This study explores the thermodynamic and vibrational properties of water in the three-dimensional environment of solvated ions and small molecules using molecular simulations. The spectrum of intermolecular vibrations in liquid solvents provides detailed information on the shape of the local potential energy surface, which in turn determines local thermodynamic properties such as the entropy. Here, we extract this information using a spatially resolved extension of the two-phase thermodynamics method to estimate hydration water entropies based on the local vibrational density of states (3D-2PT). Combined with an analysis of solute-water and water-water interaction energies, this allows us to resolve local contributions to the solvation enthalpy, entropy, and free energy. We use this approach to study effects of ions on their surrounding water hydrogen bond network, its spectrum of intermolecular vibrations, and resulting thermodynamic properties. In the three-dimensional environment of polar and nonpolar functional groups of molecular solutes, we identify distinct hydration water species and classify them by their characteristic vibrational density of states and molecular entropies. In each case, we are able to assign variations in local hydration water entropies to specific changes in the spectrum of intermolecular vibrations. This provides an important link for the thermodynamic interpretation of vibrational spectra that are accessible to far-infrared absorption and Raman spectroscopy experiments. Our analysis provides unique microscopic details regarding the hydration of hydrophobic and hydrophilic functional groups, which enable us to identify interactions and molecular degrees of freedom that determine relevant contributions to the solvation entropy and consequently the free energy.
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http://dx.doi.org/10.1021/acs.jctc.7b00184 | DOI Listing |
Molecules
January 2025
Istituto di Biostrutture e Bioimmagini-CNR (IBB-CNR), Via De Amicis 95, I-80145 Napoli, Italy.
We perform DFT calculations with different hybrid (ωB97X-D and M05-2X) and double hybrid (B2PLYP-D3 and ωB2PLYP) functionals to characterize the lowest energy triplet excited states of naphthalene monomer and dimers in different stacking arrangements and to simulate their absorption spectra. We show that both excimer and localized triplet minima exist. In the former, the spin density is delocalized over the two monomers, adopting a face-to-face arrangement with a short inter-molecular distance.
View Article and Find Full Text PDFChem Biodivers
January 2025
Universidad Nacional de Tucuman Facultad de Bioquimica Quimica y Farmacia, Chemistry, Av. Kirchner 1900, 4000, San Miguel de Tucumán, ARGENTINA.
(Z)-3-butylamino-4,4,4-trifluoro-1-(2-hydroxyphenyl)but-2-en-1-one (1), a new β-aminoenone, has been investigated in terms of its intra- and intermolecular interactions. Vibrational, electronic and NMR spectroscopies were used for the characterization, while X-ray diffraction methods afforded the determination of the crystal structure. The compound is arranged in the crystal lattice as centre-symmetric H-bonded dimeric aggregates (C2/c monoclinic space group).
View Article and Find Full Text PDFJ Chem Phys
January 2025
Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Two-dimensional (2D) vibrational spectroscopy is a powerful means of investigating the structure and dynamics of complex molecules in condensed phases. However, even in theory, analysis of 2D spectra resulting from complex inter- and intra-molecular motions using only molecular dynamics methods is not easy. This is because molecular motions comprise complex multiple modes and peaks broaden and overlap owing to various relaxation processes and inhomogeneous broadening.
View Article and Find Full Text PDFNano Lett
January 2025
Synergetic Extreme Condition High-Pressure Science Center, State Key Laboratory of Superhard Materials, College of Physics, Jilin University, Changchun 130012, China.
Covalent-organic frameworks (COFs) are dynamic covalent porous organic materials constructed from emissive molecular organic building blocks. However, most two-dimensional (2D) COFs are nonemissive or weakly emissive in the solid state owing to the intramolecular rotation and vibration together with strong π-π interactions. Herein, we report a pressure strategy to achieve the bright multicolor emission from yellow to red in the 2D triazine triphenyl imine COF (TTI-COF).
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China.
Intermolecular hydrogen bonds between carboxyl (COO) and amino groups are a common weak interaction in proteins. Infrared (IR) spectral assignment of such an intermolecular hydrogen bond provides a fingerprint for studying protein-protein interactions as its absorption frequency is affected by the molecular electrostatic environment. Temperature-dependent FTIR and temperature-jump time-resolved IR absorbance difference spectra of several typical amino acids and those of wild type and single-site mutated αB-crystallin were performed.
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