Energies Of Solute Molecules Research Articles

Concentration Depth Profile-Based Multilayer Sorption Surface Tension Model for Aqueous Solutions.

Surface tension of chemically complex aqueous droplets is significant to atmospheric aerosol particle dynamics and fate. Isotherm-based predictive surface tension models are available which consider one layer of solute molecules sorbed at the liquid-vapor interface. However, the concentration depth profile (CDP) of solute molecules near the surface is continuous, making the single monolayer assumption inappropriate. Here, this work extends the isotherm framework by dividing the surface region into multiple layers to capture the continuity of the spatial distribution of solute molecules for binary solutions. Partition functions are established based on the displacement of water molecules by solute molecules. The number of displaced water molecules and energy of solute molecules at the surface and in the bulk are key model parameters relating surface tension and solute activity. Number densities of surface molecules from molecular dynamic (MD) simulations available in the literature are applied to determine model parameters. Finally, the model is extended to predict surface tension for mixture solutions, considering both independent and dependent adsorptions of different solute species to the liquid-vapor interface. The proposed model works well for both electrolyte and nonelectrolyte solutions and their mixtures from pure solvent to pure solute.

MMPBSA.py: An Efficient Program for End-State Free Energy Calculations

MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.

Excited States and Photochemistry of Bicyclo[1.1.0]butane

Calculations on the excited states of bicyclo[1.1.0]butane in the gas phase by different theoretical methods using several basis sets were performed. In general, the agreement between calculated and experimental excitation energies for bicyclo[1.1.0]butane in the gas phase is very good. Reviews of the solution-phase photochemistry of bicyclo[1.1.0]butane as well as previous calculations on the ground and excited states of bicyclo[1.1.0]butane are given to provide a necessary perspective of the photochemistry of bicyclo[1.1.0]butane in solution. To simulate the solution-phase photochemistry of bicyclo[1.1.0]butane, a well potential is added to the Kirkwood-Onsager model for obtaining solvation energies of molecules in solution. The addition of the well potential gives rise to a blue-shift of all gas-phase excitation energies in solution. However, there is also the very important added effect of providing an increase in Rydberg-valence mixing of solution-phase excited states. It is this mixing of antibonding valence character into the solution-phase excited states that is necessary to explain the solution-phase photochemistry of bicyclo[1.1.0]butane through bond-breaking and the formation of a conical intersection intermediate.

Electronic excitation energies of molecules in solution within continuum solvation models: Investigating the discrepancy between state-specific and linear-response methods

In a recent article [R. Cammi, S. Corni, B. Mennucci, and J. Tomasi, J. Chem. Phys. 122, 104513 (2005)], we demonstrated that the state-specific (SS) and the linear-response (LR) approaches, two different ways to calculate solute excitation energies in the framework of quantum-mechanical continuum models of solvation, give different excitation energy expressions. In particular, they differ in the terms related to the electronic response of the solvent. In the present work, we further investigate this difference by comparing the excitation energy expressions of SS and LR with those obtained through a simple model for solute-solvent systems that bypasses one of the basic assumptions of continuum solvation models, i.e., the use of a single Hartree product of a solute and a solvent wave function to describe the total solute-solvent wave function. In particular, we consider the total solute-solvent wave function as a linear combination of the four products of two solute states and two solvent electronic states. To maximize the comparability with quantum-mechanical continuum model the resulting excitation energy expression is recast in terms of response functions of the solvent and quantities proper for the solvated molecule. The comparison of the presented expressions with the LR and SS ones enlightens the physical meaning of the terms included or neglected by these approaches and shows that SS agrees with the results of the four-level model, while LR includes a term classified as dispersion in previous treatments and neglects another related to electrostatic. A discussion on the possible origin of the LR flaw is finally given.

Electronic excitation energies of molecules in solution: State specific and linear response methods for nonequilibrium continuum solvation models

We present a formal comparison between the two different approaches to the calculation of electronic excitation energies of molecules in solution within the continuum solvation model framework, taking also into account nonequilibrium effects. These two approaches, one based on the explicit evaluation of the excited state wave function of the solute and the other based on the linear response theory, are here proven to give formally different expressions for the excitation energies even when exact eigenstates are considered. Calculations performed for some illustrative examples show that this formal difference has sensible effects on absolute solvatochromic shifts (i.e., with respect to gas phase) while it has small effects on relative (i.e., nonpolar to polar solvent) solvatochromic shifts.

Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions

The efficient evaluation of electrostatic energies of macromolecules in aqueous solutions is useful for many problems in theoretical structural biology. A continuum method based on the generalized Born (GB) approximation is implemented here. It is shown that the choice of the dielectric discontinuity surface is critical for obtaining correct electrostatic energies of molecules in solution. In addition, it is demonstrated that an electrostatic model validated on solvation energies (vacuum to water transfer) might not be appropriate for energies in solution and might not yield correct energy ranking of ligand/protein complexes. The agreement between the GB approach and the finite difference solution of the Poisson equation is shown to be very good for both the molecular and the solvent accessible surface. The discrepancies between the GB and the finite difference approach are much lower than the ones due to the use of different surfaces.

Energies of solute molecules from an atom charge–dipole interaction model with a surrounding dielectric: Application to Gibbs energies of proton transfer between carboxylic acids in water

An expression is derived for the electrostatic energy of an array of charged, polarizable atoms representing a solute molecule in a cavity in a dielectric continuum, using a generalization of the theory of the reaction field. Explicit formulas are obtained for the case of a spherical cavity. The formulas are used to calculate Gibbs energies and entropies of proton transfer between carboxylic acids in water, using atom polarizabilities from previous studies and atom charges on the COOH and COO− groups which are optimzed to fit experimental Gibbs energies of proton transfer between acyclic carboxylic acids involving monovalent anions. A cavity radius increment is likewise optimized. The optimized fit is good, and the parameters are reasonably consistent with data from other sources (charges from molecular orbital theory, experimental dipole moments, and partial molal volumes). Calculations for reactions involving divalent anions or bicyclo[2.2.2]octane-1-carboxylic acids yield correct Gibbs energies with the same atom charges, but small adjustments are required in the cavity radius increment. Entropies for the reactions involving acyclic acids are calculated assuming that the entropy change arises solely from changes of bulk solvent properties with temperature. The results are in fair agreement with experiment in some cases, but show large discrepancies in others, due in part to a large sensitivity of the entropy to the parameters of the model. Overall, the results support the view that variations in ionization energies of carboxylic acids arise largely from electrostatic interactions.