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Computation
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Calculations in Solution
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Calculations in Solution

A special issue of Computation (ISSN 2079-3197). This special issue belongs to the section "Computational Chemistry".

Deadline for manuscript submissions: closed (31 January 2024) | Viewed by 7310

Special Issue Editor

Prof. Dr. Liliana Mammino

E-Mail Website
Guest Editor
Faculty of Science, Engineering and Agriculture, University of Venda, Thohoyandou 0950, South Africa
Interests: computational chemistry; computational studies of biologically active molecules; chemistry education; cross-discipline explorations; education for sustainability

Special Issue Information

Dear Colleagues,

Many industrial processes, all the processes occurring within living organisms, and the processes occurring in the water bodies in our planet are all processes in which the relevant molecules are in solution. Solute molecules and solvent molecules interact, and these interactions cause changes in many properties of solute molecules, such as their conformational preferences, energetics, separation of the various types of energy levels and, therefore, electronic and IR spectra, NMR signals, the way in which molecules of different solutes interact with each other, etc. This Special Issue of Computation is devoted to the theoretical/computational study of molecules and molecular processes in solution. The scope of the Special Issue is broad, extending to all the aspects of these studies, from theoretical modeling to the study of specific molecules, classes of molecules or processes.

Prof. Dr. Liliana Mammino
Guest Editor

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. Computation is an international peer-reviewed open access monthly 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 1800 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

  • theoretical aspects of the study of molecules in solution
  • solvent effects on the molecular properties of specific molecules or class of molecules
  • considering the presence and effects of solvents in the study of biological activities
  • considering the effects of solvents in the design of industrial processes

Published Papers (5 papers)

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Research

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21 pages, 2656 KiB  
Article
Implicit and Explicit Solvent Effects on the Global Reactivity and the Density Topological Parameters of the Preferred Conformers of Caespitate
by Andrea Moreno-Ceballos, María Eugenia Castro, Norma A. Caballero, Liliana Mammino and Francisco J. Melendez
Computation 2024, 12(1), 5; https://doi.org/10.3390/computation12010005 - 03 Jan 2024
Viewed by 1516
Abstract
In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol [...] Read more.
In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol with biological activity. Acylphloroglucinols have attracted attention for treating tuberculosis due to their structural characteristics, highlighting the stabilizing effect of their intramolecular hydrogen bonds (IHBs). In this work, a conformational search for the caespitate was performed using the MM method. Posteriorly, DFT calculations with the APFD functional were used for full optimization and vibrational frequencies, obtaining stable structures. A population analysis was performed to predict the distribution of the most probable conformers. The calculations were performed in the gas phase and solution using the implicit SMD model for water, chloroform, acetonitrile, and DMSO solvents. Additionally, the multiscale ONIOM QM1/QM2 model was used to simulate the explicit solvent. The implicit and explicit solvent effects were evaluated on the global reactivity indexes using the conceptual-DFT approach. In addition, the QTAIM approach was applied to analyze the properties of the IHBs of the most energetically and populated conformers. The obtained results indicated that the most stable and populated conformer is in the gas phase, and chloroform has an extended conformation. However, water, acetonitrile, and DMSO have a hairpin shape. The optimized structures are well preserved in explicit solvent and the interaction energies for the IHBs were lower in explicit than implicit solvents due to non-covalent interactions formed between the solvent molecules. Finally, both methodologies, with implicit and explicit solvents, were validated with 1H and 13C NMR experimental data. In both cases, the results agreed with the experimental data reported in the CDCl3 solvent. Full article
(This article belongs to the Special Issue Calculations in Solution)
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12 pages, 1364 KiB  
Article
How Sn(IV) Influences on the Reaction Mechanism of 11, tri-Butyl p-Coumarate and Its tri-Butyl-tin p-Coumarate Considering the Solvent Effect: A DFT Level Study
by Rogelio A. Delgado-Alfaro and Zeferino Gómez-Sandoval
Computation 2023, 11(11), 220; https://doi.org/10.3390/computation11110220 - 03 Nov 2023
Viewed by 1071
Abstract
Antioxidants are molecules that neutralize free radicals. In general, the reaction mechanisms of antioxidants are well known. The main reaction mechanisms of antioxidants are electron transfer (ET), hydrogen transfer (HT), and radical adduction formation (RAF). The study of these mechanisms is helpful in [...] Read more.
Antioxidants are molecules that neutralize free radicals. In general, the reaction mechanisms of antioxidants are well known. The main reaction mechanisms of antioxidants are electron transfer (ET), hydrogen transfer (HT), and radical adduction formation (RAF). The study of these mechanisms is helpful in understanding how antioxidants control high free radical levels in the cell. There are many studies focused on determining the main mechanism of an antioxidant to neutralize a wide spectrum of radicals, mainly reactive oxygen species (ROS)-type radicals. Most of these antioxidants are polyphenol-type compounds. Some esters, amides, and metal antioxidants have shown antioxidant activity, but there are few experimental and theoretical studies about the antioxidant reaction mechanism of these compounds. In this work, we show the reaction mechanism proposed for two esters, 11, tri-butyl p-coumarate and its tri-butyl-tin p-coumarate counterpart, using Sn(IV). We show how Sn(IV) increases the electron transfer in polar media and the H transfer in non-polar media. Even though the nature of esters could be polar or non-polar compounds, the antioxidant activity is good for the Sn(IV)-p-coumarate complex in non-polar media. Full article
(This article belongs to the Special Issue Calculations in Solution)
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9 pages, 2371 KiB  
Article
Solvent Effects in the Regioselective N-Functionalization of Tautomerizable Heterocycles Catalyzed by Methyl Trifluoromethanesulfonate: A Density Functional Theory Study with Implicit Solvent Model
by Nelson H. Morgon, Srijit Biswas, Surajit Duari and Aguinaldo R. de Souza
Computation 2022, 10(10), 172; https://doi.org/10.3390/computation10100172 - 26 Sep 2022
Cited by 1 | Viewed by 1296
Abstract
Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, [...] Read more.
Methyl trifluoromethanesulfonate was found to catalyze the reaction of the nucleophilic substitution of the hydroxyl group of alcohols by N-heterocycles followed by X- to N- alkyl group migration (X = O, S) to obtain N-functionalized benzoxazolone, benzothiazolethione, indoline, benzoimidazolethione and pyridinone derivatives. A high degree of solvent dependency on the yield of the products was observed during optimization of the reaction parameters. The yield of the product was found to be 0%, 48% and 70% in acetonitrile, 1,2-dichloroethane and chloroform, respectively. The mechanism of the reaction was established through experiments as well as DFT calculations. The functional B3LYP and 6-311++G(d) basis function sets were used to optimize the molecular geometries. D3 Grimme empiric dispersion with Becke–Johnson dumping was employed, and harmonic vibrational frequencies were calculated to characterize the stationary points on the potential energy surface. To ensure that all the stationary points were smoothly connected to each other, intrinsic reaction coordinate (IRC) analyses were performed. The influence of solvents was considered using the solvation model based on density (SMD). The free energy profiles of the mechanisms were obtained with vibrational unscaled zero-point vibrational energy (ZPE), thermal, enthalpy, entropic and solvent corrections. Full article
(This article belongs to the Special Issue Calculations in Solution)
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14 pages, 5935 KiB  
Article
Naphthenic Acids Aggregation: The Role of Salinity
by Renato D. Cunha, Livia J. Ferreira, Ednilsom Orestes, Mauricio D. Coutinho-Neto, James M. de Almeida, Rogério M. Carvalho, Cleiton D. Maciel, Carles Curutchet and Paula Homem-de-Mello
Computation 2022, 10(10), 170; https://doi.org/10.3390/computation10100170 - 22 Sep 2022
Cited by 3 | Viewed by 1959
Abstract
Naphthenic Acids (NA) are important oil extraction subproducts. These chemical species are one of the leading causes of marine pollution and duct corrosion. For this reason, understanding the behavior of NAs in different saline conditions is one of the challenges in the oil [...] Read more.
Naphthenic Acids (NA) are important oil extraction subproducts. These chemical species are one of the leading causes of marine pollution and duct corrosion. For this reason, understanding the behavior of NAs in different saline conditions is one of the challenges in the oil industry. In this work, we simulated several naphthenic acid species and their mixtures, employing density functional theory calculations with the MST-IEFPCM continuum solvation model, to obtain the octanol–water partition coefficients, together with microsecond classical molecular dynamics. The latter consisted of pure water, low-salinity, and high-salinity environment simulations, to assess the stability of NAs aggregates and their sizes. The quantum calculations have shown that the longer chain acids are more hydrophobic, and the classical simulations corroborated: that the longer the chain, the higher the order of the aggregate. In addition, we observed that larger aggregates are stable at higher salinities for all the studied NAs. This can be one factor in the observed low-salinity-enhanced oil recovery, which is a complex phenomenon. The simulations also show that stabilizing the aggregates induced by the salinity involves a direct interplay of Na+ cations with the carboxylic groups of the NAs inside the aggregates. In some cases, the ion/NA organization forms a membrane-like circular structural arrangement, especially for longer chain NAs. Full article
(This article belongs to the Special Issue Calculations in Solution)
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Review

Jump to: Research

49 pages, 7574 KiB  
Review
The Study of Molecules and Processes in Solution: An Overview of Questions, Approaches and Applications
by Neani Tshilande, Liliana Mammino and Mireille K. Bilonda
Computation 2024, 12(4), 78; https://doi.org/10.3390/computation12040078 - 09 Apr 2024
Viewed by 611
Abstract
Many industrial processes, several natural processes involving non-living matter, and all the processes occurring within living organisms take place in solution. This means that the molecules playing active roles in the processes are present within another medium, called solvent. The solute molecules are [...] Read more.
Many industrial processes, several natural processes involving non-living matter, and all the processes occurring within living organisms take place in solution. This means that the molecules playing active roles in the processes are present within another medium, called solvent. The solute molecules are surrounded by solvent molecules and interact with them. Understanding the nature and strength of these interactions, and the way in which they modify the properties of the solute molecules, is important for a better understanding of the chemical processes occurring in solution, including possible roles of the solvent in those processes. Computational studies can provide a wealth of information on solute–solvent interactions and their effects. Two major models have been developed to this purpose: a model viewing the solvent as a polarisable continuum surrounding the solute molecule, and a model considering a certain number of explicit solvent molecules around a solute molecule. Each of them has its advantages and challenges, and one selects the model that is more suitable for the type of information desired for the specific system under consideration. These studies are important in many areas of chemistry research, from the investigation of the processes occurring within a living organism to drug design and to the design of environmentally benign solvents meant to replace less benign ones in the chemical industry, as envisaged by the green chemistry principles. The paper presents a quick overview of the modelling approaches and an overview of concrete studies, with reference to selected crucial investigation themes. Full article
(This article belongs to the Special Issue Calculations in Solution)
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