Structural characterization by infrared multiple photon dissociation spectroscopy of protonated gas-phase ions obtained by electrospray ionization of cysteine and dopamine

Structural characterization of protonated gas-phase ions of cysteine and dopamine by infrared multiple photon dissociation (IRMPD) spectroscopy using a free electron laser in combination with theory based on DFT calculations reveals the presence of two types of protonated dimer ions in the electrospray mass spectra of the metabolites. In addition to the proton-bound dimer of each species, the covalently bound dimer of cysteine (bound by a disulfide linkage) has been identified. The dimer ion of m/z 241 observed in the electrospray mass spectra of cysteine has been identified as protonated cystine by comparison of the experimental IRMPD spectrum to the IR absorption spectra predicted by theory and the IRMPD spectrum of a standard. Formation of the protonated covalently bound disulfide-linked dimer ions (i.e. protonated cystine) from electrospray of cysteine solution is consistent with the redox properties of cysteine. Both the IRMPD spectra and theory indicate that in protonated cystine the covalent disulfide bond is retained and the proton is involved in intramolecular hydrogen bonding between the amine groups of the two cysteine amino acid units. For cysteine, the protonated covalently bound dimer (m/z 241) dominated the mass spectrum relative to the proton-bound dimer (m/z 243), but this was not the case for dopamine, where the protonated monomer and the proton-bound dimer were both observed as major ions. An extended conformation of the ethylammonium side chain of gas-phase protonated dopamine monomer was verified from the correlation between the predicted IR absorption spectra and the experimental IRMPD spectrum. Dopamine has the same extended ethylamine side chain conformation in the proton-bound dopamine dimer identified in the mass spectra of electrosprayed dopamine. The structure of the proton-bound dimer of dopamine is confirmed by calculations and the presence of an IR band due to the shared proton. The presence of the shared proton in the protonated cystine ion can be inferred from the IRMPD spectrum.

Vibrational spectra,normal coordinate analyses,and molecular configurations of crystalline propionic acid

Temperature dependence of the IR spectra of crystalline propionic acid were examined in the temperature range 242–50 K. The intensities of most absorption bands increased on lowering the temperature, but some bands diminished until they disappeared at temperatures lower than about 120 K. Normal coordinate analyses indicate that the former bands are due to the stable cis dimer and the latter due to the less stable trans dimer which would be produced from the cis dimer by simultaneous proton transfer along two hydrogen bonds.     

A comparative study of dimerization of chlorophylls and pheophytins by fluorescence and odmir

Optical and ODMR data for dimers of pheophytin a and b and chlorophyll a and b are presented. It is proposed that pheophytin a forms a parallel dimer arising from π-π interaction, binding being essentially different from that in the corresponding chlorophyll dimer. The dimer of phcophytin a is less stable (K ≈ 10⁴ ol/mol) than that of chlorophyll a(K ≈ 10⁶ ol/mol).     

Photocleavage of dimers of coumarin and 6-alkylcoumarins

The cleavage of four coumarin dimers, the syn-head-to-tail (ht) dimer of parent coumarin (syn-ht-CC1), the anti- and syn-hh dimers of 6-methylcoumarin (anti-hh-CC2 and syn-hh-CC2, respectively) and the anti-hh dimer of 6-dodecylcoumarin (anti-hh-CC3), was studied by UV–vis and IR spectroscopy and HPLC upon direct 254 nm irradiation as well as sensitized excitation. The quantum yield of dimer splitting is Φ_sp = 0.1–0.3 in various solvents and the effects of structure and solvent polarity are small. In certain solvents some of the dimers produced CO₂ along with the monomers in the splitting reaction. Electron transfer from dimers to the triplet state of sensitizers, such as benzophenone or 9,10-anthraquinone, was observed in acetonitrile.     

Four-wave mixing spectroscopy of molecular dimers. Application to dimers of pentacene in p-terphenyl

Dispersive coherent Stokes-Raman scattering (CSRS) experiments on pentacene dimers in p-terphenyl were performed to locate the corresponding singly excited, delocalized, dimer levels. In addition the CNRS technique was used to locate the doubly excited dimer state. Future experiments exploring the dynamics of this novel state are discussed.     

Temperature-dependent dephasing of delocalized dimer states of pentacene in p-terphenyl: picosecond photon echo experiments

Optical dephasing of pentacene dimers in p-terphenyl is studied. Dimer statesR₃ and R₄ exhibit an exponential temperature activation of T′₂ which is inconsistent with a mechanism involving scattering between delocalized dimer states. Other dephasing mechanisms are discussed. An upper limit is placed on the relaxation rate from the upper dimer state, R₁, to R₃     

Electrochemical oxidation of 9-methylxanthine

The electrochemical oxidation of 9-methylxanthine proceeds via four voltammetric oxidation peaks at the pyrolytic graphite electrode. The first voltammetric oxidation peak (peak I_a) is a 1e reaction giving a radical which dimerizes to 8,8′-bi-9-methyl-9H-purine-2,6-(1H, 3H)-dione. Peak II_a is a further 2e electrooxidation of the peak I_a dimer to another yellow dimer 8,8′-bi-9-methyl-9H-purine-2,6-(1H)-dione-3,5-(3H)-diiminylidene. This dimer is not very stable and it hydrolyzes to 1-methyl allantoin. Peak III_a is an adsorption pre-peak to peak IV_a which corresponds, overall, to a direct 4e?4H⁺ electrooxidation of 9-methylxanthine to an unstable diimine of 9-methyluric acid. Hydrolysis of this diimine leads to a variety of ultimate products.     

Excitonic interactions in covalently-linked porphyrin dimers

We have studied the absorption spectra, emission spectra, and fluorescence excitation polarization spectra of a series of free base and diprotonated etioporphyrin-I dimers covalently linked through (CH₂)_n bridges, n = 0–8. The absorption spectra of the n = 0 and n = 1 dimer show red shifts, which are largest (≈15 mm) for the Soret band of the n = 0 dimer. The Soret bands of the diprotonated dimers n = 0–3 show splitting (≈500–1000 cm^?1) which can be interpreted by an exciton model assuming a reasonable geometry. The fluorescence spectra and quantum yields are similar to that of the monomer, except for the same red shift seen in absorption; however, the n = 0 diprotonated dimer shows an anomalo vibronic structure. The fluorescence excitation polarization spectra for the n = 0 and the n = 1 dimers differ substantially from the monomer; dimers n ? 3 have fluorescence excitation polarization spectra that suggest that some of the excitation stays localized in one moiety while the r hops to the dimer partner.     

Application of electrospray mass spectrometry in probing protein-protein and protein-ligand noncovalent interactions

A novel mass spectrometry-based methodology using electrospray ionization (ESI) is described for the detection of protein-protein [interferon (IFN)-γ dimer] and protein-ligand [ras-guanosine diphosphate (GDP)] noncovalent interactions. The method utilizes ESI from aqueous solution at appropriate pH. The presence of the noncovalent complex of the IFN-γ dimer was confirmed by the observed average molecular weight of 33,819 Da. The key to the detection of the IFN-γ dimer is the use of an alkaline solution (pH ≈ 9) for sample preparation and for mass spectrornetry analysis. The effect of the declustering energy in the region of the ion sampling orifice and focusing quadrupole on the preservation of the gas-phase noncovalent complex (IFN-γ dimer) was also studied. The effect of the declustering energy on complex dissociation was further extended to probe the noncovalent protein-ligand association of ras-GDP. It was found that little energy is required to dissociate the IFN-γ dimer, whereas a substantial amount of energy is required to dissociate the gas-phase ras-GDP complex.     

Reactions of cyclo-octatetraene and its derivatives—VII: Reactions of cyclo-octatetraene tetramer and of the dimer heptacyclo[8.6.0.02,6.03,9.07,15.08,12.011,16]hexadeca-4,13-diene

Supplementary evidence has been obtained for the formulation of the cyclo-octatetraene tetramer as 1. Thus tetracyano-ethylene gives a 2:1 adduct 7, and at ca 310° the tetramer fragments cleanly to afford the cyclo-octatetraene dimer 9. Additions to dimer 9 may be effected selectively at the 4,5-double bond, and occur in the exo-mode. The generation of tetrachlorobenzyne from 3,4,5,6-tetrachlorobenzenediazonium carboxylate in tetrahydrofuran results in the ether-ester 22.     

Organometallic compound with Lewis base—IV : Dimerization of methyl crotonate by aluminum alkyl-tertiary amine complex

Aluminum alkyl-tertiary amine complex was found to induce the catalytic dimerization of methyl crotonate (MCr) to dimethyl 2-methylpent-4-ene-1,3-dicarboxylate (1) and dimethyl 2-methylpent-cis-3-ene-1,3-dicarboxylate (2). The of the γ-hydrogen of the MCr molecule. Dimer 2 is formed through the isomerization of dimer 1. The complex of AlR₃ with a bidentate ligand, sparteine, produces dimer 1, selectively. The complex of AlR₃ with monodentate ligand NEt₃, on the other hand, induces the isomerization of dimer 1 to the cis-form of dimer 2. The coordination number of aluminum alkyl-tertiary amine complex seems to control the dimerization mechanism of MCr.     

Synthesis of chiral polymers containing thioetherified cinchonidinium repeating units and their application to asymmetric catalysis

A thiol-ene reaction of dithiol and two equivalents of cinchonidine afforded a thioetherified cinchonidine dimer. The dimer was treated with benzyl bromide to give a quaternary ammonium dimer. An ion exchange reaction of the cinchonidinium dimer and disodium disulfonate gave polymers containing chiral quaternary ammonium repeating units in their main-chain structures. Another type of chiral polymer was synthesized by quaternization polymerization. Repeated quaternization reactions between the thioetherified cinchonidine dimer and dihalides yielded chiral polymers containing cinchonidinium structures in their main chains. Both of these chiral polymers were successfully used as catalysts for the asymmetric alkylation of N-diphenylmethylene glycine tert-butyl ester. The chiral cinchonidinium polymers explored in this study showed excellent catalytic activity in asymmetric alkylation reactions and were reused several times without loss of activity.     

The Ras dimer structure

Oncogenic mutated Ras is a key player in cancer, but despite intense and expensive approaches its catalytic center seems undruggable. The Ras dimer interface is a possible alternative drug target. Dimerization at the membrane affects cell growth signal transduction. In vivo studies indicate that preventing dimerization of oncogenic mutated Ras inhibits uncontrolled cell growth. Conventional computational drug-screening approaches require a precise atomic dimer model as input to successfully access drug candidates. However, the proposed dimer structural models are controversial. Here, we provide a clear-cut experimentally validated N-Ras dimer structural model. We incorporated unnatural amino acids into Ras to enable the binding of labels at multiple positions via click chemistry. This labeling allowed the determination of multiple distances of the membrane-bound Ras-dimer measured by fluorescence and electron paramagnetic resonance spectroscopy. In combination with protein–protein docking and biomolecular simulations, we identified key residues for dimerization. Site-directed mutations of these residues prevent dimer formation in our experiments, proving our dimer model to be correct. The presented dimer structure enables computational drug-screening studies exploiting the Ras dimer interface as an alternative drug target.

By combining the incorporation of unnatural amino acids, click chemistry, FRET and EPR distance measurements, protein modeling and biomolecular simulations, we obtained an unambiguous Ras dimer structural model and disrupt the dimer by mutagenesis.     

Laccase (EC 1.10.3.2) catalyses the conversion of procyanidin B-2 (epicatechin dimer) to type A-2

We report here the conversion of procyanidin B-2 (epicatechin dimer) to the procyanidin A-2 dimer by laccase (EC 1.10.3.2). The identity of the A-2 dimer was determined by its mass spectrum (m/z = 577), as well as by comparison with a product formed with the DPPH (2,2-diphenyl-1-picrylhydrazyl) radical. This latter system was previously shown to transform procyanidin type-B to type-A. Other quinonoid-type products, including an oxidation product (m/z = 574.6) of A-2, were also observed. We propose that in plants the conversion of natural procyanidins type-B to type-A might occur by enzymatic means rather than via a radical process as was previously suggested.     

Water-soluble supramolecular porphyrin dimer: self-organization of mono(imidazolyl)-substituted Zn porphyrin to a special-pair type dimer in water

Tris(4-carboxylphenyl)-mono(N-methylimidazolyl)-substituted Zn porphyrin was synthesized as a precursor for a water-soluble supramolecular porphyrin dimer. The dimer formation was performed in a NaHCO₃ aq solution (pH 8.4) and phosphate buffer solutions (pH 7.4-9.0). The split Soret bands of Zn porphyrin observed in the absorption spectra clearly showed self-organization to a special-pair type slipped cofacial dimer via metal coordination of imidazole even in water.     

Indenone chemistry—III: Use of the 2-carboethoxymethyl-6-methoxyindenone in the synthesis of the gibbane skeleton

The 2-carboethoxymethyl-6-methoxyindenone 5 has been synthesized in good yield. The endo head-to-tail dimer 6 and the exo head-to-tail dimer 7 can be synthesized stereoselectively from the indenone 5. Diels Alder addition of 5 to 1,3-butadiene affords the 7-methoxy-9aα-carboethoxymethyl-9a, 1,4aα, 4-tetrahydrofluorenone 8. The corresponding acid 9 can be cyclised to the 2 - methoxy - 4bαH - gibba - A,5 - tetraene - 8,10 - dione 10.     

First enantiopure phosphapalladacycle with planar chirality. X-Ray study of the racemic dimer and (Spl,SCSN)-diastereomer of its prolinate derivative

The first P,C-cyclopalladated complex with planar chirality was prepared by direct cyclopalladation of prochiral di-tert-butyl(ferrocenylmethyl)phosphine. Resolution of the racemic dimer was achieved through separation of its diastereomeric (S)-prolinate derivatives. The palladacycle structure was confirmed by the ¹H NMR spectra of the dimer and its triphenylphosphine adduct and an X-ray diffraction study of the racemic dimeric complex. The absolute configuration of the planar chirality was determined by an X-ray diffraction investigation of one of two diastereomers of the (S)-prolinate derivative.     

IR Study of Monomer–Dimer Self-association of 2,2-Dimethyl-3-ethyl-3-pentanol in n-Octane: Determination of the Molar Absorptivities of Monomer and Dimer Bands, and Dimerization Constants Using Novel Equations

The monomer–dimer self-association equilibrium of 2,2-dimethyl-3-ethyl-3-pentanol in n-octane has been studied by IR spectroscopy at four temperatures (288, 298, 308, and 318 K). The solute was chosen to restrict the self-association between solute molecules to dimerization only, owing to steric hindrance of the bulky chains in the vicinity of the OH group. Two linear equations have been derived for the treatment of the experimental data. One of these equations was used to treat the data of the concentration dependent integrated absorbance of the monomer bands for each temperature to obtain the monomer molar absorptivity, ε _m, and dimerization constant, K. The other equation was used to treat the data of concentration-dependent dimer bands to obtain the dimer molar absorptivity, ε _d, and K. Thus, the dimerization constant was determined by two methods. Since the same thermodynamic quantity K is obtained from either the monomer bands or the dimer bands, the difference between them at a given temperature can serve as an assessment of the quality of the experiment. The standard enthalpy and entropy of dimerization were also obtained from a van’t Hoff plot.     

Composition and structure of activated complexes in stereoselective deprotonation of cyclohexene oxide by a mixed dimer of chiral lithium amide and lithiated imidazole

Stereoselective deprotonation of cyclohexene oxide, using a mixed dimer built of the chiral lithium amide, lithium (1R,2S)-N-methyl-1-phenyl-2-pyrrolidinyl-propanamide, and 2-lithio-1-methylimidazole, has been studied. The composition of the rate limiting activated complex was determined by kinetics to be built from one mixed dimer molecule and one epoxide molecule. Based on this knowledge computational chemistry has been applied to gain insight into possible structures of the activated complexes.     

Stacking of triphenylene: characterization of the potential energy surface

The interaction potential energy of triphenylene dimer has been calculated with Møller–Plesset second-order perturbation theory for various geometrical configurations. Different types of geometrical perturbations such as rotation, displacements and their combinations are studied in terms of their effects on the stability of the dimer. Minimum energy conformers for face to face, rotated, parallel displaced and T-shape structures are obtained. For the unsubstituted triphenylene, the 35° rotation of one of the monomers results in the global minimum. However, the dimer is still very flexible in terms of displacements. A helical structure seems to be the most stable form for the trimer. For large stacked clusters, the two body forces dominate the interactions while at small monomer–monomer separation, three body terms behave like z ^?9 where z is the vertical distance between two adjacent monomers.