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Molecular Spectroscopy and Computations of Solvation Phenomena of Bioorganic Molecules: New Insights and Applications

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Bioorganic Chemistry".

Deadline for manuscript submissions: 31 December 2025 | Viewed by 739

Special Issue Editors


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Guest Editor
Institute of Chemistry, University of Opole, 48, Oleska Street, 45-052 Opole, Poland
Interests: nuclear magnetic shielding tensor; GIAO NMR; indirect spin-spin coupling constants; ZPV corrections to nuclear magnetic shielding; temperature correction (TC); solvent effect; relativistic corrections (RC); bioactive compounds; natural products
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Section of Organic Chemistry & Biochemistry, Department of Chemistry, University of Ioannina, GR-45110 Ioannina, Greece
Interests: bioorganic chemistry; natural product chemistry; NMR spectroscopy; structural biology; food chemistry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The structure and dynamics of ionic solvation are some of the most attractive subjects in chemistry, and numerous studies have been published since 1930s. Thus, a fairly large number of monographs summarizing results of various scattering and spectroscopic methods and quantum chemical calculations have been published. On the contrary, solvation phenomena of bioorganic compounds have received less attention, although they are of fundamental importance in a variety of chemical, physical, and biological processes. X-ray crystallography can provide high-resolution structural data of bioorganic molecules; however, the static structures obtained and the limited number of solvent molecules from crystalline samples do not provide sufficiently accurate descriptions of solvent binding and dynamics. Thus, several spectroscopic and quantum chemical methods have been published in the last few decades to investigate the role of solvents:

  • In structural and conformational analysis;
  • In diastereo- and enantioselective reactions;
  • In the improvement of stereoselectivity, which could be of importance in structure–activity relationships;
  • In bioorganic catalysis.

Several of the above advancements are summarized in the classical book of Reichart and Welton (Solvents and Solvent Effects in Organic Chemistry, John Wiley and Sons (2011)). Nevertheless, there is a need for source material describing important spectroscopic and computational developments and applications in bioorganic solvation phenomena over the last 15 years. The present Special Issue “Molecular Spectroscopy and Computations of Solvation Phenomena of Bioorganic Molecules: New Insights and Applications” aims to underscore the recent advances of solvation phenomena in determining critical structural, thermodynamic, and dynamic properties of bioorganic molecules not only for specialists but also for neophytes in this exciting field.

Prof. Dr. Teobald Kupka
Prof. Dr. Ioannis P. Gerothanassis
Guest Editors

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Keywords

  • bioorganic molecules
  • solvation phenomena
  • spectroscopic methods
  • quantum chemical methods

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Published Papers (2 papers)

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Research

22 pages, 3080 KB  
Article
Comprehensive Speciation and Computational Study of Cu2+ and Zn2+ Complexation with O-Phosphorylethanolamine and O-Phosphorylcholine in Aqueous Solution
by Federica Carnamucio, Chiara Abate, Massimiliano Cordaro, Claudia Foti, Salvatore Donato, Franz Saija, Giuseppe Cassone and Ottavia Giuffrè
Molecules 2025, 30(19), 3923; https://doi.org/10.3390/molecules30193923 - 29 Sep 2025
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Abstract
An extensive study on the interactions between O-phosphorylethanolamine (PEA) and O-phosphorylcholine (PPC), Cu2+ and Zn2+, is thoroughly described. The formation constants were determined at different temperatures (15 ≤ t/°C ≤ 37) and ionic strengths (0.15 ≤ I/mol L−1 [...] Read more.
An extensive study on the interactions between O-phosphorylethanolamine (PEA) and O-phosphorylcholine (PPC), Cu2+ and Zn2+, is thoroughly described. The formation constants were determined at different temperatures (15 ≤ t/°C ≤ 37) and ionic strengths (0.15 ≤ I/mol L−1 ≤ 0.97) by potentiometric titrations. For the Zn2+-PEA/-PPC systems, speciation models were also confirmed by 1H NMR titrations at t = 25 °C and I = 0.15 mol L−1 in NaCl. Sequestering abilities were calculated under different temperatures and physiological conditions. Density Functional Theory (DFT) calculations along with enhanced sampling of the conformational space were performed aimed to better elucidate the Cu2+-, Zn2+- PEA/PPC molecular interactions and their relative stabilities. Overall, both experiments and computer simulations showed that the complex species involved in the Cu2+–PEA system exhibited a significant and selective stability, particularly in conditions simulating cerebrospinal fluid. While the binding molecular mechanisms were elucidated via DFT supplemented by automized conformational search, the computational binding energies trend qualitatively follows the experimental logK behavior across the Cu2+-, Zn2+- PEA/PPC complexes. These results highlight the potential physiological role of PEA in modulating free copper levels and regulating its redox activity in pathological conditions, such as Wilson’s Disease (WD). Full article
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30 pages, 10527 KB  
Article
A Thorough Understanding of Methylrhodium(III)–Porphyrin Photophysics: A DFT/TDDFT Study
by Piotr Lodowski and Maria Jaworska
Molecules 2025, 30(19), 3855; https://doi.org/10.3390/molecules30193855 - 23 Sep 2025
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Abstract
Rhodium–porphyrin complexes are characterised by their ability to activate C-H and C-C bonds and, therefore, find applications in synthesis and catalysis. Axial rhodoporphyrin ligands are susceptible to photodissociation under the influence of light. DFT and TDDFT calculations were performed to investigate the mechanism [...] Read more.
Rhodium–porphyrin complexes are characterised by their ability to activate C-H and C-C bonds and, therefore, find applications in synthesis and catalysis. Axial rhodoporphyrin ligands are susceptible to photodissociation under the influence of light. DFT and TDDFT calculations were performed to investigate the mechanism of photodissociation of the methyl ligand from the methylrhodium(III)–porphyrin complex (MeRhPor). Various photolysis pathways of the rhodium–methyl bond were investigated, including photolysis from states in the Q and Soret bands. Photolysis from triplet states was also considered. Based on the calculations, the most probable mechanism for photodissociation of the methyl ligand was proposed. The methyl-rhodium binding energy in the methylrhodium(III)–porphyrin complex and the energy of formation of the rhodium–porphyrin radical dimer formed by methyl dissociation were also calculated. Full article
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