Model of peptide bond-aromatic ring interaction: correlated ab initio quantum chemical study.

J Phys Chem B

Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, Flemingovo namesti 2, 166 10 Prague 6, Czech Republic.

Published: August 2007

Aromatic ring-peptide bond interactions (modeled as benzene and formamide, N-methylformamide and N-methylacetamide) are studied by means of advanced computational chemistry methods: second-order Möller-Plesset (MP2), coupled-cluster single and double excitation model [CCSD(T)], and density functional theory with dispersion (DFT-D). The geometrical preferences of these interactions as well as their interaction energy content, in both parallel and T-shaped arrangements, are investigated. The stabilization energy reaches a value of over 5 kcal/mol for the N-methylformamide-benzene complex at the CCSD(T)/complete basis set (CBS) level. Decomposition of interaction energy by the DFT-symmetry-adapted perturbation treatment (SAPT) technique shows that the parallel and T-shaped arrangements, although similar in their total interaction energies, differ significantly in the proportion of electrostatic and dispersion terms.

Download full-text PDF

Source
http://dx.doi.org/10.1021/jp072859+DOI Listing

Publication Analysis

Top Keywords

interaction energy
8
parallel t-shaped
8
t-shaped arrangements
8
model peptide
4
peptide bond-aromatic
4
bond-aromatic ring
4
interaction
4
ring interaction
4
interaction correlated
4
correlated initio
4

Similar Publications

For paediatric patients suffering from neurofibromatosis, Selumetinib (SEL) is the only approved drug. Here an original ecofriendly and high pace method is introduced using 96- microwell spectrophotometric assay (MW-SPA) to measure SEL content in bulk and commercial pharmaceutical formulation (Koselugo capsules). This assay was relied on in-microwell formation of a coloured charge transfer complex (CTC) upon interaction of SEL with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ).

View Article and Find Full Text PDF

Quinone extraction drives atmospheric carbon monoxide oxidation in bacteria.

Nat Chem Biol

January 2025

Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia.

Diverse bacteria and archaea use atmospheric CO as an energy source for long-term survival. Bacteria use [MoCu]-CO dehydrogenases (Mo-CODH) to convert atmospheric CO to carbon dioxide, transferring the obtained electrons to the aerobic respiratory chain. However, it is unknown how these enzymes oxidize CO at low concentrations and interact with the respiratory chain.

View Article and Find Full Text PDF

Recent advancements in the understanding of the alterations in mitochondrial biogenesis in Alzheimer's disease.

Mol Biol Rep

January 2025

Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research, Raebareli Transit Campus, Bijnour-Sisendi Road, Sarojini Nagar, Lucknow, Uttar Pradesh, 226002, India.

Alzheimer's disease (AD) is a common neurodegenerative disease characterized by progressive memory loss and cognitive decline. The processes underlying the pathophysiology of AD are still not fully understood despite a great deal of research. Since mitochondrial dysfunction affects cellular energy metabolism, oxidative stress, and neuronal survival, it is becoming increasingly clear that it plays a major role in the development of AD.

View Article and Find Full Text PDF

Cells use 'active' energy-consuming motor and filament protein networks to control micrometre-scale transport and fluid flows. Biological active materials could be used in dynamically programmable devices that achieve spatial and temporal resolution that exceeds current microfluidic technologies. However, reconstituted motor-microtubule systems generate chaotic flows and cannot be directly harnessed for engineering applications.

View Article and Find Full Text PDF

Excitons, bound electron-hole pairs, influence the optical properties in strongly interacting solid-state systems and are typically most stable and pronounced in monolayer materials. Bulk systems with large exciton binding energies, on the other hand, are rare and the mechanisms driving their stability are still relatively unexplored. Here, we report an exceptionally large exciton binding energy in single crystals of the bulk van der Waals antiferromagnet CrSBr.

View Article and Find Full Text PDF

Want AI Summaries of new PubMed Abstracts delivered to your In-box?

Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!