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The value of the Mo\ller–Plesset third order calculations is examined. An efficient method for the evaluation of the gradient of the MP3 energy is reported, and it has been programmed for both restricted and unrestricted Hartree–Fock wave functions. Large basis set calculations (TZ2P or better) are reported for the optimization of geometries and the determination of harmonic frequencies (which are obtained by finite differences of analytic gradients). The molecules selected are NH2, PH2, AsH2, H2O, NH3, H2CO, HCN, and C2H2. For the closed shell systems, the RMP3 predictions for bond lengths are inferior (approx. 0.006 Å) to RMP2 predictions (approx. 0.003 Å) for single bonds, and for multiple bonds the RMP3 bond lengths are too short by approximately the same amount (approx. 0.01 Å) that RMP2 are too long. For the open shell systems, the UMP3 geometrical parameters show only a marginal improvement over UMP2, except for PH2 where the bond length error is reduced to 0.003 Å. The results for harmonic frequencies show a similar comparison between MP2 and MP3. On the basis of this experience, it appears that large scale calculations at the MP3 level are not recommended; MP2 calculations with a large basis set are much cheaper and provide results with a similar, if not superior, accuracy. [ABSTRACT FROM AUTHOR]

The present study aims to characterize the electronically low-lying doublet states of the SNS molecule in detail. From an analysis of the eigenvalues and eigenvectors of the molecular orbital (MO) Hessian at the self-consistent-field (SCF) level, the corresponding rotations amongst the high-lying occupied and low-lying unoccupied molecular orbitals highlight nine low-lying doublet states worthy of study. Three bent (2A1, 2B2, and 2A2), three ring (2B1, 2A2, and 2A1), and three linear (2Πu and two 2Πg) structural isomers with doublet electronic states have been investigated at the SCF, configuration interaction with single and double excitations (CISD), and complete active space (CAS) SCF levels of theory with five different basis sets, double zeta (DZ) through triple zeta plus double polarization (TZ+2P). At the SCF level of theory, the stability of the wave functions and the energetics of the above mentioned doublet states are discussed in terms of the molecular orbital (MO) Hessian. The MO Hessian is often shown to properly predict the energetic ordering of the different electronic states. [ABSTRACT FROM AUTHOR]

The importance of the consideration of water molecules in the structural interpretation of ligand-derived pharmacophore models is explored. We compare and combine results from recently introduced methods for bound-water molecule identification in protein binding sites and ligand-superposition-based pharmacophore derivation, for the interpretation of ligand-derived pharmacophore models. In the analysis of thymidine kinase (HSV-1) and poly (ADP-ribose) polymerase (PARP), the concurrent application of both methods leads to an agreement in the prediction of tightly bound water molecules as key pharmacophoric points in the binding site of these proteins. This agreement has implications for approaching binding site analysis and consensus drug design, as it highlights how pharmacophore-based models of binding sites can include interaction features not only with protein groups but also with bound water molecules. [ABSTRACT FROM AUTHOR]