A new approach is proposed to more accurately estimate the energies of H-bond interactions in thr... more A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system.
Journal of Chemical Information and Modeling, 2001
Partial atomic charges are significant descriptors in predicting the water solubilities of crysta... more Partial atomic charges are significant descriptors in predicting the water solubilities of crystalline organic compounds from their chemical structures. Lipophilicity remains the predominant factor. It was also found that quantitative estimates of hydrogen bond strengths (hydrogen bond factors) play important roles. These descriptors can be easily interpreted to guide chemists to the synthesis of compounds with increased or decreased water solubility. This work is based on a set of 22 compounds the aqueous solubilities of which were determined by a new potentiometric method, pSOL, and were confirmed, in part, by the traditional shake-flask method. A new software package, HYBOTPLUS, furnished the partial atomic charges and hydrogen bond factors.
QSPR analyses of a data set containing experimental partition coefficients in the three systems o... more QSPR analyses of a data set containing experimental partition coefficients in the three systems octanol-water, water-gas, and octanol-gas for 98 chemicals have shown that it is possible to calculate any partition coefficient in the system 'gas phase/octanol/water' by three different approaches: (1) from experimental partition coefficients obtained in the corresponding two other subsystems. However, in many cases these data may not be available. Therefore, a solution may be approached (2), a traditional QSPR analysis based on e.g. HYBOT descriptors (hydrogen bond acceptor and donor factors, SigmaCa and SigmaCd, together with polarisability alpha, a steric bulk effect descriptor) and supplemented with substructural indicator variables. (3) A very promising approach which is a combination of the similarity concept and QSPR based on HYBOT descriptors. In this approach observed partition coefficients of structurally nearest neighbours of a compound-of-interest are used. In addition, contributions arising from differences in alpha, SigmaCa, and SigmaCd values between the compound-of-interest and its nearest neighbour(s), respectively, are considered. In this investigation highly significant relationships were obtained by approaches (1) and (3) for the octanol/gas phase partition coefficient (log Log).
Stability constants of potassium, sodium, and benzylammonium salts with 18C5 are determined in wa... more Stability constants of potassium, sodium, and benzylammonium salts with 18C5 are determined in water, methanol, and acetonitrile by potentiometric titrations. The corresponding free energies DeltaG agree within the error with those obtained from calorimetric titrations. In comparison to 18C6 the DeltaG values are lower by 14 to 16 kJ/mol, with methanol or acetonitrile as solvent and K(+) or benzylammonium salts. Differences in the calorimetrically determined binding enthalpies DeltaH between 18C6 and 18C5 are usually even larger. In water, however, the DeltaG differences between the 18C5 and 18C6 complexes become almost negligible. The D(3)d-like conformation of such crown ethers can be evaluated for the first time by NOE methods using the less symmmetrical 18C5. The NMR data indicate also the absence of significant conformational changes upon complexation, in line with molecular mechanics calculations (CHARMm). These show that the low binding constants of K(+) with 18C5 are due to the expulsion of the cation due to one C-H bond pointing toward the cavity, leading to larger K(+).O distances. The CHARMm calculated gas phase energy difference between the K(+) crown complexes of 26 kJ/mol agrees approximately with experimental differences.
A new approach is proposed to more accurately estimate the energies of H-bond interactions in thr... more A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system.
Journal of Chemical Information and Modeling, 2001
Partial atomic charges are significant descriptors in predicting the water solubilities of crysta... more Partial atomic charges are significant descriptors in predicting the water solubilities of crystalline organic compounds from their chemical structures. Lipophilicity remains the predominant factor. It was also found that quantitative estimates of hydrogen bond strengths (hydrogen bond factors) play important roles. These descriptors can be easily interpreted to guide chemists to the synthesis of compounds with increased or decreased water solubility. This work is based on a set of 22 compounds the aqueous solubilities of which were determined by a new potentiometric method, pSOL, and were confirmed, in part, by the traditional shake-flask method. A new software package, HYBOTPLUS, furnished the partial atomic charges and hydrogen bond factors.
QSPR analyses of a data set containing experimental partition coefficients in the three systems o... more QSPR analyses of a data set containing experimental partition coefficients in the three systems octanol-water, water-gas, and octanol-gas for 98 chemicals have shown that it is possible to calculate any partition coefficient in the system 'gas phase/octanol/water' by three different approaches: (1) from experimental partition coefficients obtained in the corresponding two other subsystems. However, in many cases these data may not be available. Therefore, a solution may be approached (2), a traditional QSPR analysis based on e.g. HYBOT descriptors (hydrogen bond acceptor and donor factors, SigmaCa and SigmaCd, together with polarisability alpha, a steric bulk effect descriptor) and supplemented with substructural indicator variables. (3) A very promising approach which is a combination of the similarity concept and QSPR based on HYBOT descriptors. In this approach observed partition coefficients of structurally nearest neighbours of a compound-of-interest are used. In addition, contributions arising from differences in alpha, SigmaCa, and SigmaCd values between the compound-of-interest and its nearest neighbour(s), respectively, are considered. In this investigation highly significant relationships were obtained by approaches (1) and (3) for the octanol/gas phase partition coefficient (log Log).
Stability constants of potassium, sodium, and benzylammonium salts with 18C5 are determined in wa... more Stability constants of potassium, sodium, and benzylammonium salts with 18C5 are determined in water, methanol, and acetonitrile by potentiometric titrations. The corresponding free energies DeltaG agree within the error with those obtained from calorimetric titrations. In comparison to 18C6 the DeltaG values are lower by 14 to 16 kJ/mol, with methanol or acetonitrile as solvent and K(+) or benzylammonium salts. Differences in the calorimetrically determined binding enthalpies DeltaH between 18C6 and 18C5 are usually even larger. In water, however, the DeltaG differences between the 18C5 and 18C6 complexes become almost negligible. The D(3)d-like conformation of such crown ethers can be evaluated for the first time by NOE methods using the less symmmetrical 18C5. The NMR data indicate also the absence of significant conformational changes upon complexation, in line with molecular mechanics calculations (CHARMm). These show that the low binding constants of K(+) with 18C5 are due to the expulsion of the cation due to one C-H bond pointing toward the cavity, leading to larger K(+).O distances. The CHARMm calculated gas phase energy difference between the K(+) crown complexes of 26 kJ/mol agrees approximately with experimental differences.
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Papers by Oleg Raevsky