The Raman spectra of serine and 3,3-dideutero-serine in aqueous solution

The Raman spectra of serine [[alpha]-amino-[beta]-hydroxypropionic acid; HOCH2CH(NH3)+COO-] and 3,3-dideutero-serine [HOCD2CH(NH3)+COO-] in aqueous solution were studied in the range 4000-300 cm-1. The data obtained for the deuterated compound are novel and provide compelling evidence that previously reported assignments for the undeuterated amino acid should be revised.http://www.sciencedirect.com/science/article/B6THW-4KNMB16-1/1/19da7b30f32b5efeacb053228a66c4a

Infrared and Raman spectroscopic characterization of the hydrogen-bonding network in l-serine crystal

The IR spectra (4000-400 cm-1) of neat and isotopically substituted (ND/OD <= 10% D and [congruent with]30% D) polycrystalline l-serine ([alpha]-amino-[beta]-hydroxypropionic acid; HO-CH2-CH(NH3)+-COO-) were recorded in the temperature range 300-10 K and assigned. The isotopic-doping/low-temperature methodology, which allows for decoupling of individual proton vibrational modes from the crystal bulk vibrations, was used for estimating the lengths and energies of the different H-bonds present in l-serine crystal. To this end, the frequency shifts observed in both the NH/OH stretching and out-of-plane bending spectral regions (relatively to reference values for these vibrations in non-hydrogen-bonded l-serine molecules) were used, together with previously developed empirical correlations between these spectral parameters and the H-bond properties. In addition, the room-temperature Raman spectrum (4000-150 cm-1) of a single crystal of neat l-serine was also recorded and interpreted. A systematic comparison was made between the spectroscopic data obtained currently for l-serine and previously for dl-serine, revealing that the vibrational spectra of the two crystals reflect well the different characteristics of their hydrogen-bond networks, and also correlate accurately with the different susceptibility of the two crystals to pressure-induced strain.http://www.sciencedirect.com/science/article/B6THW-4K4WMR3-2/1/211ac428c09ebc9eb45cf3b81d93fcb

Low-temperature infrared spectra and hydrogen bonding in polycrystalline dl-serine and deuterated derivatives

The FT-IR spectra of polycrystalline dl-serine [[alpha]-amino-[beta]-hydroxypropionic acid; HO-CH2-CH(NH3)+-COO-] and isotopically substituted [ND/ODAlcohol (90% D); CD2 (>98% D)] dl-serine were recorded in the range 4000-500 cm-1 in the temperature range 300-10 K, and fully assigned. The isotopic-doping/low-temperature methodology, which allows for decoupling of individual proton vibrational modes from the crystal bulk vibrations, was used to estimate the energies of the different H-bonds present in dl-serine crystal. To this end, the frequency shifts observed in both the NH/OH stretching and out-of-plane bending spectral regions (relatively to reference values for these vibrations in non-hydrogen-bonded dl-serine molecules) were used, together with previously developed empirical correlations. The results are compared with available structural data on this amino acid.http://www.sciencedirect.com/science/article/B6THW-4J91R39-2/1/f8f35f435466c8a5204879d330cbade

Preferred Conformers and Photochemical (λ > 200 nm) Reactivity of Serine and 3,3-Dideutero-Serine In the Neutral Form

A systematic investigation of the conformational potential energy surface of neutral serine [HOCH2CHNH2COOH] and 3,3-dideutero-serine [HOCD2CHNH2COOH] was undertaken, revealing the existence of 61 different minima. The structures and vibrational spectra of the most stable conformers, which were estimated to have relative energies within 7 kJ mol-1 and account for ca. 93% of the total conformational population at room temperature, were calculated at both the MP2 and DFT/BLYP levels of theory with the 6-311++G(d,p) basis-set and used to interpret the spectroscopic data obtained for the compounds isolated in low-temperature inert matrixes. The assignment of the main spectral infrared features observed in the range 4000−400 cm-1 to the most stable conformers of serine was undertaken. In addition, UV irradiation (λ > 200 nm) of the matrix-isolated compounds was also performed, leading to decarboxylation, which was found to be strongly dependent on the conformation assumed by the reactant molecule

Identification of stillbirths in NSW linked population health datasets

This manuscript has not been submitted for publication. It compares stillbirth reporting from four different population data sources, and develops an algorithm for maximum identification of definite and probable stillbirths in linked population data while avoiding false positive and duplicate reports. By placing the results on this repository we are hoping to inform future use of population data for research on stillbirths in NSW.This work was supported by the Stillbirth Foundation Australia. Christine Roberts is supported by a NHMRC Senior Research Fellowship (APP1021025). We thank the NSW Ministry of Health for access to the population health data and the Centre for Health Record Linkage (CHeReL) for linking the data sets

Foldamers of β-peptides : conformational preference of peptides formed by rigid building blocks : The first MI-IR spectra of a triamide nanosystem

To determine local chirality driven conformational preferences of small aminocyclobutane-1-carboxylic acid derivatives, X-(ACBA) n -Y, their matrix-isolation IR spectra were recorded and analyzed. For the very first time model systems of this kind were deposited in a frozen (~10 K) noble gas matrix to reduce line width and thus, the recorded sharp vibrational lines were analyzed in details. For cis-(S,R)-1 monomer two “zigzag” conformers composed of either a six or an eight-membered H-bonded pseudo ring was identified. For trans-(S,S)-2 stereoisomer a zigzag of an eight-membered pseudo ring and a helical building unit were determined. Both findings are fully consistent with our computational results, even though the relative conformational ratios were found to vary with respect to measurements. For the dimers (S,R,S,S)-3 and (S,S,S,R)-4 as many as four different cis,trans and three different trans,cis conformers were localized in their matrix-isolation IR (MI-IR) spectra. These foldamers not only agree with the previous computational and NMR results, but also unambiguously show for the first time the presence of a structure made of a cis,trans conformer which links a “zigzag” and a helical foldamer via a bifurcated H-bond. The present work underlines the importance of MI-IR spectroscopy, applied for the first time for triamides to analyze the conformational pool of small biomolecules. We have shown that the local chirality of a β-amino acid can fully control its backbone folding preferences. Unlike proteogenic α-peptides, β- and especially (ACBA) n type oligopeptides could thus be used to rationally design and influence foldamer’s structural preferences

Molecular structure and vibrational spectra of methyl glycolate and methyl α-hydroxy isobutyrate

Conformational isomerism in isolated and liquid methyl glycolate and methyl α-hydroxy isobutyrate was investigated by a concerted molecular orbital and vibrational spectroscopic approach (infrared and Raman). The molecular structures, relative energies, dipole moments and vibrational spectra of the various possible conformers of the studied compound were calculated, using the extended 6-31G* basis set at the HF-SCF ab initio level of theory. The theoretical results were then used to interpret infrared and Raman data obtained under different experimental conditions. It was found that both in the liquid and gaseous phase the studied molecules exist in two experimentally observed conformational states, the Cs point group Syn–syn conformer (Ss), which exhibits an intramolecular OH⋯O hydrogen bond, being the most stable form. As expected, the relative populations of the second more stable conformers increase in the liquid phase, since intermolecular interactions tend to reduce the importance of the intramolecular H-bonding that is the main stabilizing factor of the Ss forms

Matrix-Isolated Diglycolic Anhydride: Vibrational Spectra and Photochemical Reactivity

The structure of diglycolic anhydride (1,4-dioxane-2,6-dione; DGAn) isolated in a low-temperature argon matrix at 10 K was studied by means of FTIR spectroscopy. Interpretation of the experimental vibrational spectrum was assisted by theoretical calculations at the DFT(B3LYP)/aug-cc-pVTZ level. The optimized structure of the isolated DGAn molecule adopts an envelope conformation, which was found to resemble closely the structure of DGAn in a crystal. The UV-induced (λ > 240 nm) photolysis of the matrix-isolated compound was also investigated. In order to identify the main species resulting from irradiation of the monomeric DGAn, a comparison between the DFT(B3LYP)/aug-cc-pVTZ calculated spectra of the putative products and the experimental data was carried out. The observed photoproducts can be explained by a model involving four channels: (a) 1,3-dioxolan-4-one + CO; (b) CO2 + CO + oxirane; (c) formaldehyde + ketene + CO2; (d) oxiran-2-one + oxiran-2-one. As a whole, the experiments indicated that the C−O−C bridge, connecting the two CO groups, is the most reactive fragment in the molecule excited with UV light. This observation was confirmed by the natural bond orbital (NBO) analysis revealing that the most important NBO interactions are those between the carbonyl groups and the adjacent C−O and C−C bonds

Entropy effects in conformational distribution and conformationally dependent UV-induced photolysis of serine monomer isolated in solid argon

Monomeric serine can be trapped in low temperature argon matrices in different conformers, which can be classified in three groups (A, B, C) accordingly to the main intramolecular interaction they exhibit: A (OHA...N hydrogen bond), B (OHC...N) and C (OHA...O) (subscripts A and C stand for alcohol and carboxylic group, respectively). The OHC...N intramolecular interaction found in B-type conformers is considerably stronger than both the OHA...N and OHA...O hydrogen bonds, and leads to reduce the abundance of B-type form relatively to A and C forms at high temperatures due to entropy effects. When submitted to UV irradiation ([lambda]>200 nm), the main observed photoprocess is decarboxylation, leading to production of CO2 and ethanolamine. A less important photochemical process is also observed, where the compound undergoes decarbonylation, with formation of CO, H2O and acetamide. The two observed photoprocesses were found to be dependent on the conformation assumed by the reactant molecule, with A- and C-type conformers of serine undergoing decarboxylation and B-type conformers decarbonylation.http://www.sciencedirect.com/science/article/B6TGS-4HH81VW-3/1/d77a65d2ed3aed1faa11df13313e2b8

Preferred Conformers and Photochemical (λ > 200 nm) Reactivity of Serine and 3,3-Dideutero-Serine In the Neutral Form

A systematic investigation of the conformational potential energy surface of neutral serine [HOCH2CHNH2COOH] and 3,3-dideutero-serine [HOCD2CHNH2COOH] was undertaken, revealing the existence of 61 different minima. The structures and vibrational spectra of the most stable conformers, which were estimated to have relative energies within 7 kJ mol-1 and account for ca. 93% of the total conformational population at room temperature, were calculated at both the MP2 and DFT/BLYP levels of theory with the 6-311++G(d,p) basis-set and used to interpret the spectroscopic data obtained for the compounds isolated in low-temperature inert matrixes. The assignment of the main spectral infrared features observed in the range 4000−400 cm-1 to the most stable conformers of serine was undertaken. In addition, UV irradiation (λ > 200 nm) of the matrix-isolated compounds was also performed, leading to decarboxylation, which was found to be strongly dependent on the conformation assumed by the reactant molecule