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26 pages, 1298 KB

Open AccessArticle

Quantum Chemical (QC) Calculations and Linear Solvation Energy Relationships (LSER): Hydrogen-Bonding Calculations with New QC-LSER Molecular Descriptors

by Costas Panayiotou

Liquids 2024, 4(4), 663-688; https://doi.org/10.3390/liquids4040037 - 4 Oct 2024

Cited by 5 | Viewed by 2639

Abstract

A new method, based on quantum chemical calculations, is proposed for the thermodynamically consistent reformulation of QSPR-type Linear Free-Energy Relationship (LFER) models. This reformulation permits the extraction of valuable information on intermolecular interactions and its transfer in other LFER-type models, in acidity/basicity scales, [...] Read more.

A new method, based on quantum chemical calculations, is proposed for the thermodynamically consistent reformulation of QSPR-type Linear Free-Energy Relationship (LFER) models. This reformulation permits the extraction of valuable information on intermolecular interactions and its transfer in other LFER-type models, in acidity/basicity scales, or even in equation-of-state models. New molecular descriptors of electrostatic interactions are derived from the distribution of molecular surface charges obtained from COSMO-type quantum chemical calculations. The widely used and very successful Abraham’s Linear Solvation Energy Relationship (LSER) model is selected as the reference LSER model for the calculations in solute–solvent systems as well as in solute self-solvation. Hydrogen-bonding free energies, enthalpies, and entropies are now derived for a variety of common solutes. The capacity of the method to address the role of conformational changes in solvation quantities is discussed. The perspectives of the LSER model with the implementation of the new descriptors are also discussed. Full article

(This article belongs to the Special Issue Recent Advances in the Behavior of Liquids in Honor of Prof. Dr. William Acree Jr.)

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14 pages, 1461 KB

Open AccessArticle

Simulating and Predicting Adsorption of Organic Pollutants onto Black Phosphorus Nanomaterials

by Lihao Su, Ya Wang, Zhongyu Wang, Siyu Zhang, Zijun Xiao, Deming Xia and Jingwen Chen

Nanomaterials 2022, 12(4), 590; https://doi.org/10.3390/nano12040590 - 9 Feb 2022

Cited by 12 | Viewed by 3546

Abstract

Layered black phosphorus (BP) has exhibited exciting application prospects in diverse fields. Adsorption of organics onto BP may influence environmental behavior and toxicities of both organic pollutants and BP nanomaterials. However, contributions of various intermolecular interactions to the adsorption remain unclear, and values [...] Read more.

Layered black phosphorus (BP) has exhibited exciting application prospects in diverse fields. Adsorption of organics onto BP may influence environmental behavior and toxicities of both organic pollutants and BP nanomaterials. However, contributions of various intermolecular interactions to the adsorption remain unclear, and values of adsorption parameters such as adsorption energies (E_ad) and adsorption equilibrium constants (K) are lacking. Herein, molecular dynamic (MD) and density functional theory (DFT) was adopted to calculate E_ad and K values. The calculated E_ad and K values for organics adsorbed onto graphene were compared with experimental ones, so as to confirm the reliability of the calculation methods. Polyparameter linear free energy relationship (pp-LFER) models on E_ad and logK were developed to estimate contributions of different intermolecular interactions to the adsorption. The adsorption in the gaseous phase was found to be more favorable than in the aqueous phase, as the adsorbates need to overcome cohesive energies of water molecules onto BP. The affinity of the aromatics to BP was comparable to that of graphene. The pp-LFER models performed well for predicting the E_ad and K values, with external explained variance ranging from 0.90 to 0.97, and can serve as effective tools to rank adsorption capacities of organics onto BP. Full article

(This article belongs to the Special Issue Computational Study of Nanomaterials)

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21 pages, 3692 KB

Open AccessArticle

Catalytic Pyrolysis of Aliphatic Carboxylic Acids into Symmetric Ketones over Ceria-Based Catalysts: Kinetics, Isotope Effect and Mechanism

by Tetiana Kulik, Borys Palianytsia and Mats Larsson

Catalysts 2020, 10(2), 179; https://doi.org/10.3390/catal10020179 - 3 Feb 2020

Cited by 22 | Viewed by 7122

Abstract

Ketonization is a promising way for upgrading bio-derived carboxylic acids from pyrolysis bio-oils, waste oils, and fats to produce high value-added chemicals and biofuels. Therefore, an understanding of its mechanism can help to carry out the catalytic pyrolysis of biomass more efficiently. Here [...] Read more.

Ketonization is a promising way for upgrading bio-derived carboxylic acids from pyrolysis bio-oils, waste oils, and fats to produce high value-added chemicals and biofuels. Therefore, an understanding of its mechanism can help to carry out the catalytic pyrolysis of biomass more efficiently. Here we show that temperature-programmed desorption mass spectrometry (TPD-MS) together with linear free energy relationships (LFERs) can be used to identify catalytic pyrolysis mechanisms. We report the kinetics of the catalytic pyrolysis of deuterated acetic acid and a reaction series of linear and branched fatty acids into symmetric ketones on the surfaces of ceria-based oxides. A structure–reactivity correlation between Taft’s steric substituent constants Es* and activation energies of ketonization indicates that this reaction is the sterically controlled reaction. Surface D_3-n-acetates transform into deuterated acetone isotopomers with different yield, rate, E^≠, and deuterium kinetic isotope effect (DKIE). The obtained values of inverse DKIE together with the structure–reactivity correlation support a concerted mechanism over ceria-based catalysts. These results demonstrate that analysis of Taft’s correlations and using simple equation for estimation of DKIE from TPD-MS data are promising approaches for the study of catalytic pyrolysis mechanisms on a semi-quantitative level. Full article

(This article belongs to the Special Issue Catalysis for the Production of Sustainable Fuels and Chemicals)

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23 pages, 5814 KB

Open AccessArticle

Predicting the Blood-Brain Barrier Permeability of New Drug-Like Compounds via HPLC with Various Stationary Phases

by Małgorzata Janicka, Małgorzata Sztanke and Krzysztof Sztanke

Molecules 2020, 25(3), 487; https://doi.org/10.3390/molecules25030487 - 23 Jan 2020

Cited by 35 | Viewed by 8862

Abstract

The permeation of the blood-brain barrier is a very important consideration for new drug candidate molecules. In this research, the reversed-phase liquid chromatography with different columns (Purosphere RP-18e, IAM.PC.DD2 and Cosmosil Cholester) was used to predict the penetration of the blood-brain barrier by [...] Read more.

The permeation of the blood-brain barrier is a very important consideration for new drug candidate molecules. In this research, the reversed-phase liquid chromatography with different columns (Purosphere RP-18e, IAM.PC.DD2 and Cosmosil Cholester) was used to predict the penetration of the blood-brain barrier by 65 newly-synthesized drug-like compounds. The linear free energy relationships (LFERs) model (log BB = c + eE + sS + aA + bB + vV) was established for a training set of 23 congeneric biologically active azole compounds with known experimental log BB (BB = C_blood/C_brain) values (R² = 0.9039). The reliability and predictive potency of the model were confirmed by leave-one-out cross validation as well as leave-50%-out cross validation. Multiple linear regression (MLR) was used to develop the quantitative structure-activity relationships (QSARs) to predict the log BB values of compounds that were tested, taking into account the chromatographic lipophilicity (log k_w), polarizability and topological polar surface area. The excellent statistics of the developed MLR equations (R² > 0.8 for all columns) showed that it is possible to use the HPLC technique and retention data to produce reliable blood-brain barrier permeability models and to predict the log BB values of our pharmaceutically important molecules. Full article

(This article belongs to the Section Analytical Chemistry)

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19 pages, 2968 KB

Open AccessArticle

Skin Permeation of Solutes from Metalworking Fluids to Build Prediction Models and Test A Partition Theory

by Jacqueline M. Hughes-Oliver, Guangning Xu and Ronald E. Baynes

Molecules 2018, 23(12), 3076; https://doi.org/10.3390/molecules23123076 - 24 Nov 2018

Cited by 1 | Viewed by 3599

Abstract

Permeation of chemical solutes through skin can create major health issues. Using the membrane-coated fiber (MCF) as a solid phase membrane extraction (SPME) approach to simulate skin permeation, we obtained partition coefficients for 37 solutes under 90 treatment combinations that could broadly represent [...] Read more.

Permeation of chemical solutes through skin can create major health issues. Using the membrane-coated fiber (MCF) as a solid phase membrane extraction (SPME) approach to simulate skin permeation, we obtained partition coefficients for 37 solutes under 90 treatment combinations that could broadly represent formulations that could be associated with occupational skin exposure. These formulations were designed to mimic fluids in the metalworking process, and they are defined in this manuscript using: one of mineral oil, polyethylene glycol-200, soluble oil, synthetic oil, or semi-synthetic oil; at a concentration of 0.05 or 0.5 or 5 percent; with solute concentration of 0.01, 0.05, 0.1, 0.5, 1, or 5 ppm. A single linear free-energy relationship (LFER) model was shown to be inadequate, but extensions that account for experimental conditions provide important improvements in estimating solute partitioning from selected formulations into the MCF. The benefit of the Expanded Nested-Solute-Concentration LFER model over the Expanded Crossed-Factors LFER model is only revealed through a careful leave-one-solute-out cross-validation that properly addresses the existence of replicates to avoid an overly optimistic view of predictive power. Finally, the partition theory that accompanies the MCF approach is thoroughly tested and found to not be supported under complex experimental settings that mimic occupational exposure in the metalworking industry. Full article

(This article belongs to the Special Issue Solid-Phase Microextraction)

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12 pages, 1369 KB

Open AccessArticle

On the Nature of the Transition State Characterizing Gated Molecular Encapsulations

by Xiaoyong Lu, Bao-Yu Wang, Shigui Chen and Jovica D. Badjić

Molecules 2014, 19(9), 14292-14303; https://doi.org/10.3390/molecules190914292 - 11 Sep 2014

Cited by 3 | Viewed by 7463

Abstract

Gated molecular encapsulations, with baskets of type 1, are postulated to occur by the mechanism in which solvent molecule penetrates the inner space of 1, through one of its apertures, while the residing guest simultaneously departs the cavity. In the transition [...] Read more.

Gated molecular encapsulations, with baskets of type 1, are postulated to occur by the mechanism in which solvent molecule penetrates the inner space of 1, through one of its apertures, while the residing guest simultaneously departs the cavity. In the transition state of the exchange, three pyridine-based gates are proposed to assume an open position with both incoming solvent and departing guest molecules interacting with the concave surface of the host. The More O’Ferrall-Jencks diagram and linear free energy relationships (LFERs) suggest a more advanced departure of the guest when bigger solvents partake in the displacement. Full article

(This article belongs to the Special Issue Intramolecular Hydrogen Bonding)

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16 pages, 291 KB

Open AccessArticle

Kinetic Studies that Evaluate the Solvolytic Mechanisms of Allyl and Vinyl Chloroformate Esters

by Malcolm J. D'Souza, Aaron F. Givens, Peter A. Lorchak, Abigail E. Greenwood, Stacey L. Gottschall, Shannon E. Carter and Dennis N. Kevill

Int. J. Mol. Sci. 2013, 14(4), 7286-7301; https://doi.org/10.3390/ijms14047286 - 2 Apr 2013

Cited by 2 | Viewed by 8456

Abstract

At 25.0 °C the specific rates of solvolysis for allyl and vinyl chloroformates have been determined in a wide mix of pure and aqueous organic mixtures. In all the solvents studied, vinyl chloroformate was found to react significantly faster than allyl chloroformate. Multiple [...] Read more.

At 25.0 °C the specific rates of solvolysis for allyl and vinyl chloroformates have been determined in a wide mix of pure and aqueous organic mixtures. In all the solvents studied, vinyl chloroformate was found to react significantly faster than allyl chloroformate. Multiple correlation analyses of these rates are completed using the extended (two-term) Grunwald-Winstein equation with incorporation of literature values for solvent nucleophilicity (N_T) and solvent ionizing power (Y_Cl). Both substrates were found to solvolyze by similar dual bimolecular carbonyl-addition and unimolecular ionization channels, each heavily dependent upon the solvents nucleophilicity and ionizing ability. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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18 pages, 459 KB

Open AccessArticle

Use of Linear Free Energy Relationships (LFERs) to Elucidate the Mechanisms of Reaction of a γ-Methyl-β-alkynyl and an ortho-Substituted Aryl Chloroformate Ester

by Malcolm J. D’Souza, Jaci A. Knapp, Gabriel A. Fernandez-Bueno and Dennis N. Kevill

Int. J. Mol. Sci. 2012, 13(1), 665-682; https://doi.org/10.3390/ijms13010665 - 10 Jan 2012

Cited by 11 | Viewed by 9944

Abstract

The specific rates of solvolysis of 2-butyn-1-yl-chloroformate (1) and 2-methoxyphenyl chloroformate (2) are studied at 25.0 °C in a series of binary aqueous-organic mixtures. The rates of reaction obtained are then analyzed using the extended Grunwald-Winstein (G-W) equation and [...] Read more.

The specific rates of solvolysis of 2-butyn-1-yl-chloroformate (1) and 2-methoxyphenyl chloroformate (2) are studied at 25.0 °C in a series of binary aqueous-organic mixtures. The rates of reaction obtained are then analyzed using the extended Grunwald-Winstein (G-W) equation and the results are compared to previously published G-W analyses for phenyl chloroformate (3), propargyl chloroformate (4), p-methoxyphenyl choroformate (5), and p-nitrophenyl chloroformate (6). For 1, the results indicate that dual side-by-side addition-elimination and ionization pathways are occurring in some highly ionizing solvents due to the presence of the electron-donating γ-methyl group. For 2, the analyses indicate that the dominant mechanism is a bimolecular one where the formation of a tetrahedral intermediate is rate-determining. Full article

(This article belongs to the Special Issue Correlation Analysis Applied to Solvolysis Reactions)

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14 pages, 377 KB

Open AccessArticle

Correlation of the Rates of Solvolysis of Neopentyl Chloroformate—A Recommended Protecting Agent

by Malcolm J. D’Souza, Shannon E. Carter and Dennis N. Kevill

Int. J. Mol. Sci. 2011, 12(2), 1161-1174; https://doi.org/10.3390/ijms12021161 - 15 Feb 2011

Cited by 13 | Viewed by 9801

Abstract

The specific rates of solvolysis of neopentyl chloroformate (1) have been determined in 21 pure and binary solvents at 45.0 °C. In most solvents the values are essentially identical to those for ethyl and n-propyl chloroformates. However, in aqueous-1,1,1,3,3,3-hexafluoro-2-propanol mixtures [...] Read more.

The specific rates of solvolysis of neopentyl chloroformate (1) have been determined in 21 pure and binary solvents at 45.0 °C. In most solvents the values are essentially identical to those for ethyl and n-propyl chloroformates. However, in aqueous-1,1,1,3,3,3-hexafluoro-2-propanol mixtures (HFIP) rich in fluoroalcohol, 1 solvolyses appreciably faster than the other two substrates. Linear free energy relationship (LFER) comparison of the specific rates of solvolysis of 1 with those for phenyl chloroformate and those for n-propyl chloroformate are helpful in the mechanistic considerations, as is also the treatment in terms of the Extended Grunwald-Winstein equation. It is proposed that the faster reaction for 1 in HFIP rich solvents is due to the influence of a 1,2-methyl shift, leading to a tertiary alkyl cation, outweighing the only weak nucleophilic solvation of the cation possible in these low nucleophilicity solvents. Full article

(This article belongs to the Special Issue Correlation Analysis Applied to Solvolysis Reactions)

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