In this work we address a specific experimental and theoretical question regarding the influence of a conformational population in the modeling of photoelectron circular dichroism (PECD) spectroscopy. In the past two decades, PECD has revealed a rich and complex phenomenology in molecular processes with unprecedented insight, especially in molecular geometry sensitivity. Since the early development of this spectroscopy, theory has pointed out the importance of conformer influence on PECD; in particular, the rotation of methyl groups was surprisingly found to be responsible for strong modulation of the PECD signal. Here, to advance understanding of the effect of rotations, we have chosen to study norcamphor, a single-conformer molecule, as a benchmark for a PECD comparison between experiment and theory at the density functional theory (DFT) and time-dependent density functional theory (TDDFT) levels. The excellent agreement between experimental data and theory for norcamphor sheds light on the influence of rotations and gives a solid explanation for the reasonable qualitative agreement in the PECD of camphor, where three methyl groups are added to the same molecular structure.
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http://dx.doi.org/10.1039/d1cp05416c | DOI Listing |
Chiral amines and amino alcohols form an important category of molecules employed in the designing of new drugs and catalyst. Herein, we present a helically-twisted stereodynamic dialdehyde probe 1 for the determining of absolute configuration, and enantiomeric excess of chiral amine and amino alcohols. Probe 1 is based on the pyridine-2,6-dicarboxamide (PDC) core and undergoes rapid interconversion between the P- and M- conformers.
View Article and Find Full Text PDFJ Phys Chem A
December 2024
Department of Chemistry, University of Georgia, 302 East Campus Road, Athens, Georgia 30602, United States.
Vacuum-ultraviolet (VUV) absorption spectroscopy enables electronic transitions that offer the unambiguous identification of molecules. As target molecules become more complex, multifunctional species present a great challenge to both experimental and computational spectroscopy. This research reports both experimental and theoretical studies of oxiranes.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Chemistry, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, India.
Herein, we have investigated the effect of microhydration on the secondary structure of a capped dipeptide Boc-DPro-Gly-NHBn-OMe (Boc = tert-butyloxycarbonyl, Bn = Benzyl), i.e., Pro-Gly (PG) with a single H2O molecule using gas-phase laser spectroscopy combined with quantum chemistry calculations.
View Article and Find Full Text PDFbioRxiv
September 2024
Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.
Small molecule ligands exhibit a diverse range of conformations in solution. Upon binding to a target protein, this conformational diversity is generally reduced. However, ligands can retain some degree of conformational flexibility even when bound to a receptor.
View Article and Find Full Text PDFACS Chem Biol
August 2024
Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80305, United States.
The engineering of novel protein-ligand binding interactions, particularly for complex drug-like molecules, is an unsolved problem, which could enable many practical applications of protein biosensors. In this work, we analyzed two engineered biosensors, derived from the plant hormone sensor PYR1, to recognize either the agrochemical mandipropamid or the synthetic cannabinoid WIN55,212-2. Using a combination of quantitative deep mutational scanning experiments and molecular dynamics simulations, we demonstrated that mutations at common positions can promote protein-ligand shape complementarity and revealed prominent differences in the electrostatic networks needed to complement diverse ligands.
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