Production of Similar Fragments from the Glycine, Alanine, and Methionine Amino Acid Molecules Under Low-Energy Electron Impact L.G

Vol. 128 (2015) ACTA PHYSICA POLONICA A No. 1 Production of Similar Fragments from the Glycine, Alanine, and Methionine Amino Acid Molecules under Low-Energy Electron Impact L.G. Romanovaa, J. Tamulieneb, V.S. Vuksticha, T.A. Snegurskayac, A.V. Pappa and A.V. Snegurskya;* aInstitute of Electron Physics, Ukrainian National Academy of Sciences, 21 Universitetska str., 88017 Uzhgorod, Ukraine bVilnius University, Institute of Theoretical Physics and Astronomy, 12 A. Go²tauto str., 01108, Vilnius, Lithuania cUzhgorod National University, Department of Physics, 46 Pidhirna str., 88000 Uzhgorod, Ukraine (Received March 30, 2015; in nal form April 24, 2015) Production of the ionic fragments of the same chemical composition due to a low-energy electron impact on the glycine, alanine, and methionine amino acid molecules has been studied both experimentally and theoretically. The mass-spectrometric technique was applied to detect the above ionic fragments within the 1720 a.m.u. mass range with the ±0:25 a.m.u. resolution, while the density functional theory based theoretical approach allowed the relevant species to be identied and the mechanisms of their production to be claried. A special attention has been paid to analysis of the geometrical structures of the molecules under study as well to nding the appearance potentials of their fragments with the accuracy of ±0:1 eV. DOI: 10.12693/APhysPolA.128.15 PACS: 34.50.Lf, 34.90.+q 1. Introduction electrons are of a primary interest from the viewpoint of tracing the consequences of malignant transformations in Amino acids being biologically relevant organic sub- living cells under the inuence of ionizing radiation and stances involved in the live organisms include gener- also provide useful radiation therapy eect on tumors in ally the amine (NH2) and the carboxylic acid (COOH) human beings [5]. functional groups. Their generic formula looks like The studies of the basic mechanisms of the amino acid H2NCHRCOOH (R being an organic substituent, the so- molecule structural changes caused by low-energy elec- called side-chain [1]). Amino acids also serve as build- tron impact are far from being complete despite their ing blocks of proteins and intermediates in metabolism. undoubted signicance. According to the National Insti- The chemical properties of these molecules determine the tute of Standards (NIST) database [6], the available rele- biological activity of the proteins. In addition, proteins vant data are a bit disputable, while those on the parent contain the necessary information needed to determine molecule ionization thresholds and fragment appearance the structure and the stability of the live organism. This energies are extremely scarce. is an important eld of scientic research, and today it is still one of the most important tasks of modern biological and chemical science [2]. Regarding the possible degradation of amino acids under the external impact, it is a well-known fact that ionizing radiation causes in live tissue the irreversible eects at the genetic level [3]. The mechanism of such degradation does not include the direct action of high-energy Fig. 1. Structural formulae of the molecules under study. ionizing radiation only, because the inuence of the processes related to the low-energy secondary electrons ap- pears to be signicant [4]. Secondary products of ion- In our previous papers (see, e.g. [79]), we have stud- izing radiation in living tissues are capable of damaging ied both experimentally and theoretically fragmenta- the structural units of nucleic acids and proteins leading, tion of the glycine, alanine, and methionine molecules in particular, to dissociative ionization with both posi- by low-energy (below 150 eV) electrons and noticed tive and negative-ion production. Thus, the low-energy yield of some fragments of the above three molecules having the same chemical composition not comparing their production mechanisms. Therefore, the aim of the present paper was to study the mechanisms of their *corresponding author; e-mail: [email protected] production and compare these mechanisms with each other. The amino acid glycine, alanine, and methionine (15) 16 L.G. Romanova et al. molecules (see schematic view in Fig. 1) have dier- electron gun provided an electron current Ie = 30−50 µA ent substituents R: H, CH3 and C2H4SCH3. One within a wide (0150 eV) energy range with the energy of them (methionine) involves not only the main con- spread < 0.3 eV (full width at the half-maximum of the stituents such as carbon and hydrogen, but also the sul- beam energy distribution) [10]. The experimental ap- fur atom. The above molecules present good example pearance potentials were determined by means of a t- for predicting the inuence of substituents on the pro- ting technique based on the least-squares method approx- cess of fragmentation of the core part (H2NCHCOOH) imation using the MarquardtLevenberg algorithm de- of the amino acid. To our knowledge, no similar data are scribed in detail in our previous studies (see. e.g. [710]). present in literature. The accuracy of the appearance potential determination was not worse than ±0:1 eV. The energy dependences 2. Experimental of ionization and dissociative ionization cross-sections to be measured in the incident electron energy range from In our study, we used a conventional magnetic mass- the threshold up to 150 eV. The ions produced in the spectrometer MI-1201 (see, e.g. [10]) as the mass- ion source and extracted by the electric eld entered a separator unit enabling the fragments of electron magnetic ion separator and were detected by means of molecule interaction to be identied. Figure 2 shows the an electrometer. schematic diagram of the experimental setup. The ex- The data acquisition and processing system was con- perimental apparatus developed and applied is based, as trolled by a PC. Special measures were taken to stabi- already mentioned above, on the magnetic mass spectro- lize the mass analyzer transmission, thus, making the meter capable of operating within the 1720 a.m.u. mass of the fragment under study to be reliably xed. mass range. High sensitivity (≈10−16 A) and resolu- An electron energy scale was calibrated with respect to tion (±0:25 a.m.u.) of the mass analyzer enabled the known ionization thresholds for argon atom and nitrogen fragments of the target molecule to be reliably separated molecule (see below) with the accuracy not worse than and detected even at low levels of ion currents reaching ±0:1 eV. The molecular beam M (see Fig. 2) was directed the ion detector (see Fig. 2). to the ionization chamber normally to the electron beam (the beams intersect in the gure plane). The experimental procedure was as follows. First both electron and molecular beam sources were put into operation and after reaching the optimal conditions of beam generation a mass spectrum of the molecules under study was measured. The masses of the fragments produced were then xed and the energy dependences of the relevant ion yields were measured. Elec- tron energy was varied with an energy step of 0.10.3 eV enabling the threshold areas of the dissociative ionization functions for all the fragments under study to be measured. In this case the problem of the incident electron energy scale calibration becomes very signicant. To calibrate the above energy scale we have measured the threshold areas of the ionization functions for the two Fig. 2. Schematic diagram of the experimental setup test gases Ar and N2. The experimental ionization and supporting electrical circuits. thresholds were determined by means of a tting technique is based on a least-squares method approximation The primary molecular beam ( in Fig. 2) was formed M using the MarquardtLevenberg algorithm suggested by by means of an eusion source with a resistive oven Maerk's group (see, e.g., our earlier paper [11]). providing target molecule concentrations not less than 1010 molecule/cm3. The operating temperature of the 3. Theoretical molecular beam source was varied up to 200 ◦C being controlled by a thermocouple allowing the temperature The structures of the molecules and their fragments dependences of the fragment yields to be determined. were studied using the generalized gradient approxima- As it has been shown in our previous papers [79], the tion for the exchange-correlation potential in the den- linear behaviour of the above temperature dependences sity functional theory (DFT) as it is described by the (plotted in the semi-logarithmic scale) within the temper- Becke three-parameter hybrid functional, applying the ature range of 50120 ◦C indicated unambiguously that non-local correlation provided by Lee, Yang, and Parr. production of the above fragments due to the thermal The DFT method is commonly referred to as B3LYP [12], degradation of the parent molecule was negligible. i.e. as a representative standard one described in more The temperature and pressure conditions of the molec- detail below. The cc-pVTZ basis set was used as well [13]. ular beam formation excluded the possibility of molecular The structures of the molecule isomers/conformers and cluster formation. A specially designed three-electrode their fragments under study were optimized globally Production of Similar Fragments from the Glycine, Alanine. 17 without any symmetry constraint. The bond order and the bond length of the molecule conformers were investi- gated to nd the weaker bonds possible to be destructed. Additionally, the vibration spectrum was evaluated to predict the possible elongation of bonds and the change of the angle aiming to analyze the most probable fragments produced due to electron impact. On the other hand, the results on the vibration modes were analyzed to be sure that the equilibrium point of the molecular systems was found. In order to model the fragmentation processes, the possible fragment anions, cations and fragments with a zero charge were evaluated.

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