Vibrational CD studies of the solution conformation of simple alanyl peptides as a function of pH

The CH-stretching vibrational CD (VCD) spectra of glycyl-L-alanine, L-alanylglycine, and L-alanyl-L-alanine have been studied at neutral, high, and low pH in D2O solution. The intense positive VCD band attributed to the C alpha H stretch of the alanyl residue in glycyl-L-alanine at neutral pH is absent in L-alanylglycine. In contrast to the VCD spectra of L-alanine, the positive methine-stretching VCD band in glycyl-L-alanine and L-alanyl-L-alanine is still present at pH 2. Based on the ring current mechanism, the VCD spectra are consistent with the presence of a five-membered CO...HN intramolecular hydrogen-bonded ring between the C-terminal carboxylate and peptide NH groups at neutral and high pH; and a seven-membered COH...O = C hydrogen-bonded ring between the C-terminal carboxyl OH and peptide C = O groups at low pH. In the N-terminal alanyl residue, the peptide C = O group is hydrogen bonded to the NH trans to the methine bond. The CH-stretching VCD spectra of L-alanyl-L-alanyl-L-alanine at neutral pH are consistent with two intramolecularly hydrogen-bonded conformations for the central alanyl residue.     

Theoretical and pH dependent surface enhanced Raman spectroscopy study on caffeine

The surface enhanced Raman spectroscopy (SERS) spectrum of caffeine is recorded on a silver colloid at different pH values. It is discussed on the basis of the SERS "surface selection rules" in order to characterize its vibrational behavior on such a biological artificial model. To improve the previous assignments in the Raman spectrum and for a reliable, detailed analysis of SERS spectra, density functional theory calculations (structural parameters, harmonic vibrational wavenumbers, total electron density, and natural population analysis of the molecule) are performed for the anhydrous form of caffeine and the results are discussed. The predicted geometry and vibrational Raman spectra are in good agreement with the experimental data. The flat orientation of the mainly chemisorbed caffeine attached through the pi electrons and the lone pair of nonmethylated N atoms of the imidazole ring are proposed to occur at neutral and basic pH values. At acid pH values caffeine is probably adsorbed on the Ag surface through one or both oxygen atoms, more probably through the O atom of the conjugated carbonyl group with an end-on orientation. However, the changes in the overall SERS spectral pattern seem to indicate the electromagnetic mechanism as being the dominant one.     

Synthesis of 18O-Labelled chlorophyll derivatives at carbonyl oxygen atoms by acidic hydrolysis of the ethylene ketal and acetal

The ethylene ketal of pyropheophorbides, chlorophylls possessing the 13-keto carbonyl group and lacking the 13(2)-methoxycarbonyl group, reacted with H(2)(18)O (ca. 95% 18O atom) by acidic hydrolysis to give efficiently and regioselectively 13(1)-18O-oxo-labelled compounds (ca. 92% 18O). The resulting 18O-labelled chlorin was modified by several chemical reactions to afford some derivatives with little loss of the 18O atom. Following the same procedures, 3(1),13(1)-doubly-18O-labelled pyrochlorophyll derivatives were also prepared. All the synthetic 18O-labelled compounds were identified by FAB-mass and vibrational spectra. Especially, in the vibrational spectroscopic results including IR and resonance Raman spectra, an about 30 cm(-1) wavenumber down-shift of the 3- and/or 13-C[double bond]O stretching vibrational bands was observed by exchanging 3(1)- or 13(1)-oxo-oxygen atom from 16O to 18O.     

Metal complexes of anti-inflammatory drugs. Part III. Nictindole complexes of copper(II) halides

The preparation and properties of the copper(II) halide complexes CuX₂(NIDOL)₂ (where X = Cl, Br) are reported for the anti-inflammatory drug nictindole (NIDOL). The diffuse reflectance spectra, magnetic moments and electron spin resonance spectra are consistent with a tetragonally distorted pseudo-octahedral environment around the copper(II) ions. The infrared spectra indicate monodentate coordination of the neutral drug to the central metal ion via the nitrogen atom of the pyridine ring.     

A theoretical investigation on the conformation and the interaction of CHF2OCF2CHF2 (desflurane II) with one water molecule

The conformation and the interaction of CHF₂OCF₂CHF₂ (desflurane II) with one water molecule is investigated theoretically using the ab initio MP2/aug-cc-pvdz and DFT-based M062X/6-311++G(d,p) methods. The calculations include the optimized geometries, the harmonic frequencies of relevant vibrational modes along with a natural bond orbital (NBO) analysis including the NBO charges, the hybridization of the C atom and the intra- and intermolecular hyperconjugation energies. In the two most stable conformers, the CH bond of the F₂HCO- group occupies the gauche position. The hyperconjugation energies are about the same for both conformers and the conformational preference depends on the interaction between the non-bonded F and H atoms. The deprotonation enthalpies of the CH bonds are about the same for both conformers, the proton affinity of the less stable conformer being 3 kcal mol^?1 higher. Both conformers of desflurane II interact with water forming cyclic complexes characterized by CH…O and OH…F hydrogen bonds. The binding energies are moderate, ranging from ?2.4 to ?3.2 kcal mol^?1 at the MP2 level. The origin of the blue shifts of the ν(CH) vibrations is analyzed. In three of the complexes, the water molecule acts as an electron donor. Interestingly, in these cases a charge transfer is also directed to the non bonded OH group of the water molecule. This effect seems to be a property of polyfluorinated ethers.     

The effect of ring size on vibrational spectroscopy and hydrogen bonding properties for the complexes between small ring carbonyl compounds with HF and HCl: Theoretical analysis

The effect of the molecular structure on the properties of C = O…HX (X = F, Cl) bonds was investigated in a set of small cyclic carbonyl compounds, using vibrational spectroscopy and B3LYP/6–311G** calculations. Two main effects were studied: the size of the ring and the inclusion of oxygen atoms in the ring. In these complexes the C = O and H–X participating bonds in the hydrogen–bond are elongated, while others bonds are compressed. The calculated vibrational spectra were interpreted and band assignments were reported. Surface potential energy calculations are carried out with scanning HCl and HF near oxygen atom.     

Structural fluctuations of myoglobin from normal-modes,M?ssbauer,Raman, and absorption spectroscopy.

A normal-mode analysis of carbon monoxymyoglobin (MbCO) and deoxymyoglobin (Mb) with 170 water molecules is performed for (54)Fe and (57)Fe. A projection is defined that extracts iron out-of-plane vibrational modes and is used to calculate spectra that can be compared with those from resonance Raman scattering. The calculated spectra and the isotopic shift (57)Fe versus (54)Fe agree with the experimental data. At low temperatures the average mean square fluctuations (MSFs) of the protein backbone atoms agree with molecular dynamics simulation. Below 180 K the MSFs of the heme iron agree with the data from Mossbauer spectroscopy. The MSFs of the iron atom relative to the heme are an order of magnitude smaller than the total MSFs of the iron atom. They agree with the data from optical absorption spectroscopy. Thus the MSFs of the iron atom as measured by Mossbauer spectroscopy can be used to probe the overall motion of the heme within the protein matrix, whereas the Gaussian thermal line broadening of the Soret band and the resonance Raman bands can be used to detect local intramolecular iron-porphyrin motions.     

Resonance Raman investigations of chloroperoxidase, horseradish peroxidase, and cytochrome c using Soret band laser excitation.

Resonance Raman spectra of the heme protein chloroperoxidase in its native and reduced forms and complexed with various small ions are obtained by using laser excitation in the Soret region (350-450 nm). Additionally, Raman spectra of horseradish peroxidase, cytochrome P-450cam, and cytochrome c, taken with Soret excitation, are presented and discussed. The data support previous findings that indicate a strong analogy between the active site environments of chloroperoxidase and cytochrome P-450cam. The Raman spectra of native chloroperoxidase are found to be sensitive to temperature and imply that a high leads to low spin transition of the heme iron atom takes place as the temperature is lowered. Unusual peak positions are also found for native and reduced chloroperoxidase and indicate a weakening of porphyrin ring bond strengths due to the presence of a strongly electron-donating axial ligand. Enormous selective enhancements of vibrational modes at 1360 and 674 cm-1 are also observed in some low-spin ferrous forms of the enzyme. These vibrational frequencies are assigned to primary normal modes of expansion of the prophyrin macrocycle upon electronic excitation.     

Six-coordinate phosphorus compounds. Crystal structures and dynamic NMR studies of phosphoranes containing chelating ligands

Hexacoordination of the neutral phosphorus compounds 4–6 is evidenced by their high field ³¹P NMR chemical shifts and is further substantiated by the crystal structure of 5 and 6.5 contains the potentially bis-chelating ligand Ar = (C₆H₃(CH₂NMe₂)₂-2,6) and 6 the same ligand with a protonated amino group. In both cases the compounds exhibit slightly distorted octahedral geometry. In compound 5, only one NMe₂ group is coordinated to the phosphorus atom with an N → P bond of 2.063 Å. In compound 6, the NMe₂ group is coordinated to the phosphorus atom with an N → P bond of 2.007 Å while the dimethylammonium substituent is pointing away from the phosphorus atom forming a hydrogen bridge with two oxygen atoms. The fluxional behavior of these three novel six-coordinate phosphorus compounds was studied by dynamic ¹H NMR spectroscopy.     

Structure and energetics of small iron clusters

Electronic properties of Fe(2-10) clusters and their ions are described by an all-electron ab initio density functional theory computational analysis using the Handy's OPTX exchange and the gradient-corrected correlation functional of Perdew, Burke and Ernzerhof with a triple-zeta valence basis set plus polarization functions. Ground state structures, magnetic moments, dissociation energies, binding energies, IR vibrational spectra, vertical and adiabatic ionization energies, and electron affinities are reported. Two possible states for Fe(2) which are separated by 81.54 meV are described as possible Fe(2), while the septet (ground state) yields an accurate bond distance (error of 0.02??); the nonet yields a precise vibrational frequency (error of 10.1?cm(-1)). Fe(2) binding energy (0.05 eV/atom error) more closely resembles experimental data than any other previously reported computational methods. In addition, the Fe(6) is found to be the most stable cluster within our set being analyzed.     

New effective inhibitors of the Abelson kinase

The effects of substituents on the aryl ring were studied by the preparation and testing of several PD173955 analogs. Inserting a single carbon atom into the C–N bond in the aniline subunit (PDC) reduced the kinase inhibition by a factor of 200. Despite its decreased affinity for Abl compared with PD173955, PDC exhibits a Ki very similar to that reported for Imatinib. Increased water solubility is also gained by replacing the thiomethyl group with an amino or glycyl moiety. For both PD173955 and PDC, the analogs with amino groups in place of the methylthio group are 10 times more inhibitory than the parent molecules. Two molecules were identified with Kis about three orders of magnitude lower than reported for Imatinib.     

Oligosaccharide sequence determination using B/E linked field scanning or tandem mass spectrometry of phosphatidylethanolamine derivatives

Product ion mass spectral data of [M + H]+ ions of oligosaccharides, mainly tetra- and pentasaccharides, as their dipalmitoyl phosphatidylethanolamine derivatives were obtained using both liquid secondary ion mass spectrometry with B/E linked scanning and fast atom bombardment ionization with collision-induced dissociation/tandem mass spectrometry. Both methods give similar positive product ion spectra of equivalent high sensitivity (detection limits of approximately 50 pmol) that principally contain glycosidic cleavage ions retaining the reducing end of the molecule from which monosaccharide sequence can be deduced. A series of ions from fission of the phosphate ester bond together with glycosidic cleavage are present in the tandem mass spectra and B/E linked scan spectra when helium collision gas is used. Monosaccharide linkage position of isomeric molecules is reflected in the intensity of glycosidic fragmentation, without retention of the oxygen atom, with decreasing cleavage in the order 1-3 greater than 1-4 greater than 1-6 linkage. Fucose and N-acetylhexosamines show an increased degree of fragmentation over hexose sugars. The application of product ion spectra of derivatized oligosaccharides is demonstrated for characterizing mixed samples and also the acquisition of spectra directly from the silica surface of high-performance thin-layer chromatography plates.     

Time-resolved FTIR difference spectroscopy for the study of photosystem I with high potential naphthoquinones incorporated into the A1 binding site

Time–resolved step-scan Fourier transform infrared difference spectroscopy has been used to study cyanobacterial photosystem I photosynthetic reaction centers from Synechocystis sp. PCC 6803 (S6803) with four high-potential, 1,4-naphthoquinones incorporated into the A₁ binding site. The high-potential naphthoquinones are 2-chloro-, 2-bromo-, 2,3-dichloro- and 2,3-dibromo-1,4-naphthoquinone. “Foreign minus native” double difference spectra (DDS) were constructed by subtracting difference spectra for native photosystem I (with phylloquinone in the A₁ binding site) from corresponding spectra obtained using photosystem I with the different quinones incorporated. To help assess and assign bands in the difference and double difference spectra, density functional theory based vibrational frequency calculations for the different quinones in solvent, or in the presence of a single asymmetric H– bond to either a water molecule or a peptide backbone NH group, were undertaken. Calculated and experimental spectra agree best for the peptide backbone asymmetrically H– bonded system. By comparing multiple sets of double difference spectra, several new bands for the native quinone (phylloquinone) are identified. By comparing calculated and experimental spectra we conclude that the mono-substituted halogenated NQs can occupy the binding site in either of two different orientations, with the chlorine or bromine atom being either ortho or meta to the H– bonded CO group.     

Ligand effects due to resonance character in LAuCCH<Superscript>−</Superscript> (L = F,Cl, Br,I, CCH) complexes: an NBO/NRT analysis

The organogold complexes of LAuCCH^? (L?=?F, Cl, Br, I, CCH) were investigated using natural bond orbital/natural resonance theory (NBO/NRT) methods. The NBO/NRT results strongly support the general resonance-type three-center-four-electron (3c/4e) picture of LAuCCH: L^?: Au–CCH ? L–Au :CCH^?, arising from hyperconjugation interactions. The sums of ionic and covalent contributions to both L–Au and Au–CCH bonds are all slightly larger than that due to the additional π-back bonding within the 3c/4e hyperbonded triad. This complementary relationship between L–Au and Au–CCH bond orders implies a competing relationship between the ancillary ligand and CCH around the gold atom. We discuss the ligand effects in the LAuCCH^? series on the basis of this competing relationship.     

Fast atom bombardment tandem mass spectrometric analysis of N-carbamoylamino acids.

Using fast atom bombardment (FAB) and tandem mass spectrometry (MS/MS), we examined 12 synthetic N-carbamoylamino acids (CAA) as tert-butyldimethylsilyl (TBDMS) derivatives. In FAB mass spectrometry and FAB MS/MS, spectra of protonated molecules for CAA provide specific cleavages involving the TBDMS carbamoyl moiety. The daughter scan spectrum of the parent ion indicated that it was useful for structural elucidation and differentiation of structural isomers of CAA. We have also identified each CAA separately in a mixture using a neutral loss scan for characteristic ions. In addition, we demonstrated that CAA in urine samples from patients with ornithine carbamoyl transferase deficiency gave collision-induced dissociation (CID) spectra which correspond well with CID spectra obtained using synthetically prepared CAA.     

Analysis of derivatized ceramides and neutral glycosphingolipids by high-performance tandem mass spectrometry

Microscale reduction of ceramides and neutral glycosphingolipids has been evaluated as a means of improving their analysis by fast atom bombardment mass spectrometry, alone and in combination with tandem mass spectrometry. Reduction (conversion of the amide to an amine) of native ceramides and glycosphingolipids containing one to three sugars yields derivatives that show significant signal enhancement. This sensitivity increase allows the acquisition of normal and tandem fast atom bombardment mass spectra from a submicrogram amount of sample. Concomitant permethylation is required for glycosphingolipids that contain more than three sugars. Collision induced dissociation mass spectra of protonated molecular ions, recorded on a four sector instrument, show improved fragmentation allowing the simultaneous characterization of both the ceramide and carbohydrate portions of glycosphingolipids. The reductions are carried out at the nanogram to microgram level with borane, reacting the solid sample with condensed reagent vapor. The borane reduction method has been adapted for this class of substances by adding an oxidation step in order to convert unsaturated lipids to hydroxylated derivatives by oxidation of the resulting organoborane. This approach, used in conjunction with tandem mass spectrometry, allows the determination of olefinic bond location. Labeled derivatives have been prepared by reacting the substrates with trideuterioborane and were used to ascertain the fragmentations and localize olefinic bonds. The collision induced fragmentation of reduced ceramides and neutral glycosphingolipids is only weakly affected by the presence of additional functionalities, such as methoxyl (after permethylation) and hydroxyl groups (resulting from hydroboration and oxidation), a characteristic which facilitates interpretation of the spectra of unknown compounds.     

Difference FT-IR study of a novel biochemical preparation of photosystem II.

There are two redox-active tyrosines in photosystem II, the water-splitting complex, that form neutral tyrosine radicals. One of these tyrosine radicals, D., is stable and has an unknown function. The other redox-active tyrosine, Z, acts to transfer oxidizing equivalents from the primary chlorophyll donor of photosystem II to the manganese cluster, where water oxidation occurs. In an attempt to obtain more information about Z and its interaction with its environment, we have begun a study using Fourier-transform infrared (FT-IR) vibrational spectroscopy. To facilitate these studies, we have developed a procedure to isolate spinach photosystem II complexes with an antenna size of approximately 100-110 chlorophylls per reaction center. These complexes show an approximately 2-fold increase in the specific activity of oxygen evolution over the activity of the starting material, photosystem II membranes. Although fully solubilized in detergent, these complexes retain the 24- and 18-kDa extrinsic proteins and exhibit no calcium chloride requirement for optimal oxygen evolution. In manganese-depleted photosystem II samples, Z. can be accumulated in the light. In the dark, the tyrosine radical is reduced and reprotonated to form the neutral tyrosine. Since this process is reversible and light-dependent, we have used light-minus-dark difference FT-IR spectroscopy to observe the vibrational difference spectrum that is associated with the oxidation of this residue. As a control, EPR spectra were measured under identical conditions to assess the amount of Z. that accumulated in the light. We also hope to use difference FT-IR to identify the amino acid with which Z may form a hydrogen bond.(ABSTRACT TRUNCATED AT 250 WORDS)     

Aggregation of chlorophylls in monolayers. V. The effect of water on chlorophyll a and chlorophyll b in mono and multilayer arrays

The nature of the interactions between water molecules and monolayers and multilayers of chlorophyll a (Chl a), and monolayers and multilayers of Chl b. obtained by the Langmuir-Blodgett technique, is examined by infrared spectroscopy. Following deposition of the monolayer or multilayer of Chl a or Chl b onto a plate, repetitive scans showed some modifications in the infrared spectra which are interpreted as a reorganization of the molecules as some water molecules leave the array. Drying the sample further modifies the spectra, which indicates the departure of more tenacious water molecules. Putting the sample in a moist atmosphere does not restore the original spectrum. This is an indication of a nonreversibie reorganization in the chlorophyll array. The spectra of the monolayer of chlorophyll are much more complicated than those of the multilayer, owing to the nonintegrating effect of the monolayer, which reveals the perturbing effect of the different dielectric milieux on each functional group. On the basis of the analysis of the spectra and the information gathered from the surface pressure isotherms, a model is proposed for the monolayer arrangement at the air/water interface which implies two set of dimers of water per molecule of chlorophyll. One pair of dimers constitutes the water of the first kind and is composed of vapor-like dimers. This kind of water is situated between the porphyrin planes of chlorophyll molecules and is easily removed from the monolayer. The second pair of dimers is composed of water of the second and third kinds situated between the Mg atom of the chlorophyll molecules and the water of the subphase. The second kind of water is closest to the Mg atom and is the most difficult one to remove. The third kind of water is closest to the surface and its mobility is intermediate between that of water of the first kind and that of water of the second kind. Comparing the infrared spectra of a freshly prepared monolayers of Chl a with the resonance Raman spectra of intact chloroplasts (M. Lutz, Biochim. Biophys. Acta 460 (1977) 408), we notice great similarities. This is an indication that the model we propose for the monolayer of Chl a could play an important role in the chloroplast.     

1H- and 13C-NMR studies of N-acetyl-L-alanine methylester and N-acetyl-L-alanine methylamide. I. Self-association

The ¹H- and ¹³C-NMR spectra of N-acetyl-L -alanine methylester and N-acetyl-L -alanine methylamide were measured to examine the modes of self-association of these molecules in solution. The different dilution shifts between these molecules seem to correspond to the difference in the associated state for each molecule. Consequently, for the former molecule, a dimer model forming the intermolecular hydrogen bond through Ala NH hydrogen atom in one molecule to Ala C?O oxygen atom in another molecule was proposed. Another dimer model, which coincides with that proposed recently by Neel and coworkers, was proposed for the latter molecule. This second dimer model forms an intermolecular hydrogen bond through the NH of the N-methylamide group in one molecule to the acetyl C?O in another molecule.