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Advance in Molecular Thermodynamics
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Advance in Molecular Thermodynamics

A special issue of J (ISSN 2571-8800). This special issue belongs to the section "Chemistry & Material Sciences".

Deadline for manuscript submissions: closed (15 September 2022) | Viewed by 28795

Special Issue Editor

Prof. Dr. Fumio Hirata

E-Mail
Guest Editor
Theoretical and Computational Molecular Science, Institute for Molecular Science, Okazaki, Aich, Japan
Interests: molecular thermodynamics; solvation; electronic structure; chemical reactions; molecular recognition; electrochmical processes; biomolecules; functions; fluctuation

Special Issue Information

Dear Colleagues

“Thermodynamics” is one of the oldest but the most fundamental concept of modern science and technology. This field of science was founded by the giants in science such as Kelvin, Carnot, Planck, and so on. The development of the science was originally motivated by the industrial need, or to improve the efficiency of the steam engine. The science is very general but phenomenological, and it does not tell, by itself, anything about the molecular processes buried in the phenomena. It is the thermodynamics on a molecular scale, or the molecular thermodynamics, that features the latest advances in this field of science over the last few decades. The development has been driven by the theoretical methodologies, the statistical mechanics of molecular liquids, and the molecular simulation. The important feature of those methodologies is to be able to treat solvents in atomistic detail, which discriminates them from the phenomenological thermodynamics such as the continuum solvent model. Recent advances in experimental methods represented by the transient grating spectroscopy and the pressure NMR technique are another motivating force for the advance.

The Special Issue aims to review the advances in the molecular thermodynamics over the last few decades, and to explore a new frontier in the field of science. Research areas may include, but are not limited to, the following: solvent effects on chemical reactions, microscopic characterization of phase diagrams, structural stability and fluctuation of protein, molecular recognition in biomolecules, biomolecular functions including enzymatic reactions, pharmaceutical design, and electrochemical devices.

We cordially invite you to submit a high-quality original research paper or review to this Special Issue, “Advance in Molecular Thermodynamics”.

Prof. Dr. Fumio Hirata
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 papers will be 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. J is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. 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

  • molecular thermodynamics
  • solvation
  • chemical reactions
  • molecular recognition
  • electrochemical processes
  • fluctuation

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Published Papers (8 papers)

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Editorial

Jump to: Research, Review

2 pages, 158 KiB  
Editorial
Advance in Molecular Thermodynamics
by Fumio Hirata
J 2021, 4(2), 84-85; https://doi.org/10.3390/j4020007 - 23 Apr 2021
Viewed by 1683
Abstract
“Thermodynamics” is one of the oldest but the most fundamental concepts of modern science and technology [...] Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)

Research

Jump to: Editorial, Review

12 pages, 7450 KiB  
Article
Structural Stability Analysis of Proteins Using End-to-End Distance: A 3D-RISM Approach
by Yutaka Maruyama and Ayori Mitsutake
J 2022, 5(1), 114-125; https://doi.org/10.3390/j5010009 - 14 Feb 2022
Cited by 3 | Viewed by 3218
Abstract
The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of [...] Read more.
The stability of a protein is determined from its properties and surrounding solvent. In our previous study, the total energy as a sum of the conformational and solvation free energies was demonstrated to be an appropriate energy function for evaluating the stability of a protein in a protein folding system. We plotted the various energies against the root mean square deviation, required as a reference structure. Herein, we replotted the various energies against the end-to-end distance between the N- and C-termini, which is not a required reference and is experimentally measurable. The solvation free energies for all proteins tend to be low as the end-to-end distance increases, whereas the conformational energies tend to be low as the end-to-end distance decreases. The end-to-end distance is one of interesting measures to study the behavior of proteins. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
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7 pages, 625 KiB  
Article
Accurate Absorption Energy Calculations in Solution Using the Reference Interaction Site Model Self-Consistent Field Including the Constrained Spatial Electron Density Distribution
by Daisuke Yokogawa
J 2021, 4(4), 638-644; https://doi.org/10.3390/j4040046 - 22 Oct 2021
Viewed by 2126
Abstract
The solvation effect is an important factor determining the properties of molecules in solution. The reference interaction site model (RISM) is a powerful method to treat the solvation effect with pair-correlation functions, such as a radial distribution function. This study developed a hybrid [...] Read more.
The solvation effect is an important factor determining the properties of molecules in solution. The reference interaction site model (RISM) is a powerful method to treat the solvation effect with pair-correlation functions, such as a radial distribution function. This study developed a hybrid method between quantum mechanics and RISM using the spatial electron density distributions on each atomic site (RISM-SCF-cSED). Sophisticated quantum mechanical approaches can be used to consider the solvation effect because the computational cost of RISM-SCF-cSED is reasonable. In this study, the absorption energies of 5-(dimethylamino)-2,4-pentadienal in various solutions were calculated using RISM-SCF-cSED. The experimental data were well reproduced with an average errors of ∼0.06 eV, using multi-reference perturbation theory. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
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10 pages, 769 KiB  
Article
Benchmarking Free Energy Calculations in Liquid Aliphatic Ketone Solvents Using the 3D-RISM-KH Molecular Solvation Theory
by Dipankar Roy and Andriy Kovalenko
J 2021, 4(4), 604-613; https://doi.org/10.3390/j4040044 - 13 Oct 2021
Cited by 1 | Viewed by 2481
Abstract
The three-dimensional reference interaction site model of the molecular solvation theory with the Kovalenko–Hirata closure is used to calculate the free energy of solvation of organic solutes in liquid aliphatic ketones. The ketone solvent sites were modeled using a modified united-atom force field. [...] Read more.
The three-dimensional reference interaction site model of the molecular solvation theory with the Kovalenko–Hirata closure is used to calculate the free energy of solvation of organic solutes in liquid aliphatic ketones. The ketone solvent sites were modeled using a modified united-atom force field. The successful application of these solvation models in calculating ketone–water partition coefficients of a large number of solutes supports the validation and benchmarking reported here. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
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Review

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20 pages, 433 KiB  
Review
Principal Component Analysis and Related Methods for Investigating the Dynamics of Biological Macromolecules
by Akio Kitao
J 2022, 5(2), 298-317; https://doi.org/10.3390/j5020021 - 20 Jun 2022
Cited by 15 | Viewed by 7079
Abstract
Principal component analysis (PCA) is used to reduce the dimensionalities of high-dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing [...] Read more.
Principal component analysis (PCA) is used to reduce the dimensionalities of high-dimensional datasets in a variety of research areas. For example, biological macromolecules, such as proteins, exhibit many degrees of freedom, allowing them to adopt intricate structures and exhibit complex functions by undergoing large conformational changes. Therefore, molecular simulations of and experiments on proteins generate a large number of structure variations in high-dimensional space. PCA and many PCA-related methods have been developed to extract key features from such structural data, and these approaches have been widely applied for over 30 years to elucidate macromolecular dynamics. This review mainly focuses on the methodological aspects of PCA and related methods and their applications for investigating protein dynamics. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
12 pages, 1621 KiB  
Review
Applications of Time-Resolved Thermodynamics for Studies on Protein Reactions
by Masahide Terazima
J 2022, 5(1), 186-197; https://doi.org/10.3390/j5010014 - 8 Mar 2022
Viewed by 2445
Abstract
Thermodynamics and kinetics are two important scientific fields when studying chemical reactions. Thermodynamics characterize the nature of the material. Kinetics, mostly based on spectroscopy, have been used to determine reaction schemes and identify intermediate species. They are certainly important fields, but they are [...] Read more.
Thermodynamics and kinetics are two important scientific fields when studying chemical reactions. Thermodynamics characterize the nature of the material. Kinetics, mostly based on spectroscopy, have been used to determine reaction schemes and identify intermediate species. They are certainly important fields, but they are almost independent. In this review, our attempts to elucidate protein reaction kinetics and mechanisms by monitoring thermodynamic properties, including diffusion in the time domain, are described. The time resolved measurements are performed mostly using the time resolved transient grating (TG) method. The results demonstrate the usefulness and powerfulness of time resolved studies on protein reactions. The advantages and limitations of this TG method are also discussed. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
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16 pages, 2553 KiB  
Review
Recent Developments of Computational Methods for pKa Prediction Based on Electronic Structure Theory with Solvation Models
by Ryo Fujiki, Toru Matsui, Yasuteru Shigeta, Haruyuki Nakano and Norio Yoshida
J 2021, 4(4), 849-864; https://doi.org/10.3390/j4040058 - 10 Dec 2021
Cited by 6 | Viewed by 4000
Abstract
The protonation/deprotonation reaction is one of the most fundamental processes in solutions and biological systems. Compounds with dissociative functional groups change their charge states by protonation/deprotonation. This change not only significantly alters the physical properties of a compound itself, but also has a [...] Read more.
The protonation/deprotonation reaction is one of the most fundamental processes in solutions and biological systems. Compounds with dissociative functional groups change their charge states by protonation/deprotonation. This change not only significantly alters the physical properties of a compound itself, but also has a profound effect on the surrounding molecules. In this paper, we review our recent developments of the methods for predicting the Ka, the equilibrium constant for protonation reactions or acid dissociation reactions. The pKa, which is a logarithm of Ka, is proportional to the reaction Gibbs energy of the protonation reaction, and the reaction free energy can be determined by electronic structure calculations with solvation models. The charge of the compound changes before and after protonation; therefore, the solvent effect plays an important role in determining the reaction Gibbs energy. Here, we review two solvation models: the continuum model, and the integral equation theory of molecular liquids. Furthermore, the reaction Gibbs energy calculations for the protonation reactions require special attention to the handling of dissociated protons. An efficient method for handling the free energy of dissociated protons will also be reviewed. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
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29 pages, 5343 KiB  
Review
Structure and Properties of Supercritical Water: Experimental and Theoretical Characterizations
by Norio Yoshida, Masaru Matsugami, Yuichi Harano, Keiko Nishikawa and Fumio Hirata
J 2021, 4(4), 698-726; https://doi.org/10.3390/j4040049 - 2 Nov 2021
Cited by 6 | Viewed by 4202
Abstract
Water in the supercritical region of the phase diagram exhibits a markedly different structure and properties from that at ambient conditions, which is useful in controlling chemical reactions. Nonetheless, the experimental, as well as theoretical, characterization of the substance is not easy because [...] Read more.
Water in the supercritical region of the phase diagram exhibits a markedly different structure and properties from that at ambient conditions, which is useful in controlling chemical reactions. Nonetheless, the experimental, as well as theoretical, characterization of the substance is not easy because the region is next to the critical point. This article reviews the experimental as well as theoretical studies on water in the supercritical region and its properties as a solvent for chemical reactions, as carried out by the authors and based on small-angle X-ray scattering and the statistical mechanics theory of molecular liquids, also known as reference interaction-site model (RISM) theory. Full article
(This article belongs to the Special Issue Advance in Molecular Thermodynamics)
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