Interaction energy, single water molecules

The quantitative comparisons with the available experimental data are less favorable in this case. The transition state and product in water appear to be shifted up in energy by about 15 kcal/mol. The computed curves are more in line with experimental data for ketones, where formation of hydrates is far less favorable than for formaldehyde. The discrepancy likely comes from an overly exothermic hydration energy for the charge-localized hydroxide ion, which lowers the reactant end of the pmfs. This results from the use of two-body potential functions, that is, the TIP4P water molecules are not polarized by the ion, so water-water repulsions between molecules in the first solvent shell are underestimated. Until the polarization can be explicitly treated, ions that have attractive interactions with single water molecules greater than about 18-20 kcal/mol should probably be avoided. For example, CN would be less problematic since its single molecule hydration enthalpy is only 14 kcal/mol, versus 25 for... 

In the last years the problem of the proper theoretical treatment of solvation effects in DNA has been solved to a great extent (17). In a number of publications the interaction energy between water molecules and the nucleotide bases (28), base pairs (29), single (30), and double helices (31) of DNA has been calculated. Recently, also the complete solvent structure of a B-DNA double helix fragment with 12 base pairs and the corresponding sugar and phosphate units has been determined (32). In these Monte Carlo simulations, 447 water molecules have been included and their interaction energies and probability distributions (at a temperature of 300 K) have been calculated. In recent publications the Na+ ion structure of B-DNA at different humidities, ionic concentrations and temperature has been presented (33). 

The ab initio calculations were completed for a CO2 molecule, a single water molecule, and the C02 H20 complex for multiple levels of theory and basis sets in order to calculate the interaction energy of the complex. Interaction energies were calculated as follows ... 

The literature force field models were used with the TIP3P water model to calculate the interaction of the CO2 with a single water molecule, as was done in the ab initio calculations presented above [22-24], When the literature CO2 complexes were compared to the ab initio complexes, the Steele model provided the best match with the ab initio data, with an interaction energy and distance of... 

Table 12-4. Computed interaction energies (in kcal/mol) of a single water molecule and a monomolecular water layer, respectively, with the two different (001) kaolinite surfaces...

Figure 2. Interaction energy at the SCF and MP2 levels ( ) and the corresponding counterpoise corrected levels (o) for a single water molecule approaching the carbonyl oxygen atom of formic acid.

We have made the following approximate calculation to estimate protein-water interactions by a less cumbersome procedure it is assumed that the protein molecule has a unique fixed structure determined by x-ray crystallography and interactions are calculated between the protein and a single water molecule in the absence of other solvent molecules. Using this simple system, one may consider all positions and orientations of the single water molecule relative to the protein in a step-wise manner. We present here the result of this calculation for the crystal of bovine pancreatic trypsin inhibitor (BPTI). The calculated energy, mapped in three dimensions, is a highly informative description of the crystal s solvent space. 

This analysis of water structure in the crystal of a protein, based on consideration of crystallographically-determined water locations and of a map of the energy of interaction of a single water molecule with the protein, demonstrates what we believe to... 

---