Aromatic groups can engage in an interesting class of noncovalent interactions termed π-π interactions, which play a pivotal role in stabilizing a variety of molecular architectures, including nucleic acids, proteins, and supramolecular assemblies. When the aromatic compounds interact with each other in an aqueous environment, their association is facilitated by the hydrophobic effect-the trend of nonpolar solutes to aggregate in a polar solution. To develop an in-depth understanding of hydrophobic association, we investigate in the present work π-π interactions in water, employing as a paradigm the benzene dimer. Using DFT-CES, a mean-field QM/MM method recently developed by our group, we describe the benzene solute at a quantum-mechanical level. Full consideration of detailed solute-electron density enables an optimal description of the solute-solvent interactions, leading to an accurate prediction of hydration free energies. In π-stacking of benzene, we find an entropic stabilization associated with the shrinkage of the solvent-excluded volume, which agrees with the theory of hydrophobic effect at subnanoscales. However, at the equilibrium binding distance of the benzene dimer, we find that the entropic stabilization nearly cancels out due to the enthalpic cost required for dewetting the internal space. Such an enthalpy-entropy compensation leads the association free energy to be predominantly dictated by the solute-solute interaction enthalpy. The present work offers new insight into the mechanistic role of water and the primary thermodynamic driving force of hydrophobic association.
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http://dx.doi.org/10.1021/acs.jctc.8b00880 | DOI Listing |
J Am Chem Soc
January 2025
Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.
Stacking interactions are a recurring motif in supramolecular chemistry and biochemistry, where a persistent theme is a preference for parallel-displaced aromatic rings rather than face-to-face π-stacking. This is typically explained in terms of quadrupole-quadrupole interactions between the arene moieties but that interpretation is inconsistent with accurate calculations, which reveal that the quadrupolar picture is qualitatively wrong. At typical π-stacking distances, quadrupolar electrostatics may differ in sign from an exact calculation based on charge densities of the interacting arenes.
View Article and Find Full Text PDFChem Sci
December 2024
Department of Chemistry and Biochemistry, University of California, San Diego La Jolla California 92093 USA
Metal-organic frameworks (MOFs) can be prepared from oligomeric organic ligands to prepare materials referred to as oligoMOFs. Studies of oligoMOFs are relatively limited, with most existing reports focused on fundamental structure-property relationships. In this report, functional groups, such as terminal alkynes and pyridine groups, are installed on the tether between 1,4-benzene dicarboxylic acid (Hbdc) groups of the dimer ligands.
View Article and Find Full Text PDFActa Crystallogr E Crystallogr Commun
January 2025
Department of Chemistry, Bahir Dar University, PO Box 79, Bahir Dar, Ethiopia.
The asymmetric unit of the title compound, CHN·Br·CFI, contains one 2,2,6,6 tetra-methyl-piperidine-1-ium cation, one 1,2,3,4-tetra-fluoro-5,6-di-iodo-benzene mol-ecule, and one uncoordinated bromide anion. In the crystal, the bromide anions link the 2,2,6,6-tetra-methyl-piperidine mol-ecules by inter-molecular C-H⋯Br and N-H⋯Br hydrogen bonds, leading to dimers, with the coplanar 1,2,3,4-tetra-fluoro-5,6-di-iodo-benzene mol-ecules filling the space between them. There is a π-π interaction between the almost parallel benzene rings [dihedral angle = 10.
View Article and Find Full Text PDFSci Rep
December 2024
Department of Biophysics, Faculty of Environmental Biology, University of Life Sciences in Lublin, Akademicka 13, 20-950, Lublin, Poland.
We present a comprehensive spectroscopic study supported by theoretical quantum chemical calculations conducted on a molecular system (4-(5-methyl-1,3,4-thiadiazol-2-yl)benzene-1,3-diol (C1) and the antibiotic Amphotericin B (AmB)) that exhibits highly synergistic properties. We previously reported the strong synergism of this molecular system and now wish to present related stationary measurements of UV-Vis absorption, fluorescence, and fluorescence anisotropy in a polar, aprotic solvent (DMSO and a PBS buffer), followed by time-resolved fluorescence intensity and anisotropy decay studies using different ratios of the selected 1,3,4-thiadiazole derivative to Amphotericin B. Absorption spectra measured for the system revealed discrepancies in terms of the shapes of absorption bands, particularly in PBS.
View Article and Find Full Text PDFJ Phys Chem Lett
January 2025
Molecular Spectroscopy Laboratory, RIKEN, 2-1 Hirosawa Wako, Saitama 351-0198, Japan.
[Pt(NCN)MeCN] (NCN = 1,3-di(2-pyridyl)benzene, MeCN = acetonitrile) forms oligomers in the ground state due to metallophilic interactions, and a Pt-Pt bond is formed with photoexcitation. Ultrafast excited-state dynamics of the [Pt(NCN)MeCN] dimer in acetonitrile is investigated by femtosecond time-resolved absorption (TA) and picosecond emission spectroscopy. The femtosecond TA signals exhibit 60 cm oscillations arising from the Pt-Pt stretching motion in the S dimer.
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