A novel approach to the analysis of substituent effects: quantitative description of ionization energies and gas basicity of amines

Partial physicochemical properties and relative stability of polyhydroxylated dibenzofurans: theoretical and experimental study

Polyhydroxylated dibenzofuran (PHODF) is an important degradation product of polychlorinated dibenzofuran (PCDF). Four types of hydrogen bonds (the one between a hydroxyl and the oxygen atom in the matrix, between hydroxyls at ortho positions, between the oxygen atom of hydroxyl at position 1 and the hydrogen atom of the matrix at position 9, and between hydroxyls at positions 1 and 9) exist in PHODFs. The energies of the hydrogen bonds were ascertained by comparing the two configurational isomers as approximately 8-11 kJ mol⁻¹, 16-21 kJ mol⁻¹, 5-8 kJ mol⁻¹ and 23-25 kJ mol⁻¹, respectively. An experiment was designed to verify the bond energies, and the entrance geometry on main paths was studied by AIM 2000 program. The most stable in each group of configurational isomers was ascertained on the basis of evaluating the effect of hydrogen bonds. Their thermodynamic properties (standard state entropy S°, standard enthalpy Δ(f)H° and standard Gibbs energy of formation Δ(f)G°) were calculated from the combination of density functional theory (DFT) at B3LYP/6-311G** level and isodesmic reactions. Octanol/water partition coefficients (log K(ow)) were calculated on line with molinspiration methodology based on group contributions. The number and position of hydroxyl substitution (N(PHOS)) can be a good indicator of these properties for all stable PHODF congeners. The configurations most likely to form are those with a hydrogen bond (Type IV). How intramolecular hydrogen bond influences ionization was also investigated and the first-order ionization constant for each stable conformation was obtained with the self-consistent reaction field (SCRF) method.

Use of molecular electrostatic potential for quantitative assessment of inductive effect

Density functional theory computations at the B3LYP/6-31G(d,p) level have been carried out for three types of model compounds, viz. (i) 4-substituted bicyclo[2.2.2]octane carboxylic acids, (ii) anions of 4-substituted bicyclo[2.2.2]octane carboxylic acids and (iii) 4-substituted quinuclidines where the substituents are NO(2), CN, Cl, Br, CF(3), F, CHO, CH(2)Cl, COOH, COCH(3), CONH(2), OH, OCH(3), C(6)H(5), NH(2), H, CH(3), CH(2)CH(3), CH(CH(3))(2), and C(CH(3))(3) to study the dependencies between molecular electrostatic potential minimum (V(min)) and the inductive substituent constant sigma(I). All the three model systems show excellent linear correlation between V(min) and sigma(I) suggesting that the calculation of V(min) parameter in these systems offers a simple and efficient computational approach for the evaluation of inductive substituent constants. The calculated linear equation for the models (i), (ii), and (iii) are V(min) = 12.982 sigma(I)- 48.867, V(min) = 13.444 sigma(I)- 182.760, and V(min) = 18.100 sigma(I)- 65.785, respectively. Considering the simplicity of the quinuclidine model, V(min) value at the nitrogen lone pair region of a 4-substituted quinuclidine system is recommended for the evaluation of sigma(I). Further, the additivity effect of sigma(I) is tested on multiply substituted quinuclidine and bicyclo[2.2.2]octane carboxylic acid derivatives using the V(min) approach and the results firmly supported the additivity rule of inductive effect. The systems showing considerable deviations from the additivity rule are easily recognized as those showing either steric effect or intramolecular hydrogen bond interactions at the V(min) response site. However, the distance relation of sigma(I) is not well represented in the caged molecular systems.

Progressive Docking: A Hybrid QSAR/Docking Approach for Accelerating In Silico High Throughput Screening

A combination of protein-ligand docking and ligand-based QSAR approaches has been elaborated, aiming to speed-up the process of virtual screening. In particular, this approach utilizes docking scores generated for already processed compounds to build predictive QSAR models that, in turn, assess hypothetical target binding affinities for yet undocked entries. The "progressive docking" has been tested on drug-like substances from the NCI database that have been docked into several unrelated targets, including human sex hormone binding globulin (SHBG), carbonic anhydrase, corticosteroid-binding globulin, SARS 3C-like protease, and HIV1 reverse transcriptase. We demonstrate that progressive docking can reduce the amount of computations 1.2- to 2.6-fold (when compared to traditional docking), while maintaining 80-99% hit recovery rates. This progressive-docking procedure, therefore, substantially accelerates high throughput screening, especially when using high accuracy (slower) docking approaches and large-sized datasets, and has allowed us to identify several novel potent nonsteroidal SHBG ligands.

Ultrafast Intramolecular Charge Transfer and Internal Conversion with Tetrafluoro-aminobenzonitriles

The five 2,3,5,6-tetrafluoro-4-aminobenzonitriles XABN4F with a dimethyl-amino (DMABN4F), diethyl-amino (DEABN4F), azetidinyl (AZABN4F), methyl-amino (MABN4F) or amino (ABN4F) group undergo ultrafast intramolecular charge transfer (ICT) at room temperature, in the polar solvent acetonitrile (MeCN) as well as in the nonpolar n-hexane. ICT also takes place with the corresponding non-fluorinated aminobenzonitriles DMABN, DEABN and AZABN in MeCN, whereas for these molecules in n-hexane only minor (DMABN, DEABN) or no (AZABN) ICT fluorescence is detected. For the secondary (MABN) and primary (ABN) amines, an ICT reaction does not occur, which makes ABN4F the first electron donor/acceptor molecule with an NH(2) group for which ICT is observed. The ICT state of the XABN4Fs has a dipole moment of around 14 D, clearly smaller than that of DMABN (17 D). This difference is attributed to the electron withdrawing from the CN group to the phenyl ring, exerted by the four F-substituents. The reaction from the initially prepared locally excited (LE) to the ICT state in n-hexane proceeds in the sub-picosecond time range: 0.35 ps (DMABN4F), 0.29 ps (DEABN4F) and 0.13 ps (AZABN4F), as determined from femtosecond transient absorption measurements. In the highly polar solvent MeCN, an ICT reaction time of around 90 fs is observed for all five XABN4Fs, irrespective of the nature of their amino group. This shows that with these molecules in MeCN the ICT reaction rate is limited by the solvent dielectric relaxation time of MeCN, for which a value of around 90 fs has been reported. It is therefore concluded that, during this ultrashort ICT reaction, a large-amplitude motion such as a full 90 degrees twist of the amino group is unlikely to occur in the XABN4Fs. The ICT state of the XABN4Fs is strongly quenched via internal conversion (IC), with a lifetime tau'(0) (ICT) down to 3 ps, possibly by a reaction passing through a conical intersection made accessible due to a deformation of the phenyl group by out-of-plane motions induced by vibronic coupling between low-lying pisigma* and pipi* states in the XABN4Fs.

Application of 'inductive' QSAR descriptors for quantification of antibacterial activity of cationic polypeptides

On the basis of the inductive QSAR descriptors we have created a neural network-based solution enabling quantification of antibacterial activity in the series of 101 synthetic cationic polypeptides (CAMEL-s). The developed QSAR model allowed 80% correct categorical classification of antibacterial potencies of the CAMEL-s both in the training and the validation sets. The accuracy of the activity predictions demonstrates that a narrow set of 3D sensitive 'inductive' descriptors can adequately describe the aspects of intra- and intermolecular interactions that are relevant for antibacterial activity of the cationic polypeptides. The developed approach can be further expanded for the larger sets of biologically active peptides and can serve as a useful quantitative tool for rational antibiotic design and discovery.

Synthesis and in vitro biological evaluation of fluoro-substituted-4-phenyl-1,2,3,6-tetrahydropyridines as monoamine oxidase B substrates

The substrate properties of three beta-fluoro-4-phenyl-1,2,3,6-tetrahydropyridines related to the proneurotoxin 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine have been examined in an effort to evaluate the contribution of electronic parameters to the MAO-B catalyzed allylic-alpha-carbon oxidation of the tetrahydropyridinyl system. The design, synthesis, and biological evaluation of these analogues are presented and correlations to amine ionization potentials versus substrate activity are discussed.

Inductive Electronegativity Scale. Iterative Calculation of Inductive Partial Charges

A number of novel QSAR descriptors have been introduced on the basis of the previously elaborated models for steric and inductive effects. The developed "inductive" parameters include absolute and effective electronegativity, atomic partial charges, and local and global chemical hardness and softness. Being based on traditional inductive and steric substituent constants these 3D descriptors provide a valuable insight into intramolecular steric and electronic interactions and can find broad application in structure-activity studies. Possible interpretation of physical meaning of the inductive descriptors has been suggested by considering a neutral molecule as an electrical capacitor formed by charged atomic spheres. This approximation relates inductive chemical softness and hardness of bound atom(s) with the total area of the facings of electrical capacitor formed by the atom(s) and the rest of the molecule. The derived full electronegativity equalization scheme allows iterative calculation of inductive partial charges on the basis of atomic electronegativities, covalent radii, and intramolecular distances. A range of inductive descriptors has been computed for a variety of organic compounds. The calculated inductive charges in the studied molecules have been validated by experimental C-1s Electron Core Binding Energies and molecular dipole moments. Several semiempirical chemical rules, such as equalized electronegativity's arithmetic mean, principle of maximum hardness, and principle of hardness borrowing could be explicitly illustrated in the framework of the developed approach.

A new method for estimation of homolytic C-H bond dissociation enthalpies

In this work we have quantitatively analyzed substituent effects on the homolytic bond dissociation enthalpy of 79 different compounds using a method based on discrete distance dependent atomic contributions to a molecular property. The resulting empirical relationship can be used to predict C-H bond dissociation enthalpies (within +/-10 kJ mol(-1)) for molecules where resonance contributions and captodative stabilization are insignificant. For species where captodative stabilization of the corresponding C-centered radical is possible, the method clearly overestimates the C-H bond dissociation enthalpy.