J | Special Issue : Advance in Molecular Thermodynamics

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

Open AccessArticle

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

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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

Open AccessArticle

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 2249

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

Open AccessReview

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 10 | Viewed by 4901

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

Open AccessReview

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

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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

Open AccessReview

Recent Developments of Computational Methods for pK_a 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 7 | Viewed by 3429

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

K_{a}

, the equilibrium constant for protonation reactions or acid dissociation reactions. The

p K_{a}

, which is a logarithm of

K_{a}

, 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

Open AccessReview

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 3482

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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