Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution

Cabani, Sergio; Gianni, Paolo; Mollica, Vincenzo; Lepori, Luciano

doi:10.1007/bf00646936

Cited by 960 publications

(806 citation statements)

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“…In the case of the series of 1,3-dimethyl-5-alkyluracils (6,17,19,20) [5,6,19], 1,6-dimethyl-3-alkyluracils (7,(24)(25)(26) [8,11] and 1,3-dimethyl-6-alkyluracils (10,21-23) [5,11] erratic changes were observed to occur in the values of the enthalpy of hydration. The higher values of the enthalpy increment correspond to the odd number of CH 3 groups added while the lower values correspond to those with the even n CH 2 number.…”

Section: Discussion and Resultsmentioning

confidence: 98%

Aqueous solutions of pyrimidine nucleic acid bases. Solute-solvent interactions

Zielenkiewicz¹

1999

Pure and App Chemis

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Abstract:The data previously reported on the enthalpy of hydration, partial molar volumes and heat capacities of alkylated pyrimidine nucleic acid bases, e.g. uracil, thymine and cytosine, were correlated with the following structural parameters: molecular volume, volume of solvation shell, accessible molecular surface area and its atomic partition as well as and electrostatic potential charge. The simple additivity scheme of group contributions was also taken into consideration. The correlations obtained are presented and discussed. The results of the investigations clearly show that polar interactions are decisive in structuring the water around the solute molecules.

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Section: Discussion and Resultsmentioning

confidence: 98%

Aqueous solutions of pyrimidine nucleic acid bases. Solute-solvent interactions

Zielenkiewicz¹

1999

Pure and App Chemis

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“…Transfer energetics of model compounds are generally interpreted in terms of groups additivity in which the contribution of a functional group is assumed to be independent of neighboring functional groups (Nichols et al, 1976;Cabani et al, 1981; Makhatadze&Privalov, 1990; Spolar et al ., 1992). Group additivity has been applied previously to analyzing cyclic dipeptide dissolution energetics ).…”

Section: Structural Energeticsmentioning

confidence: 99%

Energetics of hydrogen bonding in proteins: A model compound study

1996

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Differences in the energetics of amide-amide and amide-hydroxyl hydrogen bonds in proteins have been explored from the effect of hydroxyl groups on the structure and dissolution energetics of a series of crystalline cyclic dipeptides. The calorimetrically determined energetics are interpreted in light of the crystal structures of the studied compounds. Our results indicate that the amide-amide and amide-hydroxyl hydrogen bonds both provide considerable enthalpic stability, but that the amide-amide hydrogen bond is about twice that of the amide-hydroxyl. Additionally, the interaction of the hydroxyl group with water is seen most readily in its contributions to entropy and heat capacity changes. Surprisingly, the hydroxyl group shows weakly hydrophobic behavior in terms of these contributions. These results can be used to understand the effects of mutations on the stability of globular proteins.Keywords: calorimetry; enthalpy; heat capacity; hydrogen bonding; hydroxyl; model compounds; solvation Hydrogen bonds are ubiquitous in biological molecules and their contribution to the stability of these structures is of fundamental importance. Numerous studies have been performed in an attempt to quantitate the energetics of hydrogen bonding in proteins and other biological macromolecules. In spite of the considerable effort that has gone into such studies, there remains disagreement in the current literature regarding not only the magnitude, but even the sign of the contribution of hydrogen bonds to the thermodynamics, and especially the enthalpy, of proteins.In 1955, Schellman, analyzing the non-ideality of urea solutions, arrived at a value of -6.3 kJ mol" for the AH" of formation of an amide hydrogen bond (i.e., a hydrogen bond between NH and C=O groups from amide linkages) in aqueous solution (Schellman, 1955). However, a subsequent study by Klotz and Franzen (1962) looked at the dimerization of N-methyl-acetamide in aqueous solution and concluded that the AH" of formation of an amide hydrogen bond in water was zero. These studies indicated a AH" of hydrogen bond formation in water between -8 and -13 kJ mol", consistent with the earlier report of Schellman. Recent calorimetric studies on the unfolding of an alanine-based a-helix peptide also support a favorable AH" of amide hydrogen bond formation in water (Scholtz et al., 1991).Although there now is general agreement that the A H o of hydrogen bond formation in water can be favorable, it has been suggested recently that the unfavorable AH" of dehydrating polar groups upon transfer to the protein interior or into a proteinprotein interface might result in an overall unfavorable A H o for the burial of hydrogen bonded polar groups (Yang et al., 1992; Makhatadze & Privalov, 1993). These conclusions are based on experimental values for the AH" of transferring model compounds from vapor into water or on theoretical calculations of this process. The precision of such approaches is questionable because they generally require taking the difference between large...

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“…The mapping function g is simply the product of the row vector of the frequencies and the column vector of the group contributions. GC methods have been proposed by Hine and Mookerjee, 30 Meylan and Howard, 31 Cabani and co-workers, 32 and Wendoloski and co-workers. 33 A further class of GC methods, based on solvent accessible surface areas (SASAs), has been proposed by Eisenberg and Malachlan 34 and improved by Hou et al 35 In the molecular-structure-based methods, molecular descriptors such as topological indices, quantum-chemical descriptors, geometrical and electrostatic descriptors, and so forth are used to encode (function f) the molecules.…”

Section: Prediction Of the Solvation Free Energymentioning

confidence: 99%

Predicting Physical−Chemical Properties of Compounds from Molecular Structures by Recursive Neural Networks

Bernazzani

Duce

Micheli

et al. 2006

J. Chem. Inf. Model.

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In this paper, we report on the potential of a recently developed neural network for structures applied to the prediction of physical chemical properties of compounds. The proposed recursive neural network (RecNN) model is able to directly take as input a structured representation of the molecule and to model a direct and adaptive relationship between the molecular structure and target property. Therefore, it combines in a learning system the flexibility and general advantages of a neural network model with the representational power of a structured domain. As a result, a completely new approach to quantitative structure-activity relationship/ quantitative structure-property relationship (QSPR/QSAR) analysis is obtained. An original representation of the molecular structures has been developed accounting for both the occurrence of specific atoms/groups and the topological relationships among them. Gibbs free energy of solvation in water, ∆ solv G°, has been chosen as a benchmark for the model. The different approaches proposed in the literature for the prediction of this property have been reconsidered from a general perspective. The advantages of RecNN as a suitable tool for the automatization of fundamental parts of the QSPR/QSAR analysis have been highlighted. The RecNN model has been applied to the analysis of the ∆ solv G°in water of 138 monofunctional acyclic organic compounds and tested on an external data set of 33 compounds. As a result of the statistical analysis, we obtained, for the predictive accuracy estimated on the test set, correlation coefficient R ) 0.9985, standard deviation S ) 0.68 kJ mol -1 , and mean absolute error MAE ) 0.46 kJ mol -1 . The inherent ability of RecNN to abstract chemical knowledge through the adaptive learning process has been investigated by principal components analysis of the internal representations computed by the network. It has been found that the model recognizes the chemical compounds on the basis of a nontrivial combination of their chemical structure and target property.

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Group contributions to the thermodynamic properties of non-ionic organic solutes in dilute aqueous solution

Cited by 960 publications

References 20 publications

Aqueous solutions of pyrimidine nucleic acid bases. Solute-solvent interactions

Aqueous solutions of pyrimidine nucleic acid bases. Solute-solvent interactions

Energetics of hydrogen bonding in proteins: A model compound study

Predicting Physical−Chemical Properties of Compounds from Molecular Structures by Recursive Neural Networks

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