H/D exchange kinetics: Experimental evidence for formation of different b fragment ion conformers/isomers during the gas-phase peptide sequencing

Electrospray ionization (ESI) Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) combined with H/D exchange reactions was utilized to explore the existence of different b₅⁺ and b₄⁺ fragment ion conformers/isomers of hexapeptide WHWLQL in the gas phase. Distinct H/D exchange trends for protonated WHWLQL ([M + H]⁺) and its b₅⁺ and b₄⁺ fragment ions (with ND₃) were observed. Isolated ¹²C_all isotopomers of both b₅⁺ and b₄⁺ fragment ions yielded bimodal distributions of H/D exchanged product ions. The H/D exchange reaction kinetics also confirmed that b₅⁺ and b₄⁺ fragment ions exist as combination of slow-exchanging (“s”) and fast-exchanging (“f”) species. The calculated rate constant for the first labile hydrogen exchange of [M + H]⁺ (k_{[M + H]} ⁺ = 3.80 ± 0.7 × 10⁻¹⁰ cm³ mol⁻¹ s⁻¹) was ∼30 and ∼5 times greater than those for the “s” and “f” species of b₅⁺, respectively. Data from H/D exchange of isolated “s” species at longer ND₃ reaction times confirmed the existence of different conformers or isomers for b₅⁺ fragment ions. The sustained off-resonance irradiation collision-activated dissociation (SORI-CAD) of WHWLQL combined with the H/D exchange reactions indicate that “s” and “f” species of b₅⁺ and b₄⁺ fragment ions can be produced in the ICR cell as well as the ESI source. The significance of these observations for detailed understanding of protein sequencing and ion fragmentation pathways is discussed.     

Measurement of the rate constants of the reactions of the chlorine atom with C<Subscript>3</Subscript>F<Subscript>7</Subscript>I and CF<Subscript>3</Subscript>I using the resonance fluorescence of chlorine atoms

The rate constants of the reactions of the chlorine atom with C₃F₇I (k ₁) and CF₃I (k ₂) have been measured using the resonance fluorescence of chlorine atoms in a flow reactor at 295 K: k ₁ = (5.2 ± 0.3) × 10⁻¹² cm³ molecule⁻¹ s⁻¹ and k ₂ = (7.4 ± 0.6) × 10⁻¹³ cm³ molecule⁻¹ s⁻¹. No iodine atoms have been detected in the reaction products.     

DFT calculation of α-cyclodextrin dimers. contribution of hydrogen bonds to the energy of formation

The structures and energies of formation of α-cyclodextrin (α-CD) dimers formed according to the “head-to-head” (HH), “head-to-tail” (HT), and “tail-to-tail” (TT) modes, harmonic vibrational frequencies, and intensities of IR bands of the IR transitions were calculated by the DFT/PBE density functional method with full geometry optimization without symmetry restrictions. The spectral data were transformed into spectral patterns. An α-CD molecule can exist in two isomeric forms close in energy, namely, α-CD⁻ and α-CD⁺, with different directions of the ring intramolecular hydrogen bonds. Among the three α-CD⁻ dimers, the highest dimerization energy (E _d/kcal mol⁻¹) belongs to the HH⁻ (68.9), TT⁻ (43.4), and HT⁻ (24.8) dimers. The strength of the α-CD⁺ dimers decreases in the series: TT⁺ (56.7), HT⁺ (49.4), and HH⁺ (42.4). The energies E _H of hydrogen bonds were calculated from the low-frequency shifts of bands of stretching vibrations of the OH groups involved in the formation of these hydrogen bonds. The E _H value for each dimer correlates with E _d. A possibility of formation of intermolecular hydrogen bonds is a driving force of association of α-CD molecules in aqueous solutions. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 8, pp. 1289–1296, August, 2006.     

An application of near-infrared and mid-infrared spectroscopy to the study of selected tellurite minerals: xocomecatlite,tlapallite and rodalquilarite

Near-infrared and mid-infrared spectra of three tellurite minerals have been investigated. The structures and spectral properties of copper bearing xocomecatlite and tlapallite are compared with an iron bearing rodalquilarite mineral. Two prominent bands observed at 9,855 and 9,015 cm⁻¹ are assigned to ²B_1g → ²B_2g and ²B_1g → ²A_1g transitions of Cu²⁺ ion in xocomecatlite. The cause of spectral distortion is the result of many cations of Ca, Pb, Cu and Zn in the tlapallite mineral structure. Rodalquilarite is characterised by ferric ion absorption in the range 12,300–8,800 cm⁻¹. Three water vibrational overtones are observed in xocomecatlite at 7,140, 7,075 and 6,935 cm⁻¹ whereas in tlapallite bands are shifted to lower wavenumbers at 7,135, 7,080 and 6,830 cm⁻¹. The complexity of rodalquilarite spectrum increases with the number of overlapping bands in the near-infrared. The observation of intense absorption feature near 7,200 cm⁻¹ confirms hydrogen bonding water molecules in xocomecatlite. Weak bands observed near 6,375 and 6,130 cm⁻¹ in tellurites are attributed to the hydrogen bonding between (TeO₃)²⁻ and H₂O. A number of overlapping bands at low wave numbers 4,800–4,000 cm⁻¹ are caused by combinational modes of tellurite ion. (TeO₃)²⁻ stretching vibrations are characterised by three main absorptions at ~1,070, 780 and 665 cm⁻¹. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Electrochemical behavior and parameters of hydrofullerene C60H36

Electrochemistry of hydrofullerene C₆₀H₃₆ was studied by cyclic voltammetry in THF and CH₂Cl₂ in the −47–14 °C temperature range. Hydrofullerene undergoes reversible one-electron reduction to form a radical anion in THF (E ⁰=−3.18 V (Fc⁰/Fc⁺), Fc=ferrocene) and irreversible one-electron oxidation in CH₂Cl₂ (E _p ^a =1.22 V (Fc⁰/Fc⁺)). The reduction potential was used to estimate electron affinity of hydrofullerene as EA=−0.33 eV. It was suggested that C₆₀H₃₆ is an isomer withT-symmetry in which 12 double bonds form four isolated benzenoid rings located in vertices of an imaginary inscribed tetrahedron on the molecular surface. For hydrofullerene, the “electrochemical gap” is an analog of the energy gap (HOMO−LUMO), equal to (E ^Ox−E ^Red)=4.4 V, and indicates that C₆₀H₃₆ is a sufficiently “hard” molecule with a low reactivity in redox reactions. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 11, pp. 2083–2087, November, 1999.     

Infrared spectra of cyclic ethers and their derivatives

Data for the characteristic bands of cyclic ethers are reviewed. The infrared spectra of a number of 2-mono- and 2, 5-di-substituted derivatives of tetrahydrofuran are investigated. Absorption bands at about 900 cm⁻¹ are related to pulsation vibrations, and those at about 1200 cm⁻¹ to antisymmetric skeletal vibrations, of the tetrahydrofuran ring. It is shown that to confirm the presence of a tetrahydrofuran ring in a molecule, it is necessary to take into account not only the band of valence antisymmetric vibrations of the group C-O-C (ν _C-O-C ^as 1075 cm⁻¹), but also bands due to ring pulsation vibrations (ring symmetric valence vibrations ν _sk ^s ∼ 900 cm¹).     

X-ray photoelectron study of the state of Ba atoms in YBa2Cu3O7−δ doped with Co and Zn atoms

Investigating changes in the charged state of atoms upon superconductivity-suppressing substitutions is one of the methods to examine a relationship between the electronic structure of HTSC materials and the transition temperature to the superconducting state. In this paper, we measured E_bnd of the inner levels of Ba atoms in Co- and Zn-doped YBa₂Cu₃O_7−δ by X-ray photoelectron spectroscopy. Upon copper substitution by Co and Zn atoms, E_bnd of the inner levels diminishes for Ba atoms but remains the same for Cu and O atoms. The change of E_bnd of the inner levels of Ba atoms is attributed to the change of the Fermi level position in the “anionic” sublattice of (Cu₃O_7−δ)⁷⁻. Institute of Inorganic Chemistry, Siberian Branch, Russian Academy of Sciences. Translated fromZhurnal Strukturnoi Khimii, Vol. 35, No. 4, pp. 91–95, July–August, 1994. Translated by L. Smolina     

Synthesis and spectroscopic characterisation of aurichalcite (Zn,Cu2+)5(CO3)2(OH)6; implications for Cu–ZnO catalyst precursors

The Cu–ZnO catalyst precursors with variable Cu:Zn ratio, between Zn-rich and Cu-rich compositions have been investigated by a combination of electronic and vibrational spectroscopy. Synthesized catalyst precursors exhibit two d–d transition bands of Cu²⁺ ions in a distorted octahedral symmetry, at 7,600 and 12,900 cm⁻¹ (1,315 and 775 nm). The effect of structural cation substitution (Zn²⁺ and Cu²⁺) on band shifts is observed in the spectra of the synthetic catalyst precursors. The observation of two broad features at ∼7,600 and 12,900 cm⁻¹ (1,315 and 775 nm) is a strong indication for Zn²⁺ substitution by Cu²⁺ ions. The result of multiple bands in the symmetric stretching and bending regions confirms the reduction of symmetry from D _3h to C _2v /C _s for (CO₃)²⁻ ion in aurichalcite. The synthetic aurichalcite may be used as a standard for identification of spectral properties of naturally occurring anhydrous carbonate minerals.     

Molecular dynamics calculation of spectral characteristics of water clusters in the presence of ozone molecules and chlorine ions

Simultaneous interaction of the (H₂O)₅₀ cluster with O₃ molecules and Cl⁻ ions was studied by the molecular dynamics method. Six O₃ molecules located near the cluster were absorbed by the aqueous aggregate, and Cl⁻ ions in turn left the zone of the interaction with the cluster. Some of Cl⁻ ions penetrated inside the formed (O₃)₆(H₂O)₅₀ cluster and come into collision with O₃ molecules that split the ozone molecule into atoms. When Cl⁻ ions were removed sufficiently far away from the cluster, the water cluster with absorbed O₃ molecules and O atoms was observed for 15.6 ps. The interaction of water molecules with Cl⁻ ions gives rise to an increase in the integral intensity of absorption and emission IR spectra, and also to an essential decrease in the analogous characteristics of the Raman spectrum in the frequency range of 0 ≤ ω ≤ 1000 cm⁻¹. The presence of Cl⁻ ions did not affect essentially the location of the main band in the IR spectra, but considerably changed the shape of the bands in the Raman spectrum.     

A theoretical study of the acetylide anion, HCC−

The results of various ab initio calculations are reported for the electronic ground state of the acetylide anion. An “Eyring's lake” in the T-shaped configuration is identified with six different methods (SCF, MP2, CCSD, CCSD-T, CCSD(T), and CEPA–1). The equilibrium bond lengths of HCC⁻ are estimated to be r _e (CH)=1.0689(3) ? and R _e (CC)=1.2464(2) ?, and the ground-state rotational constant is predicted to be B ₀=41636(20)MHz. The large permanent dipole moment of μ₀=−3.093D should facilitate detection of the anion by microwave spectroscopy. The band centers are predicted to be 3211.3cm⁻¹(ν₁), 511.1cm⁻¹(ν₂), and 1805.0cm⁻¹(ν₃). A large transition dipole moment of 0.477 D is calculated for the ν₂ band. Rovibrational levels of HCC⁻ up to approximately 20 000 cm⁻¹ above equilibrium are calculated with DVR-DGB and FBR methods on the basis of a previous CEPA–1 potential energy surface. Different energy patterns are found and discussed, for which anharmonic and Coriolis resonances are shown to play an important role. Received: 27 July 1998 Accepted: 12 August 1998 / Published online: 19 October 1998     

Packing of complex anions and effect of mutual ordering of heavy cations in structures with the paratungstate ion [H2W12O42]10−

The packing of [H ₂W₁₂O₄₂]¹⁰⁻ polyanions in seven known crystal structures is analyzed. The centers of the polyanions are arranged according to the law of the F- cell (3 cases) or I- cell (2 cases) or according to a more complex law. “Coherence” in the arrangement of heavy W atoms belonging to different polyanions is established: there are crystallographic planes with high concentrations of these atoms;this is an effect of superstructural ordering up to formation of the cation sublattice with light “filler” atoms (K, Mg, Na, N) partly addressed to the sites of the sublattice. Translated fromZhumal Strukturnoi Khimii, Vol. 38, No. 4, pp. 732–738, July–August, 1997.     

The kinetics of chemical reactions in the products of dissociation of the CO2−H2 gas mixture in microwave discharge

The yields of hydrogen atoms, oxygen atoms and molecules, and hydroxyl radicals after a microwave discharge in the mixture of CO₂ and H₂ were measured by ESR spectroscopy in a flow-type system. A mathematical model of the kinetics of chemical reactions downstream the microwave discharge was devised. The concentrations of particles that cannot be detected under our experimental conditions were estimated. Experimental values of the concentration sensitivity for an RE-1306 ESR spectrometer are as follows: for a pressure of 1 Torr and optimized detection conditions, H^., 10¹¹ cm⁻³; O^., 3·10¹⁰ cm⁻³; OH^., 10¹⁰ cm⁻³; O₂, 3·10¹³ cm⁻³ (Ref. 7); for a pressure of 2 Torr, H^., 5·10¹² cm⁻³; O^., 2·10¹² cm⁻³; OH^., 2.5·10¹¹ cm⁻³; O₂, 7.5·10¹⁴ cm^{−3 8} Translated fromIzvestiya Akademii Nauk, Seriya Khimicheskaya, No. 4, pp. 665–669, April, 2000.     

Spectroscopy of selected copper group minerals: ktenasite,orthoserpierite and kipushite

Near-infrared (NIR) and IR spectroscopy have been applied for the characterisation of three complex Cu–Zn sulphate/phosphate minerals, namely ktenasite, orthoserpierite and kipushite. The spectral signatures of the three minerals are quite distinct in relation to their composition and structure. The effect of structural cation substitution (Zn²⁺ and Cu²⁺) on band shifts is significant both in the electronic and in the vibrational spectra of these Cu–Zn minerals. The variable Cu:Zn ratio between Zn-rich and Cu-rich compositions shows a strong effect on Cu(II) bands in the electronic spectra. The Cu(II) spectrum is most significant in kipushite (Cu-rich) with bands displayed at high wavenumbers, 11,390 and 7,545 cm⁻¹. The isomorphic substitution of Cu²⁺ for Zn²⁺ is reflected in the NIR and IR spectroscopic signatures. The multiple bands for ν₃ and ν₄ (SO₄)²⁻ stretching vibrations in ktenasite and orthoserpierite are attributed to the reduction in symmetry of the sulphate ion from T_d to C_2V. The IR spectrum of kipushite is characterised by strong (PO₄)³⁻ vibrational modes at 1,090 and 990 cm⁻¹. The range of IR absorption is higher in ktenasite than in kipushite, while it is intermediate in orthoserpierite.     

The state of metals in the Pt/Al2O3 and (Pt-Cu)/Al2O3 catalysts as indicated by IR spectroscopy with isotope dilution of 12C16O with 13C18O molecules

Adsorption of ¹³C¹⁸O+¹²C¹⁶O mixtures on the Pt(2.9%)/γ-Al₂O₃, (Pt(2.6%)+Cu(2.7%))/γ-Al₂O₃, and (Pt(2.6%)+Cu(5.1%))/γ-Al₂O₃ catalysts was studied by FTIR spectroscopy. On the metallic Pt surface at coverages close to saturation, CO is adsorbed both strongly and weakly to form linear species for which the vibrational frequencies of the isolated ¹³C¹⁸O molecules adsorbed on Pt are ∼1940 and ∼1970 cm⁻¹, respectively. The redistribution of intensities of the high-and low-frequency absorption bands in the spectra of adsorbed ¹³C¹⁸O indicates that these linear forms are present on the adjacent metal sites. The weak adsorption is responsible for the fast isotope exchange between the gaseous CO and CO molecules adsorbed on metal. The Pt-Cu alloys, in which the electronic state of the surface Pt atoms characteristic of monometallic Pt remains unchanged, are formed on the surface of the reduced Pt-Cu bimetallic catalysts. The decrease in the vibrational frequencies of the isolated C=O bonds in the isolated Pt-CO complexes suggests that the CO molecules adsorbed on the Cu atoms affect the electronic properties of Pt. Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 831–836, May, 2007.     

Activation analysis and autoradiography of impurity distributions in silicon multilayer structures

Activation analysis and autoradiography were used to investigate the concentration distribution of contaminants in poly-Si−Si₃N₄−SiO₂−Si substrate multilayer structures (SNOS) on sampling each technological product. Samples were irradiated for 36 hrs at a thermal neutron flux of 4·10¹³n·cm⁻²·sec⁻¹. The thin films of the analysed sample were removed stepwise by selective chemical etching using appropriate masking techniques. Simultaneously autoradiographs were made of the surface of parallel samples activated under the same conditions. The concentration of the technological contaminants (e.g. Na, Cu, Au) increases in the junction interface of the layers as unambiguously shown by the results obtained. Presented at the “4th Symposium on the Recent Developments in Neutron Activation Analysis” Churchill College, Cambridge, 4–7 August, 1975.     

Influence of the out-of-plane distortions of nuclear configurations of molecules with then-AO of the heteroatom directed along theC 2 symmetry axis on spin-orbit coupling between thenπ*- and ππ*-states

This paper studies changes in the matrix elements (U_mp) of spin-orbit coupling between the nπ^*- and ππ^*-states, which are induced by the (“chair,” “bath”) distortions of the nuclear configurations of molecules. The analysis is performed for acridine molecules in which the n-p_z atomic orbital (AO) of the heteroatom is directed along the C₂ symmetry axis. Earlier, for molecules with a planar nuclear configuration of C_2v symmetry and with the heteroatom lying on the C₂ axis, we established the dependence of U_mp on the symmetry of ππ^*-states [Γ(ππ^*)=A₁ or B₂]. The values of U_mp differ by more than one order of magnitude; this is in line with the difference between the interconversion rate constants (K_isc; two or three orders). In this work we have found that this contrast in U_mp (and, accordingly, in K_isc) is retained when the nuclear configuration of the acridine molecule is distorted to the “chair” (AC-A) configuration, although the individuality of both molecular orbital types (nσ-MO and π-MO) and states nπ^* and ππ^* is annihilated to a certain extent. For the “bath” (AC-B) conformation the difference in U_mp considerably diminishes. Reasons for the changes in the matrix elements of spin-orbit coupling and rate constants of the S-T conversion are analyzed. The available energy level diagram is critically analyzed, and a slightly different diagam as well as a scheme of nonradiating deactivation of acridine are suggested. L. Ya. Karpov Physicochemical Scientific Research Institute. Translated fromZhurnal Strukturnoi Khimii, Vol. 36, No. 2, pp. 292–297, March–April, 1995. Translated by L. Smolina     

Photoinduced electron transfer of fullerenes (C60 and C70) studied by transient absorption measurements in near-IR region

Efficiencies and rates of electron transfer from various electron donors to excited fullerenes (C₆₀ and C₇₀) have been determined by observing the transient absorption bands in the near-IR region, where the anion radicals of fullerenes appear. From the rise of the absorption bands of C₆₀ ⁻⁺ and C₇₀ ⁻⁺ in the near-IR region, electron transfer takes place via the triplet states (^TC₆₀ ^* and ^TC₇₀ ^*) under appropriately low concentrations of electron donors. By analysis of the rise curves C₆₀ ⁻⁺ and C₇₀ ⁻⁺, contribution of the excited singlet states (^SC₆₀ ^* and ^SC₇₀ ^*) in addition to the route of the triplet states (^TC₆₀ ^* and ^TC₇₀ ^*) is confirmed. The quantum yield for electron transfer via the triplet states Φ_ct ^T was evaluated by the ratio of [C₆₀ ⁻⁺]/[^TC₆₀ ^*] (or [C₇₀ ⁻⁺/[^TC₇₀ ^*]). The Φ_ct ^T depends upon the donor-ability, donor concentration, and solvent polarity. The back electron-transfer process, which was evaluated by observing C₆₀ ⁻⁺, also depends upon the solvent polarity.     

XRD and UV-Vis diffuse reflectance analysis of CeO2-ZrO2 solid solutions synthesized by combustion method

A series of ceria-incorporated zirconia (Ce_1−xZr_xO₂,x = 0 to 1) solid solutions were prepared by employing the solution combustion synthesis route. The products were characterized by XRD and UV-Vis-NIR diffuse reflectance spectroscopy. The materials are crystalline in nature and the lattice parameters of the solid solution series follow Vegard’s law. Diffuse reflectance spectra of the solid solutions in the UV region show two intense bands at 250 and 297 nm which are assigned respectively to Ce³⁺ ← O²⁻and Ce⁴⁺ ← O²⁻ charge transfer transitions. The two vibrational bands in 6960 cm⁻¹ and 5168 cm⁻¹ in the NIR region indicate the presence of surface hydroxyl groups on these materials.     

Radiation chemical investigations on aqueous solutions of C60(OH)18

The ultraviolet-visible absorption spectrum of C₆₀(OH)₁₈ in water showed an absorption band with λ_max = 215 nm and other characteristic absorption bands of C₆₀ are not observed. The singlet-singlet and triplet-triplet absorption bands are not observed in the 400–900 nm region. It has low reactivity with e_aq⁻ and formed an absorption band with λ_max = 580 nm. The hydroxyl radicals react with a bimolecular rate constant of 2.4×10⁹ dm³ mol⁻¹ s⁻¹ and showed an absorption band at 540 nm.