Patrick Bultinck

Computational Medicinal Chemistry for Drug Discovery

Observing computational chemistrys proven value to the introduction of new medicines, this reference offers the techniques most frequently utilized by industry and academia for ligand design. Featuring contributions from more than fifty pre-eminent scientists, Computational Medicinal Chemistry for Drug Discovery surveys molecular structure computation, intermolecular behavior, ligand-receptor interaction, and modeling responding to market demands in its selection and authoritative treatment of topics. The book examines molecular mechanics, semi-empirical methods, wave function-based quantum chemistry, density functional theory, 3-D structure generation, and hybrid methods.

A confidence level algorithm for the determination of absolute configuration using vibrational circular dichroism or Raman optical activity

Spectral comparison is an important part of the assignment of the absolute configuration (AC) by vibrational circular dichroism (VCD), or equally by Raman optical activity (ROA). In order to avoid bias caused by personal interpretation, numerical methods have been developed to compare measured and calculated spectra. Using a neighbourhood similarity measure, the agreement between a computed and measured VCD or ROA spectrum is expressed numerically to introduce a novel confidence level measure. This allows users of vibrational optical activity (VOA) techniques (VCD and ROA) to assess the reliability of their assignment of the AC of a compound. To that end, a database of successful AC determinations is compiled along with neighbourhood similarity values between the experimental spectrum and computed spectra for both enantiomers. For any new AC determination, the neighbourhood similarities between the experimental spectrum and the computed spectra for both enantiomers are projected on the database allowing an interpretation of the reliability of their assignment.

Critical thoughts on computing atom condensed Fukui functions.

Different procedures to obtain atom condensed Fukui functions are described. It is shown how the resulting values may differ depending on the exact approach to atom condensed Fukui functions. The condensed Fukui function can be computed using either the fragment of molecular response approach or the response of molecular fragment approach. The two approaches are nonequivalent; only the latter approach corresponds in general with a population difference expression. The Mulliken approach does not depend on the approach taken but has some computational drawbacks. The different resulting expressions are tested for a wide set of molecules. In practice one must make seemingly arbitrary choices about how to compute condensed Fukui functions, which suggests questioning the role of these indicators in conceptual density-functional theory.

Critical analysis of the local aromaticity concept in polyaromatic hydrocarbons

A large number of local aromaticity indices for the benzenoid rings in polyaromatic hydrocarbons is computed. The results are interpreted, supporting Clars hypothesis, and mutual correlations are investigated. It is shown that there are good correlations between all indices that strictly allow comparing benzenoid character. Poor correlations are found with NICS. A rationale is offered, yielding the conclusion that NICS and ring current maps follow a fundamentally different path to local aromaticity. In this sense the lack of correlation is not due to a real multidimensional character of aromaticity but rather to confusion and vagueness of the aromaticity concept.

Electrostatic Potentials from Self-Consistent Hirshfeld Atomic Charges

It is shown that molecular electrostatic potentials obtained from iterative or self-consistent Hirshfeld atomic point charges agree remarkably well with the ab initio computed electrostatic potentials. The iterative Hirshfeld scheme performs nearly as well as electrostatic potential derived atomic charges, having the advantage of allowing the definition of the atom in the molecule, rather than just yielding charges. The quality of the iterative Hirshfeld charges for computing electrostatic potentials is examined for a large set of molecules and compared to other commonly used techniques for population analysis.

A New Mean-Field Method Suitable for Strongly Correlated Electrons: Computationally Facile Antisymmetric Products of Nonorthogonal Geminals.

We propose an approach to the electronic structure problem based on noninteracting electron pairs that has similar computational cost to conventional methods based on noninteracting electrons. In stark contrast to other approaches, the wave function is an antisymmetric product of nonorthogonal geminals, but the geminals are structured so the projected Schrödinger equation can be solved very efficiently. We focus on an approach where, in each geminal, only one of the orbitals in a reference Slater determinant is occupied. The resulting method gives good results for atoms and small molecules. It also performs well for a prototypical example of strongly correlated electronic systems, the hydrogen atom chain.

Negative Fukui functions: new insights based on electronegativity equalization

Fukui functions have been calculated for large numbers of organic molecules, and were found to always be positive. Numeric and algebraic considerations allowed the identification of several boundary conditions for negative values for Fukui functions. Negative Fukui functions are found to be very unlikely, except when very short interatomic distances are present. Recent hypotheses concerning the occurrence of negative Fukui functions are strongly supported by the present approach.

Electron delocalization and aromaticity in low-lying excited states of archetypal organic compounds

Aromaticity is a property usually linked to the ground state of stable molecules. Although it is well-known that certain excited states are unquestionably aromatic, the aromaticity of excited states remains rather unexplored. To move one step forward in the comprehension of aromaticity in excited states, in this work we analyze the electron delocalization and aromaticity of a series of low-lying excited states of cyclobutadiene, benzene, and cyclooctatetraene with different multiplicities at the CASSCF level by means of electron delocalization measures. While our results are in agreement with Bairds rule for the aromaticity of the lowest-lying triplet excited state in annulenes having 4nπ-electrons, they do not support Soncini and Fowlers generalization of Bairds rule pointing out that the lowest-lying quintet state of benzene and septet state of cyclooctatetraene are not aromatic.

Multidimensionality of delocalization indices and nucleus independent chemical shifts in polycyclic aromatic hydrocarbons

The aromaticity and local‐aromaticity of a large set of polycyclic aromatic hydrocarbons (PAHs) is studied using multicenter delocalization indices from generalized population analysis and the popular nucleus independent chemical shift (NICS) index. A method for the fast computation of the NICS values is introduced, using the so‐called pseudo‐π‐method. A detailed examination is made of the multidimensional nature of aromaticity. The lack of a good correlation between the NICS and the multicenter delocalization indices is reported and the grounds discussed. It is shown through a thorough statistical analysis that the NICS values arise not only from local aromaticity of the benzenoid rings, but also from other circuits. It is shown that the NICS indices do not reveal the individual aromatic nature of a specific ring, contrary to the delocalization indices.

Solvent effects on IR and VCD spectra of natural products: an experimental and theoretical VCD study of pulegone.

The VCD spectra of pulegone, dissolved in CDCl3, CD2Cl2 and CS2 have been recorded in the frequency range from 1000 to 3000 cm(-1). The assignment of the absolute configuration was performed by comparing the experimental data with theoretical spectra computed at the B3LYP/6-311+G(d,p) level. Analysis of the agreement in several spectral regions revealed significant shortcomings when comparing with vacuum calculations. It is shown that the agreement improves when the solvent effects are taken into account by a continuum model. For the measurements in CDCl3 and CD2Cl2 further improvement was found when considering explicitly 1 : 1 complexes between a pulegone and a CDCl3 or CD2Cl2 solvent molecule in vacuo, while the best agreement was obtained when embedding these in a continuum model. The presence of the chiral solute was found to induce a VCD active C-D stretch band which could be modeled also at ab initio level.