Timur I. Madzhidov

The Nature of the Interaction of Organoselenium Molecules with Diiodine

The electronic structure of charge-transfer complexes of organoselenium compounds with diiodine has been studied at several levels of theory (Hartree-Fock, second order Møller-Plesset, and density functional theory). The complexation energies, optimized geometries, and the topology of the electron density and its Laplacian distribution, including domain averaged properties, have been analyzed. Special attention was paid to the influence of basis set superposition error on the energy of complexation. A tendency of organoselenium molecules to form more covalent intermolecular bonds with electron acceptors than with nitrogen atoms or other conventional electron donors has been revealed. The changes in atomic charges under complexation follow the main trends expected for the charge transfer. By means of the interacting quantum atoms (IQA) approach it has been found that the Se···I interaction is dominated by its quantum mechanical exchange-correlation contribution, the electrostatic interaction having a minor, repulsive role. IQA data have also been used to explain the value of the Se···I-I valence angle, as well as the topological charges on the iodine atoms in the complexes studied.

Structure-Reactivity Relationships in Terms of the Condensed Graphs of Reactions

An approach for the prediction of rate constants of chemical reactions, based on the representation of a chemical reaction as a condensed graph, has been tested on more than 1000 bimolecular nucleophilic substitution reactions with neutral nucleophiles in 38 solvents. Molecular fragment descriptors, temperature, and solvent parameters characterizing solvation power have been used in the reaction modeling. The obtained models ensure a good correlation between the predicted and experimental values; the corresponding deviations are comparable with interlaboratory measurement errors.

Predictive Models for Halogen-Bond Basicity of Binding Sites of Polyfunctional Molecules

Halogen bonding (XB) strength assesses the ability of an electron‐enriched group to be involved in complexes with polarizable electrophilic halogenated or diatomic halogen molecules. Here, we report QSPR models of XB of particular relevance for an efficient screening of large sets of compounds. The basicity is described by pKBI2, the decimal logarithm of the experimental 1 : 1 (B : I2) complexation constant K of organic compounds (B) with diiodine (I2) as a reference halogen‐bond donor in alkanes at 298 K. Modeling involved ISIDA fragment descriptors, using SVM and MLR methods on a set of 598 organic compounds. Developed models were then challenged to make predictions for an external test set of 11 polyfunctional compounds for which unambiguous assignment of the measured effective complexation constant to specific groups out of the putative acceptor sites is not granted. At this stage, developed models were used to predict pKBI2 of all putative acceptor sites, followed by an estimation of the predicted effective complexation constant using the ChemEqui program. The best consensus models perform well both in cross‐validation (root mean squared error RMSE=0.39–0.47 logKBI2 units) and external predictions (RMSE=0.49). The SVM models are implemented on our website (http://infochim.u‐strasbg.fr/webserv/VSEngine.html) together with the estimation of their applicability domain and an automatic detection of potential halogen‐bond acceptor atoms.

Structure–reactivity relationship in bimolecular elimination reactions based on the condensed graph of a reaction

By means of a structural representation of the chemical reactivity as a condensed graph a model predicting rate constants of the bimolecular elimination reaction is derived for the first time. The model developed enables the prediction of rate constants of reactions proceeding in different solvents or water-organic mixtures at different temperatures. It demonstrates a good predictive performance: a mean square deviation of predicted values from experimental ones is less than 0.7 logarithmic units. An outlier analysis shows that prediction errors are mainly due to the imperfection of the training data containing unique reactions. The model is available for users at arsole.u-strasbg.fr.

Additive cooperativity of hydrogen bonds in complexes of catechol with proton acceptors in the gas phase: FTIR spectroscopy and quantum chemical calculations

Experimental study of hydrogen bond cooperativity in hetero-complexes in the gas phase was carried out by IR-spectroscopy method. Stretching vibration frequencies of O-H groups in phenol and catechol molecules as well as of their complexes with nitriles and ethers were determined in the gas phase using a specially designed cell. O-H groups experimental frequency shifts in the complexes of catechol induced by the formation of intermolecular hydrogen bonds are significantly higher than in the complexes of phenol due to the hydrogen bond cooperativity. It was shown that the cooperativity factors of hydrogen bonds in the complexes of catechol with nitriles and ethers in the gas phase are approximately the same. Quantum chemical calculations of the studied systems have been performed using density functional theory (DFT) methods. It was shown, that theoretically obtained cooperativity factors of hydrogen bonds in the complexes of catechol with proton acceptors are in good agreement with experimental values. Cooperative effects lead to a strengthening of intermolecular hydrogen bonds in the complexes of catechol on about 30%, despite the significant difference in the proton acceptor ability of the bases. The analysis within quantum theory of atoms in molecules was carried out for the explanation of this fact.

Development of "Structure-Property" Models in Nucleophilic Substitution Reactions Involving Azides

This paper reports a predictive model for the rate constant of the bimolecular nucleophilic substitution involving the azide moiety. It predicts reaction rate constants in different solvents, including organic mixtures, and with different organic and inorganic azides as reactants. The optimal descriptors describing solvent effects and a cation type in the azide salt were suggested. A reasonably good predictive performance of the model in cross-validation has been demonstrated. The model was applied to predict the rates of the reactions between sodium azide with two conformers of calixarenes as well as 3-bromopropyl phenyl ester. For sterically non-hindered molecules, a good agreement between predicted and experimental reaction rates was observed. On the other hand, the model poorly reproduces the results for sterically hindered molecules.

Automatized Assessment of Protective Group Reactivity: A Step Toward Big Reaction Data Analysis

We report a new method to assess protective groups (PGs) reactivity as a function of reaction conditions (catalyst, solvent) using raw reaction data. It is based on an intuitive similarity principle for chemical reactions: similar reactions proceed under similar conditions. Technically, reaction similarity can be assessed using the Condensed Graph of Reaction (CGR) approach representing an ensemble of reactants and products as a single molecular graph, i.e., as a pseudomolecule for which molecular descriptors or fingerprints can be calculated. CGR-based in-house tools were used to process data for 142,111 catalytic hydrogenation reactions extracted from the Reaxys database. Our results reveal some contradictions with famous Greenes Reactivity Charts based on manual expert analysis. Models developed in this study show high accuracy (ca. 90%) for predicting optimal experimental conditions of protective group deprotection.

S=o…s=o Interactions as a Driving Force for Low-Temperature Conformational Rearrangement of Stable H-Bonding {S(O)-Ch2-Ch2-OH···}2 Synthon in two Modifications of Diastereomeric Pinanyl Sulfoxides Co-Crystal

GRAPHICAL ABSTRACT For the triclinic and monoclinic modifications of diastereomeric pinanyl sulfoxides co-crystal, remarkable alterations in unit cell parameters by transition from 293 to 150 К were ascertained. Such alterations are accompanied by conformational restructuring of a stable hydrogen-bonded synthon from an “unfolded” to a “folded” form. The driving force of this restructuring is the tendency to form S=O…S=O interactions, which show up in the low-temperature phases of both polymorphs. These are well-supported by the methods of quantum chemistry (DFT, B97-D/6-31G(d,p), AIM All).

Structure–reactivity modeling using mixture-based representation of chemical reactions

We describe a novel approach of reaction representation as a combination of two mixtures: a mixture of reactants and a mixture of products. In turn, each mixture can be encoded using an earlier reported approach involving simplex descriptors (SiRMS). The feature vector representing these two mixtures results from either concatenated product and reactant descriptors or the difference between descriptors of products and reactants. This reaction representation doesn’t need an explicit labeling of a reaction center. The rigorous “product-out” cross-validation (CV) strategy has been suggested. Unlike the naïve “reaction-out” CV approach based on a random selection of items, the proposed one provides with more realistic estimation of prediction accuracy for reactions resulting in novel products. The new methodology has been applied to model rate constants of E2 reactions. It has been demonstrated that the use of the fragment control domain applicability approach significantly increases prediction accuracy of the models. The models obtained with new “mixture” approach performed better than those required either explicit (Condensed Graph of Reaction) or implicit (reaction fingerprints) reaction center labeling.

Modern Trends of Organic Chemistry in Russian Universities

This review is devoted to the scientific achievements of the departments of organic chemistry in higher schools of Russia within the past decade.