Probing the contribution of electronic coupling to the directionality of electron transfer in photosynthetic reaction centers

Subpicosecond transient absorption studies are reported for a set of Rhodobacter (R.) capsulatus bacterial photosynthetic reaction centers (RCs) designed to probe the origins of the unidirectionality of charge separation via one of two electron transport chains in the native pigment-protein complex. All of the RCs have been engineered to contain a heterodimeric primary electron donor (D) consisting of a bacteriochlorophyll (BChl) and a bacteriopheophytin (BPh). The BPh component of the M heterodimer (Mhd) or L heterodimer (Lhd) is introduced by substituting a Leu for His M200 or His L173, respectively. Previous work on primary charge separation in heterodimer mutants has not included the Lhd RC from R. capsulatus, which we report for the first time. The Lhd and Mhd RCs are used as controls against which we assess RCs that combine the heterodimer mutations with a second mutation (His substituted for Leu at M212) that results in replacement of the native L-side BPh acceptor with a BChl (beta). The transient absorption spectra reveal clear evidence for charge separation to the normally inactive M-side BPh acceptor (H(M)) in Lhd-beta RCs to form D+H(M)- with a yield of approximately 6%. This state also forms in Mhd-beta RCs but with about one-quarter the yield. In both RCs, deactivation to the ground state is the predominant pathway of D decay, as it is in the Mhd and Lhd single mutants. Analysis of the results indicates an upper limit ofV2L/V2m < or = 4 for the contribution of the electronic coupling elements to the relative rates of electron transfer to the L versus M sides of the wild-type RC. In comparison to the L/M rate ratio (kL/kM) approximately 30 for wild-type RCs, our findings indicate that electronic factors contribute approximately 35% at most to directionality with the other 65% deriving from energetic considerations, which includes differences in free energies, reorganization energies, and contributions of one- and two-step mechanisms on the two sides of the RC.     

Fragmentation of trimethoprim and other compounds containing alkoxy-phenyl groups in electrospray ionisation tandem mass spectrometry

This work describes electrospray ionisation tandem mass spectrometry studies of trimethoprim and a series of structurally similar compounds containing alkoxy-phenyl groups; using accurate mass measurement to confirm the proposed fragmentations. Radical cations were observed in the spectra obtained for some of the compounds, as well as uncommon fragmentations showing losses of CH4 and C2H6, whereas other compounds showed the formation of even electron ions. Possible structures for the fragment ions have been proposed and explanations for the different types of fragmentations based on the structures of the compounds. In addition an alternate structure for a fragment ion previously reported for tandem mass spectrometry of trimethoprim has been proposed, based on accurate mass measurement.     

Neutral and ionic aluminum,gallium, and indium compounds carrying two or three terminal ethynyl groups

The syntheses of the ionic compounds [Li(+).2 dioxane (2,6-iPr(2)C(6)H(3)N(SiMe(3))Al(C triplebond CSiMe(3))(3))(-)].0.75 dioxane (1), [(Li(+))(2).(dioxane)(7)](0.5) [2,6-iPr(2)C(6)H(3)N(SiMe(3))Ga(C triplebond CSiMe(3))(3)(-)].1.5 dioxane (2), and [(Li(+))(2).(dioxane)(7)](0.5) [2,6-iPr(2)C(6)H(3)N(SiMe(3))In(C triplebond CSiMe(3))(3)(-)].1.5 dioxane (3) by the reaction of the corresponding organo metal chloride with LiC triplebond CSiMe(3) are reported. The neutral ethynyl compounds Br-Al(C triplebond CtBu)(2).2 THF (4), Cl-Ga(C triplebond CtBu)(2).THF (5), Cl-In(C triplebond CtBu)(2).2 THF (6), Al(C triplebond CtBu)(3).C[N(Me)CMe](2) (7), Ga(C triplebond CtBu)(3).dioxane (8), and In(C triplebond CtBu)(3).NEt(3) (9) have been obtained in good yields from the reaction of AlBr(3), GaCl(3), and InCl(3) with LiC triplebond CtBu in the presence of a Lewis base. Compound 7 is the first heterocyclic carbene substituted ethynyl derivative. Aluminum and gallium compounds with three terminal ethynyl groups Al(C triplebond CPh)(3).NMe(3) (10) and Ga(C triplebond CPh)(3).NMe(3) (11) have been prepared by the reaction of AlH(3).NMe(3) or GaH(3).NMe(3) with three equivalents of phenylethyne. All the above-mentioned compounds have been structurally studied. In compound 1 the lithium ion is coordinated to the three terminal ethynyl groups, whereas in compounds 2 and 3 the lithium is coordinated to the solvent (dioxane). Compound 8 crystallizes as a coordination polymer with dioxane molecules bridging the individual gallium units.     

Direct qualitative analysis of triacylglycerols by electrospray mass spectrometry using a linear ion trap

Triacylglycerols (TAGs) isolated from a biological sample provide a challenge for mass spectrometric analysis because of the complexity of naturally occurring TAGs, which may contain different fatty acyl substituents resulting in a large number of molecular species having the identical elemental composition. We have investigated the use of mass spectrometry to obtain unambiguous information as to the individual TAG molecular species present in a complex mixture of triacylglycerols using a linear ion trap mass spectrometer. Ammonium adducts of TAGs, [M+NH4]+, were generated by electrospray ionization, which permitted the molecular weight of each TAG molecular species to be determined. The mechanisms involved in the decomposition of the [M+NH4]+ and subsequent fragment ions were investigated using deuterium labeling, MS/MS, and MS3 experiments. Collision induced decomposition of [M+NH4]+ ions resulted in the neutral loss of NH3 and an acyl side-chain (as a carboxylic acid) to generate a diacyl product ion. MS/MS data were used to identify each acyl group present for a given [M+NH4]+ ion, and this information could be combined with molecular weight data to identify possible TAG molecular species present in a biological extract. Subsequent MS3 experiments on the resultant diacyl product ions, which gave rise to acylium (RCO+) and related ions, enabled unambiguous TAG molecular assignments. These strategies of MS, MS/MS, and MS3 experiments were applied to identify components within a complex mixture of neutral lipids extracted from RAW 264.7 cells.     

Synthesis of 15N-enriched pseudouridine derivatives

[reaction: see text]. A procedure for the chemical synthesis of [3-15N]-labeled pseudouridine and a methylated derivative was developed. A suitably protected pseudouridine precursor was nitrated at N3 followed by treatment with 15NH4Cl to afford the 15N-labeled product in six steps with a 20% yield. This methodology will allow for the production of RNAs with [3-15N]pseudouridine and [3-15N-methyl]pseudouridine at specific locations.     

Design of organic semiconductors: tuning the electronic properties of pi-conjugated oligothiophenes with the 3,4-ethylenedioxythiophene (EDOT) building block

Hybrid oligothiophenes based on a various combinations of thiophene and 3,4-ethylenedioxythiophene (EDOT) groups have been synthesized. UV/Vis absorption spectra show that the number and relative positions of the EDOT groups considerably affect the width of the HOMO-LUMO gap and the rigidity of the conjugated system. Analysis of the crystallographic structure of two hybrid quaterthiophenes confirms that insertion of two adjacent EDOT units in the middle of the molecule leads to a self-rigidification of the conjugated systems by intramolecular SO interactions. Cyclic voltammetry data shows that the first oxidation potential of the oligomers decreases with increasing chain length and increasing number of EDOT groups for a given chain length. Electrochemical studies and theoretical calculations show that the positions of the EDOT units in the conjugated chain control the potential difference (DeltaE(p)) between the first and second oxidation steps. Moving the EDOT groups from the outer to the inner positions of the conjugated system increases DeltaE(p). Theoretical calculations confirm that this phenomenon reflects an increase of the intramolecular coulombic repulsion between positive charges in the dication. A thin-film field-effect transistor was fabricated by vacuum sublimation of a pentamer with alternating thiophene-EDOT structure, and the hole mobility was determined.     

Design and characterization of libraries of molecular fragments for use in NMR screening against protein targets

We have designed four generations of a low molecular weight fragment library for use in NMR-based screening against protein targets. The library initially contained 723 fragments which were selected manually from the Available Chemicals Directory. A series of in silico filters and property calculations were developed to automate the selection process, allowing a larger database of 1.79 M available compounds to be searched for a further 357 compounds that were added to the library. A kinase binding pharmacophore was then derived to select 174 kinase-focused fragments. Finally, an additional 61 fragments were selected to increase the number of different pharmacophores represented within the library. All of the fragments added to the library passed quality checks to ensure they were suitable for the screening protocol, with appropriate solubility, purity, chemical stability, and unambiguous NMR spectrum. The successive generations of libraries have been characterized through analysis of structural properties (molecular weight, lipophilicity, polar surface area, number of rotatable bonds, and hydrogen-bonding potential) and by analyzing their pharmacophoric complexity. These calculations have been used to compare the fragment libraries with a drug-like reference set of compounds and a set of molecules that bind to protein active sites. In addition, an analysis of the overall results of screening the library against the ATP binding site of two protein targets (HSP90 and CDK2) reveals different patterns of fragment binding, demonstrating that the approach can find selective compounds that discriminate between related binding sites.     

Nucleic acid analysis using an expanded genetic alphabet to quench fluorescence

Organic chemistry has made possible the synthesis of molecules that expand on Nature's genetic alphabet. Using the previously described nonstandard DNA base pair constructed from isoguanine and 5-methylisocytosine, we report a highly specific and sensitive method that allows for the fast and specific quantitation of genetic sequences in a closed tube format. During PCR amplification, enzymatic site-specific incorporation of a quencher covalently linked to isoguanine allows for the simultaneous detection and identification of multiple targets. The specificity of method is then established by analysis of thermal denaturation or melting of the amplicons. The appropriate functions of all reactions are further verified by incorporation of an independent target into the reaction mixture. We report that the method is sensitive down to the single copy level, and specificity is demonstrated by multiplexed end-point genotypic analysis of four targets simultaneously using four separate fluorescent reporters. The method is general enough for quantitative and qualitative analysis of both RNA and DNA using previously developed primer sets. Though the method described employs the commonly used PCR, the enzymatic incorporation of reporter groups into DNA site-specifically should find broad utility throughout molecular biology.     

Synthesis of 6-(perfluoroalkyl)salicylates by [3+3] cyclization of 1,3-bis(silyl enol ethers) with 3-ethoxy-1-(perfluoroalkyl)prop-2-en-1-ones

6-(Perfluoroalkyl)salicylates were prepared by [3+3] cyclization of 1,3-bis(silyl enol ethers) with 3-ethoxy-1-(perfluoroalkyl)prop-2-en-1-ones.     

Synthesis of helix 69 of Escherichia coli 23S rRNA containing its natural modified nucleosides,m(3)Psi and Psi

The synthesis of 3-methylpseudouridine (m(3)Psi) phosphoramidite, 5'-O-[benzhydryloxybis(trimethylsilyloxy)silyl]-2'-O-[bis(2-acetoxyethoxy)methyl]-3-methylpseudouridine-3'-(methyl-N,N-diisopropyl)phosphoramidite, is reported. Selective pivaloyloxymethyl protection of the Psi N1 followed by methylation at N3 was used to generate the naturally occurring pseudouridine analogue. The m(3)Psi phosphoramidite was used in combination with pseudouridine (Psi) and standard base phosphoramidites to synthesize a 19-nucleotide RNA representing helix 69 of Escherichia coli 23S ribosomal RNA (rRNA) (residues 1906-1924), containing a single m(3)Psi at position 1915 and two Psi's at positions 1911 and 1917. Our synthesis of the fully modified helix 69 RNA demonstrates the ability to make milligram quantities of RNA that can be used for further high-resolution structure studies. Site-selective introduction of the methyl group at the N3 position of pseudouridine at position 1915 causes a slight increase in the thermodynamic stability of the RNA hairpin relative to pseudouridine; RNAs containing either uridine or 3-methyluridine at position 1915 have similar stability. One-dimensional imino proton NMR and circular dichroism spectra of the modified RNAs reveal that the methyl group does not cause any substantial changes in the RNA hairpin structure.