Luis Cabellos
- Universidad Politécnica de Tapachula, Tapachula, Mexico
- *Correspondence: Gerardo Martinez-Guajardo, ; Jose Luis Cabellos,
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Vanzan M, Jones RM, Corni S, D'Agosta R, Baletto F. Exploring AuRh nanoalloys: a computational perspective on the formation and physical properties. Chemphyschem 2022; 23:e202200035. [PMID: 35156760 PMCID: PMC9314847 DOI: 10.1002/cphc.202200035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/09/2022] [Indexed: 11/12/2022]
Abstract
We studied the formation of AuRh nanoalloys (between 20–150 atoms) in the gas phase by means of Molecular Dynamics (MD) calculations, exploring three possible formation processes: one‐by‐one growth, coalescence, and nanodroplets annealing. As a general trend, we recover a predominance of Rh@Au core‐shell ordering over other chemical configurations. We identify new structural motifs with enhanced thermal stabilities. The physical features of those selected systems were studied at the Density Functional Theory (DFT) level, revealing profound correlations between the nanoalloys morphology and properties. Surprisingly, the arrangement of the inner Rh core seems to play a dominant role on nanoclusters’ physical features like the HOMO‐LUMO gap and magnetic moment. Strong charge separations are recovered within the nanoalloys suggesting the existence of charge‐transfer transitions.
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Affiliation(s)
- Mirko Vanzan
- University of Padova: Universita degli Studi di Padova, Department of Chemical Sciences, Via Marzolo 1, 35131, Padova, ITALY
| | | | - Stefano Corni
- University of Padova: Universita degli Studi di Padova, Chemical Sciences, ITALY
| | - Roberto D'Agosta
- University of the Basque Country: Universidad del Pais Vasco, Physics, SPAIN
| | - Francesca Baletto
- King's College London, Physics, Strand, WC2R 2LS, London, UNITED KINGDOM
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