Heuristic molecular lipophilicity potential (HMLP): A 2D-QSAR study to LADH of molecular family pyrazole and derivatives

The quantum chemical and structure-based technique heuristic molecular lipophilicity potential (HMLP) is used in the liver alcohol dehydrogenase (LADH) study of molecular family pyrazole and derivatives. The molecular lipophilic index LM, molecular hydrophilic index HM, lipophilic indices lss, and hydrophilic indices hss of the substitutes (fragments), and atomic lipophilicity indices las are constructed and used in QSAR study. The HMLP indices are correlated with bioactivities of 18 pyrazole derivatives according to the 2D QSAR procedure. The multiple linear regression equation between the bioactivities of pyrazole derivatives and HMLP indices are built using partial least square (PLS) with the optimal statistical quantity (r=0.987, s=0.479, F=47.19). The inhibition mechanism of LADH of the pyrazole derivatives is explained according to the physical meaning of HMLP indices. During the HMLP calculations for the 2D QSAR, the only input parameters are the atomic van der Waals radius without the need to resort to any empirical parameters. Accordingly, HMLP can provide a rigorous theoretical approach with a crystal clear physical meaning for the 2D QSAR.

Application of promolecular ASA densities to graphical representation of density functions of macromolecular systems

In this article we report the application of the Promolecular Atomic Shell Approximation (Promolecular ASA) to the graphical representation of the density function (DF) of large macromolecular systems. Promolecular ASA DF, constructed from previously computed and fitted atomic densities, provides a fast and practical representation of Molecular IsoDensity Contours (MIDCOs). These representations can be extended to macromolecular systems composed by > 1000 atoms easily and with low computational costs, allowing the visualization of protein DF. The method is at first presented with a small molecule (2,4,6-trinitrophenol), comparing the resulting ASA MIDCOs with direct ab initio contours. For macromolecular tests the Promolecular ASA densities are also applied to the generation of macromolecular density surfaces of two proteins: myoglobin (2541 atoms) and gene V protein (1362 atoms).

Molecular shape analysis of a Maillard reaction intermediate

The Maillard (browning) reaction involving the polycondensation of sugars and amino acids is believed to be an important abiotic pathway for humic substance formation in nature. However, a major drawback is that the Maillard reaction is extremely slow at temperatures encountered under normal environmental conditions. In order to elucidate some details of this process molecular shape analysis was applied to investigate the initial reaction between D-glucose and glycine to form the Amadori compound fructosylglycine which is an intermediate product in the Maillard reaction. The structure of the Amadori compound was optimized at a quantum mechanical level and its ground state electron energy calculated. Molecular Iso-Density Contours (MIDCO's), electron density contour surfaces of constant electron density, were constructed for D-glucose, glycine and fructosylglycine in order to study the steric conditions for the reaction. The calculations indicate that the Amadori compound and water on one hand and the separate entities D-glucose and glycine on the other hand are very similar to each other in terms of their ground state energy. This agrees with the experimental observation that the reaction between D-glucose and glycine to form the Amadori compound is slow.

Distributions and averages of molecular conformations

A computational technique is proposed for the study of electron density variations within a distribution of molecular conformations. These variations are defined in terms of the deviations of individual electron densities from the average density associated with the average of conformations within a conformational range of a molecule.

Fractional simplex designs for interaction screening in complex mixtures

In mixture experiments, one may be interested in estimating not only main effects but also some interactions. Main effects and significant interactions in a mixture may be estimated through appropriate mixture experiments, such as simplex-centroid designs. However, for mixtures with a large number of factors, the run size for these designs becomes impractically large. A subset of a full simplex-centroid design may be used, but the problem remains regarding which factor-level settings should be selected. In this paper, we propose a solution that considers design points with either one or p individual nonzero factor-level settings. These fractional simplex designs provide a means of screening for interactions and of investigating the behavior of many-component mixtures as a whole while greatly reducing the run size compared with full simplex-centroid designs. The means of construction of the design arrays is described, and designs for < or = 31 factors are presented. Some of the proposed methodology is illustrated using generated data.

Holographic electron density shape theorem and its role in drug design and toxicological risk assessment

Each complete, boundaryless molecular electron density is fully determined by any nonzero volume piece of the electron density cloud. This inherent feature of molecules, called the "holographic" property of molecular electron densities, provides a strong foundation for the local, quantum chemical shape analysis of various functional groups, pharmacophores, and other local molecular moieties. A proof is presented for the relevant molecular shape theorem, the "holographic electron density shape theorem", and the role of this theorem in quantum chemical, quantitative shape-activity relations (QShAR) is discussed. The quantum chemical methods of molecular shape analysis can be extended to ab initio quality electron densities of macromolecules, such as proteins, as well as to local molecular moieties, such as functional groups or pharmacophores, based on the transferability and additivity of local, fuzzy density fragments and the associated local density matrixes within the framework of the ADMA (Adjustable Density Matrix Assembler) approach. In addition to new results on chemical bonding and the development of macromolecular force methods, the new methodologies are also applicable to QShAR studies in computer-aided drug discovery and in toxicological risk assessment.

Heuristic lipophilicity potential for computer-aided rational drug design: optimizations of screening functions and parameters

In this research we test and compare three possible atom-based screening functions used in the heuristic molecular lipophilicity potential (HMLP). Screening function 1 is a power distance-dependent function, bi/[formula: see text] Ri-r [formula: see text] gamma, screening function 2 is an exponential distance-dependent function, bi exp(-[formula: see text] Ri-r [formula: see text]/d0), and screening function 3 is a weighted distance-dependent function, sign(bi) exp[-xi [formula: see text] Ri-r [formula: see text]/magnitude of bi)]. For every screening function, the parameters (gamma, d0, and xi) are optimized using 41 common organic molecules of 4 types of compounds: aliphatic alcohols, aliphatic carboxylic acids, aliphatic amines, and aliphatic alkanes. The results of calculations show that screening function 3 cannot give chemically reasonable results, however, both the power screening function and the exponential screening function give chemically satisfactory results. There are two notable differences between screening functions 1 and 2. First, the exponential screening function has larger values in the short distance than the power screening function, therefore more influence from the nearest neighbors is involved using screening function 2 than screening function 1. Second, the power screening function has larger values in the long distance than the exponential screening function, therefore screening function 1 is effected by atoms at long distance more than screening function 2. For screening function 1, the suitable range of parameter gamma is 1.0 < gamma < 3.0, gamma = 2.3 is recommended, and gamma = 2.0 is the nearest integral value. For screening function 2, the suitable range of parameter d0 is 1.5 < d0 < 3.0, and d0 = 2.0 is recommended. HMLP developed in this research provides a potential tool for computer-aided three-dimensional drug design.

Heuristic lipophilicity potential for computer-aided rational drug design

In this contribution we suggest a heuristic molecular lipophilicity potential (HMLP), which is a structure-based technique requiring no empirical indices of atomic lipophilicity. The input data used in this approach are molecular geometries and molecular surfaces. The HMLP is a modified electrostatic potential, combined with the averaged influences from the molecular environment. Quantum mechanics is used to calculate the electron density function rho(r) and the electrostatic potential V(r), and from this information a lipophilicity potential L(r) is generated. The HMLP is a unified lipophilicity and hydrophilicity potential. The interactions of dipole and multipole moments, hydrogen bonds, and charged atoms in a molecule are included in the hydrophilic interactions in this model. The HMLP is used to study hydrogen bonds and water-octanol partition coefficients in several examples. The calculated results show that the HMLP gives qualitatively and quantitatively correct, as well as chemically reasonable, results in cases where comparisons are available. These comparisons indicate that the HMLP has advantages over the empirical lipophilicity potential in many aspects. The HMLP is a three-dimensional and easily visualizable representation of molecular lipophilicity, suggested as a potential tool in computer-aided three-dimensional drug design.

Implementing knot-theoretical characterization methods to analyze the backbone structure of proteins: application to CTF L7/L12 and carboxypeptidase A inhibitor proteins

In this work we apply a recently developed method for characterizing the shape of the tertiary structure of proteins. The approach is based on a combination of graph- and knot-theoretical characterizations of Cartesian projections of the space curve describing the protein backbone. The proposed technique reduces the essential shape features to a topologically based code formed by a sequence of knot symbols and polynomials. These polynomials are topological invariants that describe the overcrossing and knotting patterns of curves derived from the molecular space curve. These descriptors are algorithmically computed. The procedure is applied to describe the structure of the carboxy terminal fragment of the L7/L12 chloroplast ribosomal protein (CTF L7/L12) and the potato carboxypeptidase A inhibitor protein (PCI), which has a set of three disulfide bridges. In the former case, we describe the protein's shape features in terms of its alpha-helices, and a backbone simplified by considering helices without internal structure. An extension of the methodology to describe disulfide bridges is discussed and applied to PCI. Changes in the knot-theoretical characterization due to possible uncertainties in the resolution of the X-ray structure, as well as the inclusion of low-frequency motions of the backbone, are also discussed.

Charge densities of atoms of conjugated styryl ketones having activity against L1210 leukemia cells

Electron density calculations were undertaken on several atoms in a series of 3-substituted-4-phenyl-3-buten-2-ones in order to gain insight into the molecular features which affect charge densities. The results indicate that substituents at position 3 alter the electron densities of the olefinic group but have little effect on the acetyl function. The compounds were tested against L1210 cells in vitro, and the results suggest that electronic--but not steric--factors are important in affecting cytotoxicity. The most active compound was 3-phenylmethylene-2,4-pentanedione (1c) with an ED50 value of 1.06 x 10(-8) M.

A method for the characterization of foldings in protein ribbon models

The ribbon model of chain macromolecules is a useful tool for analyzing some of the large-scale shape features of these complex systems. Up to now, the ribbon model has been used mostly to produce graphical displays, which are usually analyzed by visual inspection. In this work we suggest a computational method for characterizing automatically, in a concise and algebraic fashion, some of the important shape features of these ribbon models. The procedure is based on a graph-theoretical and knot-theoretical characterization of three well-defined projections of a space curve associated with the ribbon. The labeled graphs can be characterized by the handedness of the crossovers in the ribbon that are the vertices of the graph. The method can be used to provide a fully algebraic representation of the changes occurring when a molecule, such as a protein, undergoes conformational rearrangements (folding), as well as to provide a shape comparison for a pair of related molecular ribbons. This algebraic representation is well suited for easy storage, retrieval, and computer manipulation of the information on the ribbon's shape. Illustrative examples of the method are provided.

Ab initio calculations on tetramethoxymethane

Minimal basis set ab initio SCF-MO calculations were performed on the 21-atom system of tetramethoxymethane (tetramethyl orthocarbonate). The geometric configuration of this model was optimized in two conformations, one having quasi-S4 symmetry and the other D2d symmetry. The S4 conformation was found to be 8 kJ mol−1 lower in energy than the D2d conformation, at the STO-3G level. The calculated energy difference is consistent with the recently measured geometric configuration of crystalline tetrabenzyl orthocarbonate. The calculated values of the bond lengths and angles were compared to the results of an electron diffraction study of the methyl species, and agree well with experiment. The theoretical electric dipole moment was calculated to be 0.01 D.

Abinitio SCF MO calculations on the reactions of OH radical with pyridine and pyridinium ion

Relative energies of various products formed in the reaction of pyridine and pyridinium ion with the hydroxyl radical are calculated using non-empirical SCF MO techniques. The favourable electron delocalization in the meta-products, rather than the electrophilic character of the OH radical is the determining factor of relative stabilities. Calculated energy barriers along approximate reaction paths correlate with the available experimental information.

Abinitio SCF-MO calculations of features of the lowest triplet state potential surfaces of several tetraatomic carbonyl compounds

Non-empirical SCF-MO calculations have been carried out for a series of tetraatomic carbonyl compounds. Portions of the ground singlet and first triplet state potential energy surfaces, in particular those along the out-of-plane bending coordinates, have been determined. Estimates of the first triplet state out-of-plane vibrational frequencies have been calculated.

Rydberg and valence-shell transitions in the quartz ultraviolet spectra of aliphatic thiones

The electronic absorption spectra of 3,3-dimethylbutane-2-thione and 3-methylbutane-2-thione in the gas phase have been measured and the observed transitions assigned with the aid of abinitio and semi-empirical calculations. In the quartz ultraviolet region four transitions are observed. A strong, broad, structureless band is assigned to the π → π* transition and three weaker, narrower bands are assigned to Rydberg n → 4s, n → 4py and n → 4pz transitions on sulfur.

Experimental and theoretical investigation of the unusual substituent effect of the vinyl group

σ+ Substituent constants for the ortho- and para-vinyl group have been determined by the application of the linear free-energy relationship to the nitration of the β-substituted styrene derivatives.Energy changes (relative to benzene system) for the proton and hydride ion transfer to individual positions in the styrene molecule have been calculated. Both approaches indicate that the vinyl group is capable of stabilizing both positively and negatively charged transition states. The interactions of the vinyl group with other substituents in the phenyl ring are also determined. Again, stabilizing effects with respect to both π-donor and π-acceptor substituents have been demonstrated for the vinyl group.

A theoretical study on the stereochemistry and protonation of −:CH2—NO2

The molecular conformation of −:CH2NO2 is found to be planar with an extremely shallow potential curve to pyramidal inversion. This suggests that suitable substituents could conceivably perturb the System into a pyramidal configuration corresponding to double minimum on the potential surface and that a chiral carbanion might therefore exist. Rotating the NO2 group out of planarity by 90° raises the barrier to inversion at carbon by an appreciable amount.A Mulliken population analysis gives a charge distribution in which a substantial portion of the negative charge has shifted from carbon to oxygen; this is consistent with the well-known tendency of nitronate ions to undergo simultaneous competitive protonation on carbon and oxygen.

A Relationship between the Sizes and Energies of Atomic Orbitals

An approximate relationship of the form[Formula: see text]where [Formula: see text] is the mean potential acting upon and V the mean volume of an electron in a closed shell of an atom has previously been proposed. This concept of a simple relationship between the sizes and energies of atomic orbitals which is predicted by simple quantum mechanical arguments has been further examined in this present work. The potential energy for a series of two electron atoms and ions has been replaced by the total electronic energy as these two quantities are simply connected by the virial theorem. For polyelectronic atoms, a quantity per electron pair which sums to the total electronic energy has been used. The volume of the ith atomic orbital[Formula: see text]has been calculated from its size as previously defined in terms of the spherical quadratic operator evaluated at the orbital centroid of charge. A relationship of the above form between the sizes and energies of atomic orbitals holds well for core orbitals but gradually deteriorates on going from the innermost (core) to outermost (valence) shell.