Determination of the molecular structure of gaseous proline by electron diffraction, supported by microwave and quantum chemical data

Belyakov, A. V.; Гарабаджиу, А. В.; Losev, Vitalii A.; Rykov, Anatolii N.

doi:10.1007/s11224-015-0589-5

Cited by 8 publications

(3 citation statements)

References 44 publications

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“…(d) The total number of tautomers and conformers we start with is 1139 (260 tautomers +879 conformers). These are obtained based on the conformer ordering from the literature. ,− In references and − , we list the name of the acid followed by the paper wherein we started our conformational sampling. From among these 1139 tautomers and conformers, 705 of them have conformers that are less than 2 kcal/mol (628 conformers and 77 tautomers).…”

Section: Methodsmentioning

confidence: 99%

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Pereira,

Ramabhadran

2023

J. Phys. Chem. A

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The use of static electronic structure calculations to compute solution-phase pK as offers a great advantage in that a macroscopic bulk property could be computed via microscopic computations involving very few molecules. There are various sources of errors in the quantum chemical calculations though. Overcoming these errors to accurately compute pK as of a plethora of acids is an active area of research in physical chemistry pursued by both computational as well as experimental chemists. We recently developed the pK-Yay method in our attempt to accurately compute aqueous pK as of strong and weak acids. The method is fully black-box, computationally inexpensive, and is very easy for even a nonexpert to use. However, the method was thus far tested on very few molecules (only 16 in all). Herein, in order to assess the future applicability of pK-Yay, we study the effect of multiple conformers, the presence of tautomers under equilibrium, and the impact of a wide variety of functional groups (derivatives of acetic acid with substituents at various positions, dicarboxylic acids, aromatic carboxylic acids, amines and amides, phenols and thiols, and fluorine bearing organic acids). Starting with more than 1000 conformers and tautomers, this study establishes that overall errors of ∼ 1.0 pK a units are routinely obtained for a majority of the molecules. Larger errors are noted in cases where multiple charges, intramolecular hydrogen bonding, and several ionizable functional groups are simultaneously present. An important conclusion to emerge from this work is that, the computed pK as are insensitive (difference <0.5) to whether we consider multiple conformers/tautomers or only choose the most stable conformer/tautomer. Further, pK-Yay captures the stereoelectronic effects arising due to differing axial vs equatorial pattern, and is useful to predict the dominant acid–base equilibrium in a system featuring several equilibria. Overall, pK-Yay may be employed in several chemical applications featuring organic molecules and biomonomers.

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Section: Methodsmentioning

confidence: 99%

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Pereira,

Ramabhadran

2023

J. Phys. Chem. A

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“…For example, García-Revilla and coworkers studied the (O

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[ 63 ] cluster while Belyacob et al investigated. gaseous proline [ 64 ]. Moreover, Bartashevich and coworkers [ 65 ] and Mitzel et al [ 66 ] have studied the internal contacts in halogen-substituted trinitromethanes, or Cukrowski and Mangondo who investigated the interactions in beryllium complexes with nitrilotriacetic and nitrilotri-3-propionic acids [ 67 ].…”

Section: Selected Applications Of the Iqa Methodologymentioning

confidence: 99%

Interacting Quantum Atoms—A Review

et al. 2020

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The aim of this review is threefold. On the one hand, we intend it to serve as a gentle introduction to the Interacting Quantum Atoms (IQA) methodology for those unfamiliar with it. Second, we expect it to act as an up-to-date reference of recent developments related to IQA. Finally, we want it to highlight a non-exhaustive, yet representative set of showcase examples about how to use IQA to shed light in different chemical problems. To accomplish this, we start by providing a brief context to justify the development of IQA as a real space alternative to other existent energy partition schemes of the non-relativistic energy of molecules. We then introduce a self-contained algebraic derivation of the methodological IQA ecosystem as well as an overview of how these formulations vary with the level of theory employed to obtain the molecular wavefunction upon which the IQA procedure relies. Finally, we review the several applications of IQA as examined by different research groups worldwide to investigate a wide variety of chemical problems.

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“…Other works have also exploited the IQA ability to assess both intramolecular and intermolecular contacts in systems relevant in biology. For instance, the IQA analysis of the conformers of vitamin C 197 or proline 198 points out that the intramolecular HBs are the main factors determining their relative stability in the gas-phase. Considering molecular association, the IQA descriptors reveal the relative strength and the nature of the key interactions.…”

Section: Energy Decompositionsmentioning

confidence: 99%

Atoms in molecules in real space: a fertile field for chemical bonding

Pendás

Francisco

Suárez

et al. 2023

Phys. Chem. Chem. Phys.

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Determination of the molecular structure of gaseous proline by electron diffraction, supported by microwave and quantum chemical data

Cited by 8 publications

References 44 publications

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Interacting Quantum Atoms—A Review

Atoms in molecules in real space: a fertile field for chemical bonding

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Determination of the molecular structure of gaseous proline by electron diffraction, supported by microwave and quantum chemical data

Cited by 8 publications

References 44 publications

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Accurate Computation of Aqueous pKas of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Interacting Quantum Atoms—A Review

Atoms in molecules in real space: a fertile field for chemical bonding

Contact Info

Product

Resources

About

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method

Accurate Computation of Aqueous pK_as of Biologically Relevant Organic Acids: Overcoming the Challenges Posed by Multiple Conformers, Tautomeric Equilibria, and Disparate Functional Groups with the Fully Black-Box pK-Yay Method