Capture of an electron by ions in methionine and norleucine molecules

The relative cross sections of processes taking place when H⁺ and He²⁺ ions with an energy of 6z keV (z is the ionic charge) capture an electron from molecules of C₅H₁₁NO₂S methionine (proteogenic amino acid) and C₆H₁₃NO₂ norleucine (nonproteogenic amino acid) are measured by time-of-flight mass spectrometry (a methionine molecule transforms into a norleucine molecule by substituting the CH₂ group for the S heteroatom). The fragmentation pattern of resulting molecular ions is established from correlation analysis of the detection times of all fragment ions. The results are compared with experimental data for fragmentation of the same molecules ionized by electrons and photons. In these amino acids, the pattern of molecular ion fragmentation is found to depend on the type of molecule ionization. However, the detachment cross section of the COOH neutral group or residue (neutral or charged) R of a side chain of the amino acid is invariably among the largest. The relative cross sections of capture with single and double ionization of molecules are measured.     

Theory of coherent phenomena and fundamentals in nuclear resonant scattering

Muonic X-ray cascades in B, C, N, O and Ne following muonic atom formation in B₂H₆, CH₄, C₂H₆, C₄H₁₀, N₂, O₂ and Ne were investigated. The densities of the different target gases were low enough to prevent any contact of the atom or molecule on which the formation takes place with surrounding atoms or molecules during the cascade. Molecular effects of the capturing molecule are clearly seen. The observed transition yields could be reproduced by variation of only two parameters in a cascade calculation: the number of initially available electrons and the muon angular momentum distribution at the starting point of the calculation. By varying the number of electrons, the molecular effects could be described. This revised version was published online in August 2006 with corrections to the Cover Date.     

Total cross-sections for positron scattering by a series of molecules

The additivity rule is employed to obtain the total (elastic+inelastic) cross-sections for positron scattering from molecules including a number of diatomic, polyatomic molecules (H₂, N₂, HCl, CO₂, NH₃, SF₆, CH₄, C₂H₄ and C₃H₈) over an incident energy range of 10-1000 eV. The total cross-sections (TCS) of the constituent atoms of molecules are obtained by employing a complex optical model potential (composed of static, polarization and absorption potential). The present results are compared with experimental data and other theoretical calculations, good agreement is obtained in intermediate- and high-energy region. Received: 11 November 1997 / Revised: 23 March 1998 / Accepted: 16 June 1998     

A first-principles study on the adsorption behaviour of methanol and ethanol over C59B heterofullerene

In the present study, the adsorption behaviour of methanol (CH₃OH) and ethanol (C₂H₅OH) molecules over heterofullerene C₅₉B surface is studied by density functional theory calculations. This heterofullerene is obtained from C₆₀ by substituting a carbon atom with a boron atom and relaxing self-consistently the structure to the local minimum. The adsorption of CH₃OH and C₂H₅OH on the C₅₉B is exothermic and the relaxed geometries are stable. The CH₃OH and C₂H₅OH adsorption can also induce a change in the highest occupied molecular orbital and the lowest unoccupied molecular orbital energy gap of the nanocage. The dehydrogenation pathways of CH₃OH and C₂H₅OH via O–H and C–H bonds scission are also examined. The results indicate that O–H bond scission is the most favourable pathway on the C₅₉B surface.     

The scattering of He from adsorbed layers of gases on Ag(110)

The adsorption of gases on Ag(110) has been studied using inelastic He atom scattering. Vibrational spectra have been obtained for Kr, Xe, C₂H₆, C₂H₄, CH₄, CF₄, CHF₃, CO₂ and H₂O. Spectra have also been obtained for multilayers of Xe (2 layers) and C₂H₆ (3 and 4 layers) where the energy changes move to lower values. The scattering from Kr and Xe can be shown to be dispersionless as has been previously found for these adsorbates on Cu(100) and Cu(110). The energy changes for Kr and Xe are smaller than on Cu surfaces and attempts were made to account for this based on an Einstein model of the adsorbed atoms in the surface holding potential.     

Fragmentation of D- and L-enantiomers of amino acids through interaction with 3He2+ ions

The relative cross section of processes attendant on the capture of an electron by 12-keV ³He²⁺ ions are measured by time-of-flight mass spectrometry for leucine (C₆H₁₃NO₂), methionine (C₅H₁₁NO₂S), and glutmic acid (C₅H₉NO₄) molecules. No differences between the formation relative cross sections of different fragment ions for the D- and L-enantiomeric forms of the amino acids are revealed. The spectrum of glutamic acid fragments taken at temperatures above 110°C is explained by decomposition of the acid with the formation of pyroglutamic acid (C₅H₇NO₃) and water. The results are compared with published data on fragmentation of the same molecules via electron-impact ionization.     

Distinct transport properties of O2 and CH4 across a carbon nanotube

It is of fundamental importance to investigate either O₂ or CH₄ molecules across nanochannels in many areas such as breathing or separation. Thus, many researches have focused on such a single type of molecules across nanochannels. However, O₂ and CH₄ can often appear together and crucially affect human life, say, in a mine. On the basis of molecular dynamics simulations, here we attempt to investigate the mixture of O₂ and CH₄, in order to identify their different transport properties in a nanochannel. We take a single-walled carbon nanotube (SWCNT) as a model nanochannel, and find that their transport properties are distinctly different. As the concentration of O₂ increases up to a high value of 0.8, it is always faster for CH₄ molecules to transport across the SWCNT, and the total number of gas molecules transporting across the SWCNT is decreased. Meanwhile, CH₄ molecules are always dominant in the SWCNT, and the total number of O₂ or CH₄ inside the SWCNT is a constant. By calculating the van der Waals interaction between the SWCNT and O₂ or CH₄, we find that the net interaction between CH₄ and the SWCNT is much stronger. Our findings may offer some hints on how to separate CH₄ from O₂, and/or store CH₄ efficiently.     

Optical properties of clusters and molecules from real-time time-dependent density functional theory using a self-consistent field

We present a detailed study of optical absorption spectra of finite-size structures, using a method based on time-dependent density-functional theory (TDDFT), which involves a self-consistent field for the propagation of the Kohn–Sham wavefunctions in real-time. Although our approach does not provide a straightforward assignment of absorption features to corresponding transitions between Kohn–Sham orbitals, as is the case in frequency-domain TDDFT methods, it allows the use of larger timesteps while conserving total energy and maintaining stable dipole moment oscillations. These features enable us to study larger systems more efficiently. We demonstrate the efficiency of our method by applying it to a hydrogen-terminated silicon cluster consisting of 364 atoms, with and without P impurities. For cases where direct comparison to experiment can be made, we reproduce the absorption features of fifteen small molecules [N₂, O₂, O₃, NO₂, N₂O, NH₃, H₂O, H₂CO, H₂CO₃, CO₂, CH₄, C₂H₂, C₂H₄, C₂H₆, C₆H₆] and find generally good agreement with experimental measurements. Our results are useful for the detection and the determination of orientation of these molecules.     

13C-NMR Study of Some Substituted 9-Acridanone Derivatives

¹³C-NMR spectra of several 9-acridanones with different substituents both on the ring (R₁ = CH₃, OCH₃, NH₂, N(CH₃)₂, NO₂) and at the nitrogen atom (R₂ = H, CH₃ C₂H₅, CH₂-C₆H₅, C[tbnd]C-CH₃, (CH₂)₂N(C₂H₂)₂, CH=C=CH₂) have been recorded. The C-NMR chemical shifts are discussed as a function of the nature of the substituent, the importance of peri steric interactions and the electronic structure of the acridanone ring. There is a good linear relationship between the total electronic density and the chemical shifts.     

Influence of heme periphery upon electronic structúre and Mössbauer spectra parameters of hemoglobin

Quantum-chemical analysis of electronic structure peculiarities and mossbauer spectra parameters was performed for penta-coordinated complex of ferro-protoporphyrin with imidazole (Fe(+2)PPIm). Peripheral substitutes (−CH₃, −C₂H₃, −C₂H₄COOH) introduced in the porphyrin macrocycle simulated real chemical structure of protoporphyrin (PP) in heme group of Hb. Calculations displayed that doubly occupied molecular orbitals (MO) of the peripheral substitutes (−CH=CH₂ and −CH₂−CH₂−COOH) always appeared near the occupat ion border. The orientation of vinyl fragment have the essential influence upon Fe₅ dorbital populations and quadrupole splitting_AE_Q for⁵B₁ and⁵B₂ terms. The values of isomer shift were insensitive to that modification of fragment orientation.     

Reactions and anion desorption induced by low-energy electron exposure of condensed acetonitrile

Thermal desorption spectrometry (TDS) and electron stimulated desorption (ESD) are employed to investigate mechanisms responsible for the formation of C₂H₆ in electron irradiated multilayer films of acetonitrile (CH₃CN) at 30 K. Using a high sensitivity time-of-flight mass spectrometer, we observe the ESD of anionic fragments H⁻, CH₂ ⁻, CH₃ ⁻ and CN⁻. Desorption occurs following dissociative electron attachment (DEA) via several negative ion resonances in the 6 to 14 eV energy range and correlates well with a “resonant” structure seen in the TDS yield of C₂H₆ (i.e., at mass 30 amu). It is proposed that C₂H₆ is formed by the reactions of CH₃ radicals generated following DEA to CH₃CN which also yields CN⁻. Between 2 and 5 eV, a second resonant feature is seen in the C₂H₆ signal. While DEA is observed in the gas phase at these energies, no anion desorption occurs since anionic fragments likely have insufficient kinetic energy to desorb. Since the CH₂ ⁻ ion has not been observed in gas-phase measurements, we propose that it is formed, along with HCN (that is detected in TDS) when dissociation into CH₃ ⁻ and CN is hindered by adjacent molecules.     

Relative intensities in x-ray photoelectron spectra. Part VI. The spectra of He(I), He(II), Y Mζ and Zr Mζ

The 2s- and 2p-electron photoionization cross-sections at photon energies up to 190 eV have been calculated, using the RPAE method for averaged configurations of the C, N, O and Ne atoms. The RPAE method ensures a more accurate relation between the cross-sections, 2s/2p, than that obtained using the Hartree—Fock method. Within the framework of the Gelius—Siegbahn model, but with the use of theoretical atomic cross-sections, we have calculated the photoionization cross-sections for He(I), He(II), Y Mζ, Zr Mζ for CH₄, C₂H₆, C₃H₈, C₂H₄, C₂H₂, NH₃, H₂O, CN^?, N₂, CO, CO₂, N₂O and NO₂^? molecules. For CO, N₂, CO₂, N₂O and H₂O molecules, a comparison is made between the theoretical and experimental cross-sections for hν < 60 eV. The calculated absolute and relative values of the molecular-orbital cross-sections are in reasonable agreement with experiment, especially at hν ? 40 eV. The calculations correctly reproduce the change in intensities under the transition He(I) → He(II). We have shown that our calculations have a significant advantage over those performed using the PW and OPW approximations. It is shown for NO, N₂, CO, H₂O, CH₄, NH₃ and N₂O molecules that the total photoionization cross-section calculated taking into account the real structure of the molecular orbitals is in better agreement with the experimental photoabsorption cross-section than is the sum of the cross-sections for the atoms in a molecule.     

50—5000 eV电子被C4H8O,C5H10O2, C6H5CH3和C4H8O2散射的总截面

使用电子被C, H和O原子散射总截面的实验数据, 利用修正后的可加性规则计算了能量为50—5000eV的电子被4个复杂大分子C₄H₈O, C₅H₁₀O₂, C₆H₅CH₃和C₄H₈O₂散射的总截面, 并将计算结果与实验结果及其他理论计算结果进行了比较. 结果表明, 即 关键词： 电子散射 可加性规则 总截面 几何屏蔽效应     

Crystal structure of di-(L-serine) phosphate monohydrate [C3O3NH7]2H3PO4H2O

The crystal structure of di-(L-serine) phosphate monohydrate [C₃O₃NH₇]₂H₃PO₄H₂O is determined by single-crystal x-ray diffraction. The intensities of x-ray reflections are measured at temperatures of 295 and 203 K. The crystal structure is refined using two sets of intensities. It is established that, in the structure, symmetrically nonequivalent molecules of L-serine occur in two forms, namely, the monoprotonated positively charged molecule CH₂(OH)CH(NH₃)⁺COOH and the zwitterion CH₂(OH)CH(NH₃)⁺COO^?, which are linked with each other and with the H₂PO ^?₄ ion through a hydrogen-bond system involving water molecules.

     

Dependence of NMR isotropic shift averages and nuclear shielding tensors on the internal rotation of the functional group X about the C-X bond in seven simple vinylic derivatives H2C=CH-X

The ‘Gauge Including Atomic Orbitals’ (GIAO) approach is used to investigate the question of intramolecular rotation. Ab initio GIAO calculations of NMR chemical shielding tensors carried out with GAUSSIAN 94 within the SCF-Hartree-Fock approximation are described. In order to compare the calculated chemical shifts with experimental ones, it is important to use consistent nuclear shieldings for NMR reference compounds like TMS. The influence of rotating functional groups X=CH₃, CHO, NO₂, NH₂, CONH₂, COOH or C₆H₅ on the shielding tensors in seven vinylic derivatives H₂C=CH-X is studied; the molecules are propene, acrolein, nitroethylene, ethyleneamine, acrylamide, acrylic acid and styrene. We observe a marked dependence of nuclear shielding and chemical shift on the torsional movement. Different Boltzmann averages over the conformational states are considered and compared for gas phase, liquid and solid state NMR. Their applicability to model cases for rigid or freely rotating molecules and for fixed molecules (e.g. polymers or proteins) with rapidly rotating groups is discussed and simple calculation models are presented. On the basis of this work it can be concluded that intramolecular rotation clearly affects the observed averages. Effects of up to 2 ppm have been observed for isotropic chemical shifts, and up to 17 ppm difference have been observed for individual tensor components, for example, of the carboxylic ¹³C atom in acrylic acid. The variation of the shielding tensor on a nucleus in a fixed molecular backbone resulting from an attached rotating group furthermore leads to a new relaxation mechanism by chemical shift anisotropy.     

Inelastic atom scattering from layers of atoms and molecules on Cu(110)

The vibrational properties of adsorbed layers have been studied using inelastic He atom scattering. The substrate was Cu(110) viewed along the [001] and [11&#x0304;0] azimuth. The adsorbates included, Kr, Xe, CH₄, CD₄, C₂H₆, CO, CO₂ and O₂ and covered the region of both physisorption and chemisorption. Despite a range of binding energies and mass ratios the vibrational frequencies showed no dependence on the momentum change, i.e. scattering was dispersionless, although intensity changes occurred in the inelastic peaks. There seemed to be no dependence of the adsorbate spectra on coverage below a monolayer. The peaks of CH₄ and C₂H₆ appeared broader than those of Kr and Xe suggesting molecular motions. Further, CH₄ and C₂H₆ gave very similar spectra. Both energy gain and loss events were observed in the inelastic spectrum. For those adsorbates which gave multilayer adsorption (Xe, C₂H₆) changes in the spectra were observed as the second layer developed. In the latter category also, mixed layers (Xe on C₂H₆, Xe on CO and C₂H₆ on Xe) were studied.     

Flame spectra from the interaction of fluorine and some halogen-containing compounds

The cold flames generated by the interaction of gaseous fluorine and CH₃I, C₂H₅I, CH₂Cl₂, CHCl₃, and CCl₄ are described. The spectra of these flames were determined. The spectroscopic results are interpreted from the point of view of the occurrence of branching in fluorination chain reactions, when superequilibrium concentrations of chemically excited molecules are formed, the latter subsequently decaying into a radical and an atom (as in the case of the F₂+CH₃I system) or into a biradical and a saturated molecule (F₂+CH₂CI₂ system).In conclusion, the author wishes to express his gratitude to Academician V. N. Kondrat'ev, A. E. Shilov, and A. M. Chaikin for a discussion of the results and assistance in the work.     

Mass spectroscopy and ablation characteristics of nylon 6.6 in the ultraviolet

We report on the mass spectroscopic and the laser ablative characteristics of nylon 6.6 [-NH-(CH₂)₆-NH-CO-(-CH₂)₄-CO-] at 193 and 248 nm, using the ArF and KrF excimer lasers. The characteristic parameters of the laser ablative process, such as etch rate at different fluences, the threshold fluence, and the absorption coefficient for both wavelengths were determined. Even at low laser energy, there was a complete breaking of the polymeric chain bonds. The following photofragments were observed at 248 nm: H, H₂, C, CH, CH₂, N, NH, O, OH, H₂O, C₂H, C₂H₂, CN, C₂H₃, HCN, N₂, CO, C₂H₄, COH, C₂H₅, N₂H, NO, C₂H₆, H₂CO, N₂H₂, C₂, CH₂NH, O₂, C₃H₃, C₃H₄, C₃H₅, C₃H₆, CNO, HCNO, and H₂CNO. At 193 nm no photofragments were observed for m/e larger than 30 amu. The photofragments with two carbon atoms have a relatively higher probability to be dissociated from the parent monomer, than heavier photofragments with four carbon atoms. The mass spectroscopic studies and the absorption spectrum of nylon 6.6 in the ultraviolet, suggest photochemical bond-breaking at 248 and 193 nm. The monomer dissociates into fragments with the predominant mass at 28 amu for both laser wavelengths. Therefore the amide group is mainly involved in the photodissociation process of nylon 6.6 in the ultraviolet. The experimental results suggest that the photochemical dissociation of the polymeric chain is the dominant mechanism of the laser ablation of nylon 6.6 at 193 and 248 nm.     

Geometric shielding corrections for total cross section calculations of electron scattering by CH4, C2H6, C2H3F3, C2H4, C2F4, C2Cl4 and C2Cl2F2 from 30–5000?eV

To quantify the changes in the geometric shielding effect in a molecule as the incident electron energy varies, an empirical fraction, which represents the total cross section contributions of shielded atoms in a molecule at different energies, is presented. Using this empirical fraction, the total cross sections for electron scattering by CH₄, C₂H₆, C₂H₃F₃, C₂H₄, C₂F₄, C₂Cl₄ and C₂Cl₂F₂ are calculated over a wide energy range from 30 to 5000 eV by the additivity rule model at the Hartree-Fock level. The quantitative total cross sections are compared with those obtained by experiment and other theories where available. Good agreement is attained above 100 eV.     

Determination of the sites of Fe atoms in Fe-substituted Mn12

In this paper neutron diffraction experiments were performed for Fe-substituted Mn12 in order to determine the sites of Fe atoms. The results of structure refinements for the sample with our accessed highest Fe content showed that all Fe atoms occupied Mn（3） sites in the Mn12 skeleton. The x-ray absorption fine structure experiments as well as multiple scattering simulations gave the same result. Thus we concluded that Fe atoms only occupied Mn（3） sites. This conclusion also means that Fe-substituted Mn12 series only includes the four single-molecule magnets of [Mn12-xFexO12（CH3COO）16（H2O）4]·2CH3COOH·4H2O （x = 1, 2, 3, and 4）, denoted by Mn11Fe1, Mn10Fe2, MngFe3, and Mn8Fe4, respectively.