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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Physical Chemistry, Theoretical and Computational Chemistry".

Deadline for manuscript submissions: closed (30 September 2015) | Viewed by 85333

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Prof. Dr. Malcolm D´Souza

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Department of Chemistry, Wesley College, 120 N. State Street, Dover, DE 19901-3875, USA
Interests: chemical kinetics; solvolysis; LFERs (Linear Free Energy Relationships); QSARs (Quantitative Structure Activity Relationships); database user-needs analysis (database building)
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Dear Colleagues,

In solutions, there are enormous numbers of solvent molecules that are in constant kinetic interaction with other solute reactants and amongst themselves. The quantitative study of these coupled collisions, as a function of time, the stoichiometry of such chemical encounters, and any resultant changes in energy or in covalent and non-covalent chemical structures, is relevant, complex, and interesting to chemical, biological, and environmental systems. This IJMS Special Issue is dedicated to papers that examine the significance and enhance our basic understanding of chemical reaction kinetics, molecular reaction dynamics, and reaction mechanisms that occur in solutions.

Prof. Dr. Malcolm J. D'Souza
Guest Editor

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Keywords

chemical kinetics
reaction mechanisms
thermodynamics
molecular reaction dynamics
homogenous solutions
equilibrium
solution/solid interface
Arrehenius equation
free energy
hydrolysis
solvolysis
steady-state approximation

Published Papers (13 papers)

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Research

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2205 KiB

Open AccessArticle

A Theoretical Study of the Hydration of Methane, from the Aqueous Solution to the sI Hydrate-Liquid Water-Gas Coexistence

by Daniel Porfirio Luis, Alcione García-González and Humberto Saint-Martin

Int. J. Mol. Sci. 2016, 17(6), 378; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17060378 - 26 May 2016

Cited by 11 | Viewed by 5574

Abstract

Monte Carlo and molecular dynamics simulations were done with three recent water models TIP4P/2005 (Transferable Intermolecular Potential with 4 Points/2005), TIP4P/Ice (Transferable Intermolecular Potential with 4 Points/ Ice) and TIP4Q (Transferable Intermolecular Potential with 4 charges) combined with two models for methane: an all-atom one OPLS-AA (Optimal Parametrization for the Liquid State) and a united-atom one (UA); a correction for the C–O interaction was applied to the latter and used in a third set of simulations. The models were validated by comparison to experimental values of the free energy of hydration at 280, 300, 330 and 370 K, all under a pressure of 1 bar, and to the experimental radial distribution functions at 277, 283 and 291 K, under a pressure of 145 bar. Regardless of the combination rules used for σ_C,O, good agreement was found, except when the correction to the UA model was applied. Thus, further simulations of the sI hydrate were performed with the united-atom model to compare the thermal expansivity to the experiment. A final set of simulations was done with the UA methane model and the three water models, to study the sI hydrate-liquid water-gas coexistence at 80, 230 and 400 bar. The melting temperatures were compared to the experimental values. The results show the need to perform simulations with various different models to attain a reliable and robust molecular image of the systems of interest. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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1084 KiB

Open AccessArticle

The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

by Anna Aviñó, Stefania Mazzini, Raimundo Gargallo and Ramon Eritja

Int. J. Mol. Sci. 2016, 17(2), 211; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17020211 - 05 Feb 2016

Cited by 3 | Viewed by 6776

Abstract

Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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7064 KiB

Open AccessArticle

Effect of Greenhouse Gases Dissolved in Seawater

by Shigeki Matsunaga

Int. J. Mol. Sci. 2016, 17(1), 45; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17010045 - 30 Dec 2015

Cited by 8 | Viewed by 6696

Abstract

A molecular dynamics simulation has been performed on the greenhouse gases carbon dioxide and methane dissolved in a sodium chloride aqueous solution, as a simple model of seawater. A carbon dioxide molecule is also treated as a hydrogen carbonate ion. The structure, coordination number, diffusion coefficient, shear viscosity, specific heat, and thermal conductivity of the solutions have been discussed. The anomalous behaviors of these properties, especially the negative pressure dependence of thermal conductivity, have been observed in the higher-pressure region. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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1167 KiB

Open AccessCommunication

One-Electron Reduction of Penicillins in Relation to the Oxidative Stress Phenomenon

by László Szabó, Tünde Tóth, Erzsébet Takács and László Wojnárovits

Int. J. Mol. Sci. 2015, 16(12), 29673-29681; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms161226130 - 11 Dec 2015

Cited by 7 | Viewed by 5610

Abstract

Certain bactericidal antibiotics target mitochondrial components and, due to the leakage of electrons from the electron transport chain, one-electron reduction might occur that can lead to intermediates passing the electron to suitable acceptors. This study aimed at investigating the one-electron reduction mechanism of selected penicillin derivatives using pulse radiolysis techniques. Penicillins can accommodate the electron on each of their carbonyl carbon. Ketyl radicals are thus produced, which are reducing agents with possibility to interact with suitable biomolecules. A detailed mechanism of the reduction is reported. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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6069 KiB

Open AccessArticle

Primary Phenomenon in the Network Formation of Endothelial Cells: Effect of Charge

by Shunto Arai

Int. J. Mol. Sci. 2015, 16(12), 29148-29160; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms161226149 - 07 Dec 2015

Cited by 3 | Viewed by 5281

Abstract

Blood vessels are essential organs that are involved in the supply of nutrients and oxygen and play an important role in regulating the body’s internal environment, including pH, body temperature, and water homeostasis. Many studies have examined the formation of networks of endothelial cells. The results of these studies have revealed that vascular endothelial growth factor (VEGF) affects the interactions of these cells and modulates the network structure. Though almost all previous simulation studies have assumed that the chemoattractant VEGF is present before network formation, vascular endothelial cells secrete VEGF only after the cells bind to the substrate. This suggests VEGF is not essential for vasculogenesis especially at the early stage. Using a simple experiment, we find chain-like structures which last quite longer than it is expected, unless the energetically stable cluster should be compact. Using a purely physical model and simulation, we find that the hydrodynamic interaction retard the compaction of clusters and that the chains are stabilized through the effects of charge. The charge at the surface of the cells affect the interparticle potential, and the resulting repulsive forces prevent the chains from folding. The ions surrounding the cells may also be involved in this process. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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7131 KiB

Open AccessArticle

Aqueous Molecular Dynamics Simulations of the M. tuberculosis Enoyl-ACP Reductase-NADH System and Its Complex with a Substrate Mimic or Diphenyl Ethers Inhibitors

by Camilo Henrique da Silva Lima, Ricardo Bicca De Alencastro, Carlos Roland Kaiser, Marcus Vinícius Nora De Souza, Carlos Rangel Rodrigues and Magaly Girão Albuquerque

Int. J. Mol. Sci. 2015, 16(10), 23695-23722; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms161023695 - 07 Oct 2015

Cited by 16 | Viewed by 6912

Abstract

Molecular dynamics (MD) simulations of 12 aqueous systems of the NADH-dependent enoyl-ACP reductase from Mycobacterium tuberculosis (InhA) were carried out for up to 20–40 ns using the GROMACS 4.5 package. Simulations of the holoenzyme, holoenzyme-substrate, and 10 holoenzyme-inhibitor complexes were conducted in order to gain more insight about the secondary structure motifs of the InhA substrate-binding pocket. We monitored the lifetime of the main intermolecular interactions: hydrogen bonds and hydrophobic contacts. Our MD simulations demonstrate the importance of evaluating the conformational changes that occur close to the active site of the enzyme-cofactor complex before and after binding of the ligand and the influence of the water molecules. Moreover, the protein-inhibitor total steric (E_LJ) and electrostatic (E_C) interaction energies, related to Gly96 and Tyr158, are able to explain 80% of the biological response variance according to the best linear equation, pK_i = 7.772 − 0.1885 × Gly96 + 0.0517 × Tyr158 (R² = 0.80; n = 10), where interactions with Gly96, mainly electrostatic, increase the biological response, while those with Tyr158 decrease. These results will help to understand the structure-activity relationships and to design new and more potent anti-TB drugs. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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2945 KiB

Open AccessArticle

Experimental and Theoretical Investigations on the Supermolecular Structure of Isoliquiritigenin and 6-O-α-D-Maltosyl-β-cyclodextrin Inclusion Complex

by Bin Li, Benguo Liu, Jiaqi Li, Huizhi Xiao, Junyi Wang and Guizhao Liang

Int. J. Mol. Sci. 2015, 16(8), 17999-18017; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms160817999 - 04 Aug 2015

Cited by 26 | Viewed by 5620

Abstract

Isoliquiritigenin (ILTG) possesses many pharmacological properties. However, its poor solubility and stability in water hinders its wide applications. The solubility of bioactive compounds can often be enhanced through preparation and delivery of various cyclodextrin (CD) inclusion complexes. The 6-O-α-D-maltosyl-β-CD (G₂-β-CD), as one of the newest developments of CDs, has high aqueous solubility and low toxicity, especially stable inclusion characteristics with bioactive compounds. In this work, we for the first time construct and characterize the supermolecular structure of ILTG/G₂-β-CD by scanning electron microscopy (SEM), ultraviolet-visible spectroscopy (UV), Fourier transform infrared spectroscopy (FT-IR), and X-ray diffractometry (XRD). The solubility of ILTG in water at 25 °C rises from 0.003 to 0.717 mg/mL by the encapsulation with G₂-β-CD. Our experimental observations on the presence of the ILTG/G₂-β-CD inclusion complex are further supported by the ONIOM(our Own N-layer Integrated Orbital molecular Mechanics)-based QM/MM (Quantum Mechanics/Molecular Mechanics) calculations, typically substantiating these supermolecular characteristics, such as detailed structural assignments, preferred binding orientations, selectivity, solvent effects, interaction energies and forces of the ILTG/G₂-β-CD inclusion complex. Our results have elucidated how ILTG interacts with G₂-β-CD, demonstrating the primary host-guest interactions between ILTG and G₂-β-CD, characterized by hydrogen bonds, hydrophobic interactions, electrostatic forces, and conformational effects, are favored for the formation of the ILTG/G₂-β-CD inclusion. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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2361 KiB

Open AccessArticle

Solvent Properties of Water in Aqueous Solutions of Elastin-Like Polypeptide

by Luisa A. Ferreira, James T. Cole, Christian Reichardt, Nolan B. Holland, Vladimir N. Uversky and Boris Y. Zaslavsky

Int. J. Mol. Sci. 2015, 16(6), 13528-13547; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms160613528 - 12 Jun 2015

Cited by 20 | Viewed by 6034

Abstract

The phase-transition temperatures of an elastin-like polypeptide (ELP) with the (GVGVP)₄₀ sequence and solvent dipolarity/polarizability, hydrogen-bond donor acidity, and hydrogen-bond acceptor basicity in its aqueous solutions were quantified in the absence and presence of different salts (Na₂SO₄, NaCl, NaClO₄, and NaSCN) and various osmolytes (sucrose, sorbitol, trehalose, and trimethylamine N-oxide (TMAO)). All osmolytes decreased the ELP phase-transition temperature, whereas NaCl and Na₂SO₄ decreased, and NaSCN and NaClO₄ increased it. The determined phase-transition temperatures may be described as a linear combination of the solvent’s dipolarity/polarizability and hydrogen-bond donor acidity. The linear relationship established for the phase-transition temperature in the presence of salts differs quantitatively from that in the presence of osmolytes, in agreement with different (direct and indirect) mechanisms of the influence of salts and osmolytes on the ELP phase-transition temperature. Full article

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830 KiB

Open AccessArticle

Theoretical in-Solution Conformational/Tautomeric Analyses for Chain Systems with Conjugated Double Bonds Involving Nitrogen(s)

by Peter I. Nagy

Int. J. Mol. Sci. 2015, 16(5), 10767-10796; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms160510767 - 13 May 2015

Cited by 2 | Viewed by 5968

Abstract

Conformational/tautomeric transformations for X=CH–CH=Y structures (X = CH₂, O, NH and Y = NH) have been studied in the gas phase, in dichloromethane and in aqueous solutions. The paper is a continuation of a former study where s-cis/s-trans conformational equilibria were predicted for analogues. The s-trans conformation is preferred for the present molecules in the gas phase on the basis of its lowest internal free energy as calculated at the B97D/aug-cc-pvqz and CCSD(T)_CBS (coupled-cluster singles and doubles with non-iterative triples extrapolated to the complete basis set) levels. Transition state barriers are of 29–36 kJ/mol for rotations about the central C–C bonds. In solution, an s-trans form is still favored on the basis of its considerably lower internal free energy compared with the s-cis forms as calculated by IEF-PCM (integral-equation formalism of the polarizable continuum dielectric solvent model) at the theoretical levels indicated. A tetrahydrate model in the supermolecule/continuum approach helped explore the 2solute-solvent hydrogen bond pattern. The calculated transition state barrier for rotation about the C–C bond decreased to 27 kJ/mol for the tetrahydrate. Considering explicit solvent models, relative solvation free energies were calculated by means of the free energy perturbation method through Monte Carlo simulations. These calculated values differ remarkably from those by the PCM approach in aqueous solution, nonetheless the same prevalent conformation was predicted by the two methods. Aqueous solution structure-characteristics were determined by Monte Carlo. Equilibration of conformers/tautomers through water-assisted double proton-relay is discussed. This mechanism is not viable, however, in non-protic solvents where the calculated potential of mean force curve does not predict remarkable solute dimerization and subsequent favorable orientation. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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1460 KiB

Open AccessArticle

Calculated Third Order Rate Constants for Interpreting the Mechanisms of Hydrolyses of Chloroformates, Carboxylic Acid Halides, Sulfonyl Chlorides and Phosphorochloridates

by T. William Bentley

Int. J. Mol. Sci. 2015, 16(5), 10601-10623; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms160510601 - 08 May 2015

Cited by 9 | Viewed by 6612

Abstract

Hydrolyses of acid derivatives (e.g., carboxylic acid chlorides and fluorides, fluoro- and chloroformates, sulfonyl chlorides, phosphorochloridates, anhydrides) exhibit pseudo-first order kinetics. Reaction mechanisms vary from those involving a cationic intermediate (S_N1) to concerted S_N2 processes, and further to third order reactions, in which one solvent molecule acts as the attacking nucleophile and a second molecule acts as a general base catalyst. A unified framework is discussed, in which there are two reaction channels—an S_N1-S_N2 spectrum and an S_N2-S_N3 spectrum. Third order rate constants (k₃) are calculated for solvolytic reactions in a wide range of compositions of acetone-water mixtures, and are shown to be either approximately constant or correlated with the Grunwald-Winstein Y parameter. These data and kinetic solvent isotope effects, provide the experimental evidence for the S_N2-S_N3 spectrum (e.g., for chloro- and fluoroformates, chloroacetyl chloride, p-nitrobenzoyl p-toluenesulfonate, sulfonyl chlorides). Deviations from linearity lead to U- or V-shaped plots, which assist in the identification of the point at which the reaction channel changes from S_N2-S_N3 to S_N1-S_N2 (e.g., for benzoyl chloride). Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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1205 KiB

Open AccessArticle

Chemical Conversion Pathways and Kinetic Modeling for the OH-Initiated Reaction of Triclosan in Gas-Phase

by Xue Zhang, Chenxi Zhang, Xiaomin Sun, Lingyan Kang and Yan Zhao

Int. J. Mol. Sci. 2015, 16(4), 8128-8141; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms16048128 - 10 Apr 2015

Cited by 4 | Viewed by 6953

Abstract

As a widely used antimicrobial additive in daily consumption, attention has been paid to the degradation and conversion of triclosan for a long time. The quantum chemistry calculation and the canonical variational transition state theory are employed to investigate the mechanism and kinetic property. Besides addition and abstraction, oxidation pathways and further conversion pathways are also considered. The OH radicals could degrade triclosan to phenols, aldehydes, and other easily degradable substances. The conversion mechanisms of triclosan to the polychlorinated dibenzopdioxin and furan (PCDD/Fs) and polychlorinated biphenyls (PCBs) are clearly illustrated and the toxicity would be strengthened in such pathways. Single radical and diradical pathways are compared to study the conversion mechanism of dichlorodibenzo dioxin (DCDD). Furthermore, thermochemistry is discussed in detail. Kinetic property is calculated and the consequent ratio of k_add/k_total and k_abs/k_total at 298.15 K are 0.955 and 0.045, respectively. Thus, the OH radical addition reactions are predominant, the substitute position of OH radical on triclosan is very important to generate PCDD and furan, and biradical is also a vital intermediate to produce dioxin. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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Review

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2865 KiB

Open AccessReview

Mechanistic Studies of the Solvolyses of Carbamoyl Chlorides and Related Reactions

by Malcolm J. D’Souza and Dennis N. Kevill

Int. J. Mol. Sci. 2016, 17(1), 111; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms17010111 - 15 Jan 2016

Cited by 12 | Viewed by 5351

Abstract

Carbamoyl chlorides are important intermediates, both in the research laboratory and in industrial scale syntheses. The most studied and used are the disubstituted derivatives, incorporating either aryl or alkyl groups (Ar₂NCOCl or R₂NCOCl). Sometimes, the groups are tied back to give a ring and piperidino- and morpholino-derivatives are commonly encountered. Some studies have been made with two different groups attached. Solvolyses tend to occur at the carbonyl carbon, with replacement of the chloride ion. Studies of both rate and products are reviewed and the solvolysis reactions are usually S_N1, although addition of an amine leads to a superimposable bimolecular component. Many of the studies under solvolytic conditions include the application of the extended Grunwald–Winstein equation. The monosubstituted derivatives (ArNHCOCl or RNHCOCl) are less studied. They are readily prepared by the addition of HCl to an isocyanate. In acetonitrile, they decompose to set up and reach equilibrium with the isocyanate (ArNCO or RNCO) and HCl. Considering that the structurally related formyl chloride (HOCOCl) is highly unstable (with formation of HCl + CO₂), the unsubstituted carbamoyl chloride (H₂NCOCl) is remarkably stable. Recommended synthetic procedures require it to survive reaction temperatures in the 300–400 °C range. There has been very little study of its reactions. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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3078 KiB

Open AccessReview

Changes of Water Hydrogen Bond Network with Different Externalities

by Lin Zhao, Kai Ma and Zi Yang

Int. J. Mol. Sci. 2015, 16(4), 8454-8489; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms16048454 - 15 Apr 2015

Cited by 71 | Viewed by 11100

Abstract

It is crucial to uncover the mystery of water cluster and structural motif to have an insight into the abundant anomalies bound to water. In this context, the analysis of influence factors is an alternative way to shed light on the nature of water clusters. Water structure has been tentatively explained within different frameworks of structural models. Based on comprehensive analysis and summary of the studies on the response of water to four externalities (i.e., temperature, pressure, solutes and external fields), the changing trends of water structure and a deduced intrinsic structural motif are put forward in this work. The variations in physicochemical and biological effects of water induced by each externality are also discussed to emphasize the role of water in our daily life. On this basis, the underlying problems that need to be further studied are formulated by pointing out the limitations attached to current study techniques and to outline prominent studies that have come up recently. Full article

(This article belongs to the Special Issue Solution Chemical Kinetics)

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