Gradient discontinuities in calculations involving molecular surface area

The free energy of solvation of a polypeptide or a protein can be expressed in terms of the accessible surface area of the molecule. Algorithms for energy minimization or for molecular dynamics, which involve the first derivatives of the energy, including the free energy of solvation, are commonly used in the conformational analysis of proteins. Discontinuities of the first derivatives, which occur in the accessible surface area and, hence, in the solvation energy, can cause serious numerical problems. In this paper, we describe all the situations in which the gradient of the molecular surface area becomes discontinuous.     

Calculation of hydrophobic interactions from molecular dynamics,surface areas,and experimental hydrocarbon solubilities

Using experimental solubilities and partial pressures for hydrocarbon solution in water and molecular dynamics calculations of hydrocarbon water interaction energies, hydrocarbon–water cavity potentials are obtained and then plotted vs. accessible surface area. The data used is mainly for aliphatic hydrocarbons, but benzene is included. Molecular dynamics calculations of pairs of hydrocarbon molecules together with the cavity potential curve are then used to obtain hydrophobic interaction free energies between the hydrocarbon pairs. While the cavity potential change is related to a change in surface area for hydrocarbon systems, the hydrocarbon–water interaction energy is not, so that the hydrophobic binding energy is not. The results are in agreement with previous results by a different method (R.B. Hermann, In Seventh Jerusalem Symposium on Quantum Pharmacology, E. Bergman and B. Pullman, Eds., D. Reidel, Dordrecht, 1974, p. 441) in that there is little or no solvent-induced binding free energy between small hydrocarbon molecules in a dilute aqueous solution. It is proposed that the cavity potential vs. accessible surface area curve obtained here can be used together with OPLS parameters to calculate both hydrocarbon–water solvation free energies and hydrophobic interactions. © 1993 John Wiley & Sons, Inc.     

Effect of surface area on equilibrium pressure. Adsorption approach

Changing droplet radii in a liquid-vapor system is due to the phase transition on the droplet surface. As a variation of the internal energy does not depend on the way the change occurs, we can imagine that a gas condenses on a droplet surface in two stages: in the first stage, autoadsorption occurs on the liquid surface, and in the second stage, adsorbed molecules transfer into the volume by diffusion. Assuming that the energetic effects of the diffusion are independent of the surface curvature, one may conclude that if two liquid bodies differ only with respect to their geometry, the difference of enthalpies of condensation on their surfaces, DeltaH(bd), is equal to the variation of energies of autoadsorption. An estimation of DeltaH(bd) for the simple bodies is presented, and the relationship between the saturation pressure and droplet radii is derived. In the range of micrometer dimensions, the new equation and the Kelvin model lead to close results; for nanocapillaries, the Kelvin equation predicts a divergence of hysteresis loops, whereas the new equation adequately describes the observations. The classical model presumes that a surface area, A, affects the free energy, while the new approach is based on the assumption that A is the repository for the internal energy.     

Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature

New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations.     

The impact of surface area,volume, curvature,and Lennard–Jones potential to solvation modeling

This article explores the impact of surface area, volume, curvature, and Lennard–Jones (LJ) potential on solvation free energy predictions. Rigidity surfaces are utilized to generate robust analytical expressions for maximum, minimum, mean, and Gaussian curvatures of solvent–solute interfaces, and define a generalized Poisson–Boltzmann (GPB) equation with a smooth dielectric profile. Extensive correlation analysis is performed to examine the linear dependence of surface area, surface enclosed volume, maximum curvature, minimum curvature, mean curvature, and Gaussian curvature for solvation modeling. It is found that surface area and surfaces enclosed volumes are highly correlated to each other's, and poorly correlated to various curvatures for six test sets of molecules. Different curvatures are weakly correlated to each other for six test sets of molecules, but are strongly correlated to each other within each test set of molecules. Based on correlation analysis, we construct twenty six nontrivial nonpolar solvation models. Our numerical results reveal that the LJ potential plays a vital role in nonpolar solvation modeling, especially for molecules involving strong van der Waals interactions. It is found that curvatures are at least as important as surface area or surface enclosed volume in nonpolar solvation modeling. In conjugation with the GPB model, various curvature‐based nonpolar solvation models are shown to offer some of the best solvation free energy predictions for a wide range of test sets. For example, root mean square errors from a model constituting surface area, volume, mean curvature, and LJ potential are less than 0.42 kcal/mol for all test sets. © 2016 Wiley Periodicals, Inc.     

Parametrization strategy for the MolFESD concept: quantitative surface representation of local hydrophobicity

We derive a new model for the established concept of the molecular free energy surface density (MolFESD) yielding a more rigorous representation of local surface contributions to the overall hydrophobicity of a molecule. The model parametrization makes efficient use of both local and global information about solvation thermodynamics, as formulated earlier for the problem of predicting free energies of hydration. The free energy of transfer is separated into an interaction contribution and a term related to the cavity formation. Interaction and cavity components are obtained from the statistical three-dimensional (3D) free energy density and a linear combination of surface and volume terms, respectively. An appropriate molecular interaction field generated by the program Grid is used as an approximate representation of the interaction part of the 3D free energy density. We further compress the 3D density by means of a linear combination of localized surface functions allowing for the derivation of local hydrophobic contributions in the form of a free energy surface density. For a set of 400 compounds our model yields significant correlation (R(2) = 0.95, sigma = 0.57) between experimental and calculated log P values. The final model is applied to establish a correlation between partial free energies of transfer for a series of sucrose derivatives and their relative sweetness, as studied earlier in the group of the authors. We find considerable improvement regarding the rms error of the regression thus validating the presented approach.     

Line tension effects for liquid droplets on circular surface domains

We study the morphologies of single liquid droplets wetting a substrate in the presence of the line tension of the three-phase contact line. On a homogeneous substrate, the line tension leads to a discontinuous unbinding of the droplet if its volume is decreased below a critical value. For a droplet wetting a structured surface with a circular domain, a line tension contrast gives rise to discontinuous depinning transitions of the contact line from the domain boundary as the droplet volume is varied. We calculate the corresponding free energy bifurcation diagram analytically for axisymmetric droplet shapes. Numerical minimization of the droplet free energy shows that line tension contrasts can stabilize nonaxisymmetric droplet shapes, thus modifying the bifurcation diagram. These latter shapes should be accessible to experiments and can be used to reveal the presence of a line tension contrast.     

The solid surface free energy calculation. I. In defense of the multicomponent approach

The acid-base approach to the calculation of solid surface free energy and liquid-liquid interfacial tensions is a practical example of application of correlation analysis, and thus it is an approximate approach. In these limits, and provided that wide and well-obtained sets of contact angles or interfacial tension data are used for their computation, surface tension components can be considered as material properties. Although their numerical value depends on the characteristics of the chosen reference material, their chemical meaning is independent on the selected scale. Contact angles contain accessible information about intermolecular forces; using surface tension component (STC) acid-base theory, one can extract this information only making very careful use of the mathematical apparatus of correlation analysis. The specific mathematical methods used to obtain these results are illustrated by using as an example a base of data obtained by the supporters of the equation-of-state theory (EQS). The achievements are appreciably good and the agreement between STC and EQS is discussed.     

The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

The development and parameterization of a solvent potential of mean force designed to reproduce the hydration thermodynamics of small molecules and macromolecules aimed toward applications in conformation prediction and ligand binding free energy prediction is presented. The model, named SGB/NP, is based on a parameterization of the Surface Generalized Born continuum dielectric electrostatic model using explicit solvent free energy perturbation calculations and a newly developed nonpolar hydration free energy estimator motivated by the results of explicit solvent simulations of the thermodynamics of hydration of hydrocarbons. The nonpolar model contains, in addition to the more commonly used solvent accessible surface area term, a component corresponding to the attractive solute-solvent interactions. This term is found to be important to improve the accuracy of the model, particularly for cyclic and hydrogen bonding compounds. The model is parameterized against the experimental hydration free energies of a set of small organic molecules. The model reproduces the experimental hydration free energies of small organic molecules with an accuracy comparable or superior to similar models employing more computationally demanding estimators and/or a more extensive set of parameters.     

Protein surface area and retention in hydrophobic interaction chromatography

Summary Molecular surface areas accessible to a 4 ? diameter spherical probe were calculated from crystallographic data for five proteins: α-chymotrypsinogen A, lysozyme, trypsinogen, ribonuclease A and ribonuclease S. The retention factors of various proteins were measured on stationary phases having polyether- and phenylligates and with aqueous eluents containing (NH₄)₂SO₄, Na₂SO₄ or NaCl at pH 7.0. The logarithmic retention factors were plotted against the salt molality and the hydrophobic interaction parameters evaluated from the limiting slopes of the plots at high salt concentrations for the proteins in the chromatographic systems investigated. The hydrophobic interaction parameters thus obtained were linear in both the molecular surface areas of the proteins and the molal surface tension increments of the salts. The experimental results obtained with these relatively simple proteins of known molecular structure, which were available in high purity, support earlier theoretical predictions for the dependence of the hydrophobic interaction parameter on the surface area of the protein and the surface tension raising effect of the salt.     

Develop and test a solvent accessible surface area-based model in conformational entropy calculations

It is of great interest in modern drug design to accurately calculate the free energies of protein-ligand or nucleic acid-ligand binding. MM-PBSA (molecular mechanics Poisson-Boltzmann surface area) and MM-GBSA (molecular mechanics generalized Born surface area) have gained popularity in this field. For both methods, the conformational entropy, which is usually calculated through normal-mode analysis (NMA), is needed to calculate the absolute binding free energies. Unfortunately, NMA is computationally demanding and becomes a bottleneck of the MM-PB/GBSA-NMA methods. In this work, we have developed a fast approach to estimate the conformational entropy based upon solvent accessible surface area calculations. In our approach, the conformational entropy of a molecule, S, can be obtained by summing up the contributions of all atoms, no matter they are buried or exposed. Each atom has two types of surface areas, solvent accessible surface area (SAS) and buried SAS (BSAS). The two types of surface areas are weighted to estimate the contribution of an atom to S. Atoms having the same atom type share the same weight and a general parameter k is applied to balance the contributions of the two types of surface areas. This entropy model was parametrized using a large set of small molecules for which their conformational entropies were calculated at the B3LYP/6-31G* level taking the solvent effect into account. The weighted solvent accessible surface area (WSAS) model was extensively evaluated in three tests. For convenience, TS values, the product of temperature T and conformational entropy S, were calculated in those tests. T was always set to 298.15 K through the text. First of all, good correlations were achieved between WSAS TS and NMA TS for 44 protein or nucleic acid systems sampled with molecular dynamics simulations (10 snapshots were collected for postentropy calculations): the mean correlation coefficient squares (R2) was 0.56. As to the 20 complexes, the TS changes upon binding; TΔS values were also calculated, and the mean R2 was 0.67 between NMA and WSAS. In the second test, TS values were calculated for 12 proteins decoy sets (each set has 31 conformations) generated by the Rosetta software package. Again, good correlations were achieved for all decoy sets: the mean, maximum, and minimum of R2 were 0.73, 0.89, and 0.55, respectively. Finally, binding free energies were calculated for 6 protein systems (the numbers of inhibitors range from 4 to 18) using four scoring functions. Compared to the measured binding free energies, the mean R2 of the six protein systems were 0.51, 0.47, 0.40, and 0.43 for MM-GBSA-WSAS, MM-GBSA-NMA, MM-PBSA-WSAS, and MM-PBSA-NMA, respectively. The mean rms errors of prediction were 1.19, 1.24, 1.41, 1.29 kcal/mol for the four scoring functions, correspondingly. Therefore, the two scoring functions employing WSAS achieved a comparable prediction performance to that of the scoring functions using NMA. It should be emphasized that no minimization was performed prior to the WSAS calculation in the last test. Although WSAS is not as rigorous as physical models such as quasi-harmonic analysis and thermodynamic integration (TI), it is computationally very efficient as only surface area calculation is involved and no structural minimization is required. Moreover, WSAS has achieved a comparable performance to normal-mode analysis. We expect that this model could find its applications in the fields like high throughput screening (HTS), molecular docking, and rational protein design. In those fields, efficiency is crucial since there are a large number of compounds, docking poses, or protein models to be evaluated. A list of acronyms and abbreviations used in this work is provided for quick reference.     

Variations of surfactant monolayer surface density in induced steady wave regime

Fluctuations of an insoluble surfactant concentration along the free liquid surface induced by steady surface waves are considered theoretically. The energy of a waved surface is assumed to consist of surface tension, curvature, and van der Waals energy components. Dependencies of the surface tension and the bending stiffness versus the surfactant concentration are assumed to be linear relative to some reference level. The van der Waals energy is taken in the form of interaction term for a thin film. Minimization of the total energy allows the expression for the deviations of concentration to be obtained. The distribution of a surfactant concentration relative to some reference level has been found to be periodic, with a period that is half of the wave period, and the amplitude of oscillations is a function of a wave number that is very similar to the Landau expansion of the free-energy near the critical point in phase transitions.     

An examination of the basic postulates of surface chemistry: A variational calculus analysis of the classic rotating drop experiment

A demonstration, using the variational calculus, is given showing that it is impossible to describe the excess free energy in any liquid surface by the use of a single energy parameter, the surface tension, without violating the laws of motion. The addition of the required second parameter, the flexural rigidity, is shown to be adequate to explain published data on the systemn-hexadecane/glycerol, and to demonstrate that for small radii of curvature, the curvature parameter may contribute orders of magnitude more to the surface energy than the surface tension does.     

Excess densities and equimolar surfaces for spherical cavities in water

For hard spheres with a radius up to 10 A in TIP4P water under ambient conditions, the author studies how the excess number of molecules at the accessible surface depends on the radius of the cavity. Simulation results derived from excess volumes are discussed in terms of radial distribution functions (rdfs), which compare well with extended simple point charge and theoretical rdfs from the literature. The excess number of molecules at the accessible surface inserted in the expression which refers to an arbitrary dividing surface enables one to find the position of the equimolar surface. The surface tension corresponding to this dividing surface was obtained from values of the free energy of cavity formation. For radii in the range of the simulation data, its behavior with curvature is quite different from that usually shown in the literature. A model, which describes how the excess number of molecules at the accessible surface changes with the radius, is discussed in the large length limit by examining consistent rdfs described by a simple analytical form. The inclusion in the model of a logarithmic term has also been considered. Comparison with theoretical results from the literature shows a good agreement for a cavity with a radius of 20 A. For a radius of 100 A and beyond, the model predicts instead sharper density profiles. Such differences have a poor effect on the surface tension at the equimolar surface.     

Use of surface area computations to describe atom-atom interactions

Accessible surface (ASA) and atomic contact (ACA) areas are powerful tools for protein structure analysis. However, their use for analysis purposes could be extended if a relationship between them and protein stability could be found. At present, this is the case only for ASAs, which have been used to assess the contribution of the hydrophobic effect to protein stability. In the present work we study whether there is a relationship between atomic contact areas and the free energy associated to atom-atom interactions. We utilise a model in which the contribution of atomic interactions to protein stability is expressed as a linear function of the accessible surface area buried between atom pairs. We assess the validity of this hypothesis, using a set of 124 lysozyme mutants (Matthews, 1995, Adv Protein Chem, 249–278) for which both the X-ray structure and the experimental stability are known. We tested this assumption for residue representations with increasing numbers of atom types. Our results indicate that for simple residue representations, with only 4 to 5 atom types, there is not a clear linear relationship between stability and buried accessible area. However, this relationship is observed for representations with 6 to 9 atom types, where gross heterogeneities in the atom type definition are eliminated. Finally, we also study a version of the linear model in which the atom- atom interactions are represented utilising a simple function for the buried accessible area, which may be useful for protein structure prediction studies.     

FACTS: Fast analytical continuum treatment of solvation

An efficient method for calculating the free energy of solvation of a (macro)molecule embedded in a continuum solvent is presented. It is based on the fully analytical evaluation of the volume and spatial symmetry of the solvent that is displaced from around a solute atom by its neighboring atoms. The two measures of solvent displacement are combined in empirical equations to approximate the atomic (or self) electrostatic solvation energy and the solvent accessible surface area. The former directly yields the effective Born radius, which is used in the generalized Born (GB) formula to calculate the solvent-screened electrostatic interaction energy. A comparison with finite-difference Poisson data shows that atomic solvation energies, pair interaction energies, and their sums are evaluated with a precision comparable to the most accurate GB implementations. Furthermore, solvation energies of a large set of protein conformations have an error of only 1.5%. The solvent accessible surface area is used to approximate the nonpolar contribution to solvation. The empirical approach, called FACTS (Fast Analytical Continuum Treatment of Solvation), is only four times slower than using the vacuum energy in molecular dynamics simulations of proteins. Notably, the folded state of structured peptides and proteins is stable at room temperature in 100-ns molecular dynamics simulations using FACTS and the CHARMM force field.     

Total Gaussian curvature,drop shapes and the range of applicability of drop shape techniques

Drop shape techniques are used extensively for surface tension measurement. It is well-documented that, as the drop/bubble shape becomes close to spherical, the performance of all drop shape techniques deteriorates. There have been efforts quantifying the range of applicability of drop techniques by studying the deviation of Laplacian drops from the spherical shape. A shape parameter was introduced in the literature and was modified several times to accommodate different drop constellations. However, new problems arise every time a new configuration is considered. Therefore, there is a need for a universal shape parameter applicable to pendant drops, sessile drops, liquid bridges as well as captive bubbles. In this work, the use of the total Gaussian curvature in a unified approach for the shape parameter is introduced for that purpose. The total Gaussian curvature is a dimensionless quantity that is commonly used in differential geometry and surface thermodynamics, and can be easily calculated for different Laplacian drop shapes. The new definition of the shape parameter using the total Gaussian curvature is applied here to both pendant and constrained sessile drops as an illustration. The analysis showed that the new definition is superior and reflects experimental results better than previous definitions, especially at extreme values of the Bond number.     

Rationalization of the behavior of solid-liquid surface free energy of water in Cassie and Wenzel wetting states on rugged solid surfaces at the nanometer scale

The present work aims to contribute to the understanding at a molecular level of the origin of the hydrophobic nature of surfaces exhibiting roughness at the nanometer scale. Graphite-based smooth and model surfaces whose roughness dimension stretches from a few angstroms to a few nanometers were used in order to generate Cassie and Wenzel wetting states of water. The corresponding solid-liquid surface free energies were computed by means of molecular dynamics simulations. The solid-liquid surface free energy of water-smooth graphite was found to be -12.7 ± 3.3 mJ/m(2), which is in reasonable agreement with a value estimated from experiments and fully consistent with the features of the employed model. All the rugged surfaces yielded higher surface free energy. In both Cassie and Wenzel states, the maximum variation of the surface free energy with respect to the smooth surface was observed to represent up to 50% of the water model surface tension. The solid-liquid surface free energy of Cassie states could be well predicted from the Cassie-Baxter equation where the surface free energies replace contact angles. The origin of the hydrophobic nature of surfaces yielding Cassie states was therefore found to be the reduction of the number of interactions between water and the solid surface where atomic defects were implemented. Wenzel's theory was found to fail to predict even qualitatively the variation of the solid-liquid surface free energy with respect to the roughness pattern. While graphite was found to be slightly hydrophilic, Wenzel states were found to be dominated by an unfavorable effect that overcame the favorable enthalpic effect induced by the implementation of roughness. From the quantitative point of view, the solid-liquid surface free energy of Wenzel states was found to vary linearly with the roughness contour length.     

Alpha7 nicotinic acetylcholine receptor agonists: prediction of their binding affinity through a molecular mechanics Poisson-Boltzmann surface area approach

A group of agonists for the alpha7 neuronal nicotinic acetylcholine receptors (nAChRs) was investigated, and their free energies of binding DeltaG(bind) were calculated by applying the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) approach. This method, based on molecular dynamics simulations of fully solvated protein-ligand complexes, allowed us to estimate the contribution of both polar and nonpolar terms as well as the entropy to the overall free energy of binding. The calculated results were in a good agreement with the experimentally determined DeltaG(bind) values, thereby pointing to the MM-PBSA protocol as a valuable computational tool for the rational design of specific agents targeting the neuronal alpha7 nAChR subtypes.     

Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking

In molecular docking, it is challenging to develop a scoring function that is accurate to conduct high-throughput screenings. Most scoring functions implemented in popular docking software packages were developed with many approximations for computational efficiency, which sacrifices the accuracy of prediction. With advanced technology and powerful computational hardware nowadays, it is feasible to use rigorous scoring functions, such as molecular mechanics/Poisson Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) in molecular docking studies. Here, we systematically investigated the performance of MM/PBSA and MM/GBSA to identify the correct binding conformations and predict the binding free energies for 98 protein-ligand complexes. Comparison studies showed that MM/GBSA (69.4%) outperformed MM/PBSA (45.5%) and many popular scoring functions to identify the correct binding conformations. Moreover, we found that molecular dynamics simulations are necessary for some systems to identify the correct binding conformations. Based on our results, we proposed the guideline for MM/GBSA to predict the binding conformations. We then tested the performance of MM/GBSA and MM/PBSA to reproduce the binding free energies of the 98 protein-ligand complexes. The best prediction of MM/GBSA model with internal dielectric constant 2.0, produced a Spearman's correlation coefficient of 0.66, which is better than MM/PBSA (0.49) and almost all scoring functions used in molecular docking. In summary, MM/GBSA performs well for both binding pose predictions and binding free-energy estimations and is efficient to re-score the top-hit poses produced by other less-accurate scoring functions.