S. Jarmelo

Experimental (IR/Raman and 1H/13C NMR) and theoretical (DFT) studies of the preferential conformations adopted by L-lactic acid oligomers and poly(L-lactic acid) homopolymer.

L-Lactic acid (L-LA) oligomers (up to the pentamer) were studied by three complementary approaches: vibrational (IR and Raman) and NMR ((1)H and (13)C) spectroscopies and DFT calculations. Vibrational and NMR spectra of L-LA oligomers and poly(L-lactic acid) (PLLA) homopolymer were recorded at room temperature and interpreted. Further insight into the structures (conformations) of the title systems was provided by theoretical B3LYP/6-311++G(d,p) studies. Calculated energies and computed vibrational and NMR spectra of the most stable conformers of L-LA oligomers, together with the experimental vibrational and NMR spectra, enabled the characterization of the preferred conformations adopted by PLLA chains.

Trans- and cis-stilbene isolated in cryogenic argon and xenon matrices.

Monomers of trans- (TS) and cis-stilbene (CS) were isolated in cryogenic argon and xenon matrices, and their infrared (IR) spectra were fully assigned and interpreted. The interpretation of the vibrational spectra received support from theoretical calculations undertaken at the DFT(B3LYP)/6-311++G(d,p) level of theory. In situ broadband UV irradiation of the matrix-isolated CS led to its isomerization to TS, which appeared in the photolysed matrices in both non-planar and planar configurations. The non-planar species was found to convert into the more stable planar form upon subsequent annealing of the matrices at higher temperature. TS was found to be photostable under the used experimental conditions. The structure of the non-planar TS form was assigned based on the comparison of its observed IR spectrum with those theoretically predicted for different conformations of TS. Chemometrics was used to make this assignment. Additional reasoning on the structure of the studied stilbenes is presented taking as basis results of the Natural Bond Orbital analysis.

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

The low temperature crystalline and glassy phases of methyl α-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.

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

Infrared spectra of monomeric α-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).

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 (vcooling10 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.

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

Abstract 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.

Crystal and Molecular Structure of dl-Serine Hydrochloride Studied by X-Ray Diffraction, Low-Temperature Fourier Transform Infrared Spectroscopy and DFT(B3LYP) Calculations

The structure of dl-serine.HCl was studied by three complementary techniques. Experimental Fourier transform infrared (FT-IR) spectra of pure NH/OH polycrystalline dl-serine.HCl [HO-CH2-CH(NH3+)-COOH.Cl(-)] and the respective deuterated derivatives [ND/ODAlcohol/Acid (<10% and ca. 60% D)] were recorded in the region 4000-400 cm(-1) in the temperature range 300-10 K and interpreted. The assignments were confirmed by comparison with the vibrational spectra of crystalline dl- and l-serine zwitterions [HO-CH 2-CH(NH3+)-COO(-)]. Further insight into the structure of the title compound was provided by theoretical DFT(B3LYP)/6-311++G(d,p) calculations of the infrared spectra and energies of 13 different conformers. Potential energy distributions resulting from normal co-ordinate analysis were calculated for the most stable conformer ( I) in its hydrogenated and deuterated modification. Frequencies of several vibrational modes were used in the estimation of enthalpies of individual H-bonds present in the crystal, using empirical correlations between enthalpy and the frequency shift that occurs as a result of the establishment of the H-bonds. X-ray crystallography data for dl-serine.HCl were recorded for the first time and, together with the experimental vibrational spectra and the theoretical calculations, allowed a detailed characterization of its molecular structure.

Conformational preferences of 3,4-dihydroxyphenylacetic acid (DOPAC)

The conformational space of 3,4-dihydroxyphenylacetic acid (DOPAC), an important dopamine metabolite, has been investigated by quantum chemical methods (B3LYP and MP2, with the 6-311++G(d,p) basis set) and matrix-isolation infrared spectroscopy. Detailed analysis of the calculated potential energy surfaces of the molecule led to identification of thirteen unique conformers, all of them showing the acetic acid side chain out of the aromatic ring plane by 60-95°. According to the calculated Gibbs energies, the five lowest energy conformers make up 99.7% of the conformational mixture at 298.15K, exhibiting individual populations falling between 16% and 24%. The main conformational trends of this molecule were interpreted on the grounds of a thorough analysis of the structural parameters and by the application of the Natural Bond Orbital theory. The role of the intramolecular interactions on the relative stability and structure of the conformers was also investigated. The infrared spectrum of DOPAC was registered after isolation of its monomers in argon and xenon matrices. Only one of DOPAC forms populated in the gas phase could be trapped in both matrix gases. This result is in agreement with the predicted low energy barriers for conformational isomerization and is also supported by annealing experiments. The spectra of matrix-isolated model compounds, phenylacetic acid and catechol, were studied under the same experimental conditions. These data were used as references and assisted in the interpretation of the results obtained for DOPAC.

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 (lambda > 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 C=O 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.

1H NMR Spectroscopic and Quantum Chemical Studies on a Poly(ester amide) Model Compound: Nα-Benzoyl-l-Argininate Ethyl Ester Chloride. Structural Preferences for the Isolated Molecule and in Solution

The molecular structure of the L-arginine derivative, N(alpha)-benzoyl-L-argininate ethyl ester chloride (BAEEH(+).Cl(-)), was characterized by combining quantum chemical methods and (1)H NMR spectroscopy. A conformational search on the potential energy surfaces of the three lowest-energy tautomers of BAEEH(+) [A: R-N(+)H=(NH(2))(2); B: R-NH-C(=NH)N(+)H(3); C: R-N(+)H(2)-C(=NH)NH(2); R = C(6)H(5)C(=O)NH-CH(COOCH(2)CH(3))CH(2)CH(2)CH(2)-] was carried out using the semiempirical PM3 method. The lowest-energy conformations obtained using this method were then optimized at the DFT(B3LYP)/6-31++G(d,p) level of theory. For all tautomers, it was found that all low-energy conformers present folded structures, in which a H-bond interaction between the guanidinium group and the amide carbonyl oxygen atom appears to be the most relevant stabilizing factor. (1)H NMR spectra of BAEEH(+).Cl(-) in DMF-D(7) were acquired in the temperature range [-55 to 75 degrees C], providing information about the rotational motions in the guanidinium group and showing that the tautomeric form of BAEEH(+) that exists in solution is tautomer A. The interpretation of the experimental findings was supported by (1)H NMR chemical shifts obtained theoretically at the DFT(B3LYP)/6-31++G(d,p) level of approximation, using both the polarized continuum model and a BAEEH(+)-water complex model.