Linearization of moment tensor potentials for multicomponent systems with a preliminary assessment for short-range interaction energy in water dimer and trimer.

Moment tensor potentials have been recently proposed as a promising novel method of polynomial expansion for the systematic approximation of molecular potential energy surfaces. However, its current formulation for multicomponent systems has not been fully linearized and requires nonlinear optimization techniques for parameter estimation. We propose an alternative relaxed formulation of the original potential energy function where parameter optimization is expressed as a linear sparse approximation problem.

Topological Fingerprints as an Aid in Finding Structural Patterns for LRRK2 Inhibition.

Multiplet-based fingerprint mapping has been used to analyse the relationship between the structural features of potential drug candidates and the enzyme LRRK2 inhibition expressed as the inhibition constant (pKi ). For 198 structurally diverse compounds 4195 dimensional fingerprints were generated and mathematically manipulated using partial least squares (PLS) regression. A variation of PLS-BETA technique was developed for the reduction of noise by eliminating excess variables that resulted in a 636 dimensional fingerprint related to pKi .

Open computing grid for molecular science and engineering.

Grid is an emerging infrastructure for distributed computing that provides secure and scalable mechanisms for discovering and accessing remote software and data resources. Applications built on this infrastructure have great potential for addressing and solving large scale chemical, pharmaceutical, and material science problems. The article describes the concept behind grid computing and will present the OpenMolGRID system that is an open computing grid for molecular science and engineering.

A general treatment of solubility. 2. QSPR prediction of free energies of solvation of specified solutes in ranges of solvents.

As part of our general QSPR treatment of solubility (started in the preceding paper), we now present quantitative relationships between solvent structures and the solvation free energies of individual solutes. Solvation free energies of 80 diverse organic solutes are each modeled in a range from 15 to 82 solvents using our CODESSA PRO software. Significant correlations (in terms of squared correlation coefficient) are found for all the 80 solutes: the best fit is obtained for n-propylamine (R(2) = 0.

A general treatment of solubility. 1. The QSPR correlation of solvation free energies of single solutes in series of solvents.

We present an extended QSPR modeling of solubilities of about 500 substances in series of up to 69 diverse solvents. The models are obtained with our new software package, CODESSA PRO, which is furnished with an advanced variable selection procedure and a large pool of theoretically derived molecular descriptors. The squared correlation coefficients and squared standard deviations (variances) range from 0.

The present utility and future potential for medicinal chemistry of QSAR/QSPR with whole molecule descriptors.

Whole-molecule descriptors are obtained computationally from molecular structures using a variety of programs. Their applications are reviewed in the areas of solubility, bioavailability, bio- and nonbio-degradability and toxicity.

Six-membered cyclic ureas as HIV-1 protease inhibitors: a QSAR study based on CODESSA PRO approach. Quantitative structure-activity relationships.

Quantitative structure-activity relationships (QSAR) for HIV-1 protease inhibitory activity of substituted tetrahydropyrimidinones have been produced using CODESSA PRO methodology and software. The best four-parameter equation (R(2)(cv)=0.847) allowed us to reveal two main structural factors which are strongly correlated with the title activity: molecular hydrophobicity and ability to form hydrogen bonds with the target enzyme.

Prediction of ultraviolet spectral absorbance using quantitative structure-property relationships.

High performance liquid chromatography (HPLC) with ultraviolet (UV) spectrophotometric detection is a common method for analyzing reaction products in organic chemistry. This procedure would benefit from a computational model for predicting the relative response of organic molecules. Models are now reported for the prediction of the integrated UV absorbance for a diverse set of organic compounds using a quantitative structure-property relationship (QSPR) approach.

Correlation of the melting points of potential ionic liquids (imidazolium bromides and benzimidazolium bromides) using the CODESSA program.

The melting points of several imidazolium-based ionic liquids or ionic liquid analogues were correlated using the CODESSA program in order to develop predictive tools for determination of suitable ionic liquid salts. The data set consisted of melting point data (degrees C) for 104 substituted imidazolium bromides divided on the basis of the N-substituents into three subsets: A-57 compounds, B-29 compounds, and C-18 compounds. The 45 benzimidazolium bromides form set D.

QSPR correlation of the melting point for pyridinium bromides, potential ionic liquids.

In an attempt to develop predictive tools for the determination of new ionic liquid solvents, QSPR models for the melting points of 126 structurally diverse pyridinium bromides in the temperature range 30-200 degrees C were developed with the CODESSA program. Six- and two-descriptor equations with squared correlation coefficients (R(2)) of 0.788 and 0.