Vibrational Spectroscopy of Homo- and Heterochiral Amino Acid Dimers: Conformational Landscapes

Abstract

The homo- and heterochiral protonated dimers of asparagine with serine and with valine were investigated using infrared multiple-photon dissociation (IRMPD) spectroscopy. Extensive quantum-chemical calculations were used in a three-tiered strategy to screen the conformational spaces of all four dimer species. The resulting binary structures were further grouped into five different types based on their intermolecular binding topologies and subunit configurations. For each dimer species, there are eight to fourteen final conformational geometries within a 10 kJ mol−1 window of the global minimum structure for each species. The comparison between the experimental IRMPD spectra and the simulated harmonic IR features allowed us to clearly identify the types of structures responsible for the observation. The monomeric subunits of the observed homo- and heterochiral dimers are compared to the corresponding protonated/neutral amino acid monomers observed experimentally in previous IRMDP/rotational spectroscopic studies. Possible chirality and kinetic influences on the experimental IRMPD spectra are discussed.

Conformations of Steroid Hormones: Infrared and Vibrational Circular Dichroism Spectroscopy

“…We chose to use the newly developed fast conformer-rotamer ensemble sampling tool, CREST [ 43 ]. CREST has been utilized and benchmarked extensively by us and others in rotational spectroscopic studies of a wide range of molecules and non-covalently bonded clusters [ 44 , 45 , 46 ] and in IR chirality recognition studies of protonated amino acid binary aggregates [ 47 ]. Generally, the experimentally observed conformers were all identified in the CREST searches.…”

“…The further conformational search, geometry optimization and harmonic frequencies calculations were performed through a multi-tiered approach developed before [ 47 ] which include several steps: (1) search for all the CREST candidates; (2) the DFT optimizations of the CREST candidates with a relaxed convergence criterion at the revPBE-D3/def2-SVP [ 51 ] level, with the empirical D3 dispersion correction; (3) a single-point energy evaluation at the B3LYP-D3/def2-TZVP level of the optimized structures in step (2). The steps (2) and (3) were performed using Molpro [ 77 ]; (4) The final geometry optimization and harmonic frequency IR and VCD calculations were performed using the Gaussian 16 package [ 78 ].…”

Stereochemical Properties of Two Schiff-Base Transition Metal Complexes and Their Ligand by Using Multiple Chiroptical Spectroscopic Tools and DFT Calculations

“…Rather than manually going through these potential ligand conformations, we used the Conformer–Rotamer Ensemble Sampling Tool, i.e., CREST, by Grimme and co-workers [ 29 ] for systematic conformational searches. The capability of CREST to generate a nearly complete set of relevant conformations has been extensively benchmarked by gas phase spectroscopic investigations, such as rotational spectroscopic studies of a wide range of molecules and non-covalently bonded clusters [ 35 , 36 , 37 ] and IR chirality recognition studies of protonated amino acid binary aggregates [ 38 ]. For example, CREST was used to identify drastically different binary aggregates of tetrahydro-2-furoic acid observed in a jet-cooled rotational spectroscopic [ 39 ] and in a matrix-isolation VCD [ 40 ] where very different binary conformers were identified from those in solution [ 41 ].…”

“…The details of the CREST program and the multitiered approach developed before [ 38 ] are described in Section 3 , Materials and Methods. In total, 91 ligand geometries were generated after the initial CREST search.…”

Raman Optical Activity of N‐Acetyl‐L‐Cysteine in Water and in Methanol: The “Clusters‐in‐a‐Liquid” Model and ab Initio Molecular Dynamics Simulations

“…It has been successfully applied to support rotational spectroscopic studies of mid-sized organic molecules and their clusters [55,56] in identifying all low energy structural candidates, although occasional misses were also reported. [57] A multi-tiered approach developed before [58] was utilized in the current study which includes several steps: 1) the generation of CREST candidates; 2) the DFT optimizations of the CREST candidates with a relaxed convergence criteria at the revPBE-D3/def2-SVP [59] level, with the empirical D3 dispersion correction; [60,61] 3) a singlepoint energy evaluation at the B3LYP [62,63] -D3/def2-TZVP level of the optimized structures in step 2). Steps 2 and 3 were done using Molpro; [64] 4) The final geometry optimization and harmonic frequency Raman and ROA calculations were performed using the Gaussian 16 package.…”