From Atoms in Amino Acids to the Genetic Code and Protein Stability, and Backwards

Matta, Chérif F.

doi:10.1002/9783527629213.ch14

Cited by 5 publications

(12 citation statements)

References 94 publications

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“…The electron densities of the five free nucleic acid bases adenine, guanine, cytosine, thymine and uracil, were also analyzed using QTAIM (for technical details of electronic structure Electron-density descriptors as predictors | Review www.future-science.com calculations, see [60]). Aqueous partial molar volumes of four of the free bases (except guanine) and all of the five nucleosides were accurately measured by Lee and Chalikian [61] at two different temperatures (18 and 55°C).…”

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

“…Aqueous partial molar volumes of four of the free bases (except guanine) and all of the five nucleosides were accurately measured by Lee and Chalikian [61] at two different temperatures (18 and 55°C). To obtain an estimate of the group contribution of the sugar moiety to the partial molar volume, the reported partial molar volumes of the bases are subtracted from the corresponding partial molar volumes of the nucleosides [60]:…”

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

“…The sugar contributes Vsugar 0 80.4±1.0 cm 3 mol -1 within the temperature range (18-55°C). Using this transferable group contribution of the sugar moiety, the partial molar volume of guanine (not reported in [61]) is obtained from [60]:…”

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

“…The calculation of the partial molar volumes of the bases was achieved using the van der Waals' volume V(vdW) and the CSI as predictors, as was done for the amino acids. The least-square fitting yields the following regression equations at the two experimental temperatures [60]: equation 41 and equation 42 correlations that are displayed in FiguRe 8, where A is adenine, T is thymine, U is uracil, G is guanine and C is cytosine.…”

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

“…While the motivation to model the partition coefficient of the 20 genetically encoded amino acid was different in the original literature (to simulate the effect of mutation on proteins folding) [59,60], the accurate modeling of partition coefficients is of prime relevance to medicinal chemistry for the reasons outlined previously. This is what will be described in the remainder of this section, an ana lysis that has never been published before despite being based on previous calculations [59].…”

Section: Modeling Of the Partitioning Coefficient Between Two Immiscible Liquid Phasesmentioning

confidence: 99%

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Electron-Density Descriptors as Predictors in Quantitative Structure–Activity/Property Relationships and Drug Design

Matta

Arabi

2011

Future Med. Chem.

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The use of electron density-based molecular descriptors in drug research, particularly in quantitative structure--activity relationships/quantitative structure--property relationships studies, is reviewed. The exposition starts by a discussion of molecular similarity and transferability in terms of the underlying electron density, which leads to a qualitative introduction to the quantum theory of atoms in molecules (QTAIM). The starting point of QTAIM is the topological analysis of the molecular electron-density distributions to extract atomic and bond properties that characterize every atom and bond in the molecule. These atomic and bond properties have considerable potential as bases for the construction of robust quantitative structure--activity/property relationships models as shown by selected examples in this review. QTAIM is applicable to the electron density calculated from quantum-chemical calculations and/or that obtained from ultra-high resolution x-ray diffraction experiments followed by nonspherical refinement. Atomic and bond properties are introduced followed by examples of application of each of these two families of descriptors. The review ends with a study whereby the molecular electrostatic potential, uniquely determined by the density, is used in conjunction with atomic properties to elucidate the reasons for the biological similarity of bioisosteres.

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Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

Section: Modeling the Partial Molar Volumes Of The Five Nucleic Acid Basesmentioning

confidence: 99%

Section: Modeling Of the Partitioning Coefficient Between Two Immiscible Liquid Phasesmentioning

confidence: 99%

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Electron-Density Descriptors as Predictors in Quantitative Structure–Activity/Property Relationships and Drug Design

Matta

Arabi

2011

Future Med. Chem.

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Probing Electron Dynamics with the Laplacian of the Momentum Density

Sukumar

MacDougall

Levit

2012

A Matter of Density

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Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential

2014

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The electron density and the electrostatic potential are fundamentally related to the molecular hamiltonian, and hence are the ultimate source of all properties in the ground- and excited-states. The advantages of using molecular descriptors derived from these fundamental scalar fields, both accessible from theory and from experiment, in the formulation of quantitative structure-to-activity and structure-to-property relationships, collectively abbreviated as QSAR, are discussed. A few such descriptors encode for a wide variety of properties including, for example, electronic transition energies, pKa's, rates of ester hydrolysis, NMR chemical shifts, DNA dimers binding energies, π-stacking energies, toxicological indices, cytotoxicities, hepatotoxicities, carcinogenicities, partial molar volumes, partition coefficients (log P), hydrogen bond donor capacities, enzyme–substrate complementarities, bioisosterism, and regularities in the genetic code. Electronic fingerprinting from the topological analysis of the electron density is shown to be comparable and possibly superior to Hammett constants and can be used in conjunction with traditional bulk and liposolubility descriptors to accurately predict biological activities. A new class of descriptors obtained from the quantum theory of atoms in molecules' (QTAIM) localization and delocalization indices and bond properties, cast in matrix format, is shown to quantify transferability and molecular similarity meaningfully. Properties such as “interacting quantum atoms (IQA)” energies which are expressible into an interaction matrix of two body terms (and diagonal one body “self” terms, as IQA energies) can be used in the same manner. The proposed QSAR-type studies based on similarity distances derived from such matrix representatives of molecular structure necessitate extensive investigation before their utility is unequivocally established. © 2014 The Author and the Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

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From Atoms in Amino Acids to the Genetic Code and Protein Stability, and Backwards

Cited by 5 publications

References 94 publications

Electron-Density Descriptors as Predictors in Quantitative Structure–Activity/Property Relationships and Drug Design

Electron-Density Descriptors as Predictors in Quantitative Structure–Activity/Property Relationships and Drug Design

Probing Electron Dynamics with the Laplacian of the Momentum Density

Modeling biophysical and biological properties from the characteristics of the molecular electron density, electron localization and delocalization matrices, and the electrostatic potential

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