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π-π stacking interactions in tryptophan-lumiflavin-tyrosine: a structural model for riboflavin insertion into riboflavin-binding protein.
J Mol Model
January 2025
Department of Natural Sciences, University of Michigan-Dearborn, Dearborn, MI, 48128, USA.
Context: Riboflavin (RF), also known as B2 vitamin, is the precursor to flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), two co-enzymes involved in many electron transport processes. Interactions of the isoalloxazine ring, common to all three compounds, are of great interest due to their biological function in flavoproteins and relevance in the transport by the carrier protein leading to development of drug delivery strategies and non-invasive diagnostics techniques. Based on protein crystallographic data, a computational investigation of the interactions in the complexes between lumiflavin, a model compound, and aromatic amino acids, tyrosine and tryptophan, was pursued with the goal of characterizing noncovalent interactions.
View Article and Find Full Text PDFDensity functional study of physisorption of H molecules on scandium and yttrium decorated C fullerene: prospect for hydrogen storage.
J Mol Model
December 2024
Computational Materials Research Lab, Department of Physics, Indian Institute of Technology (Indian School of Mines), Dhanbad, India.
Context: Hydrogen storage in porous nanostructured compounds have recently attracted a lot of attention due to the fact that the underlying adsorption mechanism and thermodynamics provide suitable platform for room temperature adsorption and desorption of H molecules. This work reports the findings of a study on the reversible hydrogen storage capacities of Sc and Y decorated C fullerene, conducted using dispersion-corrected density functional theory (DFT) calculation. The transition metal (TM) atoms, such as Sc and Y, are identified to attach to the C-C bridge position of the C fullerene through non-covalent closed-shell interactions.
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Materials and Process Simulation Center, California Institute of Technology, Pasadena, California 91125, United States.
Noncovalent interactions (NCI) play a central role in numerous physical, chemical, and biological phenomena. An accurate description of NCI is the key to success for any theoretical study in such areas. Although quantum mechanics (QM) methods such as dispersion-corrected density functional theory are sufficiently accurate, their applications are practical only for <300 atoms and <100 ps of simulation time.
View Article and Find Full Text PDFDoes Basis Set Superposition Error Significantly Affect Post-CCSD(T) Corrections?
J Comput Chem
January 2025
Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot, Israel.
We have investigated the title question for both a subset of the W4-11 total atomization energies benchmark, and for the A24x8 noncovalent interactions benchmark. Overall, counterpoise corrections to post-CCSD(T) contributions are about two orders of magnitude less important than those to the CCSD(T) interaction energy. Counterpoise corrections for connected quadruple substitutions (Q) are negligible, and or especially so.
View Article and Find Full Text PDFSpectroscopic and Quantum Chemical Evidence of Amine-CO and Alcohol-CO Interactions: Confirming an Intriguing Affinity of CO to Monoethanolamine (MEA).
Molecules
November 2024
Department of Chemistry, Technical University of Denmark, Kemitorvet 206, 2800 Kongens Lyngby, Denmark.
A recent broadband rotational spectroscopic investigation of the cross-association mechanisms of CO with monoethanolamine (MEA) in molecular beams [F. Xie et al., , , , e202218539] revealed an intriguing affinity of CO to the hydroxy group.
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