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.

From molecular modelling to photophysics of neutral oligo- and polyfluorenes incorporated into phospholipid bilayers.

The combination of various experimental techniques with theoretical simulations has allowed elucidation of the mode of incorporation of fluorene based derivatives into phospholipid bilayers. Molecular dynamics (MD) simulations on a fully hydrated 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) bilayer, with benzene (B), biphenyl (BP), fluorene (F) and tri-(9,9-di-n-octylfluorenyl-2,7-diyl), TF, have provided insights into the topography of these molecules when they are present in the phospholipid bilayer, and suggest marked differences between the behavior of the small molecules and the oligomer. Further information on the interaction of neutral fluorenes within the phospholipid bilayer was obtained by an infrared (IR) spectroscopic study of films of DMPC and of the phospholipid with PFO deuterated specifically on its alkyl chains (DMPC-PFO-d34). This was complemented by measurements of the effect of F, TF and two neutral polymers: polyfluorene poly(9,9-di-n-octylfluorenyl-2,7-diyl), PFO, and poly(9,9-di-n-dodecylfluorenyl-2,7-diyl), PFD, on the phospholipid phase transition temperature using differential scanning calorimetry (DSC). Changes in liposome size upon addition of F and PFO were followed by dynamic light scattering. In addition, the spectroscopic properties of F, TF, PFO and PFD solubilised in DMPC liposomes (absorption, steady-state and time-resolved fluorescence) were compared with those of the same probes in typical organic solvents (chloroform, cyclohexane and ethanol). Combining the insight from MD simulations with the results at the molecular level from the various experimental techniques suggests that while the small molecules have a tendency to be located in the phospholipid head group region, the polymers are incorporated within the lipid bilayers, with the backbone predominantly orthogonal to the phospholipid alkyl chains and with interdigitation of them and the PFO alkyl chains.

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.

Study of Nα-benzoyl-L-argininate ethyl ester chloride, a model compound for poly(ester amide) precursors: x-ray diffraction, infrared and Raman spectroscopies, and quantum chemistry calculations.

Poly(ester amide)s (PEAs) are lacking in structural and spectroscopic information. This paper reports a structural and spectroscopic characterization of N(α)-benzoyl-L-argininate ethyl ester chloride (BAEEH(+)·Cl(-)), an important amino acid derivative and an adequate PEAs' model compound. Crystals of BAEEH(+)·Cl(-) obtained by slow evaporation in an ethanol∕water mixture were studied by different complementary techniques. X-ray analysis shows that BAEEH(+)·Cl(-) crystallizes in the chiral space group P2(1). There are two symmetry independent cations (and anions) in the unit cell. The two cations have different conformations: in one of them, the angle between the least-squares planes of the phenyl ring and the guanidyl group is 5.1(2)°, and in the other the corresponding angle is 13.3(2)°. There is an extensive network of H-bonds that assembles the ions in layers parallel to the ab plane. Experimental FT-IR and Raman spectra of BAEEH(+)·Cl(-) were recorded at room temperature in the 3750-600 cm(-1) and 3380-100 cm(-1) regions, respectively, and fully assigned. Both structural and spectroscopic analysis were supported by quantum chemistry calculations based on different models (in vacuo and solid-state DFT simulations).

Role of guanidyl moiety in the insertion of arginine and Nalpha-benzoyl-L-argininate ethyl ester chloride in lipid membranes.

Guanidyl moieties of both arginine (Arg) and N(alpha)-benzoyl-L-argininate ethyl ester chloride (BAEE) are protonated in all environments studied, i.e., dry solid state, D(2)O solutions, and dry and hydrated lipids as suggested by DFT(B3LYP)/6-31+G(d,p) calculations. Arg and BAEE are able to insert in the lipid interphase of both DMPC and DOPC monolayers as revealed by the observed decrease in the membrane dipole potential they induce. The larger decrease in the dipole potential induced by BAEE, compared to Arg, can be explained partially by the higher affinity of the hydrophobic benzoyl and ethyl groups for the membrane phase, which allows an easier insertion of this molecule. FTIR studies indicate that the guanidyl moiety of Arg is with all probability facing the hydrophobic part of the lipids, whereas in BAEE this group is facing the water phase. Zeta potential measurements provide a direct evidence that Arg orients in the lipid interphase of phosphatidylcholine (PC) bilayers with the negative charged carboxylate group (-COO-) toward the aqueous phase.

1H NMR spectroscopic and quantum chemical studies on a poly(ester amide) model compound: Nalpha-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.

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.

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.

Preferred conformers and photochemical (lambda > 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 (lambda > 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.

Calpha-H bond-stretching frequency in alcohols as a probe of hydrogen-bonding strength: a combined vibrational spectroscopic and theoretical study of n-[1-D]propanol.

The sensitivity of the nu(C)()alpha(-)(H/D) vibrational stretching frequency to hydrogen bonding in alcohols is examined by infrared and Raman spectroscopy, supported by DFT(B3LYP)/6-311++G(d,p) calculations. The model compound studied is (R,S)-n-[1-D]propanol. It is shown that the nu(C)()alpha(-)(H/D) mode can be successfully correlated with the hydrogen-bond strength in a given solvent, provided the O-H group involved in the hydrogen bond is not acting simultaneously as a hydrogen-bond donor and acceptor. In addition, a detailed analysis of the spectroscopic features observed in both the nu(O)(-)(H) and nu(C)()alpha(-)(H/D) spectral regions of the spectra of n-propanol and (R,S)-n-[1-D]propanol, in a series of different experimental conditions, which include the matrix-isolated compound (in argon matrix), pure liquid and low-temperature glassy states, and solution in different solvents, is undertaken. This permits the contribution of the different conformers of the studied compounds to be assigned to the bands observed in the nu(O)(-)(H) and nu(C)(-)(H) spectral regions.