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Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design

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

Deadline for manuscript submissions: 31 March 2025 | Viewed by 8224

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Prof. Dr. Piotr Cysewski

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Guest Editor

Department of Physical Chemistry, Pharmacy Faculty, Collegium Medicum of Bydgoszcz, Nicolaus Copernicus University in Toruń, Kurpińskiego 5, 85-950 Bydgoszcz, Poland
Interests: theoretical chemistry; in silico modeling; solution thermodynamics; new materials screening
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Special Issue Information

Dear Colleagues,

The exploration of molecular phenomena is a multidisciplinary inquiry that spans the domains of chemistry, physics, biology, and materials science. As the Guest Editor for the upcoming Special Issue, I invite colleagues to contribute to the following potential areas and topics that can enhance our understanding of molecular structure, solvation, solute-solvent interactions, stability, and dynamics of dissolution phenomena. All kinds of submissions, including reviews, original papers, and short essays, are welcome as contributions to the various aspects of the titled phenomena. The potential themes include deciphering molecular structures and quantifying intermolecular interactions using modern electronic structure analysis, emerging computational techniques such as quantum chemistry, density functional theory, molecular dynamics, and machine learning methodologies. In particular new fresh ideas related to solvation dynamics and equilibria as well as solvation effects and mechanism are welcome. The submission of novel and innovative concepts pertaining to the dynamics and equilibria of solvation, as well as the effects and mechanisms underlying solvation is encouraged. As computational methods have progressed to the extent that the prediction and elucidation of molecular geometries have attained a high degree of sophistication the studies of real physical phenomena are possible. Hence stands as valuable tools in the realm of materials science, computational design and characterization of novel materials. The role of solvation and molecular interactions in shaping the properties of materials provides a platform for groundbreaking research, offering opportunities to engineer materials with tailored functionalities. Furthermore the amalgamation of spectroscopic techniques with computational tools offers avenues for unraveling the intricacies of molecular architecture, thereby providing insights into the forces dictating their existence and such contributions are also expected.

Prof. Dr. Piotr Cysewski
Guest Editor

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Keywords

solvation effects
solvation dynamics
designed solvents
intermolecular interactions
molecular modeling
machine learning
materials science
saturated solutions
chemical reactivity
computational techniques

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Published Papers (10 papers)

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Research

Jump to: Review

11 pages, 1330 KiB

Open AccessArticle

Simulation Studies of the Dynamics and the Connectivity Patterns of Hydrogen Bonds in Water from Ambient to Supercritical Conditions

by Dorota Swiatla-Wojcik

Molecules 2024, 29(23), 5513; https://doi.org/10.3390/molecules29235513 - 21 Nov 2024

Viewed by 347

Abstract

Pressurized high-temperature water attracts attention as a promising medium for chemical synthesis, biomass processing or destruction of hazardous waste. Adjustment to the desired solvent properties requires knowledge on the behavior of populations of hydrogen-bonded molecules. In this work, the interconnection between the hydrogen bond (HB) dynamics and the structural rearrangements of HB networks have been studied by molecular dynamics simulation using the modified central force flexible potential and the HB definition controlling pair interaction energy, HB length and HB angle. Time autocorrelation functions for molecular pairs bonded continuously and intermittently and the corresponding mean lifetimes have been calculated for conditions ranging from ambient to supercritical. A significant reduction in the continuous and intermittent lifetimes has been found between (293 K, 0.1 MPa) and (373 K, 25 MPa) and attributed to the decreasing size of patches embedded in the continuous HB network. The loss of global HB connectivity at ca. (573 K, 10 MPa) and the investigated supercritical conditions do not noticeably affect the HB dynamics. Over the whole temperature range studied, the reciprocal intermittent lifetime follows the transition state theory dependence on temperature with the activation energy of 10.4 kJ/mol. Calculations of the lifetime of molecules that do not form hydrogen bonds indicate that at supercritical temperatures, the role of reactions involving an unbound H₂O molecule as a reactant can be enhanced by lowering system density. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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13 pages, 6092 KiB

Open AccessArticle

Anchoring and Catalytic Performance of Co@C₂N Monolayer for Rechargeable Li-Se_xS_y Batteries: A First-Principles Calculations

by Xiaojing Li, Yingbo Zhang, Chenchen Liu and Shuwei Tang

Molecules 2024, 29(22), 5264; https://doi.org/10.3390/molecules29225264 - 7 Nov 2024

Viewed by 352

Abstract

Se_xS_y composite cathode materials, which offer superior theoretical capacity compared to pure selenium and improved electrochemical properties relative to pure sulfur, have aroused considerable interest in recent decades on account of their applications in electric vehicles and energy storage grids. In the current work, the feasibility of a Co@C₂N monolayer as a promising host candidate for the cathode material of Li-Se_xS_y batteries has been evaluated using first-principles calculations, and particular efforts have been devoted to underscoring the anchoring mechanism and catalytic performance of the Co@C₂N monolayer. The pronounced synergistic effects of Co-S and Li-N bonds lead to increased anchoring performance for Li₂Se_xS_y/Se_xS_y clusters on the surface of Co@C₂N monolayer, which effectively inhibit the shuttle effect. The charge density difference and Mulliken charge analysis underscores a substantial charge transfer from the Li₂Se_xS_y and Se_xS_y clusters to the Co@C₂N monolayer, which indicates a noticeable chemical interaction between them. Further electronic property calculations show that the Co@C₂N monolayer can improve the electrical conductivity of cathode materials for Li-Se_xS_y batteries by maintaining semi-metallic characteristics after anchoring of Li₂Se_xS_y/Se_xS_y clusters. Additionally, the catalytic performance of the Co@C₂N monolayer is evaluated in terms of the reduction pathway of Se₈ and the decomposition energy barrier of the Li₂SeS cluster, which highlights the catalytic role of the Co@C₂N monolayer in the formation and decomposition of the Li₂SeS cluster during the cycle processes. Overall, the Co@C₂N monolayer emerges as a promising host material and catalyst for Li-Se_xS_y batteries with remarkable anchoring and catalytic performance. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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17 pages, 7834 KiB

Open AccessArticle

Structural, Elastic, Electronic, Dynamic, and Thermal Properties of SrAl₂O₄ with an Orthorhombic Structure Under Pressure

by Hongli Guo, Huanyin Yang, Suihu Dang, Shunru Zhang and Haijun Hou

Molecules 2024, 29(21), 5192; https://doi.org/10.3390/molecules29215192 - 2 Nov 2024

Viewed by 388

Abstract

Its outstanding mechanical and thermodynamic characteristics make SrAl₂O₄ a highly desirable ceramic material for high-temperature applications. However, the effects of elevated pressure on the structural and other properties of SrAl₂O₄ are still poorly understood. This study encompassed structural, elastic, electronic, dynamic, and thermal characteristics. Band structure calculations indicate that the direct band gap of SrAl₂O₄ is 4.54 eV. In addition, the Cauchy pressures provide evidence of the brittle characteristics of SrAl₂O₄. The mechanical and dynamic stability of SrAl₂O₄ is evident from the accurate determination of its elastic constants and phonon dispersion relations. In addition, a comprehensive analysis was conducted of the relationship between specific heat and entropy concerning temperature variations. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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22 pages, 10758 KiB

Open AccessArticle

Molecular Simulation of the Water Diffusion Behavior and Electronic Properties of Boron-Nitride-Composited Mineral Oil

by Yang Wang, Wenchao Yan, Kunqi Cui, Chuanhui Cheng, Yuanyang Ren and Kai Wu

Molecules 2024, 29(18), 4500; https://doi.org/10.3390/molecules29184500 - 22 Sep 2024

Viewed by 1165

Abstract

Despite the fact that doping nanoparticles into insulating transformer oil has proven to be an effective method of enhancing its dielectric and electrical properties, it remains unclear how different types and surface conditions of nanoparticles may affect their dielectric and electrical properties. Therefore, the effect of doping various types of BN nanoparticles (nanosphere, nanotube, and nanosheet) in insulating mineral oil (MO) on the diffusion properties of water molecules and electrical properties across the BN/MO interface was investigated using molecular dynamics (MD) and Density Functional Theory (DFT) simulations. Our results show that different surface morphology and grafted functional groups in different types of BN nanoparticles have a significant impact both on the water diffusion behavior and the interfacial potential barrier across the interface between BN and MO. In the MO system directly doped by BN nanospheres, water diffusion behavior is not significantly restricted. However, grafting -NH₂ polar groups onto the BN nanoparticle surface may significantly limit the diffusion behavior of water due to the strong attraction between the -NH₂ polar groups and water molecules; the most significant effect is with nanospheres, followed by nanotubes and nanosheets. In terms of electrical properties across the interface between BN and MO, the h-BN surface (derived from BN nanosheets and nanotubes) acts as a trap for electrons in MO (−0.59 eV), while the c-BN surface (derived from BN nanospheres) acts as a potential barrier for electrons in MO (1.45 eV), and it is noteworthy that the presence of water molecules near the interface between BN and MO has little impact on the potential barriers. Advancing a fundamental understanding of the electrical and water diffusion properties of MO in correlation with the surface morphology of different types of nanoparticles is key to improving the insulation properties of oil-impregnated power transformers. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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12 pages, 402 KiB

Open AccessArticle

Calculation of Some Low-Lying Electronic Excitations of Barium Monofluoride Using the Equation of Motion (EOM)-CC3 Method with an Effective Core Potential Approach

by Marko Horbatsch

Molecules 2024, 29(18), 4356; https://doi.org/10.3390/molecules29184356 - 13 Sep 2024

Viewed by 680

Abstract

Barium monofluoride (BaF) is a polar molecule of interest in measurements of the electron electric dipole moment. For this purpose, efforts are underway to investigate this molecule embedded within cryogenic matrices, e.g., in solid Ne. For a theoretical understanding of the electronic structure of such an embedded molecule, the need arises for efficient methods which are accurate but also able to handle a number of atoms which surround the molecule. The calculation for gas-phase BaF can be reduced to involve only outer electrons by representing the inner core of Ba with a pseudopotential, while carrying out a non-relativistic calculation with an appropriate basis set. Thus, the method is effectively at a scalar-relativistic level. In this work, we demonstrate to which extent this can be achieved using coupled-cluster methods to deal with electron correlation. As a test case, the SrF(

X^{2} Σ^{+} \to B^{2} Σ^{+}

) transition is investigated, and excellent accuracy is obtained with the EOM-CC3 method. For the BaF(

X^{2} Σ^{+} \to {A^{'}}^{2} Δ

X^{2} Σ^{+} \to A^{2} Π

X^{2} Σ^{+} \to B^{2} Σ^{+}

) transitions, various coupled-cluster approaches are compared with very good agreement for EOM-CC3 with experimentally derived spectroscopic parameters, at the level of tens of

{cm}^{- 1}

. An exception is the excitation to the

{A^{'}}^{2} Δ

state, for which the energy is overestimated by

230 {cm}^{- 1}

. The poor convergence behavior for this particular state is demonstrated by providing results from calculations with basis sets of n = 3, 4, 5)-zeta quality. The calculated excitation energy for the

B^{2} Σ^{+}

state agrees better with a deperturbation analysis than with the effective spectroscopic value, with a difference of

120 {cm}^{- 1}

. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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14 pages, 2639 KiB

Open AccessArticle

Theoretical Investigation of the Effects of Aldehyde Substitution with Pyran Groups in D-π-A Dye on Performance of DSSCs

by Suzan K. Alghamdi, Abdulaziz I. Aljameel, Rageh K. Hussein, Khalled Al-heuseen, Mamduh J. Aljaafreh and Dina Ezzat

Molecules 2024, 29(17), 4175; https://doi.org/10.3390/molecules29174175 - 3 Sep 2024

Viewed by 700

Abstract

This work investigated the substitution of the aldehyde with a pyran functional group in D-π-aldehyde dye to improve cell performance. This strategy was suggested by recent work that synthesized D-π-aldehyde dye, which achieved a maximum absorption wavelength that was only slightly off the threshold for an ideal sensitizer. Therefore, DFT and TD-DFT were used to investigate the effect of different pyran substituents to replace the aldehyde group. The pyran groups reduced the dye energy gap better than other known anchoring groups. The proposed dyes showed facile intermolecular charge transfer through the localization of HOMO and LUMO orbitals on the donor and acceptor parts, which promoted orbital overlap with the TiO₂ surface. The studied dyes have HOMO and LOMO energy levels that could regenerate electrons from redox potential electrodes and inject electrons into the TiO₂ conduction band. The lone pairs of oxygen atoms in pyran components act as nucleophile centers, facilitating adsorption on the TiO₂ surface through their electrophile atoms. Pyrans increased the efficacy of dye sensitizers by extending their absorbance range and causing the maximum peak to redshift deeper into the visible region. The effects of the pyran groups on photovoltaic properties such as light harvesting efficiency (LHE), free energy change of electron injection, and dye regeneration were investigated and discussed. The adsorption behaviors of the proposed dyes on the TiO₂ (1 1 0) surface were investigated by means of Monte Carlo simulations. The calculated adsorption energies indicates that pyran fragments, compared to the aldehyde in the main dye, had a greater ability to induce the adsorption onto the TiO₂ substrate. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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10 pages, 1737 KiB

Open AccessArticle

Reproducing the Solvatochromism of Merocyanines by PCM Calculations

by Andrés Aracena, Marcos Caroli Rezende and Sebastián Pizarro

Molecules 2024, 29(17), 4103; https://doi.org/10.3390/molecules29174103 - 29 Aug 2024

Viewed by 476

Abstract

Polarizable continuum methods (PCM) have been widely employed for simulating solvent effects, in spite of the fact that they either ignore specific interactions in solution or only partially reproduce non-specific contributions. Examples of three solvatochromic dyes with a negative, a positive and a reverse behavior illustrate the achievements and shortcomings of PCM calculations and the causes for their variable success. Even when qualitatively mimicking non-specific solvent effects, departures of calculated values from experimental data may be significant (20–30%). In addition, they can utterly fail to reproduce an inverted behavior that is caused by significant specific contributions by the solvent. As shown through a theoretical model that rationalizes and predicts the solvatochromism of phenolate merocyanines based on DFT (Density Functional Theory) descriptors in the gas phase, PCM shortcomings are to be held responsible for its eventual failure to reproduce experimental data in solution. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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17 pages, 6851 KiB

Open AccessArticle

Enhancing Sulfidization and Flotation of Smithsonite Using Eco-Friendly Triethanolamine: Insights from Experimental and Simulation Studies

by Song Zhang, Guanyu Liang, Yongjun Xian and Shuming Wen

Molecules 2024, 29(14), 3433; https://doi.org/10.3390/molecules29143433 - 22 Jul 2024

Viewed by 875

Abstract

Triethanolamine (TEA) is a promising eco-friendly alternative to inorganic ammonia for enhancing surface sulfidization and flotation recovery of smithsonite. Micro-flotation experiments revealed an enhancement in smithsonite recovery to 95.21% with TEA modification, comparable to the results obtained using ammonia. The mechanisms behind the ability of TEA to enhance the sulfidization process were investigated through surface analysis and molecular dynamics simulations. TEA modification increased the content of sulfidization products, the proportion of crucial S₂²⁻ in adsorbed products, and the thickness and size of the sulfidization product layer. The complexation of TEA with Zn sites formed positively charged Zn–TEA complexes that adsorb onto the smithsonite surface. These complexes promoted negatively charged HS⁻ adsorption, creating a multi-layered adsorption structure. Moreover, TEA modification reduced the total energy required for the sulfidization. These findings open up new possibilities for using eco-friendly reagents in mineral processing, highlighting the potential of TEA in green mineral processing practices. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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20 pages, 6371 KiB

Open AccessArticle

Experimental and Theoretical Insights into the Intermolecular Interactions in Saturated Systems of Dapsone in Conventional and Deep Eutectic Solvents

by Piotr Cysewski, Tomasz Jeliński and Maciej Przybyłek

Molecules 2024, 29(8), 1743; https://doi.org/10.3390/molecules29081743 - 11 Apr 2024

Cited by 3 | Viewed by 1145

Abstract

Solubility is not only a crucial physicochemical property for laboratory practice but also provides valuable insight into the mechanism of saturated system organization, as a measure of the interplay between various intermolecular interactions. The importance of these data cannot be overstated, particularly when dealing with active pharmaceutical ingredients (APIs), such as dapsone. It is a commonly used anti-inflammatory and antimicrobial agent. However, its low solubility hampers its efficient applications. In this project, deep eutectic solvents (DESs) were used as solubilizing agents for dapsone as an alternative to traditional solvents. DESs were composed of choline chloride and one of six polyols. Additionally, water–DES mixtures were studied as a type of ternary solvents. The solubility of dapsone in these systems was determined spectrophotometrically. This study also analyzed the intermolecular interactions, not only in the studied eutectic systems, but also in a wide range of systems found in the literature, determined using the COSMO-RS framework. The intermolecular interactions were quantified as affinity values, which correspond to the Gibbs free energy of pair formation of dapsone molecules with constituents of regular solvents and choline chloride-based deep eutectic solvents. The patterns of solute–solute, solute–solvent, and solvent–solvent interactions that affect solubility were recognized using Orange data mining software (version 3.36.2). Finally, the computed affinity values were used to provide useful descriptors for machine learning purposes. The impact of intermolecular interactions on dapsone solubility in neat solvents, binary organic solvent mixtures, and deep eutectic solvents was analyzed and highlighted, underscoring the crucial role of dapsone self-association and providing valuable insights into complex solubility phenomena. Also the importance of solvent–solvent diversity was highlighted as a factor determining dapsone solubility. The Non-Linear Support Vector Regression (NuSVR) model, in conjunction with unique molecular descriptors, revealed exceptional predictive accuracy. Overall, this study underscores the potency of computed molecular characteristics and machine learning models in unraveling complex molecular interactions, thereby advancing our understanding of solubility phenomena within the scientific community. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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Review

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30 pages, 1610 KiB

Open AccessReview

A Review of Machine Learning and QSAR/QSPR Predictions for Complexes of Organic Molecules with Cyclodextrins

by Dariusz Boczar and Katarzyna Michalska

Molecules 2024, 29(13), 3159; https://doi.org/10.3390/molecules29133159 - 2 Jul 2024

Cited by 1 | Viewed by 1498

Abstract

Cyclodextrins are macrocyclic rings composed of glucose residues. Due to their remarkable structural properties, they can form host–guest inclusion complexes, which is why they are frequently used in the pharmaceutical, cosmetic, and food industries, as well as in environmental and analytical chemistry. This review presents the reports from 2011 to 2023 on the quantitative structure–activity/property relationship (QSAR/QSPR) approach, which is primarily employed to predict the thermodynamic stability of inclusion complexes. This article extensively discusses the significant developments related to the size of available experimental data, the available sets of descriptors, and the machine learning (ML) algorithms used, such as support vector machines, random forests, artificial neural networks, and gradient boosting. As QSAR/QPR analysis only requires molecular structures of guests and experimental values of stability constants, this approach may be particularly useful for predicting these values for complexes with randomly substituted cyclodextrins, as well as for estimating their dependence on pH. This work proposes solutions on how to effectively use this knowledge, which is especially important for researchers who will deal with this topic in the future. This review also presents other applications of ML in relation to CD complexes, including the prediction of physicochemical properties of CD complexes, the development of analytical methods based on complexation with CDs, and the optimisation of experimental conditions for the preparation of the complexes. Full article

(This article belongs to the Special Issue Computational and Theoretical Insights on Molecular Structure, Solvation, Interactions and New Materials Design)

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