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Advances in the Theoretical and Computational Chemistry

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Computational and Theoretical Chemistry".

Deadline for manuscript submissions: closed (30 September 2023) | Viewed by 43457

Special Issue Editors

Dr. Aurora Costales

E-Mail Website
Guest Editor
Department of Analytical and Physical Chemistry, University of Oviedo, 33006 Oviedo, Spain
Interests: theoretical and computational chemistry; materials simulations; nanoaggregates; chemical bonding theory; quantum chemical topology
Dr. Fernando Cortés-Guzmán

E-Mail Website
Guest Editor
Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City 04510, Mexico
Interests: theoretical and computational chemistry; chemical bonding theory; quantum chemical topology; molecular recognition; chemical reactivity; coordination chemistry

Special Issue Information

Dear Colleagues,

Reactivity, along with its structure, is at the core of chemistry, and is still a challenge because as the molecular or supra-molecular systems become more realistic and include explicitly more reactive environmental effects, electron transfer or photo-excitation processes, and cooperative interactions, theoretical chemistry needs to develop new approaches and algorithms to model, explain, or predict the reactivity within these systems. This Special Issue aims to provide a forum for the dissemination of the latest information on new computational and theoretical methods to describe and understand chemical reactivity.

Dr. Aurora Costales
Dr. Fernando Cortés-Guzmán
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • chemical reactivity
  • reaction mechanisms
  • potential energy surface exploration methods: ab-initio, monte-carlo, and meta molecular
  • dynamics
  • non-covalent interactions effects
  • solvent effects
  • electron transfer and redox processes
  • photochemical reactions
  • reaction forces analysis
  • reactivity prediction

Published Papers (22 papers)

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Research

20 pages, 5915 KiB  
Article
Nucleoside Analog Reverse-Transcriptase Inhibitors in Membrane Environment: Molecular Dynamics Simulations
by Anna Stachowicz-Kuśnierz, Beata Korchowiec and Jacek Korchowiec
Molecules 2023, 28(17), 6273; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28176273 - 27 Aug 2023
Viewed by 1126
Abstract
The behavior of four drugs from the family of nucleoside analog reverse-transcriptase inhibitors (zalcitabine, stavudine, didanosine, and apricitabine) in a membrane environment was traced using molecular dynamics simulations. The simulation models included bilayers and monolayers composed of POPC and POPG phospholipids. It was [...] Read more.
The behavior of four drugs from the family of nucleoside analog reverse-transcriptase inhibitors (zalcitabine, stavudine, didanosine, and apricitabine) in a membrane environment was traced using molecular dynamics simulations. The simulation models included bilayers and monolayers composed of POPC and POPG phospholipids. It was demonstrated that the drugs have a higher affinity towards POPG membranes than POPC membranes due to attractive long-range electrostatic interactions. The results obtained for monolayers were consistent with those obtained for bilayers. The drugs accumulated in the phospholipid polar headgroup region. Two adsorption modes were distinguished. They differed in the degree of penetration of the hydrophilic headgroup region. Hydrogen bonds between drug molecules and phospholipid heads were responsible for adsorption. It was shown that apricitabine penetrated the hydrophilic part of the POPC and POPG membranes more effectively than the other drugs. Van der Waals interactions between S atoms and lipids were responsible for this. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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19 pages, 3338 KiB  
Article
Computational Tool to Design Small Synthetic Inhibitors Selective for XIAP-BIR3 Domain
by Marc Farag, Charline Kieffer, Nicolas Guedeney, Anne Sophie Voisin-Chiret and Jana Sopkova-de Oliveira Santos
Molecules 2023, 28(13), 5155; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28135155 - 30 Jun 2023
Viewed by 1084
Abstract
X-linked inhibitor of apoptosis protein (XIAP) exercises its biological function by locking up and inhibiting essential caspase-3, -7 and -9 toward apoptosis execution. It is overexpressed in multiple human cancers, and it plays an important role in cancer cells’ death skipping. Inhibition of [...] Read more.
X-linked inhibitor of apoptosis protein (XIAP) exercises its biological function by locking up and inhibiting essential caspase-3, -7 and -9 toward apoptosis execution. It is overexpressed in multiple human cancers, and it plays an important role in cancer cells’ death skipping. Inhibition of XIAP-BIR3 domain and caspase-9 interaction was raised as a promising strategy to restore apoptosis in malignancy treatment. However, XIAP-BIR3 antagonists also inhibit cIAP1-2 BIR3 domains, leading to serious side effects. In this study, we worked on a theoretical model that allowed us to design and optimize selective synthetic XIAP-BIR3 antagonists. Firstly, we assessed various MM-PBSA strategies to predict the XIAP-BIR3 binding affinities of synthetic ligands. Molecular dynamics simulations using hydrogen mass repartition as an additional parametrization with and without entropic term computed by the interaction entropy approach produced the best correlations. These simulations were then exploited to generate 3D pharmacophores. Following an optimization with a training dataset, five features were enough to model XIAP-BIR3 synthetic ligands binding to two hydrogen bond donors, one hydrogen bond acceptor and two hydrophobic groups. The correlation between pharmacophoric features and computed MM-PBSA free energy revealed nine residues as crucial for synthetic ligand binding: Thr308, Glu314, Trp323, Leu307, Asp309, Trp310, Gly306, Gln319 and Lys297. Ultimately, and three of them seemed interesting to use to improve XIAP-BR3 versus cIAP-BIR3 selectivity: Lys297, Thr308 and Asp309. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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13 pages, 3011 KiB  
Article
Interaction of Water and Oxygen Molecules with Phosphorene: An Ab Initio Study
by Francesca Benini, Nicolò Bassoli, Paolo Restuccia, Mauro Ferrario and Maria Clelia Righi
Molecules 2023, 28(8), 3570; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28083570 - 19 Apr 2023
Cited by 1 | Viewed by 1210
Abstract
Phosphorene, the 2D form of black phosphorus, has recently attracted interest for optoelectronic and tribological applications. However, its promising properties are affected by the strong tendency of the layers to oxidize in ambient conditions. A significant effort has been made to identify the [...] Read more.
Phosphorene, the 2D form of black phosphorus, has recently attracted interest for optoelectronic and tribological applications. However, its promising properties are affected by the strong tendency of the layers to oxidize in ambient conditions. A significant effort has been made to identify the role of oxygen and water in the oxidation process. In this work, we introduce a first-principles study of the phosphorene phase diagram and provide a quantitative estimate of the interaction of pristine and fully oxidized phosphorene layers with oxygen and water molecules. Specifically, we study oxidized layers with oxygen coverages of 25% and 50% that keep the typical anisotropic structure of the layers. We found that hydroxilated and hydrogenated phosphorene layers are both energetically unfavorable, leading to structural distortions. We also studied the water physisorption on both pristine and oxidized layers, finding that the adsorption energy gain doubled on the oxidized layers, whereas dissociative chemisorption was always energetically unfavorable. At the same time, further oxidation (i.e., the dissociative chemisorption of O2) was always favorable, even on oxidized layers. Ab initio molecular dynamics simulations of water intercalated between sliding phosphorene layers showed that even under harsh tribological conditions water dissociation was not activated, thus further strengthening the results obtained from our static calculations. Overall, our results provide a quantitative description of the interaction of phosphorene with chemical species that are commonly found in ambient conditions at different concentrations. The phase diagram that we introduced confirms the tendency of phosphorene layers to fully oxidize due to the presence of O2, resulting in a material with improved hydrophilicity, a piece of information that is relevant for the application of phosphorene, e.g., as a solid lubricant. At the same time, the structural deformations found for the H- and OH- terminated layers undermine their electrical, mechanical, and tribological anisotropic properties and, therefore, the usage of phosphorene. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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17 pages, 3235 KiB  
Article
Crystal Structure, Chemical Bond, and Microwave Dielectric Properties of Ba1−xSrx(Zn1/3Nb2/3)O3 Solid Solution Ceramics
by Lei Xiao, Lianwen Deng, Yu Zhang, Ping Wu, Wenfei Zeng and Sen Peng
Molecules 2023, 28(8), 3451; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28083451 - 13 Apr 2023
Viewed by 1372
Abstract
Ba1−xSrx(Zn1/3Nb2/3)O3 (BSZN) perovskite ceramics are prepared using the traditional solid-state reaction method. X-ray diffraction (XRD), Scanning electron microscopy (SEM), Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS) were used to analyze the phase composition, [...] Read more.
Ba1−xSrx(Zn1/3Nb2/3)O3 (BSZN) perovskite ceramics are prepared using the traditional solid-state reaction method. X-ray diffraction (XRD), Scanning electron microscopy (SEM), Raman spectroscopy, and X-ray photoelectron spectroscopy (XPS) were used to analyze the phase composition, crystal structure, and chemical states of BSZN ceramics, respectively. In addition, the dielectric polarizability, octahedral distortion, complex chemical bond theory, and PVL theory were investigated in detail. Systematic research showed that Sr2+ addition could considerably optimize the microwave dielectric properties of BSZN ceramics. The change in τf value in the negative direction was attributed to oxygen octahedral distortion and bond energy (Eb), and the optimal value of 1.26 ppm/°C was obtained at x = 0.2. The ionic polarizability and density played a decisive role in the dielectric constant, achieving a maximum of 45.25 for the sample with x = 0.2. The full width at half-maximum (FWHM) and lattice energy (Ub) jointly contributed to improving the Q × f value, and a higher Q × f value corresponded to a smaller FWHM value and a larger Ub value. Finally, excellent microwave dielectric properties (εr = 45.25, Q × f = 72,704 GHz, and τf = 1.26 ppm/°C) were obtained for Ba0.8Sr0.2(Zn1/3Nb2/3)O3 ceramics sintered at 1500 °C for 4 h. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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17 pages, 5571 KiB  
Article
Modeling Adsorption of CO2 in Rutile Metallic Oxide Surfaces: Implications in CO2 Catalysis
by Rogelio Chávez-Rocha, Itzel Mercado-Sánchez, Ismael Vargas-Rodriguez, Joseelyne Hernández-Lima, Adán Bazán-Jiménez, Juvencio Robles and Marco A. García-Revilla
Molecules 2023, 28(4), 1776; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28041776 - 13 Feb 2023
Cited by 2 | Viewed by 1998
Abstract
CO2 is the most abundant greenhouse gas, and for this reason, it is the main target for finding solutions to climatic change. A strategy of environmental remediation is the transformation of CO2 to an aggregated value product to generate a carbon-neutral [...] Read more.
CO2 is the most abundant greenhouse gas, and for this reason, it is the main target for finding solutions to climatic change. A strategy of environmental remediation is the transformation of CO2 to an aggregated value product to generate a carbon-neutral cycle. CO2 reduction is a great challenge because of the large C=O dissociation energy, ~179 kcal/mol. Heterogeneous photocatalysis is a strategy to address this issue, where the adsorption process is the fundamental step. The focus of this work is the role of adsorption in CO2 reduction by means of modeling the CO2 adsorption in rutile metallic oxides (TiO2, GeO2, SnO2, IrO2 and PbO2) using Density Functional Theory (DFT) and periodic DFT methods. The comparison of adsorption on different metal oxides forming the same type of crystal structure allowed us to observe the influence of the metal in the adsorption process. In the same way, we performed a comparison of the adsorption capability between two different surface planes, (001) and (110). Two CO2 configurations were observed, linear and folded: the folded conformations were observed in TiO2, GeO2 and SnO2, while the linear conformations were present in IrO2 and PbO2. The largest adsorption efficiency was displayed by the (001) surface planes. The CO2 linear and folded configurations were related to the interaction of the oxygen on the metallic surface with the adsorbate carbon, and the linear conformations were associated with the physisorption and folded configurations with chemisorption. TiO2 was the material with the best performance for CO2 interactions during the adsorption. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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15 pages, 3408 KiB  
Article
Synthesis of Disubstituted Carboxonium Derivatives of Closo-Decaborate Anion [2,6-B10H8O2CC6H5]−: Theoretical and Experimental Study
by Ilya N. Klyukin, Anastasia V. Kolbunova, Alexander S. Novikov, Alexey V. Nelyubin, Andrey P. Zhdanov, Alexey S. Kubasov, Nikita A. Selivanov, Alexander Yu. Bykov, Konstantin Yu. Zhizhin and Nikolay T. Kuznetsov
Molecules 2023, 28(4), 1757; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28041757 - 13 Feb 2023
Cited by 1 | Viewed by 1497
Abstract
A comprehensive study focused on the preparation of disubstituted carboxonium derivatives of closo-decaborate anion [2,6-B10H8O2CC6H5]− was carried out. The proposed synthesis of the target product was based on the interaction between [...] Read more.
A comprehensive study focused on the preparation of disubstituted carboxonium derivatives of closo-decaborate anion [2,6-B10H8O2CC6H5]− was carried out. The proposed synthesis of the target product was based on the interaction between the anion [B10H11]− and benzoic acid C6H5COOH. It was shown that the formation of this product proceeds stepwise through the formation of a mono-substituted product [B10H9OC(OH)C6H5]−. In addition, an alternative one-step approach for obtaining the target derivative is postulated. The structure of tetrabutylammonium salts of carboxonium derivative ((C4H9)4N)[2,6-B10H8O2CC6H5] was established with the help of X-ray structure analysis. The reaction pathway for the formation of [2,6-B10H8O2CC6H5]− was investigated with the help of density functional theory (DFT) calculations. This process has an electrophile induced nucleophilic substitution (EINS) mechanism, and intermediate anionic species play a key role. Such intermediates have a structure in which one boron atom coordinates two hydrogen atoms. The regioselectivity for the process of formation for the 2,6-isomer was also proved by theoretical calculations. Generally, in the experimental part, the simple and available approach for producing disubstituted carboxonium derivative was introduced, and the mechanism of this process was investigated with the help of theoretical calculations. The proposed approach can be applicable for the preparation of a wide range of disubstituted derivatives of closo-borate anions. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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13 pages, 7216 KiB  
Article
In Silico Drug Design and Analysis of Dual Amyloid-Beta and Tau Protein-Aggregation Inhibitors for Alzheimer’s Disease Treatment
by Nisha Job, Venkatesan S. Thimmakondu and Krishnan Thirumoorthy
Molecules 2023, 28(3), 1388; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28031388 - 01 Feb 2023
Cited by 2 | Viewed by 2606
Abstract
Alzheimer’s disease (AD) is a progressive and irreversible neurodegenerative disorder that gradually leads to the state of dementia. The main features of AD include the deposition of amyloid-beta peptides (Aβ), forming senile plaques, and the development of neurofibrillary tangles due to the accumulation [...] Read more.
Alzheimer’s disease (AD) is a progressive and irreversible neurodegenerative disorder that gradually leads to the state of dementia. The main features of AD include the deposition of amyloid-beta peptides (Aβ), forming senile plaques, and the development of neurofibrillary tangles due to the accumulation of hyperphosphorylated Tau protein (p-tau) within the brain cells. In this report, seven dual-inhibitor molecules (L1–7) that can prevent the aggregation of both Aβ and p-tau are suggested. The drug-like features and identification of the target proteins are analyzed by the in silico method. L1–7 show positive results in both Blood–Brain Barrier (BBB) crossing and gastrointestinal absorption, rendering to the results of the permeation method. The molecular docking test performed for L1–7 shows binding energies in the range of −4.9 to −6.0 kcal/mol towards Aβ, and −4.6 to −5.6 kcal/mol for p-tau. The drug’s effectiveness under physiological conditions is assessed by the use of solvation models on the investigated systems. Further, the photophysical properties of L1–3 are predicted using TD-DFT studies. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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20 pages, 8654 KiB  
Article
GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems
by Anshuman Kumar, Pablo R. Arantes, Aakash Saha, Giulia Palermo and Bryan M. Wong
Molecules 2023, 28(3), 1277; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules28031277 - 28 Jan 2023
Cited by 4 | Viewed by 2083
Abstract
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we utilized a GPU-enhanced density functional tight binding (DFTB) [...] Read more.
Metadynamics calculations of large chemical systems with ab initio methods are computationally prohibitive due to the extensive sampling required to simulate the large degrees of freedom in these systems. To address this computational bottleneck, we utilized a GPU-enhanced density functional tight binding (DFTB) approach on a massively parallelized cloud computing platform to efficiently calculate the thermodynamics and metadynamics of biochemical systems. To first validate our approach, we calculated the free-energy surfaces of alanine dipeptide and showed that our GPU-enhanced DFTB calculations qualitatively agree with computationally-intensive hybrid DFT benchmarks, whereas classical force fields give significant errors. Most importantly, we show that our GPU-accelerated DFTB calculations are significantly faster than previous approaches by up to two orders of magnitude. To further extend our GPU-enhanced DFTB approach, we also carried out a 10 ns metadynamics simulation of remdesivir, which is prohibitively out of reach for routine DFT-based metadynamics calculations. We find that the free-energy surfaces of remdesivir obtained from DFTB and classical force fields differ significantly, where the latter overestimates the internal energy contribution of high free-energy states. Taken together, our benchmark tests, analyses, and extensions to large biochemical systems highlight the use of GPU-enhanced DFTB simulations for efficiently predicting the free-energy surfaces/thermodynamics of large biochemical systems. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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13 pages, 4191 KiB  
Article
Hydrophilic Silica Nanoparticles in O/W Emulsion: Insights from Molecular Dynamics Simulation
by Shasha Liu, Hengming Zhang and Shiling Yuan
Molecules 2022, 27(23), 8407; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27238407 - 01 Dec 2022
Cited by 3 | Viewed by 1284
Abstract
Previous studies have been carried out on the effect of silica nanoparticles (SNPs) on the stability of oil–water emulsions. However, the combining configuration of SNPs and oil droplets at the molecular level and the effect of SNP content on the coalescence behavior of [...] Read more.
Previous studies have been carried out on the effect of silica nanoparticles (SNPs) on the stability of oil–water emulsions. However, the combining configuration of SNPs and oil droplets at the molecular level and the effect of SNP content on the coalescence behavior of oil droplets cannot be obtained through experiments. In this paper, molecular dynamics (MD) simulation was performed to investigate the adsorption configuration of hydrophilic SNPs in an O/W emulsion system, and the effect of adsorption of SNPs on coalescence of oil droplets. The simulation results showed: (i) SNPs adsorbed on the surface of oil droplets, and excessive SNPs self-aggregated and connected by hydrogen bonds. (ii) Partially hydrophilic asphaltene and resin molecules formed adsorption configurations with SNPs, which changed the distribution of oil droplet components. Furthermore, compared with hydrophobic asphaltene, the hydrophilic asphaltene was easier to combine with SNPs. (iii) SNPs would extend the oil droplet coalescence time, and the π–π stacking structures were formed between asphaltene and asphaltene or resin molecules to enhance the connection between oil droplets during the oil droplet contact process. (iv) Enough SNPs tightly wrapped around the oil droplet, similar to the formation of a rigid film on the surface of an oil droplet, which hindered the contact and coalescence of components between oil droplets. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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10 pages, 2476 KiB  
Article
A Theoretical Study of the Halogen Bond between Heteronuclear Halogen and Benzene
by Jun Luo, Hongjing Dai, Chenglu Zeng, Dawang Wu and Maoqi Cao
Molecules 2022, 27(22), 8078; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27228078 - 21 Nov 2022
Cited by 2 | Viewed by 1398
Abstract
Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied [...] Read more.
Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied using density functional theory. The structures of the complexes between heteronuclear halogen and benzene have Cs symmetry. The interaction energies of the complexes between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene range from −27.80 to −37.18 kJ/mol, increasing with the increases in the polarity between the atoms of X and D, and are proportional to the angles of a between the Z axis and the covalent bond of heteronuclear halogen. The electron density (ρ) and corresponding Laplacian (∇2ρ) values indicate that the interaction of the heteronuclear halogen and benzene is a typical long-range weak interaction similar to a hydrogen bond. Independent gradient model analysis suggests that the van der Waals is the main interaction between the complexes of heteronuclear halogen and benzene. Symmetry-adapted perturbation theory analysis suggests that the electrostatic interaction is the dominant part in the complexes of C6H6⋯ClF, C6H6⋯ICl, C6H6⋯BrF and C6H6⋯IF, and the dispersion interaction is the main part in the complexes of C6H6⋯BrCl, C6H6⋯IBr. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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13 pages, 2625 KiB  
Article
Novel Ascorbic Acid Co-Crystal Formulations for Improved Stability
by Hui Zhang, Huahui Zeng, Mengfei Li, Yagang Song, Shuo Tian, Jing Xiong, Lan He, Yang Liu and Xiangxiang Wu
Molecules 2022, 27(22), 7998; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27227998 - 18 Nov 2022
Cited by 3 | Viewed by 1386
Abstract
A series of co-crystals of ascorbic acid were prepared with equimolar amounts of co-crystal formers (CCFs), including isonicotinic acid, nicotinic acid, 3,4-dihydroxybenzoic acid, 2,5-dihydroxybenzoic acid and m-hydroxybenzoic acid, by slow solvent evaporation and solvent-assisted grinding. The co-crystals were characterized by single-crystal X-ray diffraction [...] Read more.
A series of co-crystals of ascorbic acid were prepared with equimolar amounts of co-crystal formers (CCFs), including isonicotinic acid, nicotinic acid, 3,4-dihydroxybenzoic acid, 2,5-dihydroxybenzoic acid and m-hydroxybenzoic acid, by slow solvent evaporation and solvent-assisted grinding. The co-crystals were characterized by single-crystal X-ray diffraction spectroscopy, powder X-ray diffraction, IR spectroscopy, differential scanning calorimetry and thermogravimetric analysis. Molecular dynamics (MD) simulations further validated the interaction energy and the possible intermolecular hydrogen bonds among VC and CCFs. The co-crystals showed improved stability when exposed to different wavelengths of light, pH and temperatures compared to the free analogue, especially at higher pH (~9) and lower temperature (~4 °C). Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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17 pages, 4273 KiB  
Article
Hierarchical Virtual Screening and Binding Free Energy Prediction of Potential Modulators of Aedes Aegypti Odorant-Binding Protein 1
by Moysés F. A. Neto, Joaquín M. Campos, Amanda P. M. Cerqueira, Lucio R. de Lima, Glauber V. Da Costa, Ryan Da S. Ramos, Jairo T. Magalhães Junior, Cleydson B. R. Santos and Franco H. A. Leite
Molecules 2022, 27(20), 6777; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27206777 - 11 Oct 2022
Cited by 1 | Viewed by 1458
Abstract
The Aedes aegypti mosquito is the main hematophagous vector responsible for arbovirus transmission in Brazil. The disruption of A. aegypti hematophagy remains one of the most efficient and least toxic methods against these diseases and, therefore, efforts in the research of new chemical [...] Read more.
The Aedes aegypti mosquito is the main hematophagous vector responsible for arbovirus transmission in Brazil. The disruption of A. aegypti hematophagy remains one of the most efficient and least toxic methods against these diseases and, therefore, efforts in the research of new chemical entities with repellent activity have advanced due to the elucidation of the functionality of the olfactory receptors and the behavior of mosquitoes. With the growing interest of the pharmaceutical and cosmetic industries in the development of chemical entities with repellent activity, computational studies (e.g., virtual screening and molecular modeling) are a way to prioritize potential modulators with stereoelectronic characteristics (e.g., pharmacophore models) and binding affinity to the AaegOBP1 binding site (e.g., molecular docking) at a lower computational cost. Thus, pharmacophore- and docking-based virtual screening was employed to prioritize compounds from Sigma-Aldrich® (n = 126,851) and biogenic databases (n = 8766). In addition, molecular dynamics (MD) was performed to prioritize the most potential potent compounds compared to DEET according to free binding energy calculations. Two compounds showed adequate stereoelectronic requirements (QFIT > 81.53), AaegOBP1 binding site score (Score > 42.0), volatility and non-toxic properties and better binding free energy value (∆G < −24.13 kcal/mol) compared to DEET ((N,N-diethyl-meta-toluamide)) (∆G = −24.13 kcal/mol). Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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11 pages, 4290 KiB  
Article
A Systemic Insight into Exohedral Actinides and Endohedral Borospherenes: An&Bm and An@Bn (An=U, Np, Pu; m = 28, 32, 34, 36, 38, 40; n = 36, 38, 40)
by Peng Li, Jingbo Wei, Hao Wei, Kerong Wang, Jizhou Wu, Yuqing Li, Wenliang Liu, Yongming Fu, Feng Xie and Jie Ma
Molecules 2022, 27(18), 6047; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27186047 - 16 Sep 2022
Cited by 3 | Viewed by 1183
Abstract
A series of exohedral actinide borospherenes, An&Bm, and endohedral borospherenes, An@Bn (An=U, Np, Pu; m = 28, 32, 34, 36, 38, 40; n = 36, 38, 40), have been characterized by density functional theory calculations. The electronic structures, chemical bond [...] Read more.
A series of exohedral actinide borospherenes, An&Bm, and endohedral borospherenes, An@Bn (An=U, Np, Pu; m = 28, 32, 34, 36, 38, 40; n = 36, 38, 40), have been characterized by density functional theory calculations. The electronic structures, chemical bond topological properties and spectra have been systematically investigated. It was found that An@Bn is more stable than An&Bn in terms of structure and energy, and UB36 in an aqueous solution is the most stable molecular in this research. The IR and UV-vis spectra of An&Bm and An@Bn are computationally predicted to facilitate further experimental investigations. Charge-transfer spectroscopy decomposes the total UV-Vis absorption curve into the contributions of different excitation features, allowing insight into what form of electronic excitation the UV–Vis absorption peak is from the perspective of charge transfer between the An atoms and borospherenes. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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15 pages, 4023 KiB  
Article
Machine Learning Assisted Prediction of Power Conversion Efficiency of All-Small Molecule Organic Solar Cells: A Data Visualization and Statistical Analysis
by Norah Alwadai, Salah Ud-Din Khan, Zainab Mufarreh Elqahtani and Shahab Ud-Din Khan
Molecules 2022, 27(18), 5905; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27185905 - 11 Sep 2022
Cited by 4 | Viewed by 1675
Abstract
Organic solar cells are famous for their cheap solution processing. Their industrialization needs fast designing of efficient materials. For this purpose, testing of large number of materials is necessary. Machine learning is a better option due to cheaper prediction of power conversion efficiencies. [...] Read more.
Organic solar cells are famous for their cheap solution processing. Their industrialization needs fast designing of efficient materials. For this purpose, testing of large number of materials is necessary. Machine learning is a better option due to cheaper prediction of power conversion efficiencies. In the present work, machine learning was used to predict power conversion efficiencies. Experimental data were collected from the literature to feed the machine learning models. A detailed data visualization analysis was performed to study the trends of the dataset. The relationship between descriptors and power conversion efficiency was quantitatively determined by Pearson correlations. The importance of features was also determined using feature importance analysis. More than 10 machine learning models were tried to find better models. Only the two best models (random forest regressor and bagging regressor) were selected for further analysis. The prediction ability of these models was high. The coefficient of determination (R2) values for the random forest regressor and bagging regressor models were 0.892 and 0.887, respectively. The Shapley additive explanation (SHAP) method was used to identify the impact of descriptors on the output of models. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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14 pages, 3939 KiB  
Article
Structural, Electronic, Reactivity, and Conformational Features of 2,5,5-Trimethyl-1,3,2-diheterophosphinane-2-sulfide, and Its Derivatives: DFT, MEP, and NBO Calculations
by Nasrin Masnabadi, Mohammad R. Thalji, Huda S. Alhasan, Zahra Mahmoodi, Alexander V. Soldatov and Gomaa A. M. Ali
Molecules 2022, 27(13), 4011; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27134011 - 22 Jun 2022
Cited by 3 | Viewed by 2074
Abstract
In this study, we used density functional theory (DFT) and natural bond orbital (NBO) analysis to determine the structural, electronic, reactivity, and conformational features of 2,5,5-trimethyl-1,3,2-di-heteroatom (X) phosphinane-2-sulfide derivatives (X = O (compound 1), S (compound 2), and Se (compound 3 [...] Read more.
In this study, we used density functional theory (DFT) and natural bond orbital (NBO) analysis to determine the structural, electronic, reactivity, and conformational features of 2,5,5-trimethyl-1,3,2-di-heteroatom (X) phosphinane-2-sulfide derivatives (X = O (compound 1), S (compound 2), and Se (compound 3)). We discovered that the features improve dramatically at 6-31G** and B3LYP/6-311+G** levels. The level of theory for the molecular structure was optimized first, followed by the frontier molecular orbital theory development to assess molecular stability and reactivity. Molecular orbital calculations, such as the HOMO–LUMO energy gap and the mapping of molecular electrostatic potential surfaces (MEP), were performed similarly to DFT calculations. In addition, the electrostatic potential of the molecule was used to map the electron density on a surface. In addition to revealing molecules’ size and shape distribution, this study also shows the sites on the surface where molecules are most chemically reactive. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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21 pages, 10012 KiB  
Article
N-((1H-Pyrrol-2-yl)methylene)-6-methoxypyridin-3-amine and Its Co(II) and Cu(II) Complexes as Antimicrobial Agents: Chemical Preparation, In Vitro Antimicrobial Evaluation, In Silico Analysis and Computational and Theoretical Chemistry Investigations
by Vinusha H. Mariwamy, Shiva Prasad Kollur, Bindya Shivananda, Muneera Begum, Chandan Shivamallu, Chandan Dharmashekara, Sushma Pradeep, Anisha S. Jain, Shashanka K. Prasad, Asad Syed, Abdallah M. Elgorban, Salim Al-Rejaie, Joaquín Ortega-Castro, Juan Frau, Norma Flores-Holguín and Daniel Glossman-Mitnik
Molecules 2022, 27(4), 1436; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27041436 - 21 Feb 2022
Cited by 6 | Viewed by 2223
Abstract
Researchers are interested in Schiff bases and their metal complexes because they offer a wide range of applications. The chemistry of Schiff bases of heterocompounds has got a lot of attention because of the metal’s ability to coordinate with Schiff base ligands. In [...] Read more.
Researchers are interested in Schiff bases and their metal complexes because they offer a wide range of applications. The chemistry of Schiff bases of heterocompounds has got a lot of attention because of the metal’s ability to coordinate with Schiff base ligands. In the current study, a new bidentate Schiff base ligand, N-((1H-pyrrol-2-yl)methylene)-6-methoxypyridin-3-amine (MPM) has been synthesized by condensing 6-methoxypyridine-3-amine with pyrrole-2-carbaldehyde. Further, MPM is used to prepare Cu(II) and Co(II) metal complexes. Analytical and spectroscopic techniques are used for the structural elucidation of the synthesized compounds. Both MPM and its metal complexes were screened against Escherichia coli, Bacillus subtilis, Staphylococcus aureus and Klebsiella pneumoniae species for antimicrobial studies. Furthermore, these compounds were subjected to in silico studies against bacterial proteins to comprehend their best non-bonded interactions. The results confirmed that the Schiff base ligand show considerably higher binding affinity with good hydrogen bonding and hydrophobic interactions against various tested microbial species. These results were complemented with a report of the Conceptual DFT global reactivity descriptors of the studied compounds together with their biological scores and their ADMET computed parameters. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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24 pages, 4990 KiB  
Article
A Molecular-Wide and Electron Density-Based Approach in Exploring Chemical Reactivity and Explicit Dimethyl Sulfoxide (DMSO) Solvent Molecule Effects in the Proline Catalyzed Aldol Reaction
by Ignacy Cukrowski, George Dhimba and Darren L. Riley
Molecules 2022, 27(3), 962; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27030962 - 31 Jan 2022
Cited by 2 | Viewed by 1973
Abstract
Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays [...] Read more.
Modelling of the proline (1) catalyzed aldol reaction (with acetone 2) in the presence of an explicit molecule of dimethyl sulfoxide (DMSO) (3) has showed that 3 is a major player in the aldol reaction as it plays a double role. Through strong interactions with 1 and acetone 2, it leads to a significant increase of energy barriers at transition states (TS) for the lowest energy conformer 1a of proline. Just the opposite holds for the higher energy conformer 1b. Both the ‘inhibitor’ and ‘catalyst’ mode of activity of DMSO eliminates 1a as a catalyst at the very beginning of the process and promotes the chemical reactivity, hence catalytic ability of 1b. Modelling using a Molecular-Wide and Electron Density-based concept of Chemical Bonding (MOWED-CB) and the Reaction Energy Profile–Fragment Attributed Molecular System Energy Change (REP-FAMSEC) protocol has shown that, due to strong intermolecular interactions, the HN-C-COOH (of 1), CO (of 2), and SO (of 3) fragments drive a chemical change throughout the catalytic reaction. We strongly advocate exploring the pre-organization of molecules from initially formed complexes, through local minima to the best structures suited for a catalytic process. In this regard, a unique combination of MOWED-CB with REP-FAMSEC provides an invaluable insight on the potential success of a catalytic process, or reaction mechanism in general. The protocol reported herein is suitable for explaining classical reaction energy profiles computed for many synthetic processes. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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23 pages, 3933 KiB  
Article
Spin Orbit Coupling in Orthogonal Charge Transfer States: (TD-)DFT of Pyrene—Dimethylaniline
by Shivan Bissesar, Davita M. E. van Raamsdonk, Dáire J. Gibbons and René M. Williams
Molecules 2022, 27(3), 891; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27030891 - 28 Jan 2022
Cited by 5 | Viewed by 3738
Abstract
The conformational dependence of the matrix element for spin–orbit coupling and of the electronic coupling for charge separation are determined for an electron donor–acceptor system containing a pyrene acceptor and a dimethylaniline donor. Different kinetic and energetic aspects that play a role in [...] Read more.
The conformational dependence of the matrix element for spin–orbit coupling and of the electronic coupling for charge separation are determined for an electron donor–acceptor system containing a pyrene acceptor and a dimethylaniline donor. Different kinetic and energetic aspects that play a role in the spin–orbit charge transfer intersystem crossing (SOCT-ISC) mechanism are discussed. This includes parameters related to initial charge separation and the charge recombination pathways using the Classical Marcus Theory of electron transfer. The spin–orbit coupling, which plays a significant role in charge recombination to the triplet state, can be probed by (TD)-DFT, using the latter as a tool to understand and predict the SOCT-ISC mechanism. The matrix elements for spin–orbit coupling for acetone and 4-thio-thymine are used for benchmarking. (Time Dependent-) Density Functional Theory (DFT and TD-DFT) calculations are applied using the quantum chemical program Amsterdam Density Functional (ADF). Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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18 pages, 2253 KiB  
Article
The Discovery of New Drug-Target Interactions for Breast Cancer Treatment
by Jiali Song, Zhenyi Xu, Lei Cao, Meng Wang, Yan Hou and Kang Li
Molecules 2021, 26(24), 7474; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26247474 - 10 Dec 2021
Cited by 8 | Viewed by 2528
Abstract
Drug–target interaction (DTIs) prediction plays a vital role in probing new targets for breast cancer research. Considering the multifaceted challenges associated with experimental methods identifying DTIs, the in silico prediction of such interactions merits exploration. In this study, we develop a feature-based method [...] Read more.
Drug–target interaction (DTIs) prediction plays a vital role in probing new targets for breast cancer research. Considering the multifaceted challenges associated with experimental methods identifying DTIs, the in silico prediction of such interactions merits exploration. In this study, we develop a feature-based method to infer unknown DTIs, called PsePDC-DTIs, which fuses information regarding protein sequences extracted by pseudo-position specific scoring matrix (PsePSSM), detrended cross-correlation analysis coefficient (DCCA coefficient), and an FP2 format molecular fingerprint descriptor of drug compounds. In addition, the synthetic minority oversampling technique (SMOTE) is employed for dealing with the imbalanced data after Lasso dimensionality reduction. Then, the processed feature vectors are put into a random forest classifier to perform DTIs predictions on four gold standard datasets, including nuclear receptors (NR), G-protein-coupled receptors (GPCR), ion channels (IC), and enzymes (E). Furthermore, we explore new targets for breast cancer treatment using its risk genes identified from large-scale genome-wide genetic studies using PsePDC-DTIs. Through five-fold cross-validation, the average values of accuracy in NR, GPCR, IC, and E datasets are 95.28%, 96.19%, 96.74%, and 98.22%, respectively. The PsePDC-DTIs model provides us with 10 potential DTIs for breast cancer treatment, among which erlotinib (DB00530) and FGFR2 (hsa2263), caffeine (DB00201) and KCNN4 (hsa3783), as well as afatinib (DB08916) and FGFR2 (hsa2263) are found with direct or inferred evidence. The PsePDC-DTIs model has achieved good prediction results, establishing the validity and superiority of the proposed method. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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20 pages, 3708 KiB  
Article
Mathematical Analysis of Reaction–Diffusion Equations Modeling the Michaelis–Menten Kinetics in a Micro-Disk Biosensor
by Naveed Ahmad Khan, Fahad Sameer Alshammari, Carlos Andrés Tavera Romero, Muhammad Sulaiman and Ghaylen Laouini
Molecules 2021, 26(23), 7310; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26237310 - 02 Dec 2021
Cited by 11 | Viewed by 2705
Abstract
In this study, we have investigated the mathematical model of an immobilized enzyme system that follows the Michaelis–Menten (MM) kinetics for a micro-disk biosensor. The film reaction model under steady state conditions is transformed into a couple differential equations which are based on [...] Read more.
In this study, we have investigated the mathematical model of an immobilized enzyme system that follows the Michaelis–Menten (MM) kinetics for a micro-disk biosensor. The film reaction model under steady state conditions is transformed into a couple differential equations which are based on dimensionless concentration of hydrogen peroxide with enzyme reaction (H) and substrate (S) within the biosensor. The model is based on a reaction–diffusion equation which contains highly non-linear terms related to MM kinetics of the enzymatic reaction. Further, to calculate the effect of variations in parameters on the dimensionless concentration of substrate and hydrogen peroxide, we have strengthened the computational ability of neural network (NN) architecture by using a backpropagated Levenberg–Marquardt training (LMT) algorithm. NNs–LMT algorithm is a supervised machine learning for which the initial data set is generated by using MATLAB built in function known as “pdex4”. Furthermore, the data set is validated by the processing of the NNs–LMT algorithm to find the approximate solutions for different scenarios and cases of mathematical model of micro-disk biosensors. Absolute errors, curve fitting, error histograms, regression and complexity analysis further validate the accuracy and robustness of the technique. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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16 pages, 2585 KiB  
Article
Theoretical Analysis on Absorption of Carbon Dioxide (CO2) into Solutions of Phenyl Glycidyl Ether (PGE) Using Nonlinear Autoregressive Exogenous Neural Networks
by Naveed Ahmad Khan, Muhammad Sulaiman, Carlos Andrés Tavera Romero and Fawaz Khaled Alarfaj
Molecules 2021, 26(19), 6041; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26196041 - 05 Oct 2021
Cited by 20 | Viewed by 2158
Abstract
In this paper, we analyzed the mass transfer model with chemical reactions during the absorption of carbon dioxide (CO2) into phenyl glycidyl ether (PGE) solution. The mathematical model of the phenomenon is governed by a coupled nonlinear differential equation that corresponds [...] Read more.
In this paper, we analyzed the mass transfer model with chemical reactions during the absorption of carbon dioxide (CO2) into phenyl glycidyl ether (PGE) solution. The mathematical model of the phenomenon is governed by a coupled nonlinear differential equation that corresponds to the reaction kinetics and diffusion. The system of differential equations is subjected to Dirichlet boundary conditions and a mixed set of Neumann and Dirichlet boundary conditions. Further, to calculate the concentration of CO2, PGE, and the flux in terms of reaction rate constants, we adopt the supervised learning strategy of a nonlinear autoregressive exogenous (NARX) neural network model with two activation functions (Log-sigmoid and Hyperbolic tangent). The reference data set for the possible outcomes of different scenarios based on variations in normalized parameters (α1, α2, β1, β2, k) are obtained using the MATLAB solver “pdex4”. The dataset is further interpreted by the Levenberg–Marquardt (LM) backpropagation algorithm for validation, testing, and training. The results obtained by the NARX-LM algorithm are compared with the Adomian decomposition method and residual method. The rapid convergence of solutions, smooth implementation, computational complexity, absolute errors, and statistics of the mean square error further validate the design scheme’s worth and efficiency. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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14 pages, 3792 KiB  
Article
Initial Decomposition Mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under Shock Loading: ReaxFF Parameterization and Molecular Dynamic Study
by Lixiaosong Du, Shaohua Jin, Pengsong Nie, Chongchong She and Junfeng Wang
Molecules 2021, 26(16), 4808; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26164808 - 09 Aug 2021
Cited by 15 | Viewed by 2499
Abstract
We report a reactive molecular dynamic (ReaxFF-MD) study using the newly parameterized ReaxFF-lg reactive force field to explore the initial decomposition mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under shock loading (shock velocity >6 km/s). The new ReaxFF-lg parameters were trained from massive quantum mechanics data [...] Read more.
We report a reactive molecular dynamic (ReaxFF-MD) study using the newly parameterized ReaxFF-lg reactive force field to explore the initial decomposition mechanism of 3-Nitro-1,2,4-triazol-5-one (NTO) under shock loading (shock velocity >6 km/s). The new ReaxFF-lg parameters were trained from massive quantum mechanics data and experimental values, especially including the bond dissociation curves, valence angle bending curves, dihedral angle torsion curves, and unimolecular decomposition paths of 3-Nitro-1,2,4-triazol-5-one (NTO), 1,3,5-Trinitro-1,3,5-triazine (RDX), and 1,1-Diamino-2,2-dinitroethylene (FOX-7). The simulation results were obtained by analyzing the ReaxFF dynamic trajectories, which predicted the most frequent chain reactions that occurred before NTO decomposition was the unimolecular NTO merged into clusters ((C2H2O3N4)n). Then, the NTO dissociated from (C2H2O3N4)n and started to decompose. In addition, the paths of NO2 elimination and skeleton heterocycle cleavage were considered as the dominant initial decomposition mechanisms of NTO. A small amount of NTO dissociation was triggered by the intermolecular hydrogen transfer, instead of the intramolecular one. For α-NTO, the calculated equation of state was in excellent agreement with the experimental data. Moreover, the discontinuity slope of the shock-particle velocity equation was presented at a shock velocity of 4 km/s. However, the slope of the shock-particle velocity equation for β-NTO showed no discontinuity in the shock wave velocity range of 3–11 km/s. These studies showed that MD by using a suitable ReaxFF-lg parameter set, could provided detailed atomistic information to explain the shock-induced complex reaction mechanisms of energetic materials. With the ReaxFF-MD coupling MSST method and a cheap computational cost, one could also obtain the deformation behaviors and equation of states for energetic materials under conditions of extreme pressure. Full article
(This article belongs to the Special Issue Advances in the Theoretical and Computational Chemistry)
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