General Purpose Electronegativity Relaxation Charge Models Applied to CoMFA and CoMSIA Study of GSK-3 Inhibitors

Iterative Solvers for Empirical Partial Atomic Charges: Breaking the Curse of Cubic Numerical Complexity

Rational drug design involves a vast amount of computations to get thermodynamically reliable results and often relies on atomic charges as a means to model electrostatic interactions within the system. Computational inefficiency often hampers the development of new and wider dissemination of the known methods; thus, any source to speed up the calculations without a sacrifice in quality is warranted. At the heart of many empirical methods of calculating atomic charges is the solution of a system of linear algebraic equations (SLAE). The classical method of solving SLAE-the Gauss method-has in general case a cubic computational complexity. It is shown that the use of iterative methods for solving SLAE, characteristic to typical empirical atomic charge calculation methods, makes it possible to significantly reduce the amount of calculations and to obtain a computational complexity approaching a quadratic one. Despite the fact that this phenomenon is well-known in numerical methods, iterative solvers surprisingly do not seem to have been systematically applied to calculation of atomic charges via empirical schemes. Another finding is the relative values of the matrix elements, determined by the physical grounds of the interactions within the empirical system, generally lead to SLAE's with well-defined matrices, suited to use with iterative solvers to fasten computation compared to using the noniterative solvers. This finding broadens the applicability range of atomic charges obtained with empirical methods for such cases as, e.g., account of polarizability via "on-the-fly" recalculation of charges in changing surroundings within the force fields in molecular dynamics settings.

Influence of Descriptor Implementation on Compound Ranking Based on Multiparameter Assessment

Most of the common molecular descriptors have numerous different implementations. This can influence the results of compound prioritization based on the multiparameter assessment (MPA) approach that allows a medicinal chemist to simultaneously analyze and achieve the desired balance of the diverse and often conflicting molecular and pharmacological properties. In this study, we analyzed the feasibility of using different implementations of common descriptors (logP, logS, TPSA, logBB, hERG, nHBA) interchangeably in predesigned sets of requirements in the course of multiparameter compound optimization. The influence of methods of descriptor calculation, continuity or discreteness of their values, their applicability domains, as well as of the nature of desirability functions in an MPA profile were examined in terms of the stability of MPA compound ranking. It was shown that the interchangeable use of different methods of descriptor calculation is reliably acceptable only for continuously distributed parameters transformed by a smooth desirability function. If a descriptor in an MPA scheme is discretely distributed, only the implementation that was used for building the scoring profile may be used for assessment. An inconsistency of assessment due to different applicability domains of descriptors was also demonstrated.

Synthesis, Spectra, and Theoretical Investigations of 1,3,5-Triazines Compounds as Ultraviolet Rays Absorber Based on Time-Dependent Density Functional Calculations and three-Dimensional Quantitative Structure-Property Relationship

A series of 1,3,5-triazines were synthesized and their UV absorption properties were tested. The computational chemistry methods were used to construct quantitative structure-property relationship (QSPR), which was used to computer aided design of new 1,3,5-triazines ultraviolet rays absorber compounds. The experimental UV absorption data are in good agreement with those predicted data using the Time-dependent density functional theory (TD-DFT) [B3LYP/6-311 + G(d,p)]. A suitable forecasting model (R > 0.8, P < 0.0001) was revealed. Predictive three-dimensional quantitative structure-property relationship (3D-QSPR) model was established using multifit molecular alignment rule of Sybyl program, which conclusion is consistent with the TD-DFT calculation. The exceptional photostability mechanism of such ultraviolet rays absorber compounds was studied and confirmed as principally banked upon their ability to undergo excited-state deactivation via an ultrafast excited-state proton transfer (ESIPT). The intramolecular hydrogen bond (IMHB) of 1,3,5-triazines compounds is the basis for the excited state proton transfer, which was explored by IR spectroscopy, UV spectra, structural and energetic aspects of different conformers and frontier molecular orbitals analysis.

Simulation of Intramolecular Hydrogen Bond Dynamics in Manzamine A as a Sensitive Test for Charge Distribution Quality

Subtle balance of inter- and intramolecular hydrogen bond strength in aqueous solutions often governs the structure and dynamics of molecular species used as potential drugs and in supramolecular applications. In silico molecular dynamics study of water solution of manzamine A has been performed with different atomic charges in order to investigate the influence of charge distribution choice on predicting qualitative and quantitative features of the simulated systems. Various well known charge schemes (MK-ESP, RESP, Mulliken, AM1-BCC, Gasteiger-Hückel, Gasteiger-Marsili, MMFF94, and Dynamic Electronegativity Relaxation - DENR) led to qualitatively different pictures of dynamic behavior of the intramolecular hydrogen bond. The reported calculation framework represents a relatively rare case where differences in charge distributions lead to noticeable differences in simulated properties, thus providing a useful test case for force field and charge distribution development, provided high quality experiments are conducted to use as references.