Conformational Changes of the Alanine Dipeptide in Water–Ethanol Binary Mixtures

Spatially-Decomposed Free Energy of Solvation Based on the Endpoint Density-Functional Method

A spatially resolved version of the density-functional method for solvation thermodynamics is presented by extending the free-energy functional previously established in the one-dimensional, energy representation and formulating a new expression in a mixed four-dimensional representation (three dimensions for position and one dimension for energy). The space was further divided into a set of discrete regions with respect to the relative position of a solvent molecule from the solute, and the spatially decomposed energetics of solvation were analyzed for small molecules with a methyl, amine, or hydroxyl group and alanine dipeptide in solvent water. It was observed that the density of the solvation free energy is weakly dependent on the solute site in the excluded-volume region and is distinctively favorable in the first shells of the solute atoms that can readily form hydrogen bonds with water. The solvent-reorganization term reduces faster with the separation from the solute than the direct interaction between the solute and solvent, and the latter governs the energetics in the second shell and outer regions. The sum of the contributions to the free energy from the excluded volume and first shell was found to deviate significantly from the total sum over all the regions, implying that the solvation free energy is not spatially localized near the solute in a quantitative sense. Still, a local description was shown to be valid as confirmed by the correlation of the total value of free energy with the corresponding value obtained by integrating the free-energy density to the second shell. The theoretical framework developed in the present work to spatially decompose the solvation free energy can thus be useful to identify stabilizing or destabilizing regions of solvent proximate to a solute and to analyze the role that the displacement of interfacial water plays in the thermodynamics of molecular association.

Probing the Solute-Solvent Interaction of an Azo-Bonded Prodrug in Neat and Binary Media: Combined Experimental and Computational Study

Preferential solvation has significant importance in interpreting the molecular physicochemical properties of wide spectrum of materials in solution. In this work, the solute-solvent interaction of pro-drug Sulfasalazine (SSZ) in neat and binary media was investigated experimentally and computationally. The solute-solvent interactions of interest were spectrophotometrically probed and computationally investigated for providing insights concerning the molecular aspects of SSZ:media interaction. Experimentally, the obtained results in 1,4-dioxane:water binary mixture demonstrated a dramatic non-linear changes in the spectral behavior of SSZ indicative of the dependency of its molecular behaviors on the compositions of the molecular microenvironment in the essence of solute-solvent interaction. Computationally, geometry optimization and simulation of the absorption spectra of SSZ in media of interest were performed employing DFT and TD-DFT methods, respectively, where the solvent effects on the absorption were examined implicitly using IEFPCM method. Obtained results revealed a nonpolar nature of the molecular orbitals that are directly involved in the SSZ:medium interaction. As in good correspondence with the experimental results, these simulations demonstrated that these orbitals are of non-polar nature and hence minimally affected by polarity of the media and in turn favoring the non-polar molecular environments. On the other hand, the molecular origin of SSZ:media interaction was demonstrated explicitly through complexation of SSZ with water molecules revealing a cooperative hydrogen bonding stabilization with an average length of 1.90 Å. The findings of this work demonstrate the significance of the preferential solvation and composition of the molecular microenvironment on the physicochemical properties of molecules of pharmaceutical importance.

Effect of the solvent on the conformational behavior of the alanine dipeptide deduced from MD simulations

In general, peptides do not exhibit a well-defined conformational profile in solution. However, despite the experimental blurred picture associated with their structure, compelling spectroscopic evidence shows that peptides exhibit local order. The conformational profile of a peptide is the result of a balance between intramolecular interactions between different atoms of the molecule and intermolecular interactions between atoms of the molecule and the solvent. Accordingly, the conformational profile of a peptide will change upon the properties of the solvent it is soaked. To get insight into the balance between intra- and intermolecular interactions on the conformational preferences of the peptide backbone we have studied the conformational profile of the alanine dipeptide in diverse solvents using molecular dynamics as sampling technique. Solvents studied include chloroform, methanol, dimethyl sulfoxide, water and N-methylacetamide. Different treatments of the solvent have been studied in the present work including explicit solvent molecules, a generalized Born model and using the bulk dielectric constant of the solvent. The diverse calculations identify four major conformations with different populations in the diverse solvents: the C₇^eq only sampled in chloroform; the C₅ or extended conformation; the polyproline (PII) conformation and the right-handed α-helix conformation (α_R). The results of present calculations permit to analyze how the balance between intra- and intermolecular interactions explains the populations of the diverse conformations observed.

QM/MM Study of Substituent and Solvent Effects on the Excited State Dynamics of the Photoactive Yellow Protein Chromophore

Substituent and solvent effects on the excited state dynamics of the Photoactive Yellow Protein chromophore are studied using the average solvent electrostatic potential from molecular dynamics (ASEP/MD) method. Four molecular models were considered: the ester and thioester derivatives of the p-coumaric acid anion and their methylated derivatives. We found that the solvent produces dramatic modifications on the free energy profile of the S1 state: 1) Two twisted structures that are minima in the gas phase could not be located in aqueous solution. 2) Conical intersections (CIs) associated with the rotation of the single bond adjacent to the phenyl group are found for the four derivatives in water solution but only for thio derivatives in the gas phase. 3) The relative stability of minima and CIs is reverted with respect to the gas phase values, affecting the prevalent de-excitation paths. As a consequence of these changes, three competitive de-excitation channels are open in aqueous solution: the fluorescence emission from a planar minimum on S1, the trans-cis photoisomerization through a CI that involves the rotation of the vinyl double bond, and the nonradiative, nonreactive, de-excitation through the CI associated with the rotation of the single bond adjacent to the phenyl group. In the gas phase, the minima are the structures with the lower energy, while in solution these are the conical intersections. In solution, the de-excitation prevalent path seems to be the photoisomerization for oxo compounds, while thio compounds return to the initial trans ground state without emission.

Multiscale simulations for understanding the evolution and mechanism of hierarchical peptide self-assembly

Multiscale molecular simulations that combine and systematically link several hierarchies can provide insights into the evolution and dynamics of hierarchical peptide self-assembly from the molecular level to the mesoscale.

Solvent effects on de-excitation channels in the p-coumaric acid methyl ester anion, an analogue of the photoactive yellow protein (PYP) chromophore

Environmental effects on the deactivation channels of the PYP chromophore in the gas phase and water solution are compared at the CASPT2//CASSCF/cc-pVDZ level.