Solvent effects in tandem mass spectrometry: mechanistic studies indicating how a change in solvent conditions and pH can dramatically alter CID spectra

Dramatically different CID (collision-induced dissociation) spectra are obtained when the complex [Zn(dien-glucose)](+) is electrosprayed from acidic and basic solutions. To understand this peculiar phenomenon, an in-depth mechanistic study was performed on one of the product ions that is present when the initial complex is diluted in basic solution but absent when the complex is diluted with acidic solution. On the basis of the results of this study, the differences in the CID spectra can be rationalized by the fact that the complex electrosprayed from basic solution was kinetically trapped, with the deprotonation site distal from the metal center. Under acidic conditions, the deprotonation site is at a hydroxyl group coordinated to the metal ion. A variety of experiments support this hypothesis. The studies herein underscore the importance of using identical solvent conditions when comparing sets of CID spectra. The data also highlight a very interesting phenomenon involving deprotonation of a hydroxyl group, which was several atoms away from the Zn(II) metal center.     

Air-liquid interfaces of aqueous solutions containing ammonium and sulfate: spectroscopic and molecular dynamics studies

Investigations of the air-liquid interface of aqueous salt solutions containing ammonium (NH(4)(+)) and sulfate (SO(4)(2-)) ions were carried out using molecular dynamics simulations and vibrational sum frequency generation spectroscopy. The molecular dynamics simulations show that the predominant effect of SO(4)(2-) ions, which are strongly repelled from the surface, is to increase the thickness of the interfacial region. The vibrational spectra reported are in the O-H stretching region of liquid water. Isotropic Raman and ATR-FTIR (attenuated total reflection Fourier transform infrared) spectroscopies were used to study the effect of ammonium and sulfate ions on the bulk structure of water, whereas surface sum frequency generation spectroscopy was used to study the effect of these ions on the interfacial structure of water. Analysis of the interfacial and bulk vibrational spectra reveal that aqueous solutions containing SO(4)(2-) perturb the interfacial water structure differently than the bulk and, consistent with the molecular dynamics simulations, reveal an increase in the thickness of the interfacial region.     

Spectroscopic and computational studies of aqueous ethylene glycol solution surfaces

The combination of Monte Carlo, ab initio, and DFT computational studies of ethylene glycol (EG) and EG-water hydrogen-bonding complexes indicate that experimental vibrational spectra of EG and EG-water solution surfaces have contributions from numerous conformations of both EG and EG-water. The computed spectra, derived from harmonic vibrational frequency calculations and a theoretical Boltzmann distribution, show similarity to the experimental surface vibrational spectra of EG taken by broad-bandwidth sum frequency generation (SFG) spectroscopy. This similarity suggests that, at the EG and aqueous EG surfaces, there are numerous coexisting conformations of stable EG and EG-water complexes. A blue shift of the CH2 symmetric stretch peak in the SFG spectra was observed with an increase in the water concentration. This change indicates that EG behaves as a hydrogen-bond acceptor when solvated by additional water molecules. This also suggests that, in aqueous solutions of EG, EG-EG aggregates are unlikely to exist. The experimental blue shift is consistent with the results from the computational studies.     

Synthesis and investigation of [Cp(PMe(3))Rh(H)(H(2))](+) and its partially deuterated and tritiated isotopomers: evidence for a hydride/dihydrogen structure

Hydrogenolysis of [Cp(PMe(3))Rh(Me)(CH(2)Cl(2))](+)BAr'(4)(-) (4, Ar' = 3,5-C(6)H(3)(CF(3))(2)) in dichloromethane afforded the nonclassical polyhydride complex [Cp*PMe(3))Rh(H)(H(2))](+)BAr'(4)(-) (1), which exhibits a single hydride resonance at all accessible temperatures in the (1)H NMR spectrum. Exposure of solutions of 1 to D(2) or T(2) gas resulted in partial isotopic substitution in the hydride sites. Formulation of 1 as a hydride/dihydrogen complex was based upon T(1) (T(1)(min) = 23 ms at 150 K, 500 MHz), J(H-D) (ca. 10 Hz), and J(H-T) (ca. 70 Hz) measurements. The barrier (Delta G(++)) to exchange of hydride with dihydrogen sites was determined to be less than ca. 5 kcal/mol. Protonation of Cp(PMe(3))Rh(H)(2) (2) using H(OEt(2))(2)BAr'(4) resulted in binuclear species [(Cp(PMe(3))Rh(H))(2)(mu-H)](+)BAr'(4)(-) (3), which is formed in a reaction involving 1 as an intermediate. Complex 3 contains two terminal hydrides and one bridging hydride ligand which exchange with a barrier of 9.1 kcal/mol as observed by (1)H NMR spectroscopy. Additionally, the structures of 3 and 4, determined by X-ray diffraction, are reported.     

Genetic and genomic approaches to identify and study the targets of bioactive small molecules

Natural and synthetic bioactive small molecules form the backbone of modern therapeutics. These drugs primarily exert their effect by targeting cellular host or foreign proteins that are critical for the progression of disease. Therefore, a crucial step in the process of recognizing valuable new drug leads is identification of their protein targets; this is often a time consuming and difficult task. This report is intended to provide a comprehensive review of recent developments in genetic and genomic approaches to overcome the hurdle of discovering the protein targets of bioactive small molecules.     

A formal [3 + 3] cycloaddition reaction. Improved reactivity using alpha,beta-unsaturated iminium salts and evidence for reversibility of 6pi-electron electrocyclic ring closure of 1-oxatrienes

A detailed account regarding a formal [3 + 3] cycloaddition method using 4-hydroxy-2-pyrones and 1,3-diketones is described here. This formal cycloaddition reaction or annulation reaction is synthetically useful for constructing 2H-pyranyl heterocycles. The usage of alpha,beta-unsaturated iminium salts is significant in controlling competing reaction pathways to give exclusively 2H-pyrans. Most significantly, experimental evidence is provided to support the mechanism of this reaction that involves a sequential Knoevenagel condensation and a reversible 6pi-electron electrocyclic ring-closure of 1-oxatrienes.     

Fourier transform Raman spectroscopy: A comparison of Nd:YAG and lower-frequency sources

Fourier transform Raman instruments invariably incorporate Nd:YAG solid state lasers operating at 1064 nm. Recently, new lasers have appeared which are likely to be of appropriate power and linewidth for Raman spectroscopy and to be very economical. They emit at various wavelengths between the deep red and one micron wavelength. We have investigated whether sources in this domain are as satisfactory as Nd:YAG ones and conclude that where samples display even the slightest fluorescence with 1064 nm excitation this will be worse if shorter wavelength sources are used and unacceptably so if the source is of shorter wavelength than 900 nm. Thus as a routine analytical tool new improved sources are essential and many of the newer sources are unlikely to be satisfactory.     

A biogenetically inspired heterodimerization approach to the synthesis of the core structure of the alkaloid fissoldhimine

A biogenetically inspired heterodimerization reaction of N-substituted 2-pyrroline equivalents leads to the tricyclic core of the alkaloid fissoldhimine. Thus, pyrrolidin-2-ol derivatives, in which the nitrogen atom is substituted either with urea or thiourea functionality, serve as equivalents of the corresponding N-substituted 2-pyrrolines. Reaction of these compounds under Lewis acidic (e.g., lanthanide triflate) or Brønsted acid conditions leads to a diastereomeric form of the tricyclic core of fissoldhimine. The reaction can be envisaged to occur either via an asynchronous intermolecular inverse electron demand hetero-Diels-Alder reaction, or through a tandem Mannich/ring-closure reaction.     

Synthesis, structure, and magnetic properties of the layered copper(II) oxide Na2Cu2TeO6

A new quaternary layered transition-metal oxide, Na2Cu2TeO6, has been synthesized under air using stoichiometric (with respect to the cationic elements) mixtures of Na2CO3, CuO, and TeO2. Na2Cu2TeO6 crystallizes in the monoclinic space group C2/m with a = 5.7059(6) A, b = 8.6751(9) A, c = 5.9380(6) A, beta = 113.740(2) degrees, V = 269.05(5) A3, and Z = 2, as determined by single-crystal X-ray diffraction. The structure is composed of infinity(2)[Cu2TeO6] layers with the Na atoms located in the octahedral voids between the layers. Na2Cu2TeO6 is a green nonmetallic compound, in agreement with the electronic structure calculation and electrical resistance measurement. The magnetic susceptibility shows Curie-Weiss behavior between 300 and 600 K with an effective moment of 1.85(2) muB/Cu(II) and theta(c) = -87(6) K. A broad maximum at 160 K is interpreted as arising from short-range one-dimensional antiferromagnetic correlations. With the aid of the technique of magnetic dimers, the short-range order was analyzed in terms of an alternating chain model, with the surprising result that the stronger intrachain coupling involves a super-superexchange pathway with a Cu-Cu separation of >5 A. The J2/J1 ratio within the alternating chain refined to 0.10(1), and the spin gap is estimated to be 127 K.     

Characterization and photochemistry of 13-desmethyl bacteriorhodopsin

The photochemistry of the 13-desmethyl (DM) analogue of bacteriorhodopsin (BR) is examined by using spectroscopy, molecular orbital theory, and chromophore extraction followed by conformational analysis. The removal of the 13-methyl group permits the direct photochemical formation of a thermally stable, photochemically reversible state, P1(DM) (lambda(max) = 525 nm), which can be generated efficiently by exciting the resting state, bR(DM) with yellow or red light (lambda > 590 nm). Chromophore extraction analysis reveals that the retinal configuration in P1(DM) is 9-cis, identical to that of the retinal configuration in the native BR P1 state. Fourier transform infrared and Raman experiments on P1(DM) indicate an anti configuration around the C15=N bond, as would be expected of an O-state photoproduct. However, low-temperature spectroscopy and ambient, time-resolved studies indicate that the P1(DM) state forms primarily via thermal relaxation from the L(D)(DM) state. Theoretical studies on the BR binding site show that 13-dm retinal is capable of isomerizing into a 9-cis configuration with minimal steric hindrance from surrounding residues, in contrast to the native chromophore in which surrounding residues significantly obstruct the corresponding motion. Analysis of the photokinetic experiments indicates that the Arrhenius activation energy of the bR(DM) --> P1(DM) transition in 13-dm-BR is less than 0.6 kcal/mol (vs 22 +/-5 kcal/mol measured for the bR --> P (P1 and P2) reaction in 85:15 glycerol:water suspensions of wild type). Consequently, the P1(DM) state in 13-dm-BR can form directly from all-trans, 15-anti intermediates (bR(DM) and O(DM)) or all-trans, 15-syn (K(D)(DM)/L(D)(DM)) intermediates. This study demonstrates that the 13-methyl group, and its interactions with nearby binding site residues, is primarily responsible for channeling one-photon photochemical and thermal reactions and is limited to the all-trans and 13-cis species interconversions in the native protein.