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QSAR treatment of electronic substituent effects using frontier orbital theory and topological parameters

A methodology for the estimation of Hammett substituent constants from computational-based descriptors utilizing quantitative structure activity/property relationships (QSAR/QSPR) formalism is presented. Electronic descriptors derived from quantum chemical calculations and molecular topology were used to generate computational-based analogues of empirical Hammett substituent constants from statistical analysis. Global quantum chemical reaction indices were drawn from frontier orbital theory and density functional theory and formulated from AM1-based calculations. A localized index based on the electrotopological state index was used to encode information on individual group properties. From a training set consisting of 150 meta and para-substituted benzoic acids, statistical analysis of computational-based descriptors as a function of empirical substituent constants yielded a five-parameter QSAR/QSPR model which generates computational-based constants exhibiting a strong correlation with empirical values (r2 = 0.958). Both internal (PRESS) and external (independent testing set of benzoic acids) validation procedures suggest that the electronic effects QSAR/QSPR model derived in this work from computational-based parameters is a statistically viable paradigm. Both predicted and empirical constants were used in Hammett-type validation analyses as functions of chemical, biological, and spectroscopic data for thirty structurally diverse meta and parasubstituted aromatic testing sets. Statistical measures of ensuing correlations were examined and compared, and the empirical and predicted results were of similar quality. Validation results reveal that a large number of computational-based substituent constants can be accurately estimated from semiempirical AM1 frontier orbital energies and electronic structure information obtained directly from substituted benzoic acids without the aid of empirical parametrization.

Journal Article↗

The role of hydrated divalent metal ions in the bridging of two anionic groups. An ab initio quantum chemical and molecular mechanics study of dimethyl phosphate and formate bridged by calcium and magnesium ions.

Ab initio quantum chemical (Gaussian82) and molecular mechanics (AMBER2.0) computational techniques are employed to investigate the interaction of two anions (formate an dimethylphosphate) and a central divalent metal cation (magnesium or calcium). These systems are models for the essential GDP binding unit of the G-proteins (e.g., EF-Tu or the ras oncogene proteins) and for protein/phospholipid interactions, both of which are mediated by divalent metal cations. Various levels of hydration are utilized to examine coordination of differences between magnesium and calcium ions. Two different orientations of formate and dimethyl phosphate in direct ion contact with a magnesium ion and two waters of hydration were energy minimized with both quantum and molecular mechanics techniques. The structures and energy differences between the two orientations determined by either of the computational techniques are similar. Magnesium ion has a strong propensity to assume six coordination whereas calcium ion preferentially assumes a coordination greater than six. Likewise, water molecules attached to magnesium ion are held more rigidly than those of calcium ion, thus calcium ion is more accommodating in the exchange of water for negative ligands.

Calcium↗

Cannabidiol and phenytoin: a structural comparison.

Conformational energy maps have been computed for the antiepileptic agents phenytoin and cannabidiol by the quantum-mechanical method of perturbative configuration interaction with localized orbitals (PCILO). The computation indicates that the spatial relationship between the two rings in the two drugs is similar and close to the respective structures in the crystal. This is supported by 1H and 13C NMR measurements. Hence, both compounds fulfill the stereochemical requirements suggested for anticonvulsant drug action.

Cannabidiol↗

Reactivity of alkanes on zeolites: a computational study of propane conversion reactions.

In this work, quantum chemical methods were used to study propane conversion reactions on zeolites; these reactions included protolytic cracking, primary hydrogen exchange, secondary hydrogen exchange, and dehydrogenation reactions. The reactants, products, and transition-state structures were optimized at the B3LYP/6-31G level and the energies were calculated with CBS-QB3, a complete basis set composite energy method. The computed activation barriers were 62.1 and 62.6 kcal/mol for protolytic cracking through two different transition states, 30.4 kcal/mol for primary hydrogen exchange, 29.8 kcal/mol for secondary hydrogen exchange, and 76.7 kcal/mol for dehydrogenation reactions. The effects of basis set for the geometry optimization and zeolite acidity on the reaction barriers were also investigated. Adding extra polarization and diffuse functions for the geometry optimization did not affect the activation barriers obtained with the composite energy method. The largest difference in calculated activation barriers is within 1 kcal/mol. Reaction activation barriers do change as zeolite acidity changes, however. Linear relationships were found between activation barriers and zeolite deprotonation energies. Analytical expressions for each reaction were proposed so that accurate activation barriers can be obtained when using different zeolites as catalysts, as long as the deprotonation energies are first acquired.

Journal Article↗

1,5-Hydride shift in Wolff-Kishner reduction of (20R)-3beta,20, 26-trihydroxy-27-norcholest-5-en-22-one: synthetic, quantum chemical, and NMR studies.

Heating (20R)-3beta,20,26-trihydroxy-27-norcholest-5-en-22-one (1) with hydrazine and KOH at 160 degrees C completely converted the steroid to a diastereoisomeric mixture of the new (20R,22RS)-27-norcholest-5-ene-3beta,20,22-triols (2). Exclusive formation of 2 suggests that the expected Wolff-Kishner reduction to a methylene group at the C-22 ketone in 1 was diverted to the C-26 position by a 1,5-hydride shift. All attempts under acid conditions failed to produce a C-22 phenyl hydrazone from 1. However, reaction of 1 was reacted with phenylhydrazine in hot KOH, gave the C-26 phenylhydrazone 4 as the sole product. Evidently, under alkaline conditions, first a hydride ion undergoes an intramolecular transfer from the C-26 CH(2)OH group to the C-22 ketone in 1, and then the phenylhydrazine traps the newly formed aldehyde. To examine this hypothesis, we constructed computer-simulated transition state models from quantum chemical calculations and then compared data from these models with NMR measurements of the reaction mixtures containing 2. The NMR data showed that the C-22 diastereoisomers of 2 are formed in a nearly 1:1 ratio exactly as predicted from the energy-optimized transition states, which were calculated for intramolecular 1,5-hydride shifts that produced each of the two C-22 diastereoisomers. Accordingly, these results support the hypothesis that an intramolecular 1,5-hydride shift mechanism promotes complete conversion of 1 to 2 under classical Wolff-Kishner reduction conditions.

Aldehydes↗

Infrared overtone spectroscopy and unimolecular decay dynamics of peroxynitrous acid.

Peroxynitrous acid (HOONO) is generated in a pulsed supersonic expansion through recombination of photolytically generated OH and NO(2) radicals. A rotationally resolved infrared action spectrum of HOONO is obtained in the OH overtone region at 6971.351(4) cm(-1) (origin), providing definitive spectroscopic identification of the trans-perp (tp) conformer of HOONO. Analysis of the rotational band structure yields rotational constants for the near prolate asymmetric top, the ratio of the a-type to c-type components of the transition dipole moment for the hybrid band, and a homogeneous linewidth arising from intramolecular vibrational energy redistribution and/or dissociation. The quantum state distribution of the OH (nu=0,J(OH)) products from dissociation is well characterized by a microcanonical statistical distribution constrained only by the energy available to products, 1304+/-38 cm(-1). This yields a 5667+/-38 cm(-1) [16.2(1) kcal mol(-1)] binding energy for tp-HOONO. An equivalent available energy and corresponding binding energy are obtained from the highest observed OH product state. Complementary high level ab initio calculations are carried out in conjunction with second-order vibrational perturbation theory to predict the spectroscopic observables associated with the OH overtone transition of tp-HOONO including its vibrational frequency, rotational constants, and transition dipole moment. The same approach is used to compute frequencies and intensities of multiple quantum transitions that aid in the assignment of weaker features observed in the OH overtone region, in particular, a combination band of tp-HOONO involving the HOON torsional mode.

Journal Article↗

[Analysis of factors limiting the applications of binomial statistics in studies of mediator secretion at neuromuscular synapses].

Binomial parameters of transmitter secretion were calculated on the basis of synaptic potential analyses at frog sartorius muscle. In some synapses negative values of parameter of the p were found. These negative values often occurred at low concentrations of Ca2+ ions and small amplitude of miniature end plate potentials. The obtained data were interpreted in terms of a model which presupposes the heterogeneity of the quantum transmitter release at different sites. A computer imitation of transmitter secretion showed that the appearance of the negative p parameter values and erroneous n estimations in the experiment are related with the shape of the distribution of quantum transmitter release probability and the amplitude of miniature end plate potentials.

Animals↗

Estimation of pKa using quantum topological molecular similarity descriptors: application to carboxylic acids, anilines and phenols.

The current availability of cheap computer power enables the construction of QSARs from modern ab initio quantum chemical data. Multivariate models for three classes of compounds are developed by means of the quantum topological molecular similarity (QTMS) tool, which incorporates descriptors originating from the "Atoms in Molecules" (AIM) theory. Correlations obtained outperform the Hammett and other traditional parameters. The advantage of QTMS over semiempirical and empirical descriptors is demonstrated by the following r(2)/q(2) values: 0.920/0.891 (acids), 0.974/0.953 (anilines), and 0.952/0.884 (phenols).

Journal Article↗

Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin.

Herein, we present theoretical results aimed at elucidating the origin of the kinetic preference for penicillins over cephalosporins characteristic of the TEM/SHV subgroup of class A beta-lactamases. First, we study the conformational properties of cephalothin showing that the C2-down conformer of the dihydrothiazine ring is preferred over the C2-up one by approximately 2 kcal/mol in solution (0.4-1.4 kcal/mol in the gas phase). Second, the TEM-1 beta-lactamase complexed with cephalothin is investigated by carrying out a molecular dynamics simulation. The DeltaG(binding) energy is then estimated using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) and quantum chemical PBSA (QM-PBSA) computational schemes. The preferential binding of benzylpenicillin over cephalothin is reproduced by the different energetic calculations, which predict relative DeltaDeltaG(binding) energies ranging from 1.8 to 5.7 kcal/mol. The benzylpenicillin/cephalothin DeltaDeltaG(binding) energy is most likely due to the lower efficacy of cephalosporins than that of penicillins in order to simultaneously bind the "carboxylate pocket" and the "oxyanion hole" in the TEM-1 active site.

Anti-Bacterial Agents↗

Molecular quantum similarity measures tuned 3D QSAR: an antitumoral family validation study.

In this work, a new methodology to construct a tuned QSAR model is presented, which is based on a convex set formalism. The present procedure continues previous 3D QSAR studies, performed using molecular quantum similarity measures (MQSM). With this new computational tool, the efficiency of MQSM applied to QSAR analysis is significantly improved. A reliable QSAR model is obtained using convex linear combinations of different kinds of MQSM, corresponding to different quantum-mechanical operators related to the quantum similarity integral. The active compounds studied here, as a case study, are a set of antitumor agents, the camptothecin molecule and analogues, and the property evaluated is the topoisomerase-I inhibition activity. Before performing a tuned QSAR analysis with this particular molecular set, a simple QSAR study for all the different possible types of MQSM is carried out. In addition, another application of MQSM is presented, to determine which method can be used to optimize molecular structures in order to reproduce experimental molecular geometries as well as possible.

Animals↗

Molecular modelling in design of crop protection chemicals.

Specific examples from pesticide research are given which illustrate the types of analysis employed to design optimal inhibitors for a given receptor, based on the assumption that a congeneric series of compounds behave in a related mode in the biosystem. The examples illustrate the complementary role played by computational chemistry, X-ray crystallography and computer graphics and also raise questions as to the current limitations of existing molecular mechanics and quantum mechanics techniques.

Agriculture↗

Noise power spectra of images from digital mammography detectors.

Noise characterization through estimation of the noise power spectrum (NPS) is a central component of the evaluation of digital x-ray systems. We begin with a brief review of the fundamentals of NPS theory and measurement, derive explicit expressions for calculation of the one- and two-dimensional (1D and 2D) NPS, and discuss some of the considerations and tradeoffs when these concepts are applied to digital systems. Measurements of the NPS of two detectors for digital mammography are presented to illustrate some of the implications of the choices available. For both systems, two-dimensional noise power spectra obtained over a range of input fluence exhibit pronounced asymmetry between the orthogonal frequency dimensions. The 2D spectra of both systems also demonstrate dominant structures both on and off the primary frequency axes indicative of periodic noise components. Although the two systems share many common noise characteristics, there are significant differences, including markedly different dark-noise magnitudes, differences in NPS shape as a function of both spatial frequency and exposure, and differences in the natures of the residual fixed pattern noise following flat fielding corrections. For low x-ray exposures, quantum noise-limited operation may be possible only at low spatial frequency. Depending on the method of obtaining the 1D NPS (i.e., synthetic slit scanning or slice extraction from the 2D NPS), on-axis periodic structures can be misleadingly smoothed or missed entirely. Our measurements indicate that for these systems, 1D spectra useful for the purpose of detective quantum efficiency calculation may be obtained from thin cuts through the central portion of the calculated 2D NPS. On the other hand, low-frequency spectral values do not converge to an asymptotic value with increasing slit length when 1D spectra are generated using the scanned synthetic slit method. Aliasing can contribute significantly to the digital NPS, especially near the Nyquist frequency. Calculation of the theoretical presampling NPS and explicit inclusion of aliased noise power shows good agreement with measured values.

Biophysics↗

Hybrid quantum mechanics/molecular mechanics simulations with two-dimensional interpolated corrections: application to enzymatic processes.

Hybrid quantum mechanics/molecular mechanics (QM/MM) techniques are widely used to study chemical reactions in large systems. Because of the computational cost associated with the high dimensionality of these systems, the quantum description is usually restricted to low-level methods, such as semiempirical Hamiltonians. In some cases, the description obtained at this computational level is quite poor and corrections must be considered. We here propose a simple but efficient way to include higher-level corrections to be used in potential energy surface explorations and in the calculation of potentials of mean force. We evaluate a correction energy term as the difference between a high-level and a low-level calculation on the QM subsystem, employing either the polarized or the gas-phase wave function, obtained as a function of two geometrical coordinates relevant in the process considered. Through the use of two-dimensional bicubic splines this correction energy is included in the simulations, ensuring the continuity and derivability of the energy function. We have tested the proposed scheme with two prototypical examples: the chorismate to prephenate rearrangement catalyzed by Bacillus subtilis chorismate mutase and the catechol methylation catalyzed by catechol O-methyltransferase. In both cases the use of interpolated corrections clearly improves the energetic and geometric descriptions of the reaction.

Bacillus subtilis↗

A theoretical study on the activation of Ser70 in the acylation mechanism of cephalosporin antibiotics.

A computational study using some molecular modeling and quantum mechanical methods has been performed for determining the most favor activation process for Ser70 in the acylation mechanism for the cephalosporin antibiotics among the three proposed ones given in the literature. The computation is based on an X-ray structure of the B chain of the Bacillus licheniformis BS3 beta-lactamase-cefoxitin complex. The position of a catalytic water involved in one of the reaction mechanism is defined using the Grid20 and InsightII programs, while that of the truncated ligand is defined using the InsightII and FirstDiscovery programs. The geometry of structures of each reaction scheme is optimized at the HF/3-21 G level of theory, and then the single point energy for each reactive species in each reaction scheme is computed at the levels of HF/6-31 + G (3df, 2p) and B3LYP/6-31 + G (3df, 2p). The effect of solvent on each reaction scheme is also studied by comparing the calculation results for each reaction scheme either in gas phase or in solution using the HF/6-31 + G (3df, 2p) level of theory. A computation using the B3LYP/6-31 + G (3df, 2p) level of theory and the Polarized Continuum Model (PCM) and by treating water as a solvent is also conducted for each activation process. It is found that, energetically, the most favor activation process for Ser70 in the acylation mechanism is the one where a proton transfer is mediated by the catalytic water and the catalytic residues Glu166 and Ser70. This agrees with those observed in an ultrahigh resolution X-ray structure and a QM/MM theoretical study published recently on the same acylation process.

Acylation↗

Energy barriers and rates of tautomeric transitions in DNA bases: ab initio quantum chemical study.

Tautomeric transitions of DNA bases are proton transfer reactions, which are important in biology. These reactions are involved in spontaneous point mutations of the genetic material. In the present study, intrinsic reaction coordinates (IRC) analyses through ab initio quantum chemical calculations have been carried out for the individual DNA bases A, T, G, C and also A:T and G:C base pairs to estimate the kinetic and thermodynamic barriers using MP2/6-31G** method for tautomeric transitions. Relatively higher values of kinetic barriers (about 50-60 kcal/mol) have been observed for the single bases, indicating that tautomeric alterations of isolated single bases are quite unlikely. On the other hand, relatively lower values of the kinetic barriers (about 20-25 kcal/mol) for the DNA base pairs A:T and G:C clearly suggest that the tautomeric shifts are much more favorable in DNA base pairs than in isolated single bases. The unusual base pairing A':C, T':G, C':A or G':T in the daughter DNA molecule, resulting from a parent DNA molecule with tautomeric shifts, is found to be stable enough to result in a mutation. The transition rate constants for the single DNA bases in addition to the base pairs are also calculated by computing the free energy differences between the transition states and the reactants.

Base Pairing↗

Quest for the rings. In silico exploration of ring universe to identify novel bioactive heteroaromatic scaffolds.

Bioactive molecules only contain a relatively limited number of unique ring types. To identify those ring properties and structural characteristics that are necessary for biological activity, a large virtual library of nearly 600 000 heteroaromatic scaffolds was created and characterized by calculated properties, including structural features, bioavailability descriptors, and quantum chemical parameters. A self-organizing neural network was used to cluster these scaffolds and to identify properties that best characterize bioactive ring systems. The analysis shows that bioactivity is very sparsely distributed within the scaffold property and structural space, forming only several relatively small, well-defined "bioactivity islands". Various possible applications of a large database of rings with calculated properties and bioactivity scores in the drug design and discovery process are discussed, including virtual screening, support for the design of combinatorial libraries, bioisosteric design, and scaffold hopping.

Biological Availability↗

Dual-topology/dual-coordinate free-energy simulation using QM/MM force field.

We have developed a dual-topology/dual-coordinate free-energy simulation method for use with a QM/MM force field. By combining two parallel processes into one alchemical process, we are able to compute the double free-energy difference (delta deltaF) within a single simulation, which eliminates half of the expensive quantum-mechanical simulation in general. The method has been tested in computing the solvation free-energy differences of several molecular pairs and shows close agreement with experimental results.

Computer Simulation↗