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When a drug interacts with its receptor, the nonpolar substituent of drug and receptor proteins attract each other because they have opposite magnitude with respect to each other. X-rays structure studies reflected that the S2/S2’ pocket in HIV-1 protease enzyme are essentially hydrophobic. The residues that make up these pockets are Val-32, Ile-47, Ile-50, and Ile-84 in each monomeric polypeptidic unit of the protease enzyme. Δπ_dr and ΔSASA_dr have been used to measure the extent of hydrophobic interaction between peptidic protease inhibitors and receptor proteins (binding site: valine‒isoleucine; and catalytic site: glycine‒aspartic acid‒threonine) on the HIV-1 protease enzyme. For measurement of hydrophobic interaction, the molecular modeling and geometry optimization of all the inhibitors and the receptor amino acids have been carried out with CAChe Pro software by opting semiempirical PM3 methods. Log P was calculated using the atom-typing scheme of Ghose and Crippen, while solvent accessible surface area by conductor likes screening model. π_d, π_r, SASA_Sd and SASA_Srwell describe the hydrophobicities of the substituents and play the effective role for site selectivity for interaction of the drug with the receptor. Comparative study of values of Δπ_dr and ΔSASA_dr show the order of hydrophobic interaction with respect to amino acids: Asp > Thr > Val > Ile and Thr > Val > Asp > Ile, respectively. Further, comparative study of the values of (ΣΔπ_dr)_binding-site, (ΣΔπ_dr)_{catalytic-site}, (ΣΔSASA_dr)_binding-site, (ΣΔSASA_dr)_{catalytic-site} shows that peptidic HIV-1-PRIs interact with binding site rather than catalytic site as binding site have lower value of ΣΔπ_dr and ΣΔSASA_dr. Among the binding site, Val has maximum interaction than Ile, as it has lower vale of Δπ_dr and ΔSASA_dr.

In this research work, we have applied “Lipinski’s RO5” for pharmacokinetics (PK) study and to predict the activity of peptidic HIV-1 protease inhibitors. Peptidic HIV-1-PRIs have been taken from literature with their observed biological activities (OBAs) in term of IC50. The logarithms of the inverse of IC50 have been used as biological end point o(log1/C) in the study. For calculation of physicochemical parameters, the molecular modeling and geometry optimization of all the derivatives have been carried out with CAChe Pro software using semiempirical PM3 method. Prediction of the biological activity of the inhibitors has shown that the best QSAR model is constructed from pharmacokinetic properties, molecular weight and hydrogen bond acceptor. This also proved that these properties play important role to describe the PKs of the drugs. On the basis of the derived models one can build up a theoretical basis to access the biological activity of the compounds of the same series.

Carboxylates and their antimony(III) complexes experimentally scanned earlier for anti-leishmanial activity (IC₅₀) against five leishmanial strains viz., <i>L. major, L. major (Pak),</i><i> </i><i>L. tropica, L. mex mex, </i>and<i> L. donovani</i>. These activities have been theoretically predicted by DFT method along with quantitative structure-activity relationship (QSAR) study. Molecular modeling and geometry optimization of the all the eight compounds have been performed on workspace program of CAChe Pro software of Fujitsu by opting B88-PW91 (Becke '88; Perdew &#x26; Wang '91) GGA (generalized-gradient approximation) energy functional with DZVP (double-zeta valence polarized ) basis set in DFT (Density Functional Theory). For QSAR, multiple linear regression (MLR) analysis has been performed on Project Leader Program associated with CAChe. The reliability of correlation between experimental activities and predicted activities are r²= 0.826, r²_CV= 0.426 (<i>L. major</i>); r²= 0.905, r²_CV= 0.507 (<i>L. major (Pak)</i>); r²= 0.980, r²_CV= 0.932 (<i>L. tropica</i>); r²= 0.781, r²_CV= 0.580 (<i>L. mex mex</i>) and r²= 0.634, r²_CV= 0.376 (<i>L. donovani</i>), and a comparison of the experimental values and the values obtained by theoretical calculations has been presented pictorially that shows close resemblance.

The present work describes the geometry and electronic structures of liquid crystals of azoxybenzene group and their reactivity with respect to molecular properties: total energy, ionization potential, electron affinity, HOMO energy, LUMO energy, electronegativity, hardness and dipole moment. Literature shows that mesomorphism depends particularly on the nature of terminal groups and their linkages with parent molecule. And thus, substitution of terminal groups can help to fine tune the liquid crystal behavior and also their applications. In this work the effect of four terminal groups of same and diverse nature has been studied. For the study, the molecular modeling and geometry optimization of the compounds have been performed on workspace program of CAChe Pro 5.04 software of Fujitsu using DFT method.

Polychlorinated biphenyls (PCBs) are important class of persist organic pollutants that were used as a component of paints especially in printings, as plastificator of plastics and insulating materials in transformers and capacitors, heat transfer fluids, additives in hydraulic fluids in vacuum and turbine pumps. There is always a need to establish reliable procedures for predicting the bioconcentration potential of chemicals from the knowledge of their molecular structure, or from readily measurable properties of the substance. Hence, correlation and prediction of biococentration factors (BCFs) based on λ<SUB>max</SUB> and vibration frequencies of various bonds viz υ(C-H) and υ(C=C) of biphenyl and its fifty-seven derivatives have been made. For the study, the molecular modeling and geometry optimization of the PCBs have been performed on workspace program of CAChe Pro 5.04 software of Fujitsu using DFT method. UV-visible spectra for each compound were created by electron transition between molecular orbitals as electromagnetic radiation in the visible and ultraviolet (UV-visible) region is absorbed by the molecule. The energies of excited electronic states were computed quantum mechanically. IR spectra of transitions for each compound were created by coordinated motions of the atoms as electromagnetic radiation in the infrared region is absorbed by the molecule. The force necessary to distort the molecule was computed quantum mechanically from its equilibrium geometry and thus frequency of vibrational transitions was predicted. Project Leader Program associated with CAChe has been used for multiple linear regression (MLR) analysis using above spectroscopic data as independent variables and BCFs of PCBs as dependent variables. The reliability of correlation and predicting ability of the MLR equations (models) are judged by R<SUP>2</SUP>, R<SUP>2</SUP><SUB>adj</SUB>, se, q<SUP>2</SUP><SUB>L10O</SUB> and F values. This study reflected clearly that UV and IR spectroscopic data can be used to predict BCFs of a large number of related compounds within limited time without any difficulty.