Chemoselective Removal of Protecting Groups from O-Glycosyl Amino Acid and Peptide (Methoxyethoxy)ethyl Esters Using Lipases and Papain

The selective C-terminal deprotection of O-glycopeptide (methoxyethoxy)ethyl esters is achieved under mild conditions (pH 6.6, 37 degrees C) by enzymatic hydrolysis using papain or lipase M from Mucor javanicus to give building blocks useful for chain-extending glycopeptide synthesis. On the other hand, the selective removal of acetyl protecting groups from the saccharide portion of glycopeptides is accomplished by alternative enzymatic hydrolysis with lipase WG from wheat germ to furnish model substrates for enzymatic glycosyl transfer reactions in order to extend the carbohydrate side chain of these conjugates.     

Detection of single nucleotide polymorphisms using electrospray ionization mass spectrometry: validation of a one-well assay and quantitative pooling studies

Single nucleotide polymorphisms (SNPs) are currently being mapped and databased at a remarkable pace, providing a viable means for understanding disease susceptibility, differential drug response and human evolution. Consequently, there is an increasing demand for SNP genotyping technologies that are simple, rapid, cost effective and readily amenable to automation for high-throughput analyses. In this study, we improved the Survivor Assay, a SNP detection method based on electrospray ionization mass spectrometry (ESI-MS), with several developments. One improvement is the development of a one-well assay, requiring no off-line purification of the polymerase chain reaction product, achieved by simple addition of reagent solution into a single well. Another is the on-line separation of magnesium and dideoxynucleotides using an in-house made monolithic metal chelating column, eliminating any off-line sample preparation prior to mass spectrometric analysis. Here the Survivor Assay is extended from a proof-of-principle concept to a validated method by genotyping six SNPs from five different regions of human genomic DNA in 55 individual samples with 100% accuracy. This improved Survivor Assay eliminates the tedious and time-consuming steps of sample preparation, minimizes sample handing and offers a high-throughput analysis of SNPs by ESI-MS. The current combined preparation and analysis time is 2 min per sample. The simplicity of this method has potential for full automation and parallel chromatography and, thus, reduced analysis time. In addition, we have adapted the Survivor Assay for quantitative SNP analysis in pooled DNA samples. The capabilities and sensitivity of this approach were evaluated. We demonstrate that an allele occurring at a frequency of 2% can consistently be quantitated.     

Modified nucleosides in human serum.

Methylated purines and pyrimidines derived from the degradation of transfer ribonucleic acid have been shown to be excreted in abnormal amounts in the urine of patients with cancer. Recent technology developed by Gehrke and Kuo has allowed the separation and quantification of modified nucleosides in serum using reversed-phase high-performance liquid chromatography with diode-array measurement. Serum levels of ten modified nucleosides were measured in 37 normal healthy adults to establish normal values and to correlate activity with age and sex. In addition, serum levels of patients with several malignancies were measured to determine activity in these diseases. Levels of modified nucleosides in normal individuals were consistently reproducible and showed no significant variation among males versus females or with age. Patients with malignant diseases showed consistent elevations and these were highest in patients with more advanced disease. The evidence of no significant differences in the mean levels of modified nucleosides in serum with age or sex in normal adults and elevations in patients with malignancies demonstrate the potential value of modified nucleosides as cancer biomarkers.     

Molecular structure of ethynylbenzene from electron diffraction and ab initio molecular orbital calculations

The molecular structure and benzene ring distortions of ethynylbenzene have been investigated by gas-phase electron diffraction and ab initio MO calculations at the HF/6-31G^* and 6-3G^** levels. Least-squares refinement of a model withC _2v, symmetry, with constraints from the MO calculations, yielded the following important bond distances and angles:r _g(C _i -C _o )=1.407±0.003 Å,r _g(C _o -C _m )=1.397±0.003 Å,r _g(C _m -C _p )=1.400±0.003 Å,r _g(Cr _i -CCH)=1.436 ±0.004 Å,r _g(C=C)=1.205±0.005 Å, C _o -C _i -C _o =119.8±0.4°. The deformation of the benzene ring of ethynylbenzene given by the MO calculations, including o-C_i-C_o=119.4°, is insensitive to the basis set used and agrees with that obtained by low-temperature X-ray crystallography for the phenylethynyl fragment, C₆H₅-CC-, in two different crystal environments. The partial substitution structure of ethynylbenzene from microwave spectroscopy is shown to be inaccurate in the ipso region of the benzene ring.     

Investigation of nucleation processes under the influence of magnetic fields

The present work demonstrates the possibilities and the limits of the in situ electrochemical scanning tunneling microscopy for investigation of nucleation processes in magnetic fields on the examples of Cu and Co electrodeposition onto Au(111) electrodes from sulfate electrolytes with pH 3. Cyclic voltammograms of Cu in the underpotential range (UPD) exhibit no significant change in the cathodic and anodic peaks recorded in magnetic fields parallel to the surface. In magnetic fields of a permanent magnet, the reconstruction of Au has been annihilated during UPD of Cu. In the overpotential range, the dissolution of Cu is inhibited. This triggers the formation of a Cu–Au surface alloy. The UPD deposition of Co onto Au(111) could be proven without magnetic field, which leads to the formation of two monolayers. The nucleation in an applied field could not be observed due to higher induced fluctuations and microconvective effects. Contribution to special issue “Magnetic field effects in Electrochemistry”.     

Density functionals for inorganometallic and organometallic chemistry

We present a database of 21 bond dissociation energies for breaking metal-ligand bonds. The molecules in the metal-ligand bond energy database are AgH, CoH, CoO+, CoOH+, CrCH3+, CuOH2+, FeH, Fe(CO)5, FeO, FeS, LiCl, LiO, MgO, MnCH3NiCH2+, Ni(CO)4, RhC, VCO+, VO, and VS. We have also created databases of metal-ligand bond lengths and atomic ionization potentials. The molecules used for bond lengths are AgH, BeO, CoH, CoO+, FeH, FeO, FeS, LiCl, LiO, MgO, RhC, VO, and VS and the ionization potentials are for the following atoms: C, Co, Cr, Cu, Ni, O, and V. The data were chosen based on their diversity and expected reliability, and they are used along with three previously developed databases (transition metal dimer bond energies and bond lengths and main-group molecular atomization energies) for assessing the accuracy of several kinds of density functionals. In particular, we report tests for 42 previously defined functionals: 2 local spin density approximation (LSDA) functionals, 14 generalized gradient approximation (GGA) methods, 13 hybrid GGA methods, 7 meta GGA methods, and 8 hybrid meta GGA methods. In addition to these functionals, we also examine the effectiveness of scaling the correlation energy by testing 13 functionals with scaled or no gradient-corrected correlation energy, and we find that functionals of this kind are more accurate for metal-metal and metal-ligand bonds than any of the functionals already in the literature. We also present a readjusted GGA and a hybrid GGA with parameters adjusted for metals. When we consider these 57 functionals for metal-ligand and metal-metal bond energies simultaneously with main-group atomization energies, atomic ionization potentials, and bond lengths we find that the most accurate functional is G96LYP, followed closely by MPWLYP1M (new in this article), XLYP, BLYP, and MOHLYP (also new in this article). Four of these five functionals have no Hartree-Fock exchange, and the other has only 5%. As a byproduct of this work we introduce a convenient diagnostic, called the B1 diagnostic, for ascertaining the multireference character in a bond.     

Expanding the genetic code

Although chemists can synthesize virtually any small organic molecule, our ability to rationally manipulate the structures of proteins is quite limited, despite their involvement in virtually every life process. For most proteins, modifications are largely restricted to substitutions among the common 20 amino acids. Herein we describe recent advances that make it possible to add new building blocks to the genetic codes of both prokaryotic and eukaryotic organisms. Over 30 novel amino acids have been genetically encoded in response to unique triplet and quadruplet codons including fluorescent, photoreactive, and redox-active amino acids, glycosylated amino acids, and amino acids with keto, azido, acetylenic, and heavy-atom-containing side chains. By removing the limitations imposed by the existing 20 amino acid code, it should be possible to generate proteins and perhaps entire organisms with new or enhanced properties.