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Biomedical subjects

K W Siu

Publications and source records attributed to K W Siu.

15 recordsLinked to original sources
PubMed2001

Proton migration and tautomerism in protonated triglycine.

Proton migration in protonated glycylglycylglycine (GGG) has been investigated by using density functional theory at the B3LYP/6-31++G(d,p) level of theory. On the protonated GGG energy hypersurface 19 critical points have been characterized, 11 as minima and 8 as first-order saddle points. Transition state structures for interconversion between eight of these minima are reported, starting from a structure in which there is protonation at the amino nitrogen of the N-terminal glycyl residue following the migration of the proton until there is fragmentation into protonated 2-aminomethyl-5-oxazolone (the b(2) ion) and glycine. Individual free energy barriers are small, ranging from 4.3 to 18.1 kcal mol(-)(1). The most favorable site of protonation on GGG is the carbonyl oxygen of the N-terminal residue. This isomer is stabilized by a hydrogen bond of the type O-H.N with the N-terminal nitrogen atom, resulting in a compact five-membered ring. Another oxygen-protonated isomer with hydrogen bonding of the type O-H.O, resulting in a seven-membered ring, is only 0.1 kcal mol(-)(1) higher in free energy. Protonation on the N-terminal nitrogen atom produces an isomer that is about 1 kcal mol(-)(1) higher in free energy than isomers resulting from protonation on the carbonyl oxygen of the N-terminal residue. The calculated energy barrier to generate the b(2) ion from protonated GGG is 32.5 kcal mol(-)(1) via TS(6-->7). The calculated basicity and proton affinity of GGG from our results are 216.3 and 223.8 kcal mol(-)(1), respectively. These values are 3-4 kcal mol(-)(1) lower than those from previous calculations and are in excellent agreement with recently revised experimental values.

Energy Transfer↗
PubMed2001

Studies of 9-fluorenyl carbocations. intramolecular hydride migration in a substituted 9-fluorenyl carbocation.

The substituted fluorenyl cation, 9-(diphenylmethyl)fluoren-9-yl cation (4), is formed under stable ion conditions (low temperature/strong acid) from its corresponding alcohol 3. This ion is transformed to a substituted diphenyl methyl cation 8 at ambient temperature via an apparent 1,2-hydrogen shift. Irradiation of 9-(diphenylmethyl)fluoren-9-ol in methanol gives products derived from the corresponding cation along with radical-derived products from C-C and C-O homolysis processes. The laser flash photolysis of this alcohol gave a transient corresponding to cation 4. All of the photoproducts are derived from cation 4 or radical pathways. High level MO calculations point to a high barrier (23.8 kcal x mol(-1)) for the 1,2-hydride shift. This barrier is the consequence of the minimum energy conformation of this fluorenyl cation which is less than ideal for the periplanar geometry necessary for this process.

Journal Article↗
PubMed2001

Characterization of the product ions from the collision-induced dissociation of argentinated peptides.

Tandem mass spectrometry performed on a pool of 18 oligopeptides shows that the product ion spectra of argentinated peptides, the [bn + OH + Ag]+ ions and the [yn - H + Ag]+ ions bearing identical sequences are virtually identical. These observations suggest strongly that these ions have identical structures in the gas phase. The structures of argentinated glycine, glycylglycine, and glycylglycylglycine were calculated using density functional theory (DFT) at the B3LYP/DZVP level of theory; they were independently confirmed using HF/LANL2DZ. For argentinated glycylglycylglycine, the most stable structure is one in which Ag+ is tetracoordinate and attached to the amino nitrogen and the three carbonyl oxygen atoms. Mechanisms are proposed for the fragmentation of this structure to the [b2 + OH + Ag]+ and the [Y2 - H + Ag]+ ions that are consistent with all experimental observations and known calculated structures and energetics. The structures of the [b2 - H + Ag]+ and the [a2 - H + Ag]+ ions of glycylglycylglycine were also calculated using DFT. These results confirm earlier suggestions that the [b2 - H + Ag]+ ion is an argentinated oxazolone and the [a2 - H + Ag]+ an argentinated immonium ion.

Mass Spectrometry↗
PubMed2001

Prediction of peptide ion mobilities via a priori calculations from intrinsic size parameters of amino acid residues.

Ion mobility spectrometry (IMS) has recently been established as a powerful tool to separate the protease digest mixtures and identify their peptide components. As accurate calculation of mobilities is critical for this technique, a new rapid method based on intrinsic size parameters (ISPs) of amino acid residues has been devised. However, those parameters had to be obtained by tedious statistical analysis of a large body of experimental data. Here we demonstrate that they can instead be derived a priori, based on the stoichiometry of a residue. Our main finding is that the ISP of a residue is essentially determined by its density, that is, the average mass/size ratio of its constituent atoms. This is in accordance with an interpretation in which peptides assume compact conformations in the gas phase dominated by the solvation of ionic charge.

Algorithms↗
PubMed2000

Single-parent evolution algorithm and the optimization of Si clusters.

We describe a novel method for the structural optimization of molecular systems. Similar to genetic algorithms (GA), our approach involves an evolving population in which new members are formed by cutting and pasting operations on existing members. Unlike previous GA's, however, the population in each generation has a single parent only. This scheme has been used to optimize Si clusters with 13-23 atoms. We have found a number of new isomers that are lower in energy than any previously reported and have properties in much better agreement with experimental data.

Journal Article↗
PubMed2000

Formation of [M - nH] + mNA](m-n)+ and [M - nH + mK](m-n)+ ions in electrospray mass spectrometry of peptides and proteins.

The [M - nH + mNa](m-n)+ and [M - nH + mK](m-n)+ ions are common in the electrospray mass spectra of proteins and peptides. The feasibility of forming these ions in the gas phase via collision activation and/or ion-molecule reaction is investigated. Sodium and potassium affinities of the N-methylacetamide anion, the acetate anion, and the 1-propanamide anion have been calculated using density functional theory at the B3LYP/6-311+ +G(d,p) level of theory. These anions were chosen as models for the functional groups on a protein or peptide. These affinity values are then used to calculate reaction enthalpies of alkali hydroxides, chlorides, and hydrates with N-methylacetamide, acetic acid, the acetate anion, and 1-propanamine, model reactions that may lead to formation of the [M - nH + mNa](m-n) and [M - nH + mK](m-n)+ ions. It is found that a number of these reactions are exothermic or slightly endothermic (deltaH(o) < + 20 kcal/mol) and are accessible after collision activation in the lens region. The potential energy hypersurfaces of model reactions between NaOH and formamide as well as NaCl and formamide show relatively flat surfaces devoid of significant barriers.

Hydroxides↗
PubMed1999

Sequencing of argentinated peptides by means of electrospray tandem mass spectrometry.

A strategy for semiautomatic sequencing of argentinated (silver-containing) oligopeptides has been developed. Sequencing is based on a search algorithm that identifies a triplet peak relationship in a product ion spectrum of the [M + Ag]+ ion of an oligopeptide. The ions that constitute a triplet are [bn + OH + Ag]+, [bn - H + Ag]+, and [a(n) - H + Ag]+, which are separated by 18 and 28 m/z units, respectively. The difference in the m/z values of adjacent triplets identifies the residue that is "cleaved". Observation of the [yn + H + Ag]+ ion containing the cleaved residue confirms the assignment. Sequencing of argentinated tryptic peptides may prove useful for automated proteome analysis via the sequence tag method.

Amino Acid Sequence↗
PubMed1999

Analysis of metallothioneins by means of capillary electrophoresis coupled to electrospray mass spectrometry with sheathless interfacing.

Capillary electrophoresis (CE) coupled to electrospray mass spectrometry via sheathless interfacing has been applied to the analysis of mammalian metallothionein (MT) extracts. In a rabbit-liver extract, four (MT-2C, MT-2A, MT-2D and MT-2E) out of six known MT sub-isoforms were unambiguously identified under three CE-resolved peaks. A fourth peak was found to contain MT-1A and/or MT-2B, whose molecular masses differ by only 1 Da. Traces of non-N-acetylated MT-2D and MT-2E were observed in a fifth, minor peak. In a rat-liver extract, both MT-1 and MT-2 were resolved and identified. Non-N-acetylated MT-2 was also identified in a resolved, minor peak. Minimum detectable amounts of MTs have been estimated to be approximately 0.6 fmol per sub-isoform.

Animals↗
PubMed1999

Testicular volume of boys after inguinal herniotomy: combined clinical and radiological follow-up.

A total of 173 boys aged 10 to 179 months with previous unilateral inguinal herniotomy were called back for follow-up. Clinical and ultrasound examinations of the scrotum were performed. The interval between operation and follow-up was 6 to 123 months (mean 31.68 months). One boy (0.58%) had a more than 50% and 10 (5.8%) had a more than 25% decrease in testicular volume on the operated side when compared with the non-operated side.

Adolescent↗
PubMed1997

Collision-induced dissociation of 30 m/z unit wide windows of electrospray-generated ions sampled under lens conditions of nominally zero potential gradient.

Windows 30 m/z units wide of ions generated in electrospray and sampled under lens conditions of nominally zero potential gradient conditions were mass selected with Q1 in a triple-quadrupole mass spectrometer, fragmented in Q2, and their product ions mass analysed with Q3. A variety of analytes (equine myoglobin, bovine insulin, leucine enkephalin and PPG 1000) were examined. The windows selected sometimes contained desolvated (bare) analyte ions; more often they did not and contained only 'background' ions. For protein samples, multiply charged product ions having m/z values both lower and higher than those of the precursor ions were observed even when the precursor ion window could not have contained naked protein dimer ions. To observe significant product ions, the precursor ion window typically contained ions residing within background 'humps' that trailed protein peaks. These ions were speculated to be diverse, solvated multimeric clusters of the analyte which fragmented in Q2 to yield the characteristic product ion spectra.

Animals↗
PubMed1996

Electrospray tandem mass spectrometry of alkali metal-containing anionic complexes of tripeptide.

Collision-induced dissociation mass spectra of alkali metal-containing anionic tripeptides are reported. Both N-terminal and C-terminal product ions were observed from the precursor ions [M - 2H + X]- and [M - 3H + 2X]- where X stands for an alkali metal. The results are consistent with precursor ion structures in which an alkali metal ion is centrally located for bonding with the amino terminus, the amide nitrogen atoms, and an oxygen atom of the carboxylate terminus; the second alkali metal ion in [M - 3H + 2X]- is likely attached to the other oxygen atom of the carboxylate terminus.

Amino Acid Sequence↗
PubMed1991

Electrospray mass spectrometry: application of ion evaporation theory to amino acids.

We describe the result of applying the ion evaporation theory to a series of amino acids. The very good correlation (r = 0.98) of the natural logarithms of protonated molecule intensities observed by electrospray with the difference between the hydration free energies of molecules and the gas-phase binding free energies of molecules and protons in amino acids is consistent with the ion evaporation model. It seems that the difference in the protonated molecule intensities of amino acids obtained by electrospray can be explained by a scheme in which protonated molecules in the liquid phase are extracted into the gas phase after a charged droplet is formed.

Amino Acids↗
PubMed1989

Ion-spray mass spectrometry of marine neurotoxins.

Ion-spray mass spectrometry was investigated for the analysis of three marine neurotoxins: domoic acid, saxitoxin and tetrodotoxin. All three compounds gave positive-ion spectra with abundant ions of protonated molecules and no significant fragmentation. Domoic acid gave a negative-ion spectrum with a strong [M-H]- ion. Tandem mass spectrometry provided useful fragment-ion spectra for all compounds. Detection limits for flow injection analyses with selected-ion monitoring were determined to be 30 pg for saxitoxin, 100 pg for domoic acid and 200 pg for tetrodotoxin. Combining liquid chromatography with ion-spray mass spectrometry allowed the determination of domoic acid and some of its isomers in toxic shellfish tissue extracts.

Kainic Acid↗