IR-Induced Photoisomerization of Glycolic Acid Isolated in Low-Temperature Inert Matrices

Glycolic acid (HO−CH2−COOH) monomers isolated in low-temperature argon and krypton matrices were studied using FTIR spectroscopy. The most stable SSC conformer of the compound dominated in the matrices immediately after their deposition. Upon broadband infrared irradiation, two minor conformers (GAC and AAT) were photogenerated. No other forms of glycolic acid were populated, either thermally or photochemically. Systematic monitoring of the progress of the IR-induced phototransformations (over a time scale of 20−140 min) allowed one to distinguish between the primary (GAC) and secondary (AAT) photoproducts. The assignment of experimental spectra to the different conformers was based on the results of IR irradiation of the samples and was assisted by the theoretical calculations carried out at the MP2/aug-cc-pVDZ level. Theoretical pathways for intramolecular rotation in the glycolic acid monomer were investigated at the MP2/6-31++G(d,p) level. Lack of conformers other than SSC, GAC, and AAT in the IR-irradiated matrices was explained in terms of energy barriers separating different forms of the compound

Structure and vibrational spectra of -hydroxy isobutyric acid in the crystalline and glassy phases and isolated in inert gas matrixes

Infrared spectra of monomeric -hydroxy isobutyric acid (HIBA) isolated in argon, krypton and xenon matrixes (at 8 K) are reported. It is shown that in all the studied matrixes HIBA exists preferentially as the intramolecularly H-bonded SsC conformer, where the HOCC, OCCO and OCOH dihedrals are 0°. In addition to the SsC form, two higher energy conformers (AaT and GskC) could be observed experimentally for the first time. The spectra of the three observed conformers were assigned on the basis of density functional theory calculations (B3LYP/6-31G*) and their relative energies estimated from relative band intensities. Raman and infrared spectra of both crystalline and low temperature glassy states were also recorded and interpreted. In consonance with previously reported X-ray structural studies (W. P. J. Gaykema, J. A. Kanters and G. Roelofsen, Cryst. Struct. Commun., 1978, 7, 463), the vibrational data now obtained are consistent with the exclusive presence in the crystalline phase of molecules assuming a conformation similar to that of the lowest energy monomer observed in the matrixes (SsC conformer).Fundação para a Ciência e Tecnologia (PRAXIS QUI/10137/98), M.Sc. Grant ref. SFRH/157/2000 (Susana Jarmelo)

Structure and vibrational properties of serine in a variety of chemical and biochemical environments

As propriedades estruturais, energéticas e vibracionais da L- e DL-Ser e dos seus isotopólogos deuterados nas formas neutra e zwiteriónica, em diferentes ambientes químicos e bioquímicos, foram investigadas por espectroscopia de IR e Raman e métodos teóricos. A investigação da Superfície de Energia Potencial da serina na forma neutra foi realizada recorrendo aos métodos DFT e MP2. As estruturas e os espectros vibracionais dos confórmeros mais estáveis da serina foram calculados usando ambos os níveis de teoria e utilizados na interpretação dos resultados espectroscópicos obtidos para o composto isolado em matrizes de árgon a baixa temperatura. Os efeitos da entropia no equílibrio conformacional da serina foram também investigados. Além disso, foi efectuada irradiação in situ dos compostos isolados e realizados estudos de variação de temperatura da matriz. Os espectros de IV das amostras policristalinas puras da L- e DL-Ser e das espécies isotopicamente substítuidas foram investigados. Um método experimental assente na conjugação do uso de dopagem isotópica e de temperaturas baixas foi usado, conjuntamente com correlações empíricas, para estimar as energias e os comprimentos das diferentes ligações-de-hidrogénio presentes em ambos os cristais. Adicionalmente, os espectros de Raman dos cristais únicos da serina, crescidos através da técnica ‘hanging drop vapor diffusion’, foram investigados. Os espectros de Raman em solução aquosa da serina e 3,3-dideutero-serina foram também estudados. Uma nova aproximação na determinação da força de ligação-de-hidrogénio entre alcoóis primários e aceitadores-de-protão foi desenvolvida. A premissa fundamental usada é que a força e direccionalidade das ligações-de-hidrogénio de alcoóis primários para aceitadores-de-protão se reflecte na ligação Ca-H do grupo funcional H-Ca-O-H. O composto modelo estudado foi o (R,S)-n-[1-D]propanol. A sensibilidade da frequência vibracional de elongação nCaH/D à ligação-de-hidrogénio foi examinada por espectroscopia de IV e Raman numa série de diferentes condições experimentais e através de cálculos DFT. Por fim, foi realizada a investigação teórica das propriedades estruturais e vibracionais dos estados reagente e produto da reacção associada à fosforilação do grupo álcool da serina inserida numa proteína catalizada pela enzima ‘PKA’, através de cálculos PM3, HF e DFT

Structural and vibrational characterization of methyl glycolate in the low temperature crystalline and glassy states

The low temperature phases of methyl glycolate (MGly) were identified and characterized structurally by differential scanning calorimetry, infrared and Raman spectroscopies and molecular modeling. Within the temperature range 13–273 K, MGly may exist in three solid phases. A crystalline phase (I) can be formed from the liquid upon slow cooling [Tonset=222–227 K] or from the low temperature glassy state resulting from fast deposition of the vapour onto a cold substrate at 13 K and subsequent warming. A mixture of the glassy state and crystalline phase (I) is obtained by cooling the liquid at higher cooling rates (vcooling?10 K min–1). Upon heating this mixture, devitrification occurs at ca. 175 K, the cold liquid then formed giving rise to a second crystalline variety (II) at Tonset=198–207 K. In the glassy state, individual MGly molecules may assume the two conformational states previously observed for this compound isolated in an argon matrix and in the liquid phase [S. Jarmelo and R. Fausto, J. Mol. Struct., 1999, 509, 183]. On the contrary, the crystalline phase I was found to exhibit conformational selectivity—in this phase, all individual molecules assume a conformation analogous to the most stable conformer found for the isolated molecule and in the liquid (the syn-syn s-cis conformer, where the H–O–C–C, O–C–CO and OC–O–C dihedrals are ca. 0°). In agreement with the spectroscopic results, a molecular modeling analysis reveals that, in this phase, two non-equivalent molecules exhibiting an intramolecular OH···O hydrogen bond exist, which are connected by a relatively strong intermolecular OH···O hydrogen bond. Crystalline state II could not be characterized in detail structurally, but the thermodynamic studies seem to indicate that it corresponds to a metastable crystalline form having a more relaxed structure and a slightly higher energy than crystalline state I. The observed temperature of fusion for the two observed crystalline forms are: I, 264 K and II, 260 K.FEDER, programa PRAXIS XXI (QUI/2/2.1/412/94

The low temperature crystalline and glassy states of methyl -hydroxy-isobutyrate

The low temperature crystalline and glassy phases of methyl -hydroxy-isobutyrate (MHib) were identified and characterized structurally by differential scanning calorimetry, IR and Raman spectroscopy and molecular modeling. Within the temperature range 13–171 K, MHib exists as a glassy state, where individual molecules may assume the two conformational states previously observed for this compound isolated in an argon matrix and in the liquid phase [S. Jarmelo and R. Fausto, J. Mol. Struct., 1999, 509, 193]. At ca. 171 K, devitrification occurs and a crystalline phase may then be formed [T(onset)213 K], the enthalpy of crystallization being ca. 5 kJ mol–1. The crystalline phase was found to exhibit conformational selectivity—in this phase all individual molecules assume a conformation analogous to the most stable conformer found for the isolated molecule and in the liquid (the Syn-syn s-cis conformer, where the H–O–C–C, O–C–CO and OC–O–C dihedrals are ca. 0°). Molecular modeling and Raman data are consistent with a structural unit within the crystal where two MHib molecules form a centrosymmetrical hydrogen bonded dimer. The observed temperature of fusion [Tf(peak)] for the crystal is 240 K.Fundação para a Ciência e Tecnologia, programas PRAXIS QUI/10137/98 e SFRH/157/2000

First experimental evidence of the third conformer of glycolic acid: combined matrix isolation, FTIR and theoretical study

Abstract The FT-IR spectra of monomeric glycolic acid, GA, isolated in argon and xenon matrices (at 10 and 20 K) were studied, enabling identification of three different conformers of GA. The most stable SSC conformer involves a hydrogen bond between the carbonyl group and the hydrogen atom of the alcohol hydroxyl group. The minor GAC and AAT forms involve intramolecular hydrogen bonds between alcohol and carboxyl OH groups, with alcohol and carboxylic groups serving as proton donors, respectively. The GAC conformer, predicted by theoretical calculations (at the DFT/B3LYP and MP2 levels with the 6-31++G(d,p) and aug-ccpVDZ basis sets) as the second most stable form, was now experimentally identified for the first time

First experimental evidence of the third conformer of glycolic acid: combined matrix isolation, FTIR and theoretical study

The FT-IR spectra of monomeric glycolic acid, GA, isolated in argon and xenon matrices (at 10 and 20 K) were studied, enabling identification of three different conformers of GA. The most stable SSC conformer involves a hydrogen bond between the carbonyl group and the hydrogen atom of the alcohol hydroxyl group. The minor GAC and AAT forms involve intramolecular hydrogen bonds between alcohol and carboxyl OH groups, with alcohol and carboxylic groups serving as proton donors, respectively. The GAC conformer, predicted by theoretical calculations (at the DFT/B3LYP and MP2 levels with the 6-31++G(d,p) and aug-cc-pVDZ basis sets) as the second most stable form, was now experimentally identified for the first time.http://www.sciencedirect.com/science/article/B6TFN-4C2FHSF-7/1/8b868591b7c14f11e4cc9abeb26b9e2