Comparative matrix isolation infrared spectroscopy study of 1,3- and 1,4-diene monoterpenes (α-phellandrene and γ-terpinene).

In the present work, γ-terpinene (a 1,4-diene derivative) and α-phellandrene (1,3-diene derivative) were isolated in cryogenic argon matrices and their structures, vibrational spectra, and photochemistries were characterized with the aid of FTIR spectroscopy and quantum chemical calculations performed at the DFT/B3LYP/6-311++G(d,p) level of approximation. The molecules bear one conformationally relevant internal rotation axis, corresponding to the rotation of the isopropyl group. The calculations provide evidence of three minima on the potential energy surfaces of the studied molecules, where the isopropyl group assumes the trans, gauche+, and gauche- conformations (T, G+, G-). The signatures of all these conformers were identified in the experimental matrix infrared spectra, with the T forms dominating, in agreement with the theoretical predicted abundances in gas phase at room temperature. In situ UV (λ > 200 nm) irradiation of matrix-isolated α-phellandrene led to its isomerization into an open-ring species. The photoproduct was found to exhibit the ZE configuration of its backbone, which to be formed from the reactant molecule does not require extensive structural rearrangements of both the reagent and matrix. γ-Terpinene was photostable when subjected to irradiation under the same experimental conditions. In addition, the liquid compounds at room temperature were also investigated by FTIR-ATR and FT-Raman spectroscopies.

Conformational space and photochemistry of alpha-terpinene.

Alpha-terpinene is a natural product that is isolated from a variety of plant sources and is used in the pharmaceutical and perfume industries. In the atmosphere, under the influence of sunlight, alpha-terpinene undergoes a series of photochemical transformations and contributes to the formation of the secondary organic aerosols. In the present work, alpha-terpinene has been isolated in low-temperature xenon and argon matrices, and its structure and photochemistry were characterized with the aid of FTIR spectroscopy and DFT calculations. The theory predicts three conformers resulting from the rotation of the exocyclic CH(CH(3))(2) framework, that is, Trans (T) and Gauche (G+ and G-) forms. The two Gauche conformers were estimated to be higher in energy, by ca. 1.75 kJ mol(-1), than the most stable Trans form. The signatures of all three conformers were found to be present in the experimental low-temperature matrix spectra with the T form dominating in diluted matrices. The conformational ratio was found to shift in favor of the G+/G- forms upon annealing of the matrices as well as in the neat alpha-terpinene liquid. UV-C (lambda > 235 nm) irradiation of matrix-isolated alpha-terpinene led to its isomerization into an open-ring species, which is produced in the Z configuration and in the conformations that require the smallest structural rearrangements of both the reagent and matrix.

Unusual noncovalent interaction between the chelated Cu(II) ion and the pi bond in the vitamin B(13) complex, cis-diammine(orotato)copper(II): theoretical and vibrational spectroscopy studies.

The crystal structure of the Cu(II) complex with Vitamin B(13) (orotic acid), cis-[Cu(oro)(NH(3))(2)] has revealed the presence of unusual, noncovalent pi-type interaction between the chelated Cu(II) ion and the C horizontal lineC bond of the uracilate ring [Michalska et al. Polyhedron 2007, 26, 4303]. In this work, the origin and strength of this interaction is thoroughly investigated. Comprehensive studies of the molecular structures and vibrational spectra of the title complex have been performed by using the unrestricted density functional theory methods, B3LYP, and the newly developed M05-2X functional. Calculations at the UMP2 level were also carried out for comparison. A variety of basis sets have been employed in the DFT calculations, including aug-cc-pVTZ, D95V(d,p), SDD, and LanL2DZ. The (63)Cu/(65)Cu isotope substitution technique was applied to identify the copper-ligand vibrations in the infrared spectra. The clear-cut assignment of all the bands in the FT-IR and Raman spectra of the title complex has been made on the basis of the calculated potential energy distribution, PED. It is shown that an extremely intense band at 1210 cm(-1) in the Raman spectrum of cis-[Cu(oro)(NH(3))(2)] is diagnostic for the N-1 deprotonation of the uracilate ring and coordination to the copper(II) ion. The B3LYP functional performs better than M05-2X in predicting vibrational frequencies of this complex in the solid state. Intermolecular interactions in crystal were modeled by the supramolecular system consisting of cis-[Cu(oro)(NH(3))(2)], ethylene (above), and formaldehyde (below the copper coordination plane). The stable structure of this system has been predicted only by the M05-2X and MP2 methods, which include dispersion energy, whereas the B3LYP calculations failed in geometry optimization. The distance between the Cu atom and the C horizontal lineC bond, predicted by the M05-2X method (3.00 A) is similar to the van der Waals contacts between the stacking bases in DNA. The calculated interaction energy between the chelated Cu(II) complex and ethylene amounts to -7.33 kcal mol(-1), which is similar to that determined for stacked uracil dimer. It is concluded that the London dispersion energy plays a significant role in the noncovalent interaction between the chelated Cu(II) ion and the uracilate ring in the crystal of cis-[Cu(oro)(NH(3))(2)]. Many copper enzymes in their active sites contain the chelated Cu(II) ion and the aromatic groups (Phe, Tyr and Trp) as the potential binding sites; therefore, the noncovalent copper(II)-pi interaction can be very important for the structure and functioning of these enzymes.

Raman microspectroscopy of organic inclusions in spodumenes from Nilaw (Nuristan, Afghanistan).

The color varieties of spodumene (green spodumene, kunzite) from Nilaw mine (Nuristan, Afghanistan) have been investigated by microthermometry and Raman spectroscopy analyses. These minerals are rich in primary and secondary fluid inclusions. Measured values of temperature homogenization (T(h)) and pressure (P) for selected fluid-inclusion assemblages (I-IV) FIA in green spodumene and (I-II) FIA in kunzite ranges from 370 to 430°C, 1.16 to 1.44 kbar and 300 to 334°C, 0.81 to 1.12 kbar, respectively. The brine content and concentration varies from 4.3 to 6.6 wt.% eq. NaCl. Numerous and diverse mineral phases (quartz, feldspars, mica, beryl, zirconium, apatite, calcite, gypsum) present in this mineral as solid inclusions were studied by Raman microspectroscopy. Raman spectra of selected fluid, organic and solid inclusions were collected as line or rectangular maps and also depth profiles to study their size and contents. There appeared very interesting calcite (156, 283, 711 and 1085 cm(-1)), beryl (324, 397, 686, 1068 and 3610 cm(-1)), topaz (231, 285, 707, 780 and 910 cm(-1)) and spodumene (355, 707 and 1073 cm(-1)) inclusions accompanied by fluid and/or organic inclusions (liquid and gas hydrocarbons) with bands at 2350 cm(-1) (CO(2), N(2)), 2550 cm(-1) (H(2)S) and 2900 cm(-1) (C(2)H(6)-CH(3)). Some solid inclusions contain carbonaceous matter (D-band at ca. 1320 cm(-1) and/or G-band at ca. 1600 cm(-1)).

Nociceptin and its natural and specifically-modified fragments: Structural studies.

The vibrational structures of Nociceptin (FQ), its short bioactive fragments, and specifically-modified [Tyr¹]FQ (1-6), [His¹]FQ (1-6), and [His(1,4)]FQ (1-6) fragments were characterized. We showed that in the solid state, all of the aforementioned peptides except FQ adopt mainly turn and disordered secondary structures with a small contribution from an antiparallel ß-sheet conformation. FQ (1-11), FQ (7-17) [His¹]FQ (1-6), and [His(1,4)]FQ (1-6) have an α-helical backbone arrangement that could also slightly influence their secondary structure. The adsorption behavior of these peptides on a colloidal silver surface in an aqueous solution (pH = ∼8.3) was investigated by means of surface-enhanced Raman scattering (SERS). All of the peptides, excluding FQ (7-17), chemisorbed on the colloidal silver surfaces through a Phe4 residue, which for FQ, FQ (1-11), FQ (1-6), [Tyr¹]FQ (1-6), and [His¹]FQ (1-6) lies almost flat on this surface, while for FQ (1-13) and FQ (1-13)NH2 adopts a slightly tilted orientation with respect to the surface. The Tyr¹ residue in [Tyr¹]FQ (1-6) does not interact with the colloidal silver surface, suggesting that the Tyr¹ and Phe4 side chains are located on the opposite sides of the peptide backbone, which can be also true for His¹ and Phe4 in [His¹]FQ (1-6). The lone pair of electrons on the oxygen atom of the ionized carbonyl group of FQ (1-13) and FQ (7-17) appears to be coordinated to the colloidal silver nanoparticles, whereas in the case of the remaining peptides, it only assists in the adsorption process, similar to the --NH4 group. We also showed that upon adsorption, the secondary structure of these peptides is altered.

Matrix-isolated monomeric tryptophan: electrostatic interactions as nontrivial factors stabilizing conformers.

An extensive analysis of the conformational space of tryptophan (Trp) was performed at the B3LYP/6-311++G(d,p) level and verified by comparison with the infrared spectra of the compound isolated in low-temperature argon and xenon matrixes. Different types of conformers have been unequivocally identified in the matrixes. Type I exhibits the trans arrangement of the carboxylic group and is stabilized by an O-H...N intramolecular H-bond. Types II and III have the carboxylic group in the cis conformation and feature N-H...O=C and N-H...O-C hydrogen bonds, respectively. Three individual conformers of type I were identified in the matrixes. Other conformational degrees of freedom are related with the Calpha-Cbeta-Cgamma=C and C1-Calpha-Cbeta-Cgamma angles (chi1 and chi2, respectively). In proteins, these two dihedral angles define the conformations of the amino acid residues. In monomeric Trp, chi1 adopts the "+" (ca. +90 degrees ) and "-" (ca. -90 degrees ) orientations, while average values of -67.4, 170.5, and 67.6 degrees ("a", "b", and "c", respectively) were found for chi2. Theoretical analysis revealed two important factors in stabilizing the structures of the Trp conformers: the H-bond type and electrostatic interactions. Classified by the H-bond type, the most stable are forms I, followed by II and III. Out of possible combinations of the chi1 and chi2 dihedral angles, "a+", "b+", and "c-" were theoretically found more stable than their "a-", "b-", and "c+" counterparts. Thus, the stabilizing effect of interactions involving the pyrrole ring (which are possible in Ia+, Ib+, and Ic- conformers) is considerably higher compared to those in which the phenyl ring is engaged (existing in the Ia-, Ib-, and Ic+ forms).

Importance of entropy in the conformational equilibrium of phenylalanine: a matrix-isolation infrared spectroscopy and density functional theory study.

The conformational behavior and infrared spectrum of l-phenylalanine were studied by matrix-isolation infrared spectroscopy and DFT [B3LYP/6-311++G(d,p)] calculations. The fourteen most stable structures were predicted to differ in energy by less than 10 kJ mol(-1), eight of them with abundances higher than 5% at the temperature of evaporation of the compound (423 K). Experimental results suggest that six conformers contribute to the spectrum of the isolated compound, whereas two conformers (IIb(3) and IIIb(3)) relax in matrix to a more stable form (IIb(2)) due to low energy barriers for conformational isomerization (conformational cooling). The two lowest-energy conformers (Ib(1), Ia) differ only in the arrangement of the amino acid group relative to the phenyl ring; they exhibit a relatively strong stabilizing intramolecular hydrogen bond of the O-H...N type and the carboxylic group in the trans configuration (O=C-O-H dihedral angle ca. 180 degrees ). Type II conformers have a weaker H-bond of the N-H...O=C type, but they bear the more favorable cis arrangement of the carboxylic group. Being considerably more flexible, type II conformers are stabilized by entropy and the relative abundances of two conformers of this type (IIb(2) and IIc(1)) are shown to significantly increase with temperature due to entropic stabilization. At 423 K, these conformers are found to be the first and third most abundant species present in the conformational equilibrium, with relative populations of ca. 15% each, whereas their populations could be expected to be only ca. 5% if entropy effects were not taken into consideration. Indeed, phenylalanine can be considered a notable example of a molecule where entropy plays an essential role in determining the relative abundance of the possible low-energy conformational states and then, the thermodynamics of the compound, even at moderate temperatures. Upon UV irradiation (lambda > 235 nm) of the matrix-isolated compound, unimolecular photodecomposition of phenylalanine is observed with production of CO(2) and phenethylamine.

Rhythmic changes of some lysosomal hydrolases activity from rat liver. Rhythmic changes of acid phosphatase synthesis.

The activity of acid phosphatase (E.C.3.1.3.2.), arylsulfatase (E.C.3.1.1.23.), beta-galactosidase (E.C.3.1.1.23.), and beta-acetylglucosaminidase (E.C.3.2.1.30.) in rat liver homogenates of 4.5 month-old male rats is presented in this paper. The degradation processes are observed in rat liver homogenate after incubation. The activity of acid phosphatase and beta-acetylglucosaminidase increases, the activity in one of beta-galactosidase is constant, and arylsulfatase decreases during the time of incubation. Furthermore, the maxima of the enzyme activities shift during the incubation in the time of a day. Gel filtration of acid phosphatase on the Sephadex G-150 Superfine and DEAE-cellulose columns determinate the mutual content of acid phosphatase subunits to isoenzymes I and II in various points of a day. The greatest content of acid phosphatase subunits versus both the isoenzymes content is at 02(24), and the greatest content of isoenzyme II versus the content of isoenzymes I appears at 07(12). From these data it is clear that the period of the isoenzyme II synthesis from the subunit amounts to 5 h, while 10 h are necessary to create the isoenzyme I originated from isoenzyme II. The comparison of acid phosphatase activity before and after the homogenate filtration on the Sephadex column indicates the increase of this enzyme activity after its separation from the other proteins and other components.

Low frequency vibrational modes of oxygenated myoglobin, hemoglobins, and modified derivatives.

The low frequency resonance Raman spectra of the dioxygen adducts of myoglobin, hemoglobin, its isolated subunits, mesoheme-substituted hemoglobin, and several deuteriated heme derivatives are reported. The observed oxygen isotopic shifts are used to assign the iron-oxygen stretching (approximately 570 cm-1) and the heretofore unobserved delta (Fe-O-O) bending (approximately 420 cm-1) modes. Although the delta (Fe-O-O) is not enhanced in the case of oxymyoglobin, it is observed for all the hemoglobin derivatives, its exact frequency being relatively invariable among the derivatives. The lack of sensitivity to H2O/D2O buffer exchange is consistent with our previous interpretation of H2O/D2O-induced shifts of v(O-O) in the resonance Raman spectra of dioxygen adducts of cobalt-substituted heme proteins; namely, that those shifts are associated with alterations in vibrational coupling of v(O-O) with internal modes of proximal histidyl imidazole rather than to steric or electronic effects of H/D exchange at the active site. No evidence is obtained for enhancement of the v(Fe-N) stretching frequency of the linkage between the heme iron and the imidazole group of the proximal histidine.

Resonance raman studies of heme structural differences in subunits of deoxy hemoglobin.

Low frequency resonance Raman (RR) spectra are reported for deoxy hemoglobin (Hb), its isolated subunits, its analogue bearing methine-deuterated hemes in all four subunits (Hb-d(4)), and the hybrids bearing the deuterated heme in only one type of subunit, which are [alpha(d4)beta(h4)](2) and [alpha(h4)beta(d4)](2). Analyzed collectively, the spectra reveal subunit-specific modes that conclusively document subtle differences in structure for the heme prosthetic groups in the two types of subunits within the intact tetramer. Not surprisingly, the most significant spectral differences are observed in the gamma(7) mode that has a major contribution from out of plane bending of the methine carbons, a distortion that is believed to relieve strain in the high-spin heme prosthetic groups. The results provide convincing evidence for the utility of selectively labeled hemoglobin hybrids in unraveling the separate subunit contributions to the RR spectra of Hb and its various derivatives and for thereby detecting slight structural differences in the subunits.

Resonance Raman studies of cytochrome P450BM3 and its complexes with exogenous ligands.

Resonance Raman spectra are reported for both the heme domain and holoenzyme of cytochrome P450BM3 in the resting state and for the ferric NO, ferrous CO, and ferrous NO adducts in the absence and presence of the substrate, palmitate. Comparison of the spectrum of the palmitate-bound form of the heme domain with that of the holoenzyme indicates that the presence of the flavin reductase domain alters the structure of the heme domain in such a way that water accessibility to the distal pocket is greater for the holoenzyme, a result that is consistent with analogous studies of cytochrome P450cam. The data for the exogenous ligand adducts are compared to those previously reported for corresponding derivatives of cytochrome P450cam and document significant and important differences for the two proteins. Specifically, while the binding of substrate induces relatively dramatic changes in the nu(Fe-XY) modes of the ferrous CO, ferric NO, and ferrous NO derivatives of cytochrome P450cam, no significant changes are observed for the corresponding derivatives of cytochrome P450BM3 upon binding of palmitate. In fact, the spectral data for substrate-free cytochrome P450BM3 provide evidence for distortion of the Fe-XY fragment, even in the absence of substrate. This apparent distortion, which is nonexistent in the case of substrate-free cytochrome P450cam, is most reasonably attributed to interaction of the Fe-XY fragment with the F87 phenylalanine side chain. This residue is known to lie very close to the heme iron in the substrate-free derivative of cytochrome P450BM3 and has been suggested to prevent hydroxylation of the terminal, omega, position of long-chain fatty acids.