Characterization of Streptococcus pneumoniae N-acetylglucosamine-6-phosphate deacetylase as a novel diagnostic marker.

The identification of novel diagnostic markers of pathogenic bacteria is essential for improving the accuracy of diagnoses and for developing targeted vaccines. Streptococcus pneumoniae is a significant human pathogenic bacterium that causes pneumonia. N-acetylglucosamine-6-phosphate deacetylase (NagA) was identified in a protein mixture secreted by S. pneumoniae and its strong immunogenicity was confirmed in an immuno-proteomic assay against the anti-serum of the secreted protein mixture. In this study, recombinant S. pneumoniae NagA protein was expressed and purified to analyze its protein characteristics, immunospecificity, and immunogenicity, thereby facilitating its evaluation as a novel diagnostic marker for S. pneumoniae. Mass spectrometry analysis showed that S. pneumoniae NagA contains four internal disulfide bonds and that it does not undergo post-translational modification. S. pneumoniae NagA antibodies successfully detected NagA from different S. pneumoniae strains, whereas NagA from other pathogenic bacteria species was not detected. In addition, mice infected with S. pneumoniae generated NagA antibodies in an effective manner. These results suggest that NagA has potential as a novel diagnostic marker for S. pneumoniae because of its high immunogenicity and immunospecificity.

Simultaneous molecular formula determinations of natural compounds in a plant extract using 15 T Fourier transform ion cyclotron resonance mass spectrometry.

BACKGROUND: Plant extracts are a reservoir of pharmacologically active substances; however, conventional analytical methods can analyze only a small portion of an extract. Here, we report a high-throughput analytical method capable of determining most phytochemicals in a plant extract and of providing their molecular formulae from a single experiment using ultra-high-resolution electrospray ionization mass spectrometry (UHR ESI MS). UHR mass profiling was used to analyze natural compounds in a 70% ethanol ginseng extract, which was directly infused into a 15 T Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer for less than 10 min without a separation process. RESULTS: The UHR FT-ICR MS yielded a mass accuracy of 0.5 ppm and a mass resolving power (m/Δm) of 1,000,000-270,000 for the range m/z 290-1,100. The mass resolution was sufficient to resolve the isotopic fine structure (IFS) of many compounds in the extract. After noise removal from 1,552 peaks, 405 compounds were detected. The molecular formulae of 123 compounds, including 33 ginsenosides, were determined using the observed IFS, exact monoisotopic mass, and exact mass difference. Liquid chromatography (LC)/FT-ICR MS of the extract was performed to compare the high-throughput performance of UHR ESI FT-ICR MS. The LC/FT-ICR MS detected only 129 compounds, including 19 ginsenosides. The result showed that UHR ESI FT-ICR MS identified three times more compounds than LC/FT-ICR MS and in a relatively shorter time. The molecular formula determination by UHR FT-ICR MS was validated by LC and tandem MS analyses of three known ginsenosides. CONCLUSIONS: UHR mass profiling of a plant extract by 15 T FT-ICR MS showed that multiple compounds were simultaneously detected and their molecular formulae were decisively determined by a single experiment with ultra-high mass resolution and mass accuracy. Simultaneous molecular determination of multiple natural products by UHR ESI FT-ICR MS would be a powerful method to profile a wide range of natural compounds.

Aromatic pi-pi interaction mediated by a metal atom: structure and ionization of the bis(eta(6)-benzene)chromium-benzene cluster.

Aromatic pi-pi interaction in the presence of a metal atom has been investigated experimentally and theoretically with the model system of bis(eta(6)-benzene)chromium-benzene cluster (Cr(Bz)(2)-Bz) in which a free solvating benzene is non-covalently attached to the benzene moiety of Cr(Bz)(2). One-photon mass-analyzed threshold ionization (MATI) spectroscopy and first principles calculations are employed to identify the structure of Cr(Bz)(2)-Bz which adopts the parallel-displaced configuration. The decrease in ionization potential for Cr(Bz)(2)-Bz compared with Cr(Bz)(2), resulting from the increase of the cation-pi stabilization energy upon ionization, is consistent with the parallel-displaced structure of the cluster. Theoretical calculations give the detailed cluster structures with associated energetics, thus revealing the nature of pi-pi-metal or pi-pi-cation interactions at the molecular level.

One-photon ionization spectroscopy of jet-cooled oxazole and thiazole: the role of oxygen and sulfur in the pi-conjugation of heterocyclic compounds.

One-photon mass-analyzed threshold ionization (MATI) spectroscopy of jet-cooled oxazole and thiazole has been carried out to give the precise adiabatic ionization energies of 9.5959+/-0.0006 and 9.3633+/-0.0009 eV, respectively. The structural change upon ionization has been revealed in the vibrationally resolved one-photon MATI spectra. Simulations based on the Franck-Condon analysis using the molecular structures calculated by the density functional theory reproduce the experiment very well for both molecules. The ionization-driven structural change of thiazole is quite different from that of oxazole in terms of the detailed geometrical shape, ascribed to the difference in the pi-conjugation nature of two molecules. The role of oxygen and sulfur in the stabilization of heterocyclic systems is discussed through the inspection of the calculated molecular orbitals involved in the photoionization.

Structure of pyridazine in the S1 state: experiment and theory.

The molecular structure of pyridazine in the first electronically excited state (S(1)) is deduced from the combined use of resonance-enhanced two-photon ionization and mass-analyzed threshold ionization spectroscopic methods. The equation-of-motion coupled-cluster single and double (EOM-CCSD) calculation gives the distorted planar geometry for the most stable structure of the S(1) pyridazine. The symmetry constraint of C(2v) is relaxed to that of C(s), and consequently many in-plane vibrational modes are found to be optically active in both S(1)-S(0) and D(0)-S(1) excitation spectra, being appropriately assigned from the comparison of their frequencies with ab initio values. This indicates that the S(1)-S(0) excitation is partially localized, and provides an alternative explanation for the long-standing spectroscopic puzzle in S(1) pyridazine.

Conformationally specific vacuum ultraviolet mass-analyzed threshold ionization spectroscopy of alkanethiols: structure and ionization of conformational isomers of ethanethiol, isopropanethiol, 1-propanethiol, tert-butanethiol, and 1-butanethiol.

Conformational isomers of alkanethiols are isolated in the molecular beam, and the conformer-specific ionization dynamics have been investigated using vacuum ultraviolet mass-analyzed threshold ionization (MATI) spectroscopy. Only a single conformer of ethanethiol is observed to give the adiabatic ionization potential (IP) of 9.2922 +/- 0.0007 eV for the gauche conformer. For isopropanethiol, IP is found to be 9.1426 +/- 0.0006 for the trans conformer and 9.1559 +/- 0.0006 eV for the gauche conformer. Only two major conformational isomers are identified for 1-propanethiol, giving an IP of 9.1952 +/- 0.0006 for the trans-gauche conformer and 9.2008 +/- 0.0006 eV for the gauche-gauche conformer. The tert-butanethiol, as expected, has a single conformer with an IP of 9.0294 +/- 0.0006 eV. For 1-butanethiol, there are a number of conformers, and the assignment of the MATI bands to each conformer turns out to be nontrivial. The spectral simulation using the Franck-Condon analysis based on the density functional theory (DFT) calculations has been used for the identification of each conformational isomer in the MATI spectrum. Each conformer undergoes its unique structural change upon ionization, as revealed in the vibration resolved MATI spectrum, providing the powerful method for the spectral identification of a specific conformational isomer. The conformer specificity in the ionization-driven structural change reflects the role of the electron of the highest occupied molecular orbital (HOMO) in the conformational preference.

Clustering dynamics of the metal-benzene sandwich complex: the role of microscopic structure of the solute in the bis(eta6-benzene)chromium .Arn Clusters (n = 1-15).

Ar clustering dynamics around the metal-benzene sandwich complex, bis(eta (6)-benzene)chromium: Cr(Bz) 2, is found to occur in two distinct regimes. The shift of the ionization potential (IP) upon the addition of Ar is measured to be 151 cm (-1), and it is constant until the number of Ar solvents ( n) becomes 6. The IP shift per Ar is found to be suddenly decreased to 82 cm (-1) for the clusters of n = 7-12. The cluster distribution indicates that the n = 6 cluster is most populated in the molecular beam. These experimental findings with the aid of ab initio calculation indicate that the first six Ar solvent molecules are attached to top and bottom of Cr(Bz) 2 to give the robust structure for the Cr(Bz) 2-Ar 6 cluster whereas the next six Ar molecules are gathered on the side of the solute core to give the highly symmetric structure of the Cr(Bz) 2-Ar 12 cluster.

State-selective predissociation dynamics of methylamines: the vibronic and HD effects on the conical intersection dynamics.

The photodissociation dynamics of methylamines (CH(3)NH(2) and CD(3)ND(2)) on the first electronically excited state has been investigated using the velocity map ion imaging technique probing the H or D fragment. Two distinct velocity components are found in the H(D) translational energy distribution, implying the existence of two different reaction pathways for the bond dissociation. The high H(D) velocity component with the small internal energy of the radical fragment is ascribed to the N-H(D) fragmentation via the coupling of S(1) to the upper-lying S(2) repulsive potential energy surface along the N-H(D) bond elongation axis. Dissociation on the ground S(0) state prepared via the nonadiabatic dynamics at the conical intersection should be responsible for the slow H(D) fragment. Several S(1) vibronic states of methylamines including the zero-point level and nnu(9) states (n=1, 2, or 3) are exclusively chosen in order to explore the effect of the initial quantum content on the chemical reaction dynamics. The branching ratio of the fast and slow components is found to be sensitive to the initial vibronic state for the N-H bond dissociation of CH(3)NH(2), whereas it is little affected in the N-D dissociation event of CD(3)ND(2). The fast component is found to be more dominant in the translational distribution of D from CD(3)ND(2) than it is in that of H from CH(3)NH(2). The experimental result is discussed with a plausible mechanism of the conical intersection dynamics.

Ionization spectroscopy of conformational isomers of propanal: the origin of the conformational preference.

Two different conformational isomers of propanal, cis and gauche, are investigated by the vacuum-UV mass-analyzed threshold ionization (VUV-MATI) spectroscopy to give accurate adiabatic ionization potentials of 9.9997 +/- 0.0006 eV and 9.9516 +/- 0.0006 eV, respectively. cis-Propanal, which is the more stable conformer in the neutral state, becomes less stable in the cation compared to gauche-propanal. Vibrational structures revealed in the MATI spectra indicate that cis and gauche isomers undergo their unique structural changes upon ionization. The ionization of gauche-propanal induces a geometrical change along the conformational coordinate, suggesting that the steric effect in the ground state is diminished upon ionization. Natural bonding orbital (NBO) calculations provide the extent of hyperconjugation in each conformational isomer of propanal.

Assignment of rovibrational transitions of propyne in the region of 2934-2952 cm(-1) measured by two-color IR-vacuum ultraviolet laser photoion-photoelectron methods.

The infrared (IR) spectrum of propyne in the region of 2934-2952 cm(-1) has been recorded by the IR-vacuum ultraviolet (VUV)-photoion method. The spectrum is shown to consist of two near-resonant, but noncoupled vibrational bands: the nu2 symmetric methyl C-H stretching vibrational band and a combination vibrational band nucs. The previously unobserved Q line of the nucs band is observed. The rotational transition lines of the nu2=1 band produces IR-VUV-pulsed field ionization-photoelectron (IR-VUV-PFI-PE) signal at the C3H4+ (nu2+=1) photoionization threshold. The rotational transition lines associated with the nucs band do not produce IR-VUV-PFI-PE signal. Rotational transition lines of both vibrational bands are assigned and simulated; and ab initio calculations further confirm the assignment.

Pulsed-field ionization spectroscopy of high Rydberg states (n=50-200) of bis(eta6-benzene)chromium.

The ionization behavior of the high Rydberg states of bis(eta(6)-benzene)chromium in the presence of ac and/or dc fields has been explored. The application of an ac scrambling field at the time of laser excitation lengthens the lifetime of the Rydberg state by almost two orders of magnitude. The lifetime enhancement by the scrambling field is much more effective for n<100 than it is for n>100 Rydberg states. The pulsed-field ionization of Rydberg states of n<100 shows the typical diabatic ionization behavior for low n. The two distinct ionization behaviors observed for the relatively low (n=50-100) and high (n=100-200) Rydberg states suggest that the former originate from the optically accessed nf Rydberg series, whereas the latter are due to np Rydberg series. Based on the understanding of the ionization behavior of bis(eta(6)-benzene)chromium, the accurate ionization potential is deduced to give IP=5.4665+/-0.0003 eV. Optimization of the various electric field conditions greatly enhances the spectral sensitivity of the mass-analyzed threshold ionization (MATI) spectroscopy. The high-resolution MATI spectrum of the title molecule obtained here provides precise cationic vibrational frequencies for many skeletal and benzene ring modes. A number of vibrational modes are newly identified, and the ambiguity regarding to some mode assignments is now clearly resolved through the Frank-Condon analysis based on ab initio calculations.

Rovibrationally selected and resolved state-to-state photoionization of ethylene using the infrared-vacuum ultraviolet pulsed field ionization-photoelectron method.

By preparing ethylene [C2H4(X1Ag)] in selected rotational levels of the nu11(b1u), nu2+nu12(b1u), or nu9(b2u) vibrational state with infrared (IR) laser photoexcitation prior to vacuum ultraviolet (VUV) laser photoionization, we have recorded rotationally resolved pulsed field ionization-photoelectron (PFI-PE) spectra for C2H4+(X2B3u) in the energy region of 0-3000 cm(-1) above the ionization energy (IE) of C2H4(X1Ag). Here, nu2(ag), nu9(b2u), nu11(b1u), and nu12(b1u) represent the C-C stretching, CH2 stretching, CH2 stretching, and CH2 bending modes of C2H4(X1Ag), respectively. The fully rovibrationally resolved spectra have allowed unambiguous symmetry assignments of the observed vibrational bands, which in turn have provided valuable information on the photoionization dynamics of C2H4. The IR-VUV photoionization of C2H4(X1Ag) via the nu11(b1u) or nu2+nu12(b1u) vibrational states is found to predominantly produce vibrational states of C2H4+(X2B3u) with b1u symmetry, which cannot be observed in single-photon VUV-PFI-PE measurements of C2H4(X1Ag). The analysis of the observed IR-VUV-PFI-PE bands has provided the IE(C2H4) = 84,790.2(2) cm(-1) and accurate vibrational frequencies for the nu4+(au)[84.1(2) cm(-1)], nu12+(b1u)[1411.7(2) cm(-1)], nu4+ +nu12+(b1g)[1482.5(2) cm(-1)], nu2+(ag)[1488.3(2) cm(-1)], nu2+ + nu4+(au)[1559.2(2) cm(-1)], 2nu4+ + nu12 +(b1u)[1848.5(2) cm(-1)], 4nu4+ + nu12 +(b1u)[2558.8(2) cm(-1)], nu2+ + nu12 +(b1u)[2872.7(2) cm(-1)], and nu11+(b1u)[2978.7(2) cm(-1)] vibrational states of C2H4+(X2B3u), where nu4+ is the ion torsional state. The IE(C2H4) and the nu4+(au), nu2+(ag), and nu2+ + nu4+ (au) frequencies are in excellent accord with those obtained in previous single-photon VUV-PFI-PE measurements. The other ion vibrational frequencies represent new experimental determinations. We have also performed high-level ab initio anharmonic vibrational frequency calculations for C2H4(X1Ag) and C2H4+(X2B3u) at the CCSD(T)/aug-cc-pVQZ level for guidance in the assignment of the IR-VUV-PFI-PE spectra. All theoretical vibrational frequencies for the neutral and ion, except the ion torsional frequency, are found to agree with experimental vibrational frequencies to better than 1%.

A combined VUV synchrotron pulsed field ionization-photoelectron and IR-VUV laser photoion depletion study of ammonia.

The synchrotron based vacuum ultraviolet-pulsed field ionization-photoelectron (VUV-PFI-PE) spectrum of ammonia (NH(3)) has been measured in the energy range 10.12-12.12 eV using a room-temperature NH(3) sample. In addition to extending the VUV-PFI-PE measurement to include the v(2)(+) = 0, 10, 11, 12, and 13 and the v(1)(+) + nv(2)(+) (n = 4-9) vibrational bands, the present study also reveals photoionization transition line strengths for higher rotational levels of NH(3), which were not examined in previous PFI-PE studies. Here, v(1)(+) and v(2)(+) represent the N-H symmetric stretching and inversion vibrational modes of the ammonia cation (NH(3)(+)), respectively. The relative PFI-PE band intensities for NH(3)(+)(v(2)(+)=0-13) are found to be in general agreement with the calculated Franck-Condon factors. However, rotational simulation indicates that rotational photoionization transitions of the P-branches, particularly those for the lower v(2)(+) PFI-PE bands, are strongly enhanced by forced rotational autoionization. For the synchrotron based VUV-PFI-PE spectrum of the origin band of NH(3)(+), rotational transition intensities of the P-branch are overwhelming compared to those of other rotational branches. Similar to that observed for the nv(2)(+) (n = 0-13) levels, the v(1)(+) + nv(2)(+) (n = 4-9) levels are found to have a positive anharmonicity constant; i.e., the vibrational spacing increases as n is increased. The VUV laser PFI-PE measurement of the origin band has also been made using a supersonically cooled NH(3) sample. The analysis of this band has allowed the direct determination of the ionization energy of NH(3) as 82158.2 +/- 1.0 cm(-1), which is in good accord with the previous PFI-PE and photoionization efficiency measurements. Using the known nd(v(2)(+)=1,1(0)<--0(0)) Rydberg series of NH(3) as an example, we have demonstrated a valuable method based on two-color infrared-VUV-photoion depletion measurements for determining the rotational character of autoionizing Rydberg states.

A two-color infrared-vacuum ultraviolet laser pulsed field ionization photoelectron study of NH3.

We have observed fully rotationally resolved transitions of the photoelectron vibrational bands 2(4), 2(5), 1(1)2(1), and 1(1)2(3) for ammonia cation (NH3+) by two-color infrared (IR)-vacuum ultraviolet (VUV)- pulsed field-ionization photoelectron (PFI-PE) measurements. By preparing an intermediate rovibrational state of neutral NH(3) with a known parity by IR excitation followed by VUV-PFI-PE measurements, we show that the photoelectron parity can be determined unambiguously. The IR-VUV-PFI-PE measurement of the 2(4) band clearly reveals the formation of both even and odd l states for the photoelectrons, where l is the orbital angular momentum quantum number. This observation is consistent with the conclusion that the lack of inversion symmetry for NH3 and NH3+ allows odd/even l mixings, rendering the production of both odd and even l states for the photoelectrons. Evidence is also found, indicating that the photoionization transitions with DeltaK=0 are strongly favored compared to that with DeltaK=3. For the 2(5), 1(1)2(1), and 1(1)2(3) bands, only DeltaK=0 transitions for the production of even l photoelectron states from the J'K'=2(0) rotational level of NH3(nu1=1) are observed. The preferential formation of even l photoelectron states for these vibrational bands is attributed to the fact that the DeltaK=0 transitions for the formation of odd l photoelectron states from the 2(0) rotational level of NH3(nu1=1) are suppressed by the constraint of nuclear-spin statistics. In addition to information obtained on the photoionization dynamics of NH3, this experiment also provides a more precise value of 3232+/-10 cm-1 for the nu1+ (N-H stretch) vibrational frequency of NH3+.