Review of Chemometrics Applied to Spectroscopy: 1985-95, Part 2

INTRODUCTION

Before beginning Part 2 of this review, a caveat noted by Deming and Palasota is brought to the reader's attention: [1] “Press et al. [2] have emphasized that data ‘consist of numbers, of course. But these numbers are fed into the computer, not produced by it. These are numbers to be treated with considerable respect, never to be tampered with, nor subjected to a numerical process whose character you do not completely understand. You are well advised to acquire reverence for data that is rather diferent fiom the “sporty” attitude which is sometimes allowable, or even commendable, in other numerical tasks.’ Yet by and large within chemometrics, preprocessing often seems to be carried out with little understanding of its fundamental efect on the structure of the data.”     

Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations

Molecular dynamics simulations in explicit solvent were applied to predict the hydration free energies for 23 small organic molecules in blind SAMPL2 test. We found good agreement with experimental results, with an RMS error of 2.82 kcal/mol over the whole set and 1.86 kcal/mol over all the molecules except several hydroxyl-rich compounds where we find evidence for a systematic error in the force field. We tested two different solvent models, TIP3P and TIP4P-Ew, and obtained very similar hydration free energies for these two models; the RMS difference was 0.64 kcal/mol. We found that preferred conformation of the carboxylic acids in water differs from that in vacuum. Surprisingly, this conformational change is not adequately sampled on simulation timescales, so we apply an umbrella sampling technique to include free energies associated with the conformational change. Overall, the results of this test reveal that the force field parameters for some groups of molecules (such as hydroxyl-rich compounds) still need to be improved, but for most compounds, accuracy was consistent with that seen in our previous tests.     

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

Alchemical free energy calculations are becoming a useful tool for calculating absolute binding free energies of small molecule ligands to proteins. Here, we find that the presence of multiple metastable ligand orientations can cause convergence problems when distance restraints alone are used. We demonstrate that the use of orientational restraints can greatly accelerate the convergence of these calculations. However, even with this acceleration, we find that sufficient sampling requires substantially longer simulations than are used in many published protocols. To further accelerate convergence, we introduce a new method of configuration space decomposition by orientation which reduces required simulation lengths by at least a factor of 5 in the cases examined. Our method is easily parallelizable, well suited for cases where a ligand cocrystal structure is not available, and can utilize initial orientations generated by docking packages.     

The SAMPL4 host–guest blind prediction challenge: an overview

Prospective validation of methods for computing binding affinities can help assess their predictive power and thus set reasonable expectations for their performance in drug design applications. Supramolecular host–guest systems are excellent model systems for testing such affinity prediction methods, because their small size and limited conformational flexibility, relative to proteins, allows higher throughput and better numerical convergence. The SAMPL4 prediction challenge therefore included a series of host–guest systems, based on two hosts, cucurbit[7]uril and octa-acid. Binding affinities in aqueous solution were measured experimentally for a total of 23 guest molecules. Participants submitted 35 sets of computational predictions for these host–guest systems, based on methods ranging from simple docking, to extensive free energy simulations, to quantum mechanical calculations. Over half of the predictions provided better correlations with experiment than two simple null models, but most methods underperformed the null models in terms of root mean squared error and linear regression slope. Interestingly, the overall performance across all SAMPL4 submissions was similar to that for the prior SAMPL3 host–guest challenge, although the experimentalists took steps to simplify the current challenge. While some methods performed fairly consistently across both hosts, no single approach emerged as consistent top performer, and the nonsystematic nature of the various submissions made it impossible to draw definitive conclusions regarding the best choices of energy models or sampling algorithms. Salt effects emerged as an issue in the calculation of absolute binding affinities of cucurbit[7]uril-guest systems, but were not expected to affect the relative affinities significantly. Useful directions for future rounds of the challenge might involve encouraging participants to carry out some calculations that replicate each others’ studies, and to systematically explore parameter options.     

Synthesis,Characterization, and Structure of Some New Substituted 5,6-Fused Ring Pyridazines

Pyridazines are an important class of heterocyclic compounds as a result of their materials and commercial applications. The synthesis of 5,6-fused ring pyridazines 2a–h from 1,2-diacylcyclopentadienes (fulvenes) 1a–h is described herein. This route was quite general, and features an efficient and convenient two-step synthesis of a series of 5,6-fused ring 1,2-disubstituted pyridazines using enolized 1,2-disubstituted fulvenes in a methanolic solution of hydrazine. Full characterization of newly formed fulvene 1e and pyridazines 2a–h are reported. Single-crystal X-ray analysis confirms the molecular structure of pyridazine 2f, which displayed the expected pyridazine fused to the cyclopentadienyl moiety. Adding to their real world capabilities in electronic devices, compounds 2a–h display reasonably high stability in solution and in air at room temperature.

The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations

Journal of Computer-Aided Molecular Design - Approaches for computing small molecule binding free energies based on molecular simulations are now regularly being employed by academic and industry...