DSSP is the most commonly used method to assign protein secondary structure. It is based on a hydrogen-bond definition with an energy cutoff. To assess whether hydrogen bonds defined in a parameter-free way may give more generality while preserving accuracy, we examine a series of hydrogen-bond definitions to assign secondary structure for a series of proteins. Assignment by the strongest-acceptor bifurcated definition with provision for unassigned donor hydrogens, termed the SABLE method, is found to match DSSP with 95% agreement. The small disagreement mainly occurs for helices, turns, and bends. While there is no absolute way to assign protein secondary structure, avoiding molecule-specific cutoff parameters should be advantageous in generalizing structure-assignment methods to any hydrogen-bonded system.

A method is presented to evaluate a molecule’s entropy from the atomic forces calculated in a molecular dynamics simulation. Specifically, diagonalization of the mass-weighted force covariance matrix produces eigenvalues which in the harmonic approximation can be related to vibrational frequencies. The harmonic oscillator entropies of each vibrational mode may be summed to give the total entropy. The results for a series of hydrocarbons, dialanine and a β hairpin are found to agree much better with values derived from thermodynamic integration than results calculated using quasiharmonic analysis. Forces are found to follow a harmonic distribution more closely than coordinate displacements and better capture the underlying potential energy surface. The method’s accuracy, simplicity, and computational similarity to quasiharmonic analysis, requiring as input force trajectories instead of coordinate trajectories, makes it readily applicable to a wide range of problems.

The entropy of vaporization at a liquid’s boiling point is well approximated by Trouton’s rule and even more accurately by Hildebrand’s rule. A cell method is used here to calculate the entropy of vaporization for a range of liquids by subtracting the entropy of the gas from that of the liquid. The liquid’s entropy is calculated from the force magnitudes measured in a molecular dynamics simulation based on the harmonic approximation. The change in rotational entropy is not accounted for except in the case of liquid water. The predicted entropies of vaporization agree well with experiment and Trouton’s and Hildebrand’s rules for most liquids and for water except other liquids with hydrogen bonds. This supports the idea that molecular rotation is close to ideal at a liquid’s boiling point if hydrogen bonds are absent; if they are present, then the rotational entropy gain must be included. The method provides a molecular interpretation of those rules by providing an equation in terms of a molecule’s free volume in a liquid which depends on the force magnitudes. Free volumes at each liquid’s boiling point are calculated to be ∼1 Å3 for liquids lacking hydrogen bonds, lower at ∼0.3 Å3 for those with hydrogen bonds, and they decrease weakly with increasing molecular size.Research highlights► A method to calculate a liquid’s entropy of vaporization is proposed. ► The entropy of vaporisation depends on force magnitudes from computer simulation. ► Calculated values agree with experiment, Trouton’s rule and Hildebrand’s rule. ► Free volumes decrease for larger molecules or those with stronger interactions.

A definition that equates a hydrogen bond topologically with a local energy well in the potential energy surface is used to study the structure and dynamics of liquid water. We demonstrate the robustness of this hydrogen-bond definition versus the many other definitions which use fixed, arbitrary parameters, do not account for variable molecular environments, and cannot effectively resolve transition states. Our topology definition unambiguously shows that most water molecules are double acceptors but sizable proportions are single or triple acceptors. Almost all hydrogens are found to take part in hydrogen bonds. Broken hydrogen bonds only form when two molecules try to form two hydrogen bonds between them. The double acceptors have tetrahedral geometry, lower potential energy, entropy, and density, and slower dynamics. The single and triple acceptors have trigonal and trigonal bipyramidal geometry and when considered together have higher density, potential energy, and entropy, faster dynamics, and a tendency to cluster. These calculations use an extended theory for the entropy of liquid water that takes into account the variable number of hydrogen bonds. Hydrogen-bond switching is shown to depend explicitly on the variable number of hydrogen bonds accepted and the presence of interstitial water molecules. Transition state theory indicates that the switching of hydrogen bonds is a mildly activated process, requiring only a moderate distortion of hydrogen bonds. Three main types of switching events are observed depending on whether the donor and acceptor are already sharing a hydrogen bond. The switch may proceed with no intermediate or via a bifurcated-oxygen or cyclic dimer, both of which have a broken hydrogen bond and symmetric and asymmetric forms. Switching is found to be strongly coupled to whole-molecule vibration, particularly for the more mobile single and triple acceptors. Our analysis suggests that even though water is heterogeneous in terms of the number of hydrogen bonds, the coupling between neighbors on various length and time scales brings about greater continuity in its properties.

A practical approach that enables one to calculate the standard free energy of binding from a one-dimensional potential of mean force (PMF) is proposed. Umbrella sampling and the weighted histogram analysis method are used to generate a PMF along the reaction coordinate of binding. At each point, a restraint is applied orthogonal to the reaction coordinate to make possible the determination of the volume sampled by the ligand. The free energy of binding from an arbitrary unbound volume to the restrained bound form is calculated from the ratio of the PMF integrated over the bound region to that of the unbound. Adding the free energy changes from the standard-state volume to the unbound volume and from the restrained to the unrestrained bound state gives the standard free energy of binding. Exploration of the best choice of binding paths is also made. This approach is first demonstrated on a model binding system and then tested on the benzamidine−trypsin system for which reasonable agreement with experiment is found. A comparison is made with other methods to obtain the standard free energy of binding from the PMF.

Two theoretical formulations are proposed and compared for the loss of translational and rotational entropy upon protein−ligand binding in water. The two theories share the same approach to evaluate the translational and rotational entropy of the ligand when bound. The potential of the bound ligand is modeled by six harmonic oscillators that are parametrized from the force and torque magnitudes measured in a molecular dynamics simulation, yielding vibrational and librational entropies. In the aqueous phase, the theories differ because there is no unique way to assign the total entropy to molecules in solution. In one approach, the ligand is allowed unrestricted access to the full solution volume at the standard concentration and is assigned the same translational and rotational entropy as if it were an ideal gas. We term this a “molecule-frame” (MF) theory because it considers configurational space in the reference frame of the molecule of interest. The entropy of the solvent is penalized because it is excluded from the molecule’s volume. In the second theory, all molecules including the solvent are confined by their neighbors in mean-field configurational volumes. This we term a “system-frame” (SF) theory because the configurational space available to all molecules is considered in the reference frame of the whole system. Molecules have vibrational and librational entropy in the same way as they do when bound. In addition, the discrete size of the solvent molecules quantizes the configurational space into an effective number of minima according to the solute molecule’s standard concentration and the mean volume of a solvent molecule. This leads to the cratic entropy expressed in terms of the solute molecule’s mole fraction. The equivalent number of minima in rotational space depends on both the solute molecule’s volume and the solvent molecule’s volume. This leads to an equation for the orientational entropy based on the proposed concept of “angle fraction”. The MF and SF theories are applied to calculate the translational and rotational entropy losses involved in the formation of six different protein−ligand complexes, in two of which the ligand is water. The MF entropy losses range from −80 to −142 J K−1 mol−1 for ligands at the 1 M standard-state concentration and from −52 to −63 J K−1 mol−1 for water at the 55.6 M standard-state concentration. They depend logarithmically on both the number and strength of interactions between the ligand and protein through the forces and torques. This is observed to lead to moderate dependencies on the ligands’ moments of inertia and masses. The SF entropy losses are smaller and range from −50 to −75 J K−1 mol−1 for ligands at the 1 M standard-state concentration and from 0 to −12 J K−1 mol−1 for water. They depend logarithmically on the ligand solvent’s molecular volume and weakly on the relative strengths of the ligand’s interactions with the protein and water. The cratic entropy loss in water at the standard concentration is constant and is also demonstrated to be implicit in MF theories. Entropy losses from the two approaches are also compared with those from other computational approaches and with experiment. The use of the force and torque magnitudes leads to smaller bound volumes than are obtained from ligand-displacement approaches. The general agreement of the SF entropy losses with those from experiment suggests that the SF theory is more consistent with the assumptions made in experimental measurements than the MF solvation theories, which would require a compensating entropy gain in the solvent in order to agree.

A method to calculate the classical and quantum free energy of a liquid from a computer simulation by using cell theory [J. Chem. Phys. 2007, 126, 064504] is tested for liquid water and ice Ih against experiment as a function of temperature. This fast and efficient method reproduces reasonably well the experimental values of entropy, enthalpy, and free energy of a liquid across the supercooled, stable, and superheated range of temperatures considered. There are small differences between classical and quantum results of water at 298 K, necessitating a small correction term to reproduce water’s enthalpy of vaporisation. Only at higher temperatures is entropy underestimated by up to 9 J K−1 mol−1 as verified by thermodynamic integration calculations. Satisfactory agreement for ice, however, is only obtained by using the quantum formulation. Even then, at higher temperatures, the entropies exceed experiment by up to 15 J K−1 mol−1. Further insight into the quantum nature of water is provided by inspecting the temperature dependence of the frequencies. The harmonic approximation is further supported by the harmonic force and torque distributions and the very similar entropies obtained from the force and torque variances. All these results suggest that the single molecule harmonic oscillator approximation for water, although not exact, provides a rapid, insightful, and useful means to evaluate the thermodynamic properties of water from a computer simulation in a way that can account for the quantization of water’s energy levels.