On the mechanism of anion desorption from DNA induced by low energy electrons

Our knowledge of the mechanisms of radiation damage to DNA induced by secondary electrons is still very limited, mainly due to the large sizes of the system involved and the complexity of the interactions. To reduce the problem to its simplest form, we investigated specific electron interactions with one of the most simple model system of DNA, an oligonucleotide tetrameter compound of the four bases. We report anion desorption yields from a thin solid film of the oligonucleotide GCAT induced by the impact of 3-15 eV electrons. All observed anions (H-, O-, OH-, CN-, and OCN-) are produced by dissociative electron attachment to the molecule, which results in desorption peaks between 6 and 12 eV. Above 14 eV nonresonant dipolar dissociation dominates the desorption yields. By comparing the shapes and relative intensities of the anion yield functions from GCAT physisorbed on a tantalum substrate with those obtained from isolated DNA basic subunits (i.e., bases, deoxyribose, and phosphate groups) from either the gas phase or condensed phase experiments, it is possible to obtain more details on the mechanisms involved in low energy electron damage to DNA, particularly on those producing single strand breaks.     

Decomposition of methionine by low energy electrons

In this work, we present the results from low energy (<12 eV) electron impact on isolated methionine, Met. We show that dissociative electron attachment is the operative mechanism for the sulfur content amino-acid fragmentation. The two most dominant fragments are attributed to the (Met-H)(-) and (C(4)NOH(5))(-) ions that are formed at energy below 2 eV. The formation of the latter anion is accompanied by the loss of neutral counterparts, which are most likely a water molecule and highly toxic methanethiol, CH(3)SH. Further fragments are associated with the damage at the sulfur end of the amino acid, producing the methyl sulfide anion CH(3)S(-) or sulfur containing neutrals. In the context of radiation induced damage to biological material at the nano-scale level, the present interest of methionine arises from the implication of the molecule in biological processes (e.g., S-adenosyl methionine for the stimulation of DNA methyltransferase reactions or protein synthesis).     

Global energy minimization of alanine dipeptide via barrier function methods

This paper presents an interior point method to determine the minimum energy conformation of alanine dipeptide. The CHARMM energy function is minimized over the internal coordinates of the atoms involved. A barrier function algorithm to determine the minimum energy conformation of peptides is proposed. Lennard-Jones 6-12 potential which is used to model the van der Waals interactions in the CHARMM energy equation is used as the barrier function for this algorithm. The results of applying the algorithm for the alanine dipeptide structure as a function of varying number of dihedral angles are reported, and they are compared with that obtained from genetic algorithm approach. In addition, the results for polyalanine structures are also reported.     

Bond dissociation energy and Lewis acidity of the xenon fluoride cation

This study focuses upon the Lewis acid reactivity of XeF(+) with various bases in the gas phase and the determination of the bond dissociation energy of XeF(+). The bond dissociation energy of XeF(+) has been measured by using energy-resolved collision-induced dissociation with neon, argon, and xenon target gases. Experiments with neon target yield a 298 K bond dissociation enthalpy of 2.81 +/- 0.09 eV, and those with argon target give a similar value at 2.83 +/- 0.12 eV. When using a xenon target, a significantly lower value of 1.95 +/- 0.16 eV was observed, which corresponds closely with previous measurements and theoretical predictions. It is proposed that the lighter target gases give inefficient excitation of the XeF(+) vibration leading to dissociation at energies higher than the BDE. Novel xenon-base adducts have been prepared in a flowing afterglow mass spectrometer by termolecular addition to XeF(+) and by reaction of base with XeF(+)(H(2)O). New species have been characterized qualitatively by CID, and it is found that the products formed reflect the relative ionization energies of the fragments. Among the new xenon-containing species that have been prepared are the first examples of xenon carbonyls.     

Ab initio molecular dynamics of protonated dialanine and comparison to infrared multiphoton dissociation experiments

Finite temperature Car-Parrinello molecular dynamics simulations are performed for the protonated dialanine peptide in vacuo, in relation to infrared multiphoton dissociation experiments. The simulations emphasize the flexibility of the different torsional angles at room temperature and the dynamical exchange between different conformers which were previously identified as stable at 0 K. A proton transfer occurring spontaneously at the N-terminal side is also observed and characterized. The theoretical infrared absorption spectrum is computed from the dipole time correlation function, and, in contrast to traditional static electronic structure calculations, it accounts directly for anharmonic and finite temperature effects. The comparison to the experimental infrared multiphoton dissociation spectrum turns out very good in terms of both band positions and band shapes. It does help the identification of a predominant conformer and the attribution of the different bands. The synergy shown between the experimental and theoretical approaches opens the door to the study of the vibrational properties of complex and floppy biomolecules in the gas phase at finite temperature.     

Reactions in clusters of acetone and fluorinated acetones triggered by low energy electrons

Electron attachment to clusters of acetone (A), trifluoroacetone (TFA) and hexafluoroacetone (HFA) is studied in a crossed beam experiment with mass spectrometric detection of the anionic products. We find that the electron attachment properties in A change dramatically on going from isolated molecules to clusters. While single acetone is a very weak electron scavenger (via a dissociative electron attachment (DEA) resonance near 8.5 eV), clusters of A capture electrons at very low energy (close to 0 eV). The final ionic products consist of an ensemble of molecules (M) subjected to the loss of two neutral H₂ molecules ((M_n−2H₂)⁻, n ≥ 2). Their formation at low energies can only be explained by invoking new cyclic structures and polymers. In clusters of TFA, anionic complexes containing non-decomposed molecules (M_n⁻) including the monomer (M⁻) and ionic products formed by the loss of one and two HF molecules are observed. Loss of HF units is also interpreted by the formation of new cyclic structures in the anionic system. HFA is a comparatively stronger electron scavenger forming a non-decomposed anion via a narrow resonant feature near 0 eV in the gas phase. In HFA clusters, the non-decomposed parent anion is additionally observed at higher electron energies in the range 3–9 eV. The M⁻ signal carries signatures of self-scavenging processes, i.e., inelastic scattering by one molecule and capture of the completely slowed down electron by a second molecule within the same cluster. The scavenging spectrum is hence an image of the electronically excited states of the neutral molecule.     

A molecular dynamics study of the dielectric properties of aqueous solutions of alanine and alanine dipeptide

Molecular dynamics simulations were used to compute the frequency-dependent dielectric susceptibility of aqueous solutions of alanine and alanine dipeptide. We studied four alanine solutions, ranging in concentration from 0.13-0.55 mol/liter, and two solutions of alanine dipeptide (0.13 and 0.27 mol/liter). In accord with experiment we find a strong dielectric increment for both solutes, whose molecular origin is shown to be the zwitterionic nature of the solutes. The dynamic properties were analyzed based on a dielectric component analysis into solute, a first hydration shell, and all remaining (bulk) waters. The results of this three component decomposition were interpreted directly, as well as by uniting the solute and hydration shell component to a "suprasolute" component. In both approaches three contributions to the frequency-dependent dielectric properties can be discerned. The quantitatively largest and fastest component arises from bulk water [i.e., water not influenced by the solute(s)]. The interaction between waters surrounding the solute(s) (the hydration shell) and bulk water molecules leads to a relaxation process occurring on an intermediate time scale. The slowest relaxation process originates from the solute(s) and the interaction of the solute(s) with the first hydration shell and bulk water. The primary importance of the hydration shell is the exchange of shell and bulk waters; the self-contribution from bound water molecules is comparatively small. While in the alanine solutions the solute-water cross-terms are more important than the solute self-term, the solute contribution is larger in the dipeptide solutions. In the latter systems a much clearer separation of time scales between water and alanine dipeptide related properties is observed. The similarities and differences of the dielectric properties of the amino acid/peptide solutions studied in this work and of solutions of mono- and disaccharides and of the protein ubiquitin are discussed.     

Bond breaking energy in collision induced dissociation: A study of carbon cage fragmentation in cubane,kepone and mirex

Collision induced dissociation of the carbon cage compounds cubane, kepone and mirex breaks the cage structures. The energy available for bond breaking is thus not less than about 9 eV, and the time between energy acquisition and subsequent unimolecular fragmentation is long enough that the available energy can be concentrated in three bonds to the same carbon atom. Collision induced dissociation mass-analyzed ion kinetic energy spectra of [C₅Cl₆]^+˙ from mirex and from hexachlorocyclopentadiene are virtually identical, and similar for [C₆H₆]^+˙ ions from cubane and benzene.     

Temperature and pressure dependence of alanine dipeptide studied by multibaric-multithermal molecular dynamics simulations

We applied the multibaric-multithermal (MUBATH) molecular dynamics (MD) algorithm to an alanine dipeptide in explicit water. The MUBATH MD simulation covered a wide range of conformational space and sampled the states of PII, C5, alphaR, alphaP, alphaL, and C7(ax). On the other hand, the conventional isobaric-isothermal simulation was trapped in local-minimum free-energy states and sampled only a few of them. We calculated the partial molar enthalpy difference DeltaH and partial molar volume difference DeltaV among these states by the MUBATH simulation using the AMBER parm99 and AMBER parm96 force fields and two sets of initial conditions. We compared these results with those from Raman spectroscopy experiments. The Raman spectroscopy data of DeltaH for the C5 state against the PII state agreed with both MUBATH data with the AMBER parm96 and parm99 force fields. The partial molar enthalpy difference DeltaH for the alphaR state and the partial molar volume difference DeltaV for the C5 state by the Raman spectroscopy agreed with those for the AMBER parm96 force field. On the other hand, DeltaV for the alphaR state by the Raman spectroscopy was consistent with our AMBER-parm99 force-field result. All the experimental results fall between those of simulations using AMBER parm96 and parm99 force fields, suggesting that the ideal force-field parameters lie between those of AMBER parm96 and parm99.     

Resonant vibrational excitation and de-excitation of CO(v) by low energy electrons

Integral cross sections and rate coefficients for vibrational excitation of the excited carbon-monoxide molecule, via the (2)Pi shape resonance in the energy region from 0 to 5 eV have been calculated. Cross sections are calculated by using our recently measured cross sections for the ground level CO excitation and the most recent cross sections for elastic electron scattering, applying the principle of detailed balance. Rate coefficients are calculated for Maxwellian electron energy distribution, with mean electron energies below 5 eV. By using extended Monte Carlo simulations, electron energy distribution functions (EEDF) and rate coefficients are determined in nonequilibrium conditions, in the presence of homogeneous external electric field. Nonequilibrium rates are calculated for typical, moderate values of the electric field over gas number density ratios, E/N, from 1 to 220 Td. Maxwellian and nonequilibrium rate coefficients are compared and the difference is attributed to a specific shape of the electron energy distribution functions under considered conditions.     

Two-dimensional infrared spectroscopy of the alanine dipeptide in aqueous solution

The linear-infrared and two-dimensional infrared (2D IR) spectra in the amide-I' region of the alanine dipeptide and its (13)C isotopomers in aqueous solution (D(2)O) are reported. The two amide-I' IR transitions have been assigned unambiguously by using (13)C isotopic substitution of the carbonyl group; the amide unit at the acetyl end shows a lower transition frequency in the unlabeled species. The ratio of their transition dipole strengths remains almost unchanged upon (13)C substitution, indicating the absence of intensity transfer between two vibrators. The 2D IR cross peaks directly associated with intramode coupling in this case show a small off-diagonal anharmonicity (0.2 +/- 0.2 cm(-1)), leading to a small coupling constant (1.5 +/- 0.5 cm(-1)). The coupling and the 2D IR spectra in two different polarizations (zzzz and zxxz) are as expected for a polyproline-II (PP(II))-like conformation for dialanine, with the backbone dihedral angles (phi, psi) determined to be in the range of (-70 degrees +/- 25 degrees, +120 degrees +/- 25 degrees). Ab initio DFT calculations and normal mode decoupling analysis in the Ramachandran subspace in the neighborhood of PP(II) conformation confirm the presence of a region where the coupling is vanishingly small and support these experimental findings. The relationship between the coupling and off-diagonal anharmonicity is consolidated by examining the distribution of the latter from an ensemble averaged Hamiltonian incorporating uncorrelated diagonal frequency distributions and a small coupling (<2 cm(-1)); it is found that the most probable value for the off-diagonal anharmonicity falls into the range of experimental observations. Further, incorporating DFT results, the simulated linear-IR and 2D IR can reproduce the essential features of the measurements, including the transition frequency positions and apparent peak intensities. All the experimental results and simulations are consistent with a PP(II)-like conformation for the alanine dipeptide in aqueous solution, in which two amide-I' modes are highly localized and whose frequency distributions are uncorrelated.     

The effect of configuration of gas phase protonated ethenedicarboxylates on their low energy collision induced dissociation behaviour

Low energy collision induced dissociation (CID) spectra were measured by a triple stage quadrupole mass spectrometer for the [MH]⁺ ions of diethyl and dimethyl esters of maleic, fumaric, citraconic and mesaconic acids. A very high degree of stereospecificity was observed for the geometrically isomeric diethyl esters. The cis esters give rise to very abundant [MH? EtOH]⁺ and [MH? EtOH? C₂H₄]⁺ ions, while the trans isomers exhibit very abundant [MH? C₂H₄]⁺ and [MH? 2 C₂H₄]⁺ ions. The highly stereospecific processes indicate that the double bond configuration is retained in the protonated species under the conditions of the experiment.     

Transition metal complexes based on 2,4-dihydroxyisophthalic anhydride and its functionalized derivative

Oligomeric complex compounds of Cu(II), Ni(II), Mn(II), Zn(II), and Cd(II) with 2,4-dihydroxyisophthalic aldehyde and its bis-hydrazone on the basis of 4-pyridinecarboxylic acid hydrazide are prepared. Probable structures of the complexes are proposed, based on the results of physico-chemical investigations by the methods of IR and ¹H NMR spectroscopy, magnetochemistry and molecular weight determining by Rast’s method.     

Structure of the “adduct” of caryophyllene with maleic anhydride and its tricyclic derivative

The structure of the N-methylanilide of 3-oxo-9,12,12-trimethyl-2-oxatetracyclo-[7,6,1,0^1,60^10,13]hexadecane-5-carboxylic acid, obtained from the “adduct” of caryophyllene with maleic anhydride, has been investigated by x-ray structural analysis.     

Disinfection of seeds and sprout inhibition of potatoes with low energy electrons

Electrons at acceleration voltages of 170–190 kV reduced microbial count of seeds of adzuki bean, pot herb mustered and black gram to undetectable levels without any detrimental effects on the germination ability. However, electrons at 200 kV or higher affected the growing of black gram sprouts. The energies of electrons at the surface of seed (15 cm distance from the accelerator’s window) at acceleration voltages of 170–190 kV were estimated to be 60–90 kV, based on the stopping powers of titanium and air. Electrons at acceleration voltages of 250 kV or higher inhibited sprouting of potato tubers of various cultivars. The results suggest the efficacy of low energy electron treatment for disinfection of seeds and sprout inhibition of potatoes.     

Dynamics of amide-I modes of the alanine dipeptide in D2O

The equilibrium dynamics of the acetyl and amino amide-I groups of the alanine dipeptide were examined separately using (13)C isotopic selection and 2D IR. The population relaxation times of the amide transitions were measured to be in the range 500 fs by means of heterodyne transient grating methods. The vibrational frequency correlation functions consisted in all cases of a motionally narrowed part, a component near 800 fs, and a constant part representing a distribution of structures that is static on the few ps time scale. The intermediate time scale is attributed to fluctuations in the stretching and bending of hydrogen bonds between the carbonyl and water.     

Cyclofunctionalization of hydroxyolefins induced by arenetellurinic anhydride

Arenetellurinic anhydride reacts with hydroxyolefins in acetic acid at reflux to give cyclic ethers bearing a phenyltelluro group. A mechanism via intramolecular oxytellurinylation with arenetellurinyl acetate is proposed.     

Analysis of the adaptive multilevel splitting method on the isomerization of alanine dipeptide

We apply the adaptive multilevel splitting (AMS) method to the C _eq → C _ax transition of alanine dipeptide in vacuum. Some properties of the algorithm are numerically illustrated, such as the unbiasedness of the probability estimator and the robustness of the method with respect to the reaction coordinate. We also calculate the transition time obtained via the probability estimator, using an appropriate ensemble of initial conditions. Finally, we show how the AMS method can be used to compute an approximation of the committor function. © 2019 Wiley Periodicals, Inc.     

Characterization of ceramides by low energy collisional-activated dissociation tandem mass spectrometry with negative-ion electrospray ionization

Negative-ion electrospray ionization tandem quadrupole mass spectrometry provides a useful method for the structural characterization of ceramides. Fragment ions referring to the identities of the fatty acid substituent and of the long chain base of the molecules are readily available and the structure of ceramides can be easily determined. A unique fragmentation pathway which leads to formation of the fatty acid carboxylate anions (RCO2) was observed. This fragmentation is initiated by cleavage of the C2-C3 bond of the LCB to yield a N-acylaminoethanol anion ([RCONHCH2CH2O]-), followed by rearrangement to a carboxyethylamine ([RCO2CH2CH2NH]-) intermediate, which further dissociates to a RCO2- ion. This pathway is confirmed by the CAD tandem mass spectrum of the synthetic N-acylaminoethanol standard and of the deuterated analogs of ceramides obtained by H-D exchange. The observation of RCO2- ion species permits an unambiguous identification of the fatty acyl moiety of ceramides. Tandem mass spectrometry methods for characterization of structural isomers of ceramides using product-ion scanning and for identification of specific ceramide subclasses in biological mixtures using neutral loss scanning are also demonstrated.