Proton migration in protonated glycylglycylglycine (GGG) has been investigated by using density functional theory at the B3LYP/6-31++G(d,p) level of theory. On the protonated GGG energy hypersurface 19 critical points have been characterized, 11 as minima and 8 as first-order saddle points. Transition state structures for interconversion between eight of these minima are reported, starting from a structure in which there is protonation at the amino nitrogen of the N-terminal glycyl residue following the migration of the proton until there is fragmentation into protonated 2-aminomethyl-5-oxazolone (the b(2) ion) and glycine. Individual free energy barriers are small, ranging from 4.3 to 18.1 kcal mol(-)(1). The most favorable site of protonation on GGG is the carbonyl oxygen of the N-terminal residue. This isomer is stabilized by a hydrogen bond of the type O-H.N with the N-terminal nitrogen atom, resulting in a compact five-membered ring. Another oxygen-protonated isomer with hydrogen bonding of the type O-H.O, resulting in a seven-membered ring, is only 0.1 kcal mol(-)(1) higher in free energy. Protonation on the N-terminal nitrogen atom produces an isomer that is about 1 kcal mol(-)(1) higher in free energy than isomers resulting from protonation on the carbonyl oxygen of the N-terminal residue. The calculated energy barrier to generate the b(2) ion from protonated GGG is 32.5 kcal mol(-)(1) via TS(6-->7). The calculated basicity and proton affinity of GGG from our results are 216.3 and 223.8 kcal mol(-)(1), respectively. These values are 3-4 kcal mol(-)(1) lower than those from previous calculations and are in excellent agreement with recently revised experimental values.
Download full-text PDF |
Source |
---|---|
http://dx.doi.org/10.1021/ja0015904 | DOI Listing |
Org Biomol Chem
January 2025
Department of Chemistry, CMS College Kottayam (Autonomous), Kottayam, Kerala, 686001, India.
The Suzuki-Miyaura Coupling (SMC) reaction is a powerful method for forming carbon-carbon bonds in organic synthesis. Recent advancements in SMC reactions have introduced first-row transition metal catalysts, with zinc garnering significant interest due to its cost-effective and eco-friendly nature. Despite progress in experimental protocols, the mechanistic details of zinc-catalyzed SMC reactions are limited.
View Article and Find Full Text PDFJ 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 PDFMolecules
December 2024
Department of Chemical and Materials Engineering, Lyuliang University, Lishi 033001, China.
We studied the boron-based composite cluster BAl doped with Al atoms. The global minimum structure of the BAl cluster is a three-layer structure, consisting of three parts: an Al unit, a B ring and an isolated Al atom. Charge calculations analysis shows that the cluster can be expressed as [Al][B][Al], has 6π/6σ double aromaticity and follows the (4+2) Hückel rule.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Konan Laboratory for Oligonucleotide Therapeutics (KOLOT), 7-1-20 Minatojima-Minamimachi, Kobe 650-0047, Japan.
2',4'-methylene bridged nucleic acid/locked nucleic acid (2',4'-BNA/LNA; LNA) is a modified nucleic acid that improves the function of antisense oligonucleotide therapeutics. In particular, LNA in the DNA strand increases its binding affinity for the target RNA. Predicting the binding affinities of LNA-containing antisense oligonucleotides and RNA duplexes is useful for designing antisense oligonucleotides.
View Article and Find Full Text PDFAppl Biochem Biotechnol
January 2025
Chemistry Department, Faculty of Science, Beni-Suef University, Beni-Suef, 62514, Egypt.
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!