Resonance-assisted hydrogen bonds (RAHB) are intramolecular contacts that are characterised by being particularly energetic. This fact is often attributed to the delocalisation of π electrons in the system. In the present article, we assess this thesis via the examination of the effect of electron-withdrawing and electron-donating groups, namely -F, -Cl, -Br, -CF, -N(CH), -OCH, -NHCOCH on the strength of the RAHB in malondialdehyde by using the Quantum Theory of Atoms in Molecules (QTAIM) and the Interacting Quantum Atoms (IQA) analyses. We show that the influence of the investigated substituents on the strength of the investigated RAHBs depends largely on its position within the π skeleton. We also examine the relationship between the formation energy of the RAHB and the hydrogen bond interaction energy as defined by the IQA method of wave function analysis. We demonstrate that these substituents can have different effects on the formation and interaction energies, casting doubts regarding the use of different parameters as indicators of the RAHB formation energies. Finally, we also demonstrate how the energy density can offer an estimation of the IQA interaction energy, and therefore of the HB strength, at a reduced computational cost for these important interactions. We expected that the results reported herein will provide a valuable understanding in the assessment of the energetics of RAHB and other intramolecular interactions.
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http://dx.doi.org/10.3390/molecules26144196 | DOI Listing |
Int J Biol Macromol
January 2025
Department of Life Sciences and Systems Biology, University of Torino, Italy.
A new gene coding for an iron-containing enzyme was identified in the genome of Acinetobacter radioresistens. Bioinformatics analysis allowed the assignment of the protein to DyP peroxidases, due to the presence of conserved residues involved in heme binding and catalysis. Moreover, Ar-DyP is located in an operon coding also for other enzymes involved in iron uptake and regulation.
View Article and Find Full Text PDFChemosphere
January 2025
Environment Research Institute, Shandong University, Qingdao, 266237, PR China.
Polyethylene terephthalate (PET) waste significantly contributes to the global plastic crisis, but enzymatic conversion has become an efficient and environmentally friendly strategy to combat it. Therefore, this study explored the Re-face selective depolymerization mechanisms of a novel PET-degradation peptidase, hydrolase 202. Theoretical calculations revealed that the first step, a catalytic triad-assisted nucleophilic attack, is the rate-determining step.
View Article and Find Full Text PDFJ Med Chem
January 2025
Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstr. 7, Braunschweig 38124, Germany.
The main protease M is a clinically validated target to treat infections by the coronavirus SARS-CoV-2. Among the first reported M inhibitors was the peptidomimetic α-ketoamide , whose cocrystal structure with M paved the way for multiple lead-finding studies. We established structure-activity relationships for the series by modifying residues at the P1', P3, and P4 sites.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Hefei National Research Center for Physical Sciences at the Microscale, Department of Chemistry, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China.
The local electric field (LEF) plays an important role in the catalytic process; however, the precise construction and manipulation of the electric field microenvironment around the active site remains a significant challenge. Here, we have developed a supramolecular strategy for the implementation of a LEF by introducing the host macrocycle 18-crown-6 (18C6) into a cobalt phthalocyanine (CoPc)-containing covalent organic framework (COF). Utilizing the supramolecular interaction between 18C6 and potassium ion (K), a locally enhanced K concentration around CoPc can be built to generate a LEF microenvironment around the catalytically active Co site.
View Article and Find Full Text PDFChemistry
January 2025
Brandeis University, Chemistry, 415 South Street,, Waltham, 02453, UNITED STATES OF AMERICA.
We designed and synthesized three diacetylene monomers M1-M3 having two NH2 groups. As anticipated, the NH2 groups aided the preorganization of these monomers by N-H…N hydrogen bonding. In the crystals of monomer M1 and M2, the intermolecular N-H…N hydrogen bonding preorganized the diyne units in an orientation suitable for their topochemical polymerization, but in the case of monomer M3, the distance was slightly larger than that recommended for the topochemical reaction.
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