Quantifying the conceptual problems associated with the isotropic NICS through analyses of its underlying density.

The isotropic Nucleus Independent Chemical Shift (NICSiso) is widely considered to be a suitable descriptor for aromaticity based on the correlations it exhibits with other aromaticity descriptors. To gain more insight into the origin of these correlations, we establish causal relations between the NICSiso and the underlying current density patterns by resolving the NICSiso into its underlying density. Our results indicate that the origin of the behavior of the NICSiso can be radically different from what is generally assumed. Not only does this bring into question the robustness of applying the NICSiso beyond the realms of where good correlations with other measures of aromaticity have been established, it also points to an inherent weakness in all interpretations of NICSiso values that are not based on additional data.

Interpreting the behavior of the NICSzz by resolving in orbitals, sign, and positions.

The zz component of the nucleus independent chemical shift or the NICSzz is commonly used as a quantifier of the (anti)aromatic character of a (sub)system. One of the underlying assumptions is that a position can be found where the "aromatic" ring currents are adequately reflected in the corresponding NICSzz value. However, as the NICSzz is the result of an integration over the entire space, it no longer explicitly contains the information needed to quantify the separate contributions arising from underlying current density patterns. In this study, we will show that these contributions can be revealed by resolving the NICSzz into orbitals, sign, and positions. Our analysis of benzene in terms of these resolutions shows that the same underlying current density can lead to highly complex shielding patterns that vary greatly depending on the position of the NICSzz-probe. As such, our results indicate that any analysis solely based on NICSzz-values can lead to results that are difficult to interpret, even if the system under study is considered to be well-known. © 2017 Wiley Periodicals, Inc.

Can the current density map topology be extracted from the nucleus independent chemical shifts?

Aromatic compounds are characterised by the presence of a ring current when in a magnetic field. As a consequence, current density maps are used to assess (the degree of) aromaticity of a compound. However, often a more discrete set of so-called Nucleus Independent Chemical Shift (NICS) values is used that is derived from the current density. It is shown here that there is no simple one-to-one relationship that allows reconstructing current density maps from only NICS-values. NICS values should therefore not be used as aromaticity indices without analysis of the ab initio computed current density map.

Bond Fukui indices: comparison of frozen molecular orbital and finite differences through Mulliken populations.

Bond Fukui functions and matrices are introduced for ab initio levels of theory using a Mulliken atoms in molecules model. It is shown how these indices may be obtained from first-order density matrix derivatives without need for going to second-order density matrices as in a previous work. The importance of taking into account the nonorthogonality of the basis in ab initio calculations is shown, contrasting the present results with previous work based on Hückel theory. It is shown how the extension of Fukui functions to Fukui matrices allows getting more insight into the nature of bond Fukui functions. All presently introduced indices respect the necessary normalization conditions and include the classical single atom condensed Fukui functions.

Theoretical studies on the transport mechanism of 5-fluorouracil through cyclic peptide based nanotubes.

Cyclic peptide nanotubes (CPNTs) formed by the self-assembly of cyclic peptides (CPs) with an even number of alternate l/d amino acids are typically used in the field of the transport of ions and drug molecules across the lipid bilayer. This study investigates the transport mechanism of the antitumor drug molecule, 5-fluorouracil (5FU), through the CPNT using classical and steered molecular dynamics simulations combined with umbrella sampling. During the transport of 5FU through the CPNT, 5FU is partially desolvated because the lumen of the CPNT is too small to allow for water molecules solvating it. 5FU forms H-bonding interactions with the backbones of the CPNT and at the same time, also forms hydrophobic contacts with the backbone Cα and C atoms of the CPNT. The cooperative breaking of the H-bond and hydrophobic interactions between the CPNT and 5FU increases the pulling force to transport the 5FU from the mid-Cα region to the Cα one. The calculated free energies of binding reveal that the energy barriers for the transport of 5FU are ∼-6.0 and ∼-2.0 kcal mol(-1) in the mid-Cα and Cα plane regions, respectively.

Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition.

The stability of self-assembling cyclic peptides (CPs) is attained by the intermolecular backbone-backbone hydrogen bonding (H-bonding) interactions. In addition to these H-bonding interactions, the self-assembled CPs are further stabilized by various intermolecular side chain-side chain interactions. This study investigates the role of amino acids on the structure and stability of self-assembled CPs using classical molecular dynamics (MD) simulations and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method. The amino acids considered for the construction of model structures of cyclic peptide nanotubes (CPNTs) are Ala, Leu, Phe, Gln, Glu, and Trp. The calculated structural parameters from classical MD simulations reveal that the backbone flexibility of CPNTs composed of non-Ala residues results from an intrinsic property of the amino acids. The presence of an Ala residue at the alternate position increases the solvation of side chains of Gln residue. The occurrence of Glu residue does not favour the formation of intermolecular side chain-side chain H-bonding interactions in aqueous medium. It is evident from the calculated free energy of binding that CPNTs composed of non-polar residues are highly stable in aqueous medium. At the same time, CPNTs with polar side chains are less stable in aqueous medium. Results obtained from this study demonstrate the role played by amino acid side chains on the structure and stability of CPNTs and provide valuable suggestions for the design of CPNTs with moderate stability in various solvent environments.

Multidimensionality of delocalization indices and nucleus-independent chemical shifts in polycyclic aromatic hydrocarbons II: proof of further nonlocality.

In a recent contribution, we examined the effect of 10- and 14-center circuits on the nucleus-independent chemical shifts NICSs using multicenter bond indices (MCBIs) (Fias et al., J Comput Chem 2008, 29, 358). In this study, the nonlocal contributions to the NICS are further investigated for a larger set of polycyclic aromatic hydrocarbons (PAHs). To achieve this, the NICSs are predicted using the MCBI and compared with ab initio results. The NICSs of the central ring of perylene- and benzo-[ghi]perylene-like fragments and of coronene appear to have other nonlocal contributions than the ones previously studied. It is shown that a model based on the MCBI-ring current maps and the inclusion of new circuits proves the existence and shows the nature of these new nonlocal effects on the NICS. This new model leads to a better understanding of the differences between the NICSs and delocalization indices. The results show that the NICS value is not only significantly influenced by the higher order circuits encircling the ring at which it is evaluated but also by the local aromaticity of the surrounding rings, and occasionally, like in the case of coronene, the NICSs are even influenced by currents farther away in the molecule.

Conceptual DFT properties-based 3D QSAR: analysis of inhibitors of the nicotine metabolizing CYP2A6 enzyme.

Structure-activity relationships of 46 P450 2A6 inhibitors were analyzed using the 3D-QSAR methodology. The analysis was carried out to confront the use of traditional steric and electrostatic fields with that of a number of fields reflecting conceptual DFT properties: electron density, HOMO, LUMO, and Fukui f- function as 3D fields. The most predictive models were obtained by combining the information of the electron density with the Fukui f- function (r2 = 0.82, q2 = 0.72), yielding a statistically significant and predictive model. The generated model was able to predict the inhibition potencies of an external test set of five chemicals. The result of the analysis indicates that conceptual DFT-based molecular fields can be useful as 3D QSAR molecular interaction fields.

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-pi-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.

Prediction of blood-brain partitioning: a model based on ab initio calculated quantum chemical descriptors.

A new model for the prediction of log BB, a penetration measure through the blood-brain barrier, based on a molecular set of 82 diverse molecules is developed. The majority of the descriptors are derived from quantum chemical ab initio calculations, augmented with a number of classical descriptors. The quantum chemical information enables one to compute fundamental properties of the molecules. The best set of descriptors was selected by sequential selection and multiple linear regression was used to develop the QSAR model. The predictive capability of the model was tested using internal and external test procedures and the domain of applicability was determined to identify reliable predictions. The selected set of descriptors shows a significant correlation with the experimental log BB. The proposed model could reproduce the data with an error approaching the experimental uncertainty and satisfies the available validation procedures. The obtained results indicate that the use of quantum chemical information in describing molecules improves the behavior of the model.

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 computer program for QSAR-analysis: ARTE-QSAR.

A new computer program has been designed to build and analyze quantitative-structure activity relationship (QSAR) models through regression analysis. The user is provided with a range of regression and validation techniques. The emphasis of the program lies mainly in the validation of QSAR models in chemical applications. ARTE-QSAR produces an easy interpretable output from which the user can conclude if the obtained model is suitable for prediction and analysis.

Colonic arteriovenous malformation in a child misinterpreted as an idiopathic colonic varicosis on angiography: remarks on current classification of childhood intestinal vascular malformations.

A case of lower gastrointestinal hemorrhage in a child caused by an arteriovenous malformation (AVM) of the colon is presented. On diagnostic angiography, the lesion was misinterpretated as an idiopathic colonic varicosis because none of the characteristic features of an AVM were present. The role of angiography and shortcomings in nomenclature and classification of intestinal vascular anomalies in childhood are discussed.