In Quest of the Alanine R3 Radical: Multivariate EPR Spectral Analyses of X-Irradiated Alanine in the Solid State.

The amino acid l-α-alanine is the most commonly used material for solid-state electron paramagnetic resonance (EPR) dosimetry, due to the formation of highly stable radicals upon irradiation, with yields proportional to the radiation dose. Two major alanine radical components designated R1 and R2 have previously been uniquely characterized from EPR and electron-nuclear double resonance (ENDOR) studies as well as from quantum chemical calculations. There is also convincing experimental evidence of a third minor radical component R3, and a tentative radical structure has been suggested, even though no well-defined spectral signature has been observed experimentally. In the present study, temperature dependent EPR spectra of X-ray irradiated polycrystalline alanine were analyzed using five multivariate methods in further attempts to understand the composite nature of the alanine dosimeter EPR spectrum. Principal component analysis (PCA), maximum likelihood common factor analysis (MLCFA), independent component analysis (ICA), self-modeling mixture analysis (SMA), and multivariate curve resolution (MCR) were used to extract pure radical spectra and their fractional contributions from the experimental EPR spectra. All methods yielded spectral estimates resembling the established R1 spectrum. Furthermore, SMA and MCR consistently predicted both the established R2 spectrum and the shape of the R3 spectrum. The predicted shape of the R3 spectrum corresponded well with the proposed tentative spectrum derived from spectrum simulations. Thus, results from two independent multivariate data analysis techniques strongly support the previous evidence that three radicals are indeed present in irradiated alanine samples.

Solved? The reductive radiation chemistry of alanine.

The structural changes throughout the entire reductive radiation-induced pathway of l-α-alanine are solved on an atomistic level with the aid of periodic DFT and nudged elastic band (NEB) simulations. This yields unprecedented information on the conformational changes taking place, including the protonation state of the carboxyl group in the "unstable" and "stable" alanine radicals and the internal transformation converting these two radical variants at temperatures above 220 K. The structures of all stable radicals were verified by calculating EPR properties and comparing those with experimental data. The variation of the energy throughout the full radiochemical process provides crucial insight into the reason why these structural changes and rearrangements occur. Starting from electron capture, the excess electron quickly localizes on the carbon of a carboxyl group, which pyramidalizes and receives a proton from the amino group of a neighboring alanine molecule, forming a first stable radical species (up to 150 K). In the temperature interval 150-220 K, this radical deaminates and deprotonates at the carboxyl group, the detached amino group undergoes inversion and its methyl group sustains an internal rotation. This yields the so-called "unstable alanine radical". Above 220 K, triggered by the attachment of an additional proton on the detached amino group, the radical then undergoes an internal rotation in the reverse direction, giving rise to the "stable alanine radical", which is the final stage in the reductive radiation-induced decay of alanine.

Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations.

As the chemical structures of radiation damaged molecules may differ greatly from their undamaged counterparts, investigation and description of radiation damaged structures is commonly biased by the researcher. Radical formation from ionizing radiation in crystalline α-l-rhamnose monohydrate has been investigated using a new method where the selection of radical structures is unbiased by the researcher. The method is based on using ab initio molecular dynamics (MD) studies to investigate how ionization damage can form, change and move. Diversity in the radical production is gained by using different points on the potential energy surface of the intact crystal as starting points for the ionizations and letting the initial velocities of the nuclei after ionization be generated randomly. 160 ab initio MD runs produced 12 unique radical structures for investigation. Out of these, 7 of the potential products have never previously been discussed, and 3 products are found to match with radicals previously observed by electron magnetic resonance experiments.

Structural specificity of alkoxy radical formation in crystalline carbohydrates.

A DFT study of radiation induced alkoxy radical formation in crystalline α-l-rhamnose has been performed to better understand the processes leading to selective radical formation in carbohydrates upon exposure to ionizing radiation at low temperatures. The apparent specificity of radiation damage to carbohydrates is of great interest for understanding radiation damage processes in the ribose backbone of the DNA molecule. Alkoxy radicals are formed by deprotonation from hydroxyl groups in oxidized sugar molecules. In α-l-rhamnose only one alkoxy radical is observed experimentally even though there are four possible sites for alkoxy radical formation. In the present work, the origin of this apparently specific action of radiation damage is investigated by computationally examining all four possible deprotonation reactions from oxygen in the oxidized molecule. All calculations are performed in a periodic approach and include estimates of the energy barriers for the deprotonation reactions using the Nudged Elastic Band (NEB) method. One of the four possible radical sites is ruled out due to the lack of a suitable proton acceptor. For the other three possible sites, the reaction paths and energy profiles from primary cationic radicals to stable, neutral alkoxy radicals are compared. It is found that deprotonation from one site (corresponding to the experimentally observed radical) differs from the others in that the reaction path is less energy demanding. Hence, it is suggested that the alkoxy radical formation is not necessarily site specific, but that the observed radical is formed in much greater abundance than the others due to the different energetics of the processes and reaction products.

Identification of primary free radicals in trehalose dihydrate single crystals X-irradiated at 10 K.

Primary free radical formation in trehalose dihydrate single crystals X-irradiated at 10 K was investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques. The ENDOR results allowed the unambiguous determination of six proton hyperfine coupling (HFC) tensors. Using the EIE technique, these HF interactions were assigned to three different radicals, labeled R1, R2 and R3. The anisotropy of the EPR and EIE spectra indicated that R1 and R2 are alkyl radicals (i.e. carbon-centered) and R3 is an alkoxy radical (i.e. oxygen-centered). The EPR data also revealed the presence of an additional alkoxy radical species, labeled R4. Molecular modeling using periodic Density Functional Theory (DFT) calculations for simulating experimental data suggests that R1 and R2 are the hydrogen-abstracted alkyl species centered at C5' and C5, respectively, while the alkoxy radicals R3 and R4 have the unpaired electron localized mainly at O2 and O4'. Interestingly, the DFT study on R4 demonstrates that the trapping of a transferred proton can significantly influence the conformation of a deprotonated cation. Comparison of these results with those obtained from sucrose single crystals X-irradiated at 10 K indicates that the carbon situated next to the ring oxygen and connected to the CH(2)OH hydroxymethyl group is a better radical trapping site than other positions.

Determination of the g-, hyperfine coupling- and zero-field splitting tensors in EPR and ENDOR using extended Matlab codes.

The analysis of single crystal electron magnetic resonance (EMR) data has traditionally been performed using software in programming languages that are difficult to update, are not easily available, or are obsolete. By using a modern script-language with tools for the analysis and graphical display of the data, three MatLab® codes were prepared to compute the g, zero-field splitting (zfs) and hyperfine coupling (hfc) tensors from roadmaps obtained by EPR or ENDOR measurements in three crystal planes. Schonland's original method was used to compute the g- and hfc -tensors by a least-squares fit to the experimental data in each plane. The modifications required for the analysis of the zfs of radical pairs with S = 1 were accounted for. A non-linear fit was employed in a second code to obtain the hfc -tensor from EPR measurements, taking the nuclear Zeeman interaction of an I = ½ nucleus into account. A previously developed method to calculate the g- and hfc -tensors by a simultaneous linear fit to all data was used in the third code. The validity of the methods was examined by comparison with results obtained experimentally, and by roadmaps computed by exact diagonalization. The probable errors were estimated using functions for regression analysis available in MatLab. The software will be published at https://doi.org/10.17632/ps24sw95gz.1, Input and output examples presented in this work can also be downloaded from https://old.liu.se/simarc/downloads?l=en.

The energy dependence of lithium formate and alanine EPR dosimeters for medium energy x rays.

PURPOSE: To perform a systematic investigation of the energy dependence of alanine and lilthium formate EPR dosimeters for medium energy x rays. METHODS: Lithium formate and alanine EPR dosimeters were exposed to eight different x-ray beam qualities, with nominal potentials ranging from 50 to 200 kV. Following ionometry based on standards of absorbed dose to water, the dosimeters were given two different doses of approximately 3 and 6 Gy for each radiation quality, with three dosimeters for each dose. A reference series was also irradiated to three different dose levels at a 60Co unit. The dose to water energy response, that is, the dosimeter reading per absorbed dose to water relative to that for 60Co gamma-rays, was estimated for each beam quality. In addition, the energy response was calculated by Monte Carlo simulations and compared to the experimental energy response. RESULTS: The experimental energy response estimates ranged from 0.89 to 0.94 and from 0.68 to 0.90 for lithium formate and alanine, respectively. The uncertainties in the experimental energy response estimates were typically 3%. The relative effectiveness, that is, the ratio of the experimental energy response to that following Monte Carlo simulations was, on average, 0.96 and 0.94 for lithium formate and alanine, respectively. CONCLUSIONS: This work shows that lithium formate dosimeters are less dependent on x-ray energy than alanine. Furthermore, as the relative effectiveness for both lithium formate and alanine were systematically less than unity, the yield of radiation-induced radicals is decreased following x-irradiation compared to irradiation with 60Co y-rays.

On the identity of the radiation-induced stable alanine radical.

Using periodic DFT calculations, it is concluded that the stable radiation-induced alanine radical most probably is the result of reductive deamination and protonation of the detached amino group, yielding an NH(4)(+) ammonium ion and a negatively charged radical.

Tannic Acid Radicals in the Presence of Alkali Metal Salts and Their Impact on the Formation of Silicate-Phenolic Networks.

Polyphenolic molecules have become attractive building blocks for bioinspired materials due to their adhesive characteristics, capacity to complex ions, redox chemistry, and biocompatibility. For the formation of tannic acid (TA) surface modifications based on silicate-phenolic networks, a high ionic strength is required. In this study, we investigated the effects of NaCl, KCl, and LiCl on the formation of TA coatings and compared it to the coating formation of pyrogallol (PG) using a quartz-crystal microbalance. We found that the substitution of NaCl with KCl inhibited the TA coating formation through the high affinity of K+ to phenolic groups resulting in complexation of TA. Assessment of the radical formation of TA by electron paramagnetic resonance spectroscopy showed that LiCl resulted in hydrolysis of TA forming gallic acid radicals. Further, we found evidence for interactions of LiCl with the Siaq crosslinker. In contrast, the coating formation of PG was only little affected by the substitution of NaCl with LiCl or KCl. Our results demonstrate the interaction potential between alkali metal salts and phenolic compounds and highlight their importance in the continuous deposition of silicate-phenolic networks. These findings can be taken as guidance for future biomedical applications of silicate-phenolic networks involving monovalent ions.

Primary oxidation products of 5-methylcytosine: methyl dynamics and environmental influences.

The primary oxidation product in X-irradiated single crystals of 5-methylcytosine hemihydrate and 5-methylcytosine hydrochloride has been studied at 10 K, using electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) spectroscopies. The radical is characterized by large couplings to the methyl protons and appears to be deprotonated at N1 in both crystal systems. In the hydrochloride crystal the methyl group is completely frozen at 10 K, whereas in the hemihydrate crystal it undergoes tunneling rotation. For the hemihydrate crystal, four ENDOR lines associated with transitions within the A and E rotational states were followed in three planes of rotation. Large ENDOR shifts as measured by saturation of the high- and low-field parts of the EPR spectrum indicate that the rotation is rather slow. Sidebands due to mixing of A and E rotational states are expected for slow rotation and were observed in both the EPR and the EIE spectra. The ENDOR shifts and the sideband frequencies indicate a tunneling splitting between 40 and 60 MHz. Estimates of the barrier to rotation in both crystalline systems were calculated using cluster and single-molecule density functional theory methods, and the results are consistent with those obtained by analysis of the experimental results.

Radiation-induced radicals in glucose-1-phosphate. II. DFT analysis of structures and possible formation mechanisms.

Four radiation-induced carbon-centered radicals in dipotassium glucose-1-phosphate dihydrate single crystals are examined with DFT methods, consistently relying on a periodic computational scheme. Starting from a set of plausible radical models, EPR hyperfine coupling tensors are calculated for optimized structures and compared with data obtained from EPR/ENDOR measurements, which are described in part I of this work. In this way, an independent structural identification is made of all the radicals that were observed in the experiments (R1-R4) and tentative reaction schemes are proposed. Also, the first strong evidence for conformational freedom in sugar radicals is established: two species are found to have the same chemical composition but different conformations and consequently different hyperfine coupling tensors. Analysis of the calculated energies for all model compounds suggests that the radiation chemistry of sugars, in general, is kinetically and not necessarily thermodynamically controlled.

Radiation-induced radicals in glucose-1-phosphate. I. Electron paramagnetic resonance and electron nuclear double resonance analysis of in situ X-irradiated single crystals at 77 K.

Electron magnetic resonance analysis of radiation-induced defects in dipotassium glucose-1-phosphate dihydrate single crystals in situ X-irradiated and measured at 77 K shows that at least seven different carbon-centered radical species are trapped. Four of these (R1-R4) can be fully or partly characterized in terms of proton hyperfine coupling tensors. The dominant radical (R2) is identified as a C1-centered species, assumedly formed by a scission of the sugar-phosphate junction and the concerted formation of a carbonyl group at the neighboring C2 carbon. This structure is chemically identical to a radical recently identified in irradiated sucrose single crystals. Radical species R1 and R4 most likely are C3- and C6-centered species, respectively, both formed by a net hydrogen abstraction. R3 is suggested to be chemically similar to but geometrically different from R4. Knowledge of the identity of the sugar radicals present at 77 K provides a first step in elucidating the formation mechanism of the phosphoryl radicals previously detected after X-irradiation at 280 K. In paper II, the chemical identity, precise conformation, and possible formation mechanisms of these radical species are investigated by means of DFT calculations and elementary insight into the radiation chemistry of sugar and sugar derivatives is obtained.

Free radical conformations and conversions in X-irradiated single crystals of L-cysteic acid by electron magnetic resonance and density functional theory studies.

Single crystals of L-cysteic acid monohydrate were X-irradiated and studied at 295 K using EPR, ENDOR, and EIE techniques. Three spectroscopically different radicals were observed. These were a deamination radical reduction product (R1), and two oxidation products formed by hydrogen abstraction (radicals R2, R3). R2 and R3 were shown to exhibit the same chemical structure while exhibiting very different geometrical conformations. Cluster DFT calculations at the 6-31G(d,p) level of theory supported the experimental observations for radicals R1 and R2. It was not possible to simulate the R3 radical in any attempted cluster; hence, for this purpose a single molecule approach was used. The precursor radicals for R1, R2, and R3, identified in the low-temperature work on L-cysteic acid monohydrate by Box and Budzinski, were also investigated using DFT calculations. The experimentally determined EPR parameters for the low-temperature decarboxylated cation could only be reproduced correctly within the cluster when the carboxyl group remained in the proximity of the radical. Only one of the two observed low-temperature carboxyl anions (stable at 4 and 48 K) could be successfully simulated by the DFT calculations. Evidence is presented in support of the conclusions that the carboxyl reduction product already is protonated at 4 K and that the irreversible conversion between the two reduction products is brought forward by an umbrella-type inversion of the carboxyl group.

Proton-coupled hole transfer in X-irradiated doped crystalline cytosine.H2O.

Following exposure to X-irradiation at low temperatures, the main reactions taking place in single crystals of cytosine monohydrate doped with minute amounts of 2-thiocytosine are hole transfer (HT) from the electron-loss centers to the dopant and recombination of oxidation and reduction products, assumedly by electron transfer. A huge deuterium kinetic isotope effect (KIE; >102-103) at 100 K, together with the kinetic curves obtained and density functional theory (DFT) calculations of equilibrium energy changes, indicates that these reactions proceed through a concerted proton-coupled electron/hole transfer where the proton transfer occurs between hydrogen-bonded cytosine molecules. The temperature dependence of these reaction rates between 10 and 150 K in normal and partially deuterated samples was investigated by monitoring the growth and decay of the various radical species over time using electron paramagnetic resonance (EPR) spectroscopy. By assuming a random distribution of the hole donors and acceptors in the crystals, the data are consistent with an exponential distance-dependent rate, giving a distance decay constant (beta) around 1 A-1 for the HT, which indicates that a long-range single-step superexchange mechanism mediates the charge transfer. The reactions undergo a transition from a slow, weakly temperature-dependent rate to an Arrhenius-type rate at 40-50 K, presumably being activated by excitation of low-frequency intermolecular vibrations that couple to the process. Below this transition temperature, the transfer probability might be dominated by temperature-independent nuclear tunneling. A similar beta value in both temperature regions suggests that hopping is not activated.

Combined electron magnetic resonance and density functional theory study of 10 K X-irradiated beta-D-fructose single crystals.

Primary free radical formations in fructose single crystals X-irradiated at 10 K were investigated at the same temperature using X-band Electron Paramagnetic Resonance (EPR), Electron Nuclear Double Resonance (ENDOR) and ENDOR induced EPR (EIE) techniques. ENDOR angular variations in the three principal crystallographic planes and a fourth skewed plane allowed the unambiguous determination of five proton hyperfine coupling tensors. From the EIE studies, these hyperfine interactions were assigned to three different radicals, labeled T1, T1* and T2. For the T1 and T1* radicals, the close similarity in hyperfine coupling tensors suggests that they are due to the same type of radical stabilized in two slightly different geometrical conformations. Periodic density functional theory calculations were used to aid the identification of the structure of the radiation-induced radicals. For the T1/T1* radicals a C3 centered hydroxyalkyl radical model formed by a net H abstraction is proposed. The T2 radical is proposed to be a C5 centered hydroxyalkyl radical, formed by a net hydrogen abstraction. For both radicals, a very good agreement between calculated and experimental hyperfine coupling tensors was obtained.

Potassium sodium (2R,3R)-tartrate tetra-hydrate: the paraelectric phase of Rochelle salt at 105 K.

Rochelle salt, K(+)·Na(+)·C(4)H(4)O(6) (2-)·4H(2)O, is known for its remarkable ferroelectric state between 255 and 297 K. The current investigation, based on data collected at 105 K, provides very accurate structural information for the low-temperature paraelectric form. Unlike the ferroelectric form, there is only one tartrate molecule in the asymmetric unit, and the structure displays no disorder to large anisotropic atomic displacements.

The energy dependence of lithium formate EPR dosimeters for clinical electron beams.

The objective of this study was to investigate the potential of using polycrystalline lithium formate for EPR (electron paramagnetic resonance) dosimetry of clinical electron beams, with the main focus on the dose-to-water energy response. Lithium formate dosimeters were irradiated using (60)Co gamma-rays and 6-20 MeV electrons in a PMMA phantom to doses in the range of 3-9 Gy. A plane-parallel ion chamber was used for water-based absolute dosimetry. In addition, the electron/photon transport was simulated using the EGSnrc Monte Carlo code. From the EPR measurements, the standard deviation of single dosimeter readings was 1.2%. The experimental energy response (the lithium formate dosimeter reading per absorbed dose to water for electrons relative to that for (60)Co gamma rays) was nearly independent of the electron energy and on average 0.99 +/- 0.03. The Monte Carlo calculated energy response was on average 0.5% higher than the experimental energy response, the difference being not significant. Simulations with water and polystyrene as irradiation media indicated that the energy response of lithium formate dosimeters was nearly independent of the phantom materials. In conclusion, lithium formate EPR dosimetry of clinical electron beams provides precise dose measurements with low dependence on the electron energy.

LET effects following neutron irradiation of lithium formate EPR dosimeters.

Lithium formate electron paramagnetic resonance (EPR) dosimeters were irradiated using 60Co gamma-rays or fast neutrons to doses ranging from 5 to 20 Gy and investigated by EPR spectroscopy. Using a polynomial fitting procedure in order to accurately analyze peak-to-peak line widths of first derivative EPR spectra, dosimeters irradiated with neutrons had on average 4.4+/-0.9% broader EPR resonance lines than gamma-irradiated dosimeters. The increase in line width was slightly asymmetrical. Computer simulated first derivative polycrystalline EPR spectra of a *CO2- radical gave very good reconstructions of experimental spectra of irradiated dosimeters. The spectrum simulations could then be used as a tool to investigate the line broadening observed following neutron irradiation. It was shown that an increase in the simulated Lorentzian line width could explain both the observed line broadening and the asymmetrical effect. The ratio of the peak-to-peak amplitude of first derivative EPR spectra obtained at two different microwave powers (20 and 0.5 mW) was 7.8+/-1.2% higher for dosimeters irradiated with neutrons. The dependence of the spectrum amplitude on the microwave power was extensively investigated by fitting observations to an analytical non-linear model incorporating, among others, the spin-lattice (T1) and spin-spin (T2) relaxation times as fitting parameters. Neutron irradiation resulted in a reduction in T(2) in comparison with gamma-irradiation, while a smaller difference in T1 was found. The effects observed indicate increased local radical density following irradiation using high linear energy transfer (LET) neutrons as compared to low LET gamma-irradiation. A fingerprint of the LET may thus be found either by an analysis of the line width or of the dependence of the spectrum amplitude on the microwave power. Lithium formate is therefore a promising material for EPR dosimetry of high LET radiation.

New Evidence for Hydroxyalkyl Radicals and Light- and Thermally Induced Trapped Electron Reactions in Rhamnose.

Radical formation and trapping of radicals in X-irradiated crystals of rhamnose at 6 K were investigated using electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR) and ENDOR-induced EPR (EIE) techniques, complemented with periodic density functional theory (DFT) calculations. The two major radical species at 6 K were the O4-centered alkoxy radical and the intermolecularly trapped electron (IMTE), previously also detected by other authors. The current experimental results provided hyperfine coupling constants for these two species in good agreement with the previous data, thus providing a consistency check that improves their credibility. In addition to the O4-centered alkoxy radical and the IMTE, the C3-centered and C5-centered hydroxyalkyl radicals are the most prominent primary species at 6 K. The C3-centered radical appears in two slightly different conformations at 6 K, designated C and D. The C5-centered radical exhibits a coupling to a methyl group with tunneling rotation at 6 K, and analysis of one of the rotational substates (A) of the spin system yielded an understanding of the structure of this radical. Visible light bleaching of the IMTE at 6 K led to the C3-centered radical C, and thermal annealing above 6 K resulted in a conversion of the C to the D conformation. In addition, thermal annealing releases the IMTE, apparently resulting in the formation of the C2-centered radical. It is possible that the thermal decay of the IMTE also contributes to a small part of the C3-centered radical (D) population at 85 K. There are several other products trapped in rhamnose crystals directly after irradiation at 6 K, among which are resonance lines due to the C2 H-abstraction product. However, these other products are minority species and were not fully characterized in the current work.

Direct radiation effects to the amino acid side chain: EMR and periodic DFT of X-irradiated L-asparagine at 6 K.

Radical formation in single crystals of L-asparagine monohydrate following X-irradiation at 6 K has been investigated at 6 K and at elevated temperatures using various electron magnetic resonance (EMR) techniques such as electron paramagnetic resonance (EPR), electron nuclear double resonance (ENDOR), and ENDOR-induced EPR (EIE) spectroscopy. Molecular structures of the three free radicals stable at 6 K were assessed by detailed analysis of the experimental data and density functional theory (DFT) calculations in a periodic approach. Radical LI is assumed to result from one-electron reduction at the amide functional group in the asparagine side chain followed by protonation at the amide carbonyl oxygen by proton transfer from a neighboring molecule across a hydrogen bond. Radical LII is assigned to a one-electron reduction of the carboxyl group in the amino acid backbone, followed by proton transfer across a hydrogen bond between a carboxylic oxygen and a neighboring asparagine molecule. Radical LIII is suggested to be formed by a net CO2 abstraction from an initial one-electron oxidized amino acid backbone. For the DFT modeling of LIII at 6 K, it was chosen to include the CO2 group stably embedded in the crystalline lattice. The assignments made are discussed in relation to previous work on L-asparagine. The relevance of these results to possible charge transfer processes in protein:DNA complexes is discussed.