A simple total synthesis of (plus or minus)-dendrobine.
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Alkaloids↗
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Results for “Spectrophotometry, Infrared”
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Structure and tautomerism of the neutral and monoanionic forms of 4-thiouracil derivatives.
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Hydrogen-Ion Concentration↗
A luminescent anion sensor based on a europium hybrid complex.
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Anions↗
Formation and characterization of carbon monoxide adducts of iron "twin coronet" porphyrins. Extremely low CO affinity and a strong negative polar effect on bound CO.
The carbon monoxide (CO) adducts of iron "twin coronet" porphyrins (TCPs) are characterized by UV-vis, resonance Raman (RR), IR, and 13C NMR spectroscopies. A superstructured porphyrin, designated as TCP, was used as a common framework for the four different types of iron complexes. TCP bears two binaphthalene bridges on each side and creates two hydrophobic pockets surrounded by the bulky aromatic rings. In the CO-binding cavities, the hydroxyl groups are oriented toward the center above the heme. The iron complexes investigated are as follows: TCP (which is without a covalently linked axial ligand), TCP-PY (which has a linked pyridine ligand), and TCP-TB and TCP-TG (both of which have a linked thiolate ligand). These complexes were synthesized as ferric forms and identified by the various spectroscopic methods. The UV-vis spectra of TCP-CO and TCP-PY-CO exhibit lambda(max) at 432, 546 and 428, 541 nm, respectively. On the other hand, the CO adducts of TCP-TB and TCP-TG show typical hyperporphyrin spectra for a thiolate-ligated iron(II) porphyrin-CO complex. In the RR spectra, the nu(Fe-CO) bands were observed at 506, 489 cm(-1) (TCP), 465 cm(-1) (TCP-PY), 458, 437 cm(-1) (TCP-TG) and 429 cm(-1) (TCP-TB). Compared with the reported nu(Fe-CO) frequencies of hemoproteins and their model systems, these observed values are unusually low. Further, abnormally high nu(C-O) bands are observed at 1990 cm(-1) (TCP-CO) and 2008 cm(-1) (TCP-PY-CO) in IR spectra. The lower nu(Fe-CO) and the higher nu(C-O) frequencies can be ascribed to the strong negative polar effect caused by the vicinal hydroxyl groups in the cavity. This prediction is further supported by the observation of significant 13C shieldings exhibited by TCP-CO (delta = 202.6 ppm) and TCP-PY-CO (delta = 202.3 ppm), in comparison to hemoproteins and other heme models. The CO affinity of TCP-PY (P1/2CO = 0.017 Torr at 25 C) is unusually lower than other heme models. The unique behavior of these CO adducts is discussed in context of the TCP structures.
Binding Sites↗
The role of water bridges in directing the conformational preferences of 3-indole-propionic acid and tryptamine.
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Hydrogen Bonding↗
Engineering of highly luminescent lanthanide tags suitable for protein labeling and time-resolved luminescence imaging.
The synthesis of a new ligand LH(4) based on a glutamic acid skeleton bis-functionalized on its nitrogen atom by 6-methylene-6'-carboxy-2,2'-bipyridine chromophoric units is described. UV-vis spectrophotometric titrations revealed the formation of 1:1 M:L complexes with lanthanide(III) cations, and complexation of LH(4) with equimolar amounts of hydrated LnCl(3) salts (Ln = Eu, Gd, and Tb) gave water-soluble and stable complexes of the general formula [LnL(H(2)O)]Na, which were characterized by elemental analysis, IR, UV-vis absorption spectroscopy, (1)H NMR (Ln = Eu), and mass spectrometry. The conditional stability constant for formation of the [EuL(H(2)O)]Na complex was determined by competitive complexation experiments to be log K = 16.5 +/- 0.6 in 0.01 M TRIS/HCl buffer (pH = 7.0). In water solution, the [EuL(H(2)O)]Na and [TbL(H(2)O)]Na complexes were highly luminescent with quantum yields of 8% and 31%, respectively, despite the presence of ca. one water molecule in the first coordination sphere of the metal ions. Activation of the appended carboxylate function of the glutamate moiety in the form of an N-hydroxysuccinimidyl ester allows for the covalent linking of the complexes to primary amino groups of biological compounds. Bovine serum albumin (BSA) was labeled with both Eu or Tb complexes, and the Ln-BSA conjugates were characterized by UV-vis absorption and emission spectroscopy and MALDI-TOF mass spectrometry. Labeling ratios (number of complex molecules per BSA) of ca. 8:1 and 7:1 were established for Eu-BSA and Tb-BSA, respectively. The suitability of the tagged compound for use in bioanalytical time-resolved luminescence microscopy was established by comparison with fluorescein-labeled probes.
Glutamates↗
Magnesium tetraarylporphyrin tweezer: a CD-sensitive host for absolute configurational assignments of alpha-chiral carboxylic acids.
A protocol to determine the absolute configuration of alpha-chiral carboxylic acids based on a modified circular dichroic (CD) exciton chirality method has been developed. The protocol relies on a host-guest complexation mechanism: the chiral substrates are derivatized to give bifunctional amide conjugates ("guests") that form complexes with a dimeric magnesium porphyrin host, Mg-T (T stands for "tweezer") that acts as a "receptor". The two porphyrins in the complex adopt a preferred helicity dictated by the substituents at the chiral center in accordance with their steric sizes (assigned on the basis of conformational energy A-values) and, consequently, with the absolute configuration of the substrates under investigation. This chiroptical method, verified with a variety of chiral substrates, has been demonstrated to be reliable and generally applicable, including natural products with complex structures. Molecular modeling, NMR, and FTIR experiments of selected host-guest complexes revealed the mode of ligation of the substrates to the magnesium porphyrin species and led to clarification of the structure of the complex. When oxygen functionalities were directly attached to the chiral center, the signs of the CD couplets were opposite to those predicted on the basis of steric size. NMR and molecular modeling experiments indicated that this apparent inconsistency was due to conformational characteristics of the guest molecules. The stereochemical analysis is shown to be a sensitive technique, not only for the determination of absolute configurations of substrates but also for elucidation of their solution conformations.
Carboxylic Acids↗
Spectroscopic evidence for gas-phase formation of successive beta-turns in a three-residue peptide chain.
We report the first gas-phase spectroscopic study of a three-residue model of a peptide chain, Ac-Phe-Gly-Gly-NH2 (Ac = acetyl), using the IR/UV double resonance technique. The existence of at least five different conformers under supersonic expansion conditions is established, most of them exhibiting rather strong intramolecular H-bonds. One of the most populated conformers, however, exhibits a different H-bonding network characterized by two weak H-bonds. Comparison of the amide A and I/II experimental data with density functional theory calculations carried out on a series of selected conformations enables us to assign this conformer to two successive beta-turns along the peptide chain, the two H-bonds being of C10 type, i.e., each of them closing a 10-atom ring in the molecule. The corresponding form is found to be more stable than the 310 helix secondary structure (not observed), presumably because of specific effects due to the glycine residues.
Amides↗
Microhydration of Guanine base pairs.
We report spectroscopy of clusters of guanine base pairs with one and two water molecules. We recorded the vibronic spectra of the mass-selected GG(H2O) and GG(H2O)2 clusters using resonant two photon ionization (R2PI) and we used IR-UV double resonance spectroscopy to obtain ground state IR spectra of these clusters. We found that a single water molecule stabilizes one of two structures we had previously found for guanine dimers. Addition of a second water molecule causes no further structural change.
Base Pairing↗
Unusual ligand discrimination by a myoglobin reconstituted with a hydrophobic domain-linked heme.
New, reconstituted horse heart myoglobins possessing a hydrophobic domain at the terminal of the two heme propionate side chains were constructed. The O2 and CO bindings for the reconstituted deoxymyoglobins were examined in detail by laser flash photolysis and stopped-flow rapid mixing techniques. The artificially created domain worked as a barrier against exogenous ligand penetration into the heme pocket, whereas the bound O2 was stabilized in the reconstituted myoglobin as well as in the native one. In contrast, the CO dissociation rate for the reconstituted myoglobin increased by 20-fold compared to the native protein, suggesting that the incorporation of the hydrophobic domain onto the heme pocket perturbs the distal-site structure of the reconstituted myoglobin. As a result, the substantial ligand selectivity for the reconstituted myoglobin significantly increases in favor of O2 over CO with the M' value (= KCO/KO2) of 0.88, whereas, to the best of our knowledge, there is no myoglobin mutant in which the O2 affinity exceeds the CO one. The present work concludes that the O2 selectivity of myoglobin over CO is markedly improved by chemically modifying the heme propionates without any mutation of the amino acid residues in the distal site.
Animals↗
Intrinsic folding of small peptide chains: spectroscopic evidence for the formation of beta-turns in the gas phase.
Laser desorption of model peptides coupled to laser spectroscopic techniques enables the gas-phase observation of genuine secondary structures of biology. Spectroscopic evidence for the formation of beta-turns in gas-phase peptide chains containing glycine and phenylalanine residues establishes the intrinsic stability of these forms and their ability to compete with other stable structures. The precise characterization of local minima on the potential energy surface from IR spectroscopy constitutes an acute assessment for the state-of-the-art quantum mechanical calculations also presented. The observation of different types of beta-turns depending upon the residue order within the sequence is found to be consistent with the residue propensities in beta-turns of proteins, which suggests that the prevalence of glycine in type II and II' turns stems essentially from an energetic origin, already at play under isolated conditions.
Dipeptides↗
Dioxygen activation by a low-valent cobalt complex employing a flexible tripodal N-heterocyclic carbene ligand.
The novel versatile cobalt(I) tris-carbene complex [(TIMEN(xyl))Co]Cl (1) (where TIMEN = (tris[2-(3-arylimidazol-2-ylidene)ethyl]amine) reacts with CO, one-electron oxidizers such as CH(2)Cl(2), and O(2) to yield the cobalt complexes [(TIMEN(xyl))Co(CO)]Cl (2), [(TIMEN(xyl))Co(Cl)]Cl (3), and peroxo species [(TIMEN(xyl))Co(O(2))](BPh(4)) (5). All new complexes were fully characterized by (1)H NMR, UV/vis, and IR spectroscopy as well as superconducting quantum interference device (SQUID) magnetization measurements and single-crystal X-ray crystallography. The nucleophilic character of the eta(2)-bound dioxygen ligand in 5 was confirmed by density functional theory (DFT) studies and allows for oxygen-transfer reactions with electron-deficient organic substrates, such as benzoyl chloride.
Cobalt↗
Gas phase formation of a 3(10)-helix in a three-residue peptide chain: role of side chain-backbone interactions as evidenced by IR-UV double resonance experiments.
The first spectroscopic evidence for the gas-phase formation of helical structures in short peptide chains is reported, using the IR-UV double resonance technique and DFT quantum chemistry calculations. The study involves three chemically protected peptides, all based on the same Ac-(Ala)3-NH2, (Ac = acetyl, Ala = alanine) tripeptide, in which one of the Ala residues is substituted by the aromatic phenylalanine residue. For the three molecules, only one main conformer is observed in the supersonic expansion. IR analysis shows that the structure of this conformer is strongly dependent upon the substitution site: the helical 310-type structure is observed only when Phe occupies the central residue of the chain. The present work also emphasizes that the 310-helix formation does compete with other archetypal H-bonding patterns, such as 27-ribbon or mixed structures, whose relative energetics can be greatly influenced by a modest NH-aromatic interaction.
Amino Acid Sequence↗
Ultrafast excited-state dynamics in vitamin B12 and related cob(III)alamins.
Femtosecond transient IR and visible absorption spectroscopies have been employed to investigate the excited-state photophysics of vitamin B12 (cyanocobalamin, CNCbl) and the related cob(III)alamins, azidocobalamin (N3Cbl), and aquocobalamin (H2OCbl). Excitation of CNCbl, H2OCbl, or N3Cbl results in rapid formation of a short-lived excited state followed by ground-state recovery on time scales ranging from a few picoseconds to a few tens of picoseconds. The lifetime of the intermediate state is influenced by the sigma-donating ability of the axial ligand, decreasing in the order CNCbl > N3Cbl > H2OCbl, and by the polarity of the solvent, decreasing with increasing solvent polarity. The peak of the excited-state visible absorption spectrum is shifted to ca. 490 nm, and the shape of the spectrum is characteristic of weak axial ligands, similar to those observed for cob(II)alamin, base-off cobalamins, or cobinamides. Transient IR spectra of the upper CN and N3 ligands are red-shifted 20-30 cm(-1) from the ground-state frequencies, consistent with a weakened Co-upper ligand bond. These results suggest that the transient intermediate state can be attributed to a corrin ring pi to Co 3d(z2) ligand to metal charge transfer (LMCT) state. In this state bonds between the cobalt and the axial ligands are weakened and lengthened with respect to the corresponding ground states.
Hydroxocobalamin↗
Building up key segments of N-glycans in the gas phase: intrinsic structural preferences of the alpha(1,3) and alpha(1,6) dimannosides.
The intrinsic conformer specific vibrational spectra of two important subunits of the core pentasaccharide of N-linked glycans, the alpha(1,3) and alpha(1,6) dimannosides, have been recorded in the gas phase. Coupling these measurements with a computational exploration of their conformational landscapes has enabled their conformational assignment and has identified characteristic vibrational signatures associated with particular conformational families-including those that do or do not display inter-ring hydrogen bonding across the glycosidic linkage. In addition, the IR spectra of the monosaccharide moieties provide benchmarks, through which the conformational assignments can be refined. This introduces a general concept of modularity and secondary structure in oligosaccharides--essential for the success of similar studies on larger oligosaccharides in the future.
Carbohydrate Conformation↗
Gold nanoclusters protected by conformationally constrained peptides.
The preparation and properties of a series of gold nanoclusters protected by thiolated peptides based on the alpha-aminoisobutyric acid (Aib) unit are described. The peptides were devised to form 0-3 C=O...H-N intramolecular hydrogen bonds, as required by their 3(10)-helical structure. The monolayer-protected clusters (MPCs) were prepared, using a modified version of the two-phase Brust-Schiffrin preparation, and fully characterized with (1)H NMR spectrometry, IR and UV-vis absorption spectroscopies, transmission electron microscopy (TEM), thermogravimetric analysis (TGA), and X-ray photoelectron spectroscopy (XPS). The MPCs were obtained with core diameters in the range of 1.1-2.3 nm, depending on the reaction conditions. Structured peptides formed smaller clusters. The smallest MPC obtained is in agreement with the average formula Au(38)Pep(18). The results showed that the chemical integrity of the peptide is maintained upon monolayer formation and that the average number of peptide ligands per gold cluster is typically 75-85% the value calculated for alkanethiolate MPCs of similar sizes. The IR and NMR spectra indicated that in the monolayer the peptides are involved in both intra- and interligand C=O...H-N hydrogen bonds.
Aminoisobutyric Acids↗
Excited-state mixed-valence distortions in a diisopropyl diphenyl hydrazine cation.
Excited-state mixed valence (ESMV) occurs in the 1,2-diphenyl-1,2-diisopropyl hydrazine radical cation, a molecule in which the ground state has a symmetrical charge distribution localized primarily on the hydrazine, but the phenyl to hydrazine charge-transfer excited state has two interchangeably equivalent phenyl groups that have different formal oxidation states. Electronic absorption and resonance Raman spectra are presented. The neighboring orbital model is employed to interpret the absorption spectrum and coupling. Resonance Raman spectroscopy is used to determine the excited-state distortions. The frequencies of the enhanced modes from the resonance Raman spectra are used together with the time-dependent theory of spectroscopy to fit the two observed absorption bands that have resolved vibronic structure. The origins of the vibronic structure and relationships with the neighboring orbital model are discussed.
Cations↗
Characterization and biological activities of humic substances from mumie.
Mumie, a semihard black resin formed by long-term humification, is believed to have therapeutic properties. Although mumie has been used in folk medicine since ancient times, there is little information available concerning the physicochemical properties of its constituents and the mechanisms of its therapeutic efficacy. For this study crude mumie was fractionated into fulvic acid (FA), humic acid (HA), humin, hymatomelanic acid, and two low molecular weight fractions (LMW1 and LMW2). The FA fraction was divided into five subfractions, FA1-FA5. The mumie fractions were characterized by IR, UV-vis, and fluorescence spectroscopy. Total carbohydrate content in the fractions was analyzed using the phenol reaction method. The relative content of polar groups and nonpolar hydrocarbon fragments in the mumie fractions correlated well with solubility in an aqueous medium. Biological characterization was performed using only the FA fractions. FA1 and FA2 enhanced the production of reactive oxygen species (ROS) and nitric oxide in murine peritoneal macrophages, as determined with the use of 2',7'-dichlorofluorescin diacetate and Griess reagent, respectively. The enchancement of ROS and nitric oxide production correlated with the level of total carbohydrates in the fractions. Murine splenic lymphocytes treated with FA1 showed a dose-dependent increase in [(3)H]thymidine uptake. These findings suggest that FA derived from mumie has immunomodulatory activity.
Animals↗