Presenting data in such a fashion that they can be used by other scientists.

Data always have an experimental uncertainty, i.e. error limits within which the value is very likely to be found. Although the use of statistics is common as is the use of least squares it remains uncommon to see reported the covariance between parameters for an equation to which data have been fitted. This means that a reader cannot properly calculate the error in an extrapolated or interpolated value. Even when the uncertainties in the least squares parameters are reported, errors calculated without the covariance are often too large and almost always different from the correct values calculated using the full formula. This report will demonstrate the importance of covariance in several examples. Systematic errors are also touched on; solubilities of highly hydrophobic and highly insoluble compounds are very difficult to measure for reasons not widely enough appreciated. Aggregation leading to suspended nanodroplets or nanocrystals can lead to spuriously high apparent solubilities. Another class of systematic errors comes from using an equation which is too simple for a desired extrapolation to a value of interest. The magnitude of this possible error is presented for a number of cases. Extrapolation can lead to a value of some use even though it is very uncertain, but expected uncertainty should be pointed out. Recommendations for good publishing practice are proposed for both authors and editors.

FreeSolv: a database of experimental and calculated hydration free energies, with input files.

This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via http://www.escholarship.org/uc/item/6sd403pz .

SAMPL4, a blind challenge for computational solvation free energies: the compounds considered.

For the fifth time I have provided a set of solvation energies (1 M gas to 1 M aqueous) for a SAMPL challenge. In this set there are 23 blind compounds and 30 supplementary compounds of related structure to one of the blind sets, but for which the solvation energy is readily available. The best current values of each compound are presented along with complete documentation of the experimental origins of the solvation energies. The calculations needed to go from reported data to solvation energies are presented, with particular attention to aspects which are new to this set. For some compounds the vapor pressures (VP) were reported for the liquid compound, which is solid at room temperature. To correct from VPsubcooled liquid to VPsublimation requires ΔSfusion, which is only known for mannitol. Estimated values were used for the others, all but one of which were benzene derivatives and expected to have very similar values. The final compound for which ΔSfusion was estimated was menthol, which melts at 42 °C so that modest errors in ΔSfusion will have little effect. It was also necessary to look into the effects of including estimated values of ΔCp on this correction. The approximate sizes of the effects of inclusion of ΔCp in the correction from VPsubcooled liquid to VPsublimation were estimated and it was noted that inclusion of ΔCp invariably makes ΔGS more positive. To extend the set of compounds for which the solvation energy could be calculated we explored the use of boiling point (b.p.) data from Reaxys/Beilstein as a substitute for studies of the VP as a function of temperature. B.p. data are not always reliable so it was necessary to develop a criterion for rejecting outliers. For two compounds (chlorinated guaiacols) it became clear that inclusion represented overreach; for each there were only two independent pressure, temperature points, which is too little for a trustworthy extrapolation. For a number of compounds the extrapolation from lowest temperature at which the VP was reported to 25 °C was long (sometimes over 100°) so that it was necessary to consider whether ΔCp might have significant effects. The problem is that there are no experimental values and possible intramolecular hydrogen bonds make estimation uncertain in some cases. The approximate sizes of the effects of ΔCp were estimated, and it was noted that inclusion of ΔCp in the extrapolation of VP down to room temperature invariably makes ΔGs more negative.

Blind prediction of solvation free energies from the SAMPL4 challenge.

Here, we give an overview of the small molecule hydration portion of the SAMPL4 challenge, which focused on predicting hydration free energies for a series of 47 small molecules. These gas-to-water transfer free energies have in the past proven a valuable test of a variety of computational methods and force fields. Here, in contrast to some previous SAMPL challenges, we find a relatively wide range of methods perform quite well on this test set, with RMS errors in the 1.2 kcal/mol range for several of the best performing methods. Top-performers included a quantum mechanical approach with continuum solvent models and functional group corrections, alchemical molecular dynamics simulations with a classical all-atom force field, and a single-conformation Poisson-Boltzmann approach. While 1.2 kcal/mol is still a significant error, experimental hydration free energies covered a range of nearly 20 kcal/mol, so methods typically showed substantial predictive power. Here, a substantial new focus was on evaluation of error estimates, as predicting when a computational prediction is reliable versus unreliable has considerable practical value. We found, however, that in many cases errors are substantially underestimated, and that typically little effort has been invested in estimating likely error. We believe this is an important area for further research.

Click fleximers: a modular approach to purine base-expanded ribonucleoside analogues.

The synthesis of nucleoside analogues incorporating 4-(5-pyrimidinyl)-1,2,3-triazole aglycons as expanded purine nucleobase mimics were accessed using the copper-catalyzed azide-alkyne Huisgen cycloaddition between a ribosyl azide and 5-alkynylpyrimidines. Depending on the nature of the alkyne employed, other nucleoside analogues that possess fluorescence or potential metal-binding properties were prepared. Computational studies were undertaken on the purine analogues and indicate that the heterocycles of the unfused nucleobase prefer a coplanar arrangement and the anti-glycosidic conformer is favoured in most instances.

The SAMPL3 blind prediction challenge: transfer energy overview.

Prediction of the free energy of solvation of a small molecule, or its transfer energy, is a necessary step along the path towards calculating the interactions between molecules that occur in an aqueous environment. A set of these transfer energies were gathered from the literature for series of chlorinated molecules with varying numbers of chlorines based on ethane, biphenyl, and dibenzo-p-dioxin. This focused set of molecules were then provided as a blinded challenge to assess the ability of current computational solvation methods to accurately model the interactions between water and increasingly chlorinated compounds. This was presented as part of the SAMPL3 challenge, which represented the fourth iterative blind prediction challenge involving transfer energies. The results of this exercise demonstrate that the field in general has difficulty predicting the transfer energies of more highly chlorinated compounds, and that methods seem to be erring in the same direction.

The SAMPL2 blind prediction challenge: introduction and overview.

The interactions between a molecule and the aqueous environment underpin any process that occurs in solution, from simple chemical reactions to protein-ligand binding to protein aggregation. Fundamental measures of the interaction between molecule and aqueous phase, such as the transfer energy between gas phase and water or the energetic difference between two tautomers of a molecule in solution, remain nontrivial to predict accurately using current computational methods. SAMPL2 represents the third annual blind prediction of transfer energies, and the first time tautomer ratios were included in the challenge. Over 60 sets of predictions were submitted, and each participant also attempted to estimate the error in their predictions, a task that proved difficult for most. The results of this blind assessment of the state of the field for transfer energy and tautomer ratio prediction both indicate where the field is performing well and point out flaws in current methods.

A blind challenge for computational solvation free energies: introduction and overview.

The accompanying set of papers arose from a recent blind challenge to computational solvation energies. The challenge was based on a set of 63 drug-like molecules for which solvation energies could be extracted from the literature. While the results are encouraging, there is still need for improvement.

By how much is protonated benzene stabilized by coordination of iron tricarbonyl?

Rate and equilibrium measurements for the hydrolysis of the Fe(CO)3-coordinated cyclohexadienyl cation lead to pKR = 4.7 compared with pKR = -2.1 for the uncoordinated ion. The hydrolysis yields exo-coordinated cyclohexadienol 10(7)-fold more rapidly than its endo-isomer, despite the isomers being of similar stability. DFT calculations of the energy of isodesmic transfer of Fe(CO)3 from cyclohexadiene to benzene lead to an estimate of pKa 8 for loss of a proton from the coordinated cyclohexadienyl cation to form Fe(CO)3-coordinated benzene. This implies that the coordinated cation is 33 log units (46 kcal) less acidic than the uncoordinated ion.

Predicting small-molecule solvation free energies: an informal blind test for computational chemistry.

Experimental data on the transfer of small molecules between vacuum and water are relatively sparse. This makes it difficult to assess whether computational methods are truly predictive of this important quantity or merely good at explaining what has been seen. To explore this, a prospective test was performed of two different methods for estimating solvation free energies: an implicit solvent approach based on the Poisson-Boltzmann equation and an explicit solvent approach using alchemical free energy calculations. For a set of 17 small molecules, root mean square errors from experiment were between 1.3 and 2.6 kcal/mol, with the explicit solvent free energy approach yielding somewhat greater accuracy but at greater computational expense. Insights from outliers and suggestions for future prospective challenges of this kind are presented.

No-barrier theory: calculating rates of chemical reactions from equilibrium constants and distortion energies.

No-barrier theory is a new approach to the calculation of rate constants for reactions in solution, from the corresponding equilibrium constants. It requires relatively small molecular orbital theory calculations, and has been very successful. It is in the spirit of Marcus theory, but does not require an "intrinsic barrier". The approach is explained, with an examination of the way in which the ideas on which it is based were "in the air".

Uncatalyzed and amine catalyzed decarboxylation of acetoacetic acid: an examination in terms of No Barrier Theory.

Rate constants for decarboxylation of acetoacetic acid, its anion, and its imine with aminoacetonitrile have been calculated from equilibrium constants and distortion energies using No Barrier Theory. The mechanisms of decarboxylation of both acetoacetic acid and its imine involve preequilibrium formation of the zwitterion.