Desorption ionization combined with tandem mass spectrometry: Advantages for investigating complex lipids,disaccharides and organometallic complexes

Combining desorption ionization with tandem mass spectrometry overcomes the disadvantage of limited fragmentation accompanying desorption and permits mixtures of closely related substances to be investigated directly. These features of the combination are illustrated by completing the structure-proof of a minor component of an ornithine-containing lipid mixture isolated from Thiobacillus thiooxidans. The minor component is a homolog of the major constituent and differs from the principal component owing to the presence of a double bond in lieu of a cyclopropyl ring in one of the constituent fatty acids. Another feature of the combined method is the potentially complementary nature of collision-activated dissociation spectra of protonated and cationized biomolecules. This is illustrated by the differences in the collision-activated dissociations of the [M + Na]⁺ of sucrose, desorbed by field desorption, and [M + H]⁺, desorbed by fast atom bombardment. A third illustration is the application of field desorption and tandem mass spectrometry to an organometallic compound. The combined approach allows the ligands to be identified and the relative ligand binding energies to be approximated.     

Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs

Metabolite-sensing mRNAs, or "riboswitches," specifically interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, capable of ligand-induced structural changes, and downstream regions, harboring expression-controlling elements. We report the crystal structures of the add A-riboswitch and xpt G-riboswitch aptamer modules that distinguish between bound adenine and guanine with exquisite specificity and modulate expression of two different sets of genes. The riboswitches form tuning fork-like architectures, in which the prongs are held in parallel through hairpin loop interactions, and the internal bubble zippers up to form the purine binding pocket. The bound purines are held by hydrogen bonding interactions involving conserved nucleotides along their entire periphery. Recognition specificity is associated with Watson-Crick pairing of the encapsulated adenine and guanine ligands with uridine and cytosine, respectively.     

Elucidation of the structure of quindolinone,a minor alkaloid of cryptolepis sanguinolenta: Submilligram 1H-13c and 1H-15N heteronuclear shift correlation experiments using micro inverse-detection

Elucidation of minor natural product structures has been significantly augmented by inverse-detection; further improvement has been afforded by the development of micro inverse-detection probes. We report here the elucidation of the structure of a new alkaloid, quindolinone (5H, 10H-indolo[3,2-b]quinolin-11-one), from the West African plant Cryptolepis sanguinolenta. All nmr data for this minor, preparative hplc-isolated alkaloid, including ¹H-¹⁵N one? bond heteronuclear shift correlation (HMQC) data, were recorded on an 800 μg sample of the alkaloid dissolved in 140 μl of 100% d₆-DMSO using a 400 MHz spectrometer.     

Antihydrophobic cosolvent effects for alkylation reactions in water solution, particularly oxygen versus carbon alkylations of phenoxide ions

Antihydrophobic cosolvents such as ethanol increase the solubility of hydrophobic molecules in water, and they also affect the rates of reactions involving hydrophobic surfaces. In simple reactions of hydrocarbons, such as the Diels-Alder dimerization of 1,3-cyclopentadiene, the rate and solubility data directly reflect the geometry of the transition state, in which some hydrophobic surface becomes hidden. In reactions involving polar groups, such as alkylations of phenoxide ions or S(N)1 ionizations of alkyl halides, cosolvents in water can have other effects as well. However, solvation of hydrophobic surfaces is still important. By the use of structure-reactivity relationships, and comparing the effects of ethanol and DMSO as solvents, it has been possible to sort out these effects. The conclusions are reinforced by an ab initio computer model for hydrophobic solvation. The result is a sensible transition state for phenoxide ion as a nucleophile, using its oxygen n electrons to avoid loss of conjugation. The geometry of alkylation of aniline is very different, involving packing (stacking) of the aniline ring onto the phenyl ring of a benzyl group in the benzylation reaction. The alkylation of phenoxide ions by benzylic chlorides can occur both at the phenoxide oxygen and on ortho and para positions of the ring. Carbon alkylation occurs in water, but not in nonpolar organic solvents, and it is observed only when the phenoxide has at least one methyl substituent ortho, meta, or para. The effects of phenol substituents and of antihydrophobic cosolvents on the rates of the competing alkylation processes indicate that in water the carbon alkylation involves a transition state with hydrophobic packing of the benzyl group onto the phenol ring. The results also support our conclusion that oxygen alkylation uses the n electrons of the phenoxide oxygen as the nucleophile and does not have hydrophobic overlap in the transition state. The mechanisms and explanations for competing oxygen and carbon alkylations differ from previous proposals by others.     

Oxidation of alcohols by transition metal complexes—iv : The rhodium catalysed synthesis of esters from aldehydes and alcohols

Both RhH(CO)PPh₃)₃ and a catalyst made in _situ from RhCl₃·3H₂O, PPh₃ and Na₂CO₃ catalyse the reaction of a range of aldehydes with simple primary alcohols to give esters together with alcohols formed by reduction of the aldehydes. The proportion of ester can be increased by adding an efficient hydrogen acceptor. The reaction can also be used to produce 5- and 7-membered lactones from aromatic dialdehydes. Propan-2-ol and the _{in situ} catalyst reduce some aromatic aldehydes to the corresponding alcohols without concomitant ester formation.     

Physically based molecular device model in a transient circuit simulator

Two efficient, physically based models for the real-time simulation of molecular device characteristics of single molecules are developed. These models assume that through-molecule tunnelling creates a steady-state Lorentzian distribution of excess electron density on the molecule and provides for smooth transitions for the electronic degrees of freedom between the tunnelling, molecular-excitation, and charge-hopping transport regimes. They are implemented in the fREEDA™ transient circuit simulator to allow for the full integration of nanoscopic molecular devices in standard packages that simulate entire devices including CMOS circuitry. Methods are presented to estimate the parameters used in the models via either direct experimental measurement or density-functional calculations. The models require 6–8 orders of magnitude less computer time than do full a priori simulations of the properties of molecular components. Consequently, molecular components can be efficiently implemented in circuit simulators. The molecular-component models are tested by comparison with experimental results reported for 1,4-benzenedithiol.     

Temperature weighted histogram analysis method, replica exchange, and transition paths

We analyzed the data from a replica exchange molecular dynamics simulation using the weighted histogram analysis method to combine data from all of the temperature replicas (T-WHAM) to obtain the room-temperature potential of mean force of the G-peptide (the C-terminal beta-hairpin of the B1 domain of protein G) in regions of conformational space not sampled at room temperature. We were able to determine the potential of mean force in the transition region between a minor alpha-helical population and the major beta-hairpin population and identify a possible transition path between them along which the peptide retains a significant amount of secondary structure. This observation provides new insights into a possible mechanism of formation of beta-sheet secondary structures in proteins. We developed a novel Bayesian statistical uncertainty estimation method for any quantity derived from WHAM and used it to validate the calculated potential of mean force. The feasibility of estimating regions of the potential of mean force with unfavorable free energy at room temperature by T-WHAM analysis of replica exchange simulations was further tested on a system that can be solved analytically and presented some of the same challenges found in more complex chemical systems.     

The synthesis and characterization of α- and β-1, 1-diiodo-3,4-benzo-1-telluracyclopentane,C8H8Tel2

Elemental Tellurium reacts with α,α′-dichloro-o-xylene and NaI in 2-methoxyethanol to form 1,1-diiodo-3,4-benzo-1-telluracyclopentane in 83% yield. C₈H₈TeI₂ is molecular in acetone, methylene chloride and methyl ethyl ketone, but ionic in DMF. Two crystalline modifications of the compound have been isolated from 2-methoxyethanol. The yellow-orange or α form is monoclini?, space group P2₁/c; the orange-red or β form is also monoclinic, space group I2/c. Infrared, optical and mass spectral data, along with solution UV, NMR, molecular weight and conductivity data, suggest that the two crystalline modifications are plymorphs, possibly differing in the degree and type of heavy atom interaction. In 2-methoxyethanol the β form undergoes a solution phase transformation to the stable α form. Both forms are thermochromic.     

PHOTOREDUCTION OF SOME NITROBIPHENYL ETHER HERBICIDES TO NITRO RADICAL ANIONS BY β-CAROTENE AND RELATED COMPOUNDS

Abstract —The nitrobiphenyl ether herbicides; 4-nitrobiphenyl ether, bifenox, nitrofen, acifluorfen, acifluorfen-methyl, acifluorfen-ethyl, and oxyfluorfen were reduced to their corresponding nitro radical anions by visible light in the presence of β-carotene, lycopene, retinol, retinal, retinoic acid and retinyl acetate in anaerobic solutions at high pH. It was more difficult to obtain spectra of bifenox, nitrofen and oxyfluorfen than acifluorfen derivatives, probably due to their poor solubilities. In neutral solutions the steady-state concentration of the nitro radical anions was low due to their faster rate of dispropor-tionation and the poor solubility of β-carotene. In the presence of retinal, the nitro radical anion of acifluorfen was produced at pH 7.4. Compounds containing conjugated double bonds such as crotonaldehyde and 2.4-hexadienal also reduced acifluorfen and its derivatives to their respective nitro radical anions in the presence of light. Ubiquinone-50 which does not contain conjugated double bonds in the side chain did not reduce acifluorfen under similar conditions.