Prediction of cyclohexane-water distribution coefficient for SAMPL5 drug-like compounds with the QMPFF3 and ARROW polarizable force fields

We present the performance of blind predictions of water—cyclohexane distribution coefficients for 53 drug-like compounds in the SAMPL5 challenge by three methods currently in use within our group. Two of them utilize QMPFF3 and ARROW, polarizable force-fields of varying complexity, and the third uses the General Amber Force-Field (GAFF). The polarizable FF’s are implemented in an in-house MD package, Arbalest. We find that when we had time to parametrize the functional groups with care (batch 0), the polarizable force-fields outperformed the non-polarizable one. Conversely, on the full set of 53 compounds, GAFF performed better than both QMPFF3 and ARROW. We also describe the torsion-restrain method we used to improve sampling of molecular conformational space and thus the overall accuracy of prediction. The SAMPL5 challenge highlighted several drawbacks of our force-fields, such as our significant systematic over-estimation of hydrophobic interactions, specifically for alkanes and aromatic rings.     

Rate processes in condensed media: Basic equations

A general theory of rate processes is developed. Starting from the first principles, the non-Markovian and Markovian type equations governing relaxation processes are derived. Under certain conditions (which are specified) these equations may be approximately reduced to master equations.The theory is applied to two specific models. In one of them the electron-nuclear system is represented by two intersecting electronic energy hyper-surfaces with a continuum of degrees of freedom plus a small perturbation causing transitions between these electronic states. The equations determining the time behaviour of the electronic subsystem in the general case do not coincide with master equations and the time evolution of the system has mixed oscillatory decaying behaviour.Another model takes into account a possible competition between electronic and vibrational relaxations. The corresponding kinetic equations are derived.     

πl,π*-Absorption bands as a valuable source of information on the structure of tautomers and conformers

The presence of several π_l,π*-absorption bands in the electronic spectrum of hydroxyanthraquinones indicates the occurrence of tautomeric and conformational equilibria. The structure of tautomers and conformers can be determined from the correlation between λ_max and the sums of the constants σ^A of hydroxy and oxido groups, calculated for each isomer.     

Tautomerism of anthraquinones: III. Tautomerization and rotational isomerization as processes responsible for the appearance of several π1,π*-bands in the absorption spectra of hydroxy-substituted quinones

Hydroxy-substituted anthraquinones, naphthoquinones, and naphthacenequinones exist as equilibrium mixtures of different tautomers and rotational isomers which give rise to several π₁,π* bands in their electronic absorption spectra. Each π₁,π* band can be assigned to a particular tautomer and conformer on the basis of the substituent constants σ^A.     

Electronic Absorption Spectra and Ligand Structure in the Metal Complexes of Quinizarin

The character of the electronic absorption spectra of the metal complexes with 1,4-dihydroxy-9,10-anthraquinone depends on the ligand state, namely, on the degree of its ionization and predominant contribution of the tautomeric 9,10-, 1,10-, and 1,4-anthraquinoid resonance structures. The known complexes are classified in accordance with the ligand structure. The maximal contribution of the 1,10-anthraquinoid structure of the ligand is observed for the majority of monometal complexes, while that of 9,10-anthraquinoid structure is typical of bimetal complexes. Differences in the composite electronic absorption spectra of the mixed-ligand complexes are explained in terms of contribution of different quinizarin tautomeric forms with different degree of ionization.     

Tautomerism of anthraquinones: VIII. Tautomerism and conformations of 1,4-diamino-9,10-anthraquinone

The compound widely known as 1,4-diamino-9,10-anthraquinone is in fact an equilibrium mixture of 4,9-diamino-1,10-anthraquinone and tautomeric imino forms, 10-amino-9-hydroxy-1,4-anthraquinone 1-imine and its conformer, and 4-amino-1-hydroxy-9,10-anthraquinone 9-imine or 4,9-dihydroxy-1,10-anthraquinone diimine. Amino-imino tautomerism and rotational isomerism are responsible for fine structure of the π_l,π*-absorption of the title compound.     

New stage in the development of anthraquinone chemistry and the structure of alizarin

Chemistry of 9,10-anthraquinones is considered as chemistry of isomeric anthraquinones existing in dynamic equilibrium with each other. Diversity of electronic absorption spectra of the same compounds is determined by tautomeric transformations. Alizarin exists as equilibrium mixtures of tautomers and conformers having 9,10- and 2,9-quinoid structures. Qualitatively different compositions are inherent not only to samples of alizarin prepared or purified by different methods but also to different solvates of the same sample.     

Tautomerism of anthraquinones: XI. 1-amino-4-hydroxyanthraquinone

The disperse dye red 2C regarded as 1-amino-4-hydroxy-9,10-anthraquinone is not a 9,10-anthraquinone derivative. It is characterized by a keto-enol and amino-imine tautomerism, and it consists of equilibrium mixtures of tautomers and conformers containing 4-amino-9-hydroxy-1,10-, 9 amino-4-hydroxy-1,10-, 9 amino-10-hydroxy-1,4-anthraquinones, 9 hydroxy-1,10-anthraquinone 10-imine, and also their conformers with a single intramolecular hydrogen bond. The significant differences in the absorption spectra known for this dye originate from the dissimilar isomeric composition of the samples of this dye prepared or purified by various procedures