Hydrogen HYBOT

HYBOT-Plus (hydrogen bonding thermodynamics, calculation of local and molecular physicochemical descriptors) http //www.timtec.net/soJiware/hybot-plus.htm... 

HYBOT Hydrogen Bond Thermodynamics LCAP Long-chain arylpiperazine... 

Raevsky OA, Skvortsov VS (2002) 3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling. J Comput Aided Mol Des 16(1) 1-10... 

From 163 calculated H-bond donor and 195 calculated H-bond acceptor factors, one can get enthalpy and free energy values for 31785 reactions using Eqs. (3) and (4). Later, the number of H-bond factor values was significantly increased. A special program for calculating factor values was created and included in the HYBOT (Hydrogen Bond Thermodynamics) program [28, 29]. The current version, HYBOT-2006, has about 20000 values of H-bond acceptor factors and about 5000... 

Raevsky, 0. A. Hydrogen bond strength estimation by means of HYBOT. In Computer-Assisted Lead Finding and Optimization, Van de Waterbeemd, H., Testa, B., Folkers, G. (eds.), Wiley-VGH, Weinheim, 1997, pp. 357-378. 

Raevsky, 0. A., Grigor ev, V. Ju., Trepalin, S. V. HYBOT (Hydrogen Bond Thermodynamics) program package. Registration by Russian State Patent Agency N 990090 of 25 February 1999. 

Poorly absorbed compounds have been identified as those with a PSA > 140 A2, but considerably more scatter was found around the sigmoidal curve observed for a smaller set of compounds [78]. This is partly due to the fact that many compounds do not show only simple passive diffusion, but are also affected by active carriers, efflux mechanisms involving P-glycoprotein (P-gp) and other transporter proteins, as well as gut wall metabolism. A further refinement in the PSA approach is expected to come from taking into account the strength of the hydrogen bonds, which in principle already is the basis of the HYBOT approach described below. 

Raevsky, O., Hydrogen bond strength estimation by means of the HYBOT program package, in Computer-assisted lead finding and optimization, H. van de Waterbeemd, B. Testa and G. Folkers, eds, Verlag Helvetica Chimica Acta, Basel, 1997, 367-378. 

Raevsky and co-workers have collected a large database of thermodynamic data related to hydrogen bonding with which they have developed the HYBOT program... 

HYBOT will compute hydrogen bond donor (SCa) and acceptor (2Ca) factors that describe the donor and acceptor strengths, respectively, of a compound. Using these two parameters, the authors developed models with significant statistical quality (r2 = 0.91, q2 = 0.87) of intestinal absorption. 

The sum of hydrogen bonding donor and acceptor related E-state descriptors are well correlated with the corresponding HYBOT parameters, with r2-values of 0.8-0.95 [38]. This gives the E-state descriptors a link to experimental values, which is positive but not necessary for the purpose of generating useful models with good statistical quality for, in this case, intestinal absorption. 

The relationship between individual components appears to indicate that the first and second SaSA dimensions can be related to the first and third ALMOND dimensions, with an emphasis on the first component. The first SaSA component is dominated by size-related descriptors, e.g., the total number of heavy atoms, MW, CMR, and polarizability. These properties explain approximately 60% of the first ALMOND component, suggesting that large internode distances and high internode interaction energies dominate this component. The third ALMOND component has a weaker relationship (25%) to hydrophobicity descriptors such as CLOGP, ELogP, nonpolar surface area, and the number of nonpolar atoms [123]. Only the fourth ALMOND component appears to be related (under 25%) with hydrogen-bond-related, e.g., HYBOT descriptors, whereas the second, fifth, and sixth ALMOND... 

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