Classical and quantum mechanical calculations of conformational probability density distributions. Two-rotor molecules

In order to study the dynamical structure of a two-rotor molecule, such as acetone, as a function of temperature, conformational probability density distributions are computed by using three different approaches: the so-called current approach, the classical approach, and the quantum mechanical oscillator approach. It is found that the three procedures yield comparable results, at least at normal temperature (25°C), although the current and, especially, the classical approaches give rise to too sharp distributions when compared with the quantum mechanical results. Owing to its simplicity, the current approach may be used advantageously, and it is easily extendible to many-rotor systems. Finally, it is verified that deuteration does not affect appreciably the conformation.     

Modifications of virtual orbitals in the limited CI calculations for electron-rich molecules

The efficiency of modified virtual orbitals (MVO) of ionic type and of approximate orthogonalized natural orbitals (ONO) in the CI-SD calculations was studied for O₃ and SO₂ molecules and compared with the commonly used canonical virtual orbitals (CVOs). The systems studied represent a class of electron-rich molecules, in which the number of valence electron pairs exceeds substantially the number of formal chemical bonds. We found that the modified orbitals of the types studied appear to be less effective for these systems than in the similar calculations for the AH_n type molecules. Physical reasons for this difference were discussed. The evolution of spatial properties of virtual orbitals within the modification process was analyzed. © 1996 John Wiley & Sons, Inc.     

Similarity search profiling reveals effects of fingerprint scaling in virtual screening

Fingerprint scaling is a method to increase the performance of similarity search calculations. It is based on the detection of bit patterns in keyed fingerprints that are signatures of specific compound classes. Application of scaling factors to consensus bits that are mostly set on emphasizes signature bit patterns during similarity searching and has been shown to improve search results for different fingerprints. Similarity search profiling has recently been introduced as a method to analyze similarity search calculations. Profiles separately monitor correctly identified hits and other detected database compounds as a function of similarity threshold values and make it possible to estimate whether virtual screening calculations can be successful or to evaluate why they fail. This similarity search profile technique has been applied here to study fingerprint scaling in detail and better understand effects that are responsible for its performance. In particular, we have focused on the qualitative and quantitative analysis of similarity search profiles under scaling conditions. Therefore, we have carried out systematic similarity search calculations for 23 biological activity classes under scaling conditions over a wide range of scaling factors in a compound database containing approximately 1.3 million molecules and monitored these calculations in similarity search profiles. Analysis of these profiles confirmed increases in hit rates as a consequence of scaling and revealed that scaling influences similarity search calculations in different ways. Based on scaled similarity search profiles, compound sets could be divided into different categories. In a number of cases, increases in search performance under scaling conditions were due to a more significant relative increase in correctly identified hits than detected false-positives. This was also consistent with the finding that preferred similarity threshold values increased due to fingerprint scaling, which was well illustrated by similarity search profiling.     

Flexsim-X: a method for the detection of molecules with similar biological activity

We describe the development of the method Flexsim-X, which can be used to detect molecules with similar biological activity. This procedure is based on comparing virtual affinity fingerprints made up from docking scores of the molecules with respect to a reference set of binding sites. Using a test data set consisting of ligands from five different activity classes and randomly chosen compounds, the reference panel of binding sites was optimized in terms of size and composition. Systematic approaches as well as genetic algorithm based (GA) optimization procedures have been evaluated. Additionally, the effectiveness of the method is illustrated.     

Using free energy of binding calculations to improve the accuracy of virtual screening predictions

Virtual screening of small molecule databases against macromolecular targets was used to identify binding ligands and predict their lowest energy bound conformation (i.e., pose). AutoDock4-generated poses were rescored using mean-field pathway decoupling free energy of binding calculations and evaluated if these calculations improved virtual screening discrimination between bound and nonbound ligands. Two small molecule databases were used to evaluate the effectiveness of the rescoring algorithm in correctly identifying binders of L99A T4 lysozyme. Self-dock calculations of a database containing compounds with known binding free energies and cocrystal structures largely reproduced experimental measurements, although the mean difference between calculated and experimental binding free energies increased as the predicted bound poses diverged from the experimental poses. In addition, free energy rescoring was more accurate than AutoDock4 scores in discriminating between known binders and nonbinders, suggesting free energy rescoring could be a useful approach to reduce false positive predictions in virtual screening experiments.     

Similarity search profiles as a diagnostic tool for the analysis of virtual screening calculations

An analysis method termed similarity search profiling has been developed to evaluate fingerprint-based virtual screening calculations. The analysis is based on systematic similarity search calculations using multiple template compounds over the entire value range of a similarity coefficient. In graphical representations, numbers of correctly identified hits and other detected database compounds are separately monitored. The resulting profiles make it possible to determine whether a virtual screening trial can in principle succeed for a given compound class, search tool, similarity metric, and selection criterion. As a test case, we have analyzed virtual screening calculations using a recently designed fingerprint on 23 different biological activity classes in a compound source database containing approximately 1.3 million molecules. Based on our predefined selection criteria, we found that virtual screening analysis was successful for 19 of 23 compound classes. Profile analysis also makes it possible to determine compound class-specific similarity threshold values for similarity searching.     

Pharmacophore modelling,atom-based 3D-QSAR generation and virtual screening of molecules projected for mPGES-1 inhibitory activity

COX-2 inhibitors exhibit anticancer effects in various cancer models but due to the adverse side effects associated with these inhibitors, targeting molecules downstream of COX-2 (such as mPGES-1) has been suggested. Even after calls for mPGES-1 inhibitor design, to date there are only a few published inhibitors targeting the enzyme and displaying anticancer activity. In the present study, we have deployed both ligand and structure-based drug design approaches to hunt novel drug-like candidates as mPGES-1 inhibitors. Fifty-four compounds with tested mPGES-1 inhibitory value were used to develop a model with four pharmacophoric features. 3D-QSAR studies were undertaken to check the robustness of the model. Statistical parameters such as r² = 0.9924, q² = 0.5761 and F test = 1139.7 indicated significant predictive ability of the proposed model. Our QSAR model exhibits sites where a hydrogen bond donor, hydrophobic group and the aromatic ring can be substituted so as to enhance the efficacy of the inhibitor. Furthermore, we used our validated pharmacophore model as a three-dimensional query to screen the FDA-approved Lopac database. Finally, five compounds were selected as potent mPGES-1 inhibitors on the basis of their docking energy and pharmacokinetic properties such as ADME and Lipinski rule of five.     

Ground states of molecules. 56. MNDO calculations for molecules containing sulfur

MNDO has been extended to sulfur, but without inclusion of 3d AO s. Calculations are reported for heats of formation, geometries, dipole moments, and ionization energies of a variety of sulfur-containing molecules. The average discrepancy between calculated and observed heats of formation is larger than for compounds of other elements, a difference probably due, at least partly, to the lower accuracy of the thermochemical data for sulfur compounds. The calculated dipole moments agree well with experiment as do the calculated ionization energies, except for those corresponding to ionization from sulfur “lone-pair” orbitals which are too high by ca. 1 eV, probably as a result of the neglect in NDDO of interactions between inner and valence shell orbitals. As in the case of other third-period elements, the calculated heats of formation of compounds of sulfur in its higher valence states (S^IV, S^VI) were too positive by large amounts, due presumably to the neglect of 3d AO s.     

Ground states of molecules. 53.MNDO calculations for molecules containing chlorine

MNDO calculations of heats of formation, dipole moments, ionization potentials, and structures are reported for a wide range of compounds containing chlorine in its characteristic valence state (Cl^I) and one or more of the elements H, B, Be, C, N, O, and F. The calculated errors in the heats of formation and the dipole moments are not significantly greater than those previously reported for compounds containing no chlorine. First vertical ionization potentials were on average 0.95 eV too high. The ordering of higher cationic states was found to be correct, even for species such as Cl₂O, Cl₂, and HOCl, where ab initio–Koopmans' theorem calculations predict the incorrect ordering. The calculated energies and geometries of compounds such as CIF₃ are qualitatively incorrect, probably because of the lack of 3d atomic orbitals in the orbital basis set.     

Thermodynamic calculations for molecules with asymmetric internal rotors. II. Application to the 1,2-dihaloethanes

The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables.     

Multireference correlation in long molecules with the quadratic scaling density matrix renormalization group

We have devised a local ab initio density matrix renormalization group algorithm to describe multireference correlations in large systems. For long molecules that are extended in one of their spatial dimensions, we can obtain an exact characterization of correlation, in the given basis, with a cost that scales only quadratically with the size of the system. The reduced scaling is achieved solely through integral screening and without the construction of correlation domains. We demonstrate the scaling, convergence, and robustness of the algorithm in polyenes and hydrogen chains. We converge to exact correlation energies (in the sense of full configuration interaction, with 1-10 microE(h) precision) in all cases and correlate up to 100 electrons in 100 active orbitals. We further use our algorithm to obtain exact energies for the metal-insulator transition in hydrogen chains and compare and contrast our results with those from conventional quantum chemical methods.     

Novel inhibitors of trihydroxynaphthalene reductase with antifungal activity identified by ligand-based and structure-based virtual screening

Curvularia lunata is a dark pigmented fungus that is the causative agent of several diseases in plants and in both immunodeficient and immunocompetent patients. 1,8-Dihydroxynaphthalene-melanin is found in the cell wall of C. lunata and is believed to be the important virulence factor of dematiaceous fungi. Trihydroxynaphthalene reductase is an enzyme of the 1,8-dihydroxynaphthalene-melanin biosynthetic pathway, and it thus represents an emerging target for the development of novel fungicides and antimycotics. In the present study, we describe novel inhibitors of trihydroxynaphthalene reductase from C. lunata. These inhibitors were identified by ligand-based three-dimensional similarity searching and docking to a homology-built model and by subsequent biochemical and antifungal evaluation. Discovery of competitive inhibitors with K(i) values in low micromolar and even nanomolar concentration range proves the aplicability of homology-built model of 3HNR for hit finding by virtual screening methods.     

CNDO calculations of diamagnetic shielding in molecules

An approximate procedure for the calculation of diamagnetic shielding in molecules is presented. The method proposed is based on the ‘complete neglect of differential overlap’ (CNDO) molecular wave functions and is formulated according to the zero differential overlap (ZDO) approximation. The results obtained with several CNDO-type wave functions for diatomic and polyatomic molecules are in very good agreement with non-empirical SCF calculations. The ¹⁴N diamagnetic shielding constants in several molecules were computed and some approximations usually adopted in the interpretation of ¹⁴N chemical shifts are critically discussed. It was shown that in some cases the observed ¹⁴N chemical shifts cannot be interpreted solely in terms of the paramagnetic contribution to the shielding constant.