International Journal of Molecular Sciences

Article Valine Radiolysis by H+, He+,N+, and S15+ MeV Ions

Cíntia A. P. da Costa 1, Gabriel S. Vignoli Muniz 2, Philippe Boduch 3, Hermann Rothard 3,* and Enio F. da Silveira 1 1 Physics Department, Pontifícia Universidade Católica do Rio de Janeiro, Rua Marquês de São Vicente 225, Rio de Janeiro 22451-900, Brazil; [email protected] (C.A.P.d.C.); enio@vdg.fis.puc-rio.br (E.F.d.S.) 2 Physics Institute, Universidade de São Paulo, Rua do Matão, Sao Paulo 1371–05508-090, Brazil; [email protected] 3 Centre de Recherche sur les Ions; les Matériaux et la Photonique. Normandie Université, ENSICAEN, UNICAEN, CEA, CNRS, CIMAP, 14000 Caen, France; [email protected] * Correspondence: [email protected]



Received: 27 January 2020; Accepted: 3 March 2020; Published: 10 March 2020


Abstract: Radiolysis of biomolecules by fast ions has interest in medical applications and astrobiology. The radiolysis of solid D-valine (0.2–2 µm thick) was performed at room temperature by 1.5 MeV H+, He+,N+, and 230 MeV S15+ ion beams. The samples were prepared by spraying/dropping valine-water-ethanol solution on ZnSe substrate. Radiolysis was monitored by infrared spectroscopy 1 (FTIR) through the evolution of the intensity of the valine infrared 2900, 1329, 1271, 948, and 716 cm− bands as a function of projectile fluence. At the end of sample irradiation, residues (tholins) presenting a brownish color are observed. The dependence of the apparent (sputtering + radiolysis) destruction n cross section, σd, on the beam stopping power in valine is found to follow the power law σd = aSe , with n close to 1. Thus, σd is approximately proportional to the absorbed dose. Destruction rates due to the main galactic cosmic ray species are calculated, yielding a million year half-life for solid valine in space. Data obtained in this work aim a better understanding on the radioresistance of complex organic molecules and formation of radioproducts.

Keywords: amino acid; valine; MeV ion irradiation; radiolysis; infrared absorption spectroscopy; destruction cross section; stopping power dependence

1. Introduction Amino acids are building-blocks of proteins, essential in the dynamics of all living organisms. Moreover, they also play an important role in cell signalization, and in the innate immune system. These stable organic molecules are constituted by carbon, hydrogen, oxygen, and nitrogen. Sulfur is also present in some species. The amino acids molecular structure is constructed by one central carbon atom, called α-carbon, linked to four groups: the carboxyl radical, –COOH, the amino radical, –NH2, a hydrogen atom, –H, and a side chain, –R. Two important chemical properties are caused by the interaction between the carboxyl and amino radicals. The first one is related to the dipole moment of the amino acid, which is different in solid and gas phases. Indeed, in solid phase, the mentioned structure is preserved (particularly at high temperatures). For both polar and apolar side chains, the molecule has a significant dipole moment and is called zwitterion. In gas phase, the dipole moment is weak and the molecule is called “neutral”. In condensed phase, the proton of the –COOH group migrates to the amino one forming the zwitterion. The second chemical property concerns to the peptide bond which occurs when the hydroxyl radical of the COOH group is induced to react with the NH2 radical attached to another amino acid molecule, delivering a H2O molecule and synthesizing a peptide through a bond between the CO and NH radicals. Endoergic reactions may occur several times with nearby amino acids producing larger peptides [1].

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The discovery of amino acids in meteorites [2,3], in comets [4], and possibly in the interstellar medium [5–8] inscribed them into the portfolio of astrophysical materials. Nevertheless, finding the origin of amino acids (as well as any prebiotic material, in general) is a central question in Astrobiology. The asteroids and comets that heavily bombarded the Earth circa 4 billion years ago [9,10] probably transported prebiotics. How relevant were these molecular species for triggering life on Earth? Furthermore, given the omnipresent radiation in outer space and around the giant planets [11], once formed in astrophysical environment, can amino acids survive the interplanetary journey? How could they survive the harsh conditions of the early Earth? Ionizing radiation processes are largely used in industry, in the production and/or to increase the lifetime of biological materials, e.g., ionizing radiation induces genetic modifications in plant seeds. Therefore, knowledge about the radioresistance of complex organic molecules and the subsequent formation of radioproducts may also have importance in medical science and in the industry, as for instance in food production [12], pharmaceutics [13], and particularly in cancer treatment, shielding astronauts in space, and treating victims of irradiation by nuclear materials. Except for glycine, amino acids can exist in two optical isomeric forms, known as L and D; only L-amino acids form proteins; D-amino acids can be found in antibiotics [14] and in some bacteria cell walls [1,15]. Studies on amino acid radiolysis have already been performed. In particular, for glycine, the simplest amino acid, Gerakines et al. studied thermal effects on its dissociation by energetic protons [16]. Pilling et al. irradiated glycine with 1 MeV H+ in order to study the stability of different polymorph configurations [17]. Pilling et al. [18], Maté et al. [19], and Souza-Corrêa et al. [20] studied its dissociation by keV electrons. UV radiolysis was performed by Peeters et al. [21] and by Ferreira-Rodrigues et al. [22]. For valine, electronic sputtering by MeV heavy ions was discussed by Salehpour et al. [23], Becker et al. [24], and Sundqvist et al. [25]. The current work aims at investigating some aspects of amino acid radiolysis. Specifically, the goal is to determine amino acid destruction cross sections by light and heavy energetic projectiles over a large projectile energy range. This huge experimental task is strongly reduced if amino acid radiolysis proceeds similarly as for condensed gases: their destruction cross sections depend only on the electronic stopping power (Se) of the ion-target system and not on specific quantities such as kinetic energy, mass, and atomic number of the projectile, as well as molecular and crystalline structures of the target [26–30]. Based on these premises, we have selected the amino acid D-valine (Val) to be irradiated with MeV H+, He+,N+ and 230 MeV S15+ ions, the latter for obtaining a much 1 3 higher Se. This compound is hydrophilic, has molar mass 117.15 g mol , density 1.32 g cm , and · − · − chirality properties [31]. Although observed in meteorites [1,2], d-valine does not participate in the known biological processes; l-valine, the chiral form of the d-valine, is the isotopomer existent in living organisms, also occurs in astrophysical environment and – except for the optical activity—has the same characteristics. Fourier transform infrared absorption spectroscopy (FTIR) at room temperature was used to monitor the valine radiolysis. Data obtained in this work are a contribution for a better understanding on the radioresistance of complex organic molecules, as well as on the formation of radioproducts; our findings may have consequences to Medical Science [32] and to Astrobiology [33]. The work also shows that, although the sample degradation could be adequately monitored by any vibrational band, the absorbance evolutions as a function of fluence exhibit variations for different bands. This finding may be particularly relevant for astrophysical observations. Irradiations with low electronic stopping power projectiles were performed using 1.5 MeV H+, He+, and N+ ion beams provided by the Van de Graaff Laboratory at the Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio). Irradiations with 230 MeV S15+ projectiles were carried out at GANIL (Grand Accélérateur National d’Ions Lourds), Caen, France. Int. J. Mol. Sci. 2020, 21, 1893 3 of 21 Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 3 of 21

2. Results When a solid is bombarded by ion beams, at least three relevant material processes occur: (a) structuralWhen a solidrearrangement is bombarded of molecules, by ion beams,(b) induced at least chemical three reactions relevant (rearrangement material processes of atoms) occur: and (a) structural(c) sputtering rearrangement (emission of of atoms molecules, and molecules). (b) induced All chemical the three reactions processes (rearrangement can be monitored of atoms) by infrared and (c) sputteringspectroscopy. (emission Successive of atoms acquisition and molecules). of valine All infrared the three spectra processes during can bombardment be monitored bywith infrared different spectroscopy.ion beamsSuccessive show that acquisitionthey are very ofvaline similar: infrared for this spectra reason, during only bombardmentthe FTIR spectra with obtained different with ion the beamsH+ showand S that15+ beams they are are very displayed. similar: forIn fact, this reason,the major only difference the FTIR spectraobserved obtained in the withexperiments the H+ and is the S15+absorbancebeams are displayed.decrease rate: In fact,for the the same major beam difference flux, the observed higher in the the stopping experiments power is theof the absorbance projectile in decreasethe sample, rate: for the the greater same beamis the flux,disappearance the higher rate the stopping of valine powermolecul ofes the from projectile the sample. in the sample,The cryst thealline greaterrearrangement is the disappearance (crystallization, rate of valineamorphization, molecules pore from collapsing/compaction) the sample. The crystalline is a process rearrangement observable (crystallization,by FTIR in the amorphization, very beginning pore of irradiation collapsing and/compaction) does not involve is a process the dissociation observable or by removal FTIR in of the valine verymolecules. beginning of irradiation and does not involve the dissociation or removal of valine molecules.

2.1.2.1. Results Results from from the Vanthe Van de Graa de Graaffff Laboratory: Laboratory: H+ ,H He+, +Heand+ and N+ NIon+ Ion Beams Beams

+ 2.1.1.2.1.1. 1.5 MeV1.5 MeV H HBeam+ Beam Irradiation Irradiation + FigureFigure1 shows 1 shows the FTIRthe FTIR spectrum spectrum evolution evolution for three for three fluences fluences of the of 1.5 the MeV 1.5 MeV H beam: H+ beam: (i) zero (i) zero 15 2 fluencefluence or virginor virgin sample sample (black (black line, line, with with the the highest highest absorbances); absorbances); (ii) (ii) F =F 1.4= 1.4 ×10 1015ions ions cm cm−−2,, an 15 × 2 an intermediate fluence (red line, spectrum in the middle); and (iii) F = 9.5 10 ions15 cm , the−2 highest intermediate fluence (red line, spectrum in the middle); and (iii) F = ×9.5 × 10 ions− cm , the highest fluencefluence (blue (blue line, line, the lowestthe lowest absorbances). absorbances). For For the the highest highest fluence, fluence, allvaline all valine molecules molecules of the of samplethe sample havehave been been degraded: degraded: the the still still existing existing bands bands are attributedare attributed to daughter to daughter molecules molecules (products). (products). The The 1 onlyonly exception exception is the is the double double peak peak at ~2350at ~2350 cm cm− −which1 which is is due due to to atmospheric atmospheric CO CO22 existingexisting outside the thechamber but but inside inside the the sight sight of of the the spectrometer spectrometer IR IR beam beam (its (its absorbance absorbance varies varies with with time, time, not not with withfluence). fluence).

FigureFigure 1. Evolution 1. Evolution of the of valinethe valine infrared infrared spectrum spectrum as the as projectilethe projectile fluence fluence increases. increases. The The upper upper spectrumspectrum corresponds corresponds to the to the virgin virgin sample; sample; the the two two others others were were acquired acquired at at fluences fluences 1.4 1.4 ×10 101515and and 9.5 15 2 1 × 9.5 x 101015 ionsions cm cm−2, respectively., respectively. The The feature feature at at~2350 ~2350 cm cm−1 is dueis due to atmospheric to atmospheric CO2 COoutsideoutside the chamber the × − − 2 chamberbut inside but inside the FTIR the FTIRspectrometer; spectrometer; its absorbance its absorbance varies varies up and up down and down with withtime. time.

In FigureIn Figure2, the 2, spectrumthe spectrum evolution evolution with with fluence fluence is presented is presented for some for some selected selected bands. bands. Data Data are are 1 thethe same same as Figureas Figure1 but, 1 but, in thisin this case, case, spectra spectra for for nine nine fluences fluences are are shown shown for: for: (a) (a) 3400–2400 3400–2400 cm cm−1 and 1 1 and(b) (b) 1650–1300 1650–1300 cm cm−−1 ranges,ranges, and and (c) (c) 1271, 1271, (d) (d) 948, 948, and and (e) (e) 716 716 cm cm−1− bands.bands. At At first first sight, sight, all all bands bands seem seemto todecrease decrease proportionally proportionally with with fluence; fluence; but, but, after after detailed detailed inspection, didifferentfferent behaviorsbehaviors cancan be be remarkedremarked speciallyspecially atat thethe beginningbeginning (due(due toto compaction)compaction) andand atat thethe end end (due (due to to the the appearance appearance of of productproduct bands, bands, Figure Figure2 f)2f) of of irradiation. irradiation. At At the the end end of of irradiation irradiation the the samples samples (residues) (residues) present present a a brownishbrownish color. color. In In reference reference to to the the pioneer pioneer work work of Saganof Sagan and and Khare Khare [34 ],[34], these these radioproducts radioproducts (daughter(daughter molecules) molecules) are referredare referred to as to tholins. as tholins.

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(a) (b)

(c) (d)

(e) (f)

Figure 2. Decrease of valine absorbance as the 1.5 MeV H+ beam fluence increases for five selected 1 IR regions (a–e). Note in particular that absorbances of 1329, 1271 and 948 cm− bands disappear 1 completely, while those of 2955, 1507 and 716 cm− bands do not. The fluence legend for Figure2a is the same for all figures. Panel (f) is a zoom of (a) and (b), for the highest fluence.

1 The fact that the 1544 and 1457 cm− features increase along the irradiation (dominating the IR spectrum at the end) indicates that they are not valine bands; instead, they belong to valine daughter 1 1 molecules. Furthermore, the 3300–2400 and the 1500–1300 cm− spectral regions, as well as the 716 cm− band, present a slower decrease rate and do not disappear at the final fluence; they should be formed by two overlapping components, one due to precursor molecule bands, the other due to product bands. Table1 presents the wavenumber of the main observed valine bands. Here, the third column displays the wavenumber of products after H+ irradiation.

1

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Table 1. Evolution of valine bands as the 1.5 MeV H+ and 230 MeV S15+ projectile fluences increase. TableBand 1.identificationEvolution of and valine their bands band as thewavenumbers 1.5 MeV H +forand valine 230 MeV before S15 +irradiation;projectile fluences wavenumber increase. of Bandproducts identification after H+ and and S their15+ irradiation. band wavenumbers (a) split band for valineat lowbefore temperature: irradiation; da Costa wavenumber and da Silveira of products [33]; after(b) Kumar H+ and [35]; S15 (c)+ irradiation.Façanha Filho (a) et split al. (2008) band [36]. at low Attributions temperature: are tentative. da Costa (*) and strong da Silveira absorbance; [33]; (b)(**) Kumar low absorbance. [35]; (c) Façanha Filho et al. (2008) [36]. Attributions are tentative. (*) strong absorbance; (**) low absorbance. Band Collapses into Vibration Mode Band (cm−1) (PossibleBand Collapses Species) into Vibration Mode Band (cm 1) + 15+ − H (Possible Species)S + NH3 asy str 3150, 3050 H - + - S15+ CH3+ asy str 2960, 2940 2955, 2918 (C2H6 *) 2961, 2933 (C2H6 *) + NH3 asy+ str 3150, 3050 - - +CH3 asy str 2880, 2850 2868, 2849 (C2H6 *) 2874 (C2H6 *) CH3 asy str 2960, 2940 2955, 2918 (C2H6 *) 2961, 2933 (C2H6 *) + N-H…O 2690, 2630, 2580 - - CH3 asy str 2880, 2850 2868, 2849 (C2H6 *) 2874 (C2H6 *) b a CHN-H3 bend... +O NH2 rocking ~2109 2690, (2153 2630, 2580+ 2013) - -- - − c b a CH3 bend +CONH2 2 stretchrocking ~2109 (21531640+ 2013) - -- - + c CO2−NHstretch3 asy def. 1600,1640 1555 - - 1595 (Amine) - + NH3 asy def.- 1600, 1555- 1544, -1507 1516 1595 (Nitro) (Amine) COO-+ sy str 1520, 1430, - 1390 1544, 1457 1507 1469 (C 15162H6), (Nitro) 1394 + COO sy str- 1520, 1430,- 1390 1457- 1355 1469 (Nitro) (C2H6), 1394 - - - 1355 (Nitro) COO+/CO 1340, 1320 1339 1329 COO+/CO 1340, 1320 1339 1329 +CH3+ def. 1271, 948 - 1271 CH3 def. 1271, 948 - 1271 2 6 ** ** 885885 (C (CH2H) 6 ) b b CO2 BendCO2 Bend 775775 - - C-HC-H out bend out bend 716 716 716 716

+ TheThe integratedintegrated absorbanceabsorbance evolutionevolution withwith HH+ fluencefluence is presentedpresented inin FigureFigure3 3 for for several several valine valine bands.bands. TheThe absorbanceabsorbance isis normalizednormalized toto 11 atat FF == 0, in order to compare compaction eeffectsffects onon didifferentfferent bands.bands. TwoTwo groupsgroups cancan bebe recognized:recognized: thethe firstfirst one,one, thethe “tholin”“tholin” groupgroup [[34],34], isis constitutedconstituted byby thethe 29002900 (integrated from 3300 to 2400 cm−11) and 716 cm−1 bands which present a slow decrease with fluence; (integrated from 3300 to 2400 cm− ) and 716 cm− bands which present a slow decrease with fluence; another, the “pure valine group”, is constituted by the 1329, 1271 and 948 cm1−1 bands. The tholin another, the “pure valine group”, is constituted by the 1329, 1271 and 948 cm− bands. The tholin groupgroup includesincludes bandsbands ofof daughterdaughter molecules,molecules, whichwhich absorbabsorb IRIR wavelengthswavelengths closeclose toto the valine bands. Consequently,Consequently, the the bands bands assigned assigned to to this this group group do do not not vanish vanish completely, completely, in contrastin contrast to theto the behavior behavior of pureof pure valine valine group. group. The The absorbance absorbance decrease decrease at low at low fluences fluences is emphasized is emphasized in Figure in Figure3b. At 3b. the At very the beginningvery beginning of irradiation, of irradiation, absorbances absorbances of the of pure the valinepure valine group group exhibit exhibit an exponential an exponential behavior, behavior, while while absorbances of the 7161 cm−1 band and in particular of the 29001 cm−1 band are approximately absorbances of the 716 cm− band and in particular of the 2900 cm− band are approximately constant withconstant increasing with fluence.increasing Our fluence. interpretation Our interpretation is that these two is bandsthat these are sensitive two bands to compaction, are sensitive while to thecompaction, other three while are not. the This other means three that are valine not. porousThis means samples that are valine more transparentporous samples than compacted are more transparent than compacted1 ones in the 3300–2400 cm−1 IR region. ones in the 3300–2400 cm− IR region.

(a) (b)

FigureFigure 3.3. DependenceDependence onon fluencefluence ofof thethe integratedintegrated absorbanceabsorbance forfor severalseveral bandsbands observedobserved inin thethe H H++ beambeam irradiation:(irradiation:(aa)) upup to to the the fluence fluence 25 25 ×10 101414 ionsions cmcm-22; ;((bb)) up up to to the the fluence fluence 1 1 × 10101313 ionsions cm cm-2. Data2. × − × −

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Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 6 of 21 Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 6 of 21 Data are normalized to 1 at F = 0. The smaller slopes at high fluences exhibited by the 2900* (3300–2400, 1 shown in Figure2a) and 716* (Figure2e) cm − bands are attributed to the rising of product’s bands are normalized to 1 at F = 0. The smaller slopes at high fluences exhibited by the 2900* (3300–2400, at very close wavenumbers. (*) means overlapping−1 with product’s band. Colored lines are guides shownshown inin FigureFigure 2a)2a) andand 716*716* (Figure(Figure 2e)2e) cmcm−1 bandsbands areare attributedattributed toto thethe risingrising ofof product’sproduct’s bandsbands atat for eyes. very close wavenumbers. (*) means overlapping with product’s band. Colored lines are guides for eyes. + + 2.1.2. 1.5 MeV He + and N+ Beam Irradiations 2.1.2. 1.5 MeV He+ andand NN+ BeamBeam IrradiationsIrradiations + + Absorbance evolution obtained for the 1.5 MeV He and+ N +irradiations are presented in Figures4 Absorbance evolution obtained for the 1.5 MeV He+ and N+ irradiations are presented in Figures Absorbance evolution obtained for the 1.5 MeV He and N irradiations+ are presented in Figures and5, respectively. Data for the same five bands analyzed for the H + irradiation are again depicted. 4 and 5, respectively. Data for the same five bands analyzed for the H+ irradiation are again depicted. 4 and 5, respectively.+ Data for the same five bands analyzed for the H irradiation are again depicted. For the He + beam data, the integrated absorbances are normalized at F = 0, to facilitate a comparison For the He+ beam data, the integrated absorbances are normalized at F = 0, to facilitate a comparison For the He beam data, the integrated absorbances are normalized at F = 0, to1 facilitate a comparison of their slopes. Compaction and product formation (for the 2900 and 716 cm− bands)−1 are observed for of their slopes. Compaction and product formation (for the 2900 and 716 cm−1 bands)bands) areare observedobserved low and high fluences, respectively. forfor lowlow andand highhigh fluences,fluences, respectively.respectively.

((a)) ((b))

FigureFigure 4.4. (((aa))) Dependence DependenceDependence on onon fluence fluencefluence of ofof the thethe integrated integratedintegrated absorbance absorbanceabsorbance for forfor several severalseveral bands bandsbands observed observedobserved in the inin He thethe+ + beamHe+ beambeam irradiation. irradiation.irradiation. Data areDataData normalized areare normalizednormalized to 1 at Ftoto= 110. atat The FF == asterisk 0.0. TheThe indicatesasteriskasterisk indicatesindicates overlapping overlappingoverlapping with product’s withwith bands.product’s (b) bands. Zoom into(b)) ZoomZoom the low intointo fluence thethe lowlow region. fluencefluence Colored region.region. lines ColoredColored are guides lineslines areare for guidesguides eyes. forfor eyes.eyes.

((a)) ((b)) Figure 5. (a) Dependence on fluence of the integrated absorbance for several bands observed in the N+ Figure 5. ((a)) DependenceDependence onon fluencefluence ofof thethe integratedintegrated absorbanceabsorbance forfor severalseveral bandsbands observedobserved inin thethe beam+ irradiation. (b) Zoom into the low fluence region. Data are normalized to 1 at F = 0. Colored N+ beambeam irradiation.irradiation. ((b)) ZoomZoom intointo thethe lowlow fluencefluence region.region. DataData areare normalizednormalized toto 11 atat FF == 0.0. ColoredColored lines are guides for eyes. lineslines areare guidesguides forfor eyes.eyes. + Concerning the N + beam data, Figure5a shows the absorbance evolution of five valine bands, Concerning the N+ beambeam data,data, FigureFigure 5a5a showsshows thethe absorbanceabsorbance evolutionevolution ofof fivefive valinevaline bands,bands, normalizednormalized atat FF == 0. In agreement with observations for irradiations with other ion beams, thethe slopesslopes normalized at F = 0. In agreement1 with observations for irradiations with other ion beams, the slopes of the 2900 and 716 cm−−1 bands are lower, especially at high fluences, due to the contribution of of the 2900 and 716 cm−1 bandsbands areare lower,lower, especiallyespecially atat highhigh fluences,fluences, duedue toto thethe contributioncontribution ofof product absorbances. product absorbances. + + Compaction effects are clearly seen for H+ (Figure(Figure 3)3) atat thethe beginningbeginning ofof irradiation;irradiation; forfor HeHe+ + (Figure(Figure 4)4) andand NN+ beamsbeams (Figure(Figure 5a5a andand itsits zoomzoom inin FigureFigure 5b),5b), thisthis effecteffect isis particularlyparticularly noticeablenoticeable forfor −1 thethe 2900*2900* cmcm−1 band.band.

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Compaction effects are clearly seen for H+ (Figure3) at the beginning of irradiation; for He + (FigureInt. J. Mol.4) Sci. and 2020 N, +21beams, x FOR PEER (Figure REVIEW5a and its zoom in Figure5b), this e ffect is particularly noticeable 7 of for 21 1 the 2900* cm− band. 2.2. Results from GANIL (CIMAP Laboratory) 2.2. Results from GANIL (CIMAP Laboratory) The overall IR spectrum evolution of valine bombardment by 230 MeV S15+ projectiles is 15+ presentedThe overall in Figure IR spectrum 6a. As irradiation evolution proceeds, of valine bombardment absorbance decreases by 230 MeV equally S projectilesfor all bands. is presented This is a inhint Figure that 6theira. As correspondent irradiation proceeds, A-values absorbance do not depend decreases strongly equally on fluence. for all bands. In other This words, is a hint a given that theirband correspondentdoes not disappear A-values faster do than not another, depend stronglyso that the on deduced fluence. Invaline other destruction words, a given cross band section does is notabout disappear the same faster regardless than another, of the band so that considered. the deduced This valine is true destruction for both narrow cross section and broad is about bands. the same The regardlesslatter include of thelarge band and considered. complex structures, This is true such for as both the narrow3200–2400 and cm broad−1 and bands. 1700–1200 The lattercm−1 regions: include 1 1 largethe whole and complexfeature belongs structures, to valine such and as the collapses 3200–2400 into cmproduct− and bands 1700–1200 as fluence cm− increasesregions: (Figure the whole 6b, featureacquired belongs for the to valinehighest and flu collapsesence). As into an product illustration, bands Figure as fluence 7 compares increases (Figurethe decrease6b, acquired of three for theintegrated highest absorbances fluence). As with an illustration, fluence: the Figure (I) region7 compares corresponding the decrease to the of well-defined three integrated 2109 absorbances cm−1 band, 1 withthe (II) fluence: region theof the (I) corresponding region corresponding baseline tostructure, the well-defined and the (III) 2109 region cm− nextband, to (II) the with (II) regionthe same of thewavenumber corresponding width baseline (Figure structure,7a). At high and fluences, the (III) all region of the next three to (II)integrated with the absorbances same wavenumber decrease widthexponentially (Figure 7anda). Atproportionally high fluences, to alleach of other the three (Figure integrated 7b). At absorbanceslow fluences, decrease compaction exponentially effects are andnot visible proportionally for absorbance to each of other (I) region (Figure but7b). are At clearly low fluences, seen for compaction(II) and (III) eregions.ffects are The not sample visible was for absorbanceirradiated up of to (I) 0.92 region × 10 but13 ions are cm clearly−2, corresponding seen for (II) to and a dose (III) regions.of 23 eV Themolecule sample−1. The was 1329, irradiated 1271 and up 13 2 1 1 to948 0.92 cm−1 bands10 ions have cm disappeared− , corresponding at the end to a of dose irradiation, of 23 eV evidence molecule that− . The valine 1329, was 1271 totally and degraded. 948 cm− × bandsOn the have other disappeared hand, as presented at the end in ofFigure irradiation, 6b for the evidence 3200–2200 that valineand 1700–1200 was totally cm degraded.−1 regions, several On the 1 otherbands hand, are still as presentedseen at the in end Figure of irradiation,6b for the 3200–2200 reason why and they 1700–1200 are attributed cm − regions, to daughter several molecules. bands are stillIn Table seen at1, thethe endfourth of irradiation, column lists reason the main why theyproduct’s are attributed bands observed to daughter at molecules.the highest Influence Table1 ,with the fourthpossible column attributions. lists the main product’s bands observed at the highest fluence with possible attributions.

(a) (b)

Figure 6.6. ((aa)) Valine Valine IR spectra as aa functionfunction ofof projectileprojectile fluence.fluence. The The first first spectrum at the toptop corresponds to the non-irradiated sample and the 4th one was acquired at the end of the irradiation. −1 ((b)) ZoomZoom ofof thethe 3200–27003200–2700 andand 1700–12001700–1200 cmcm− regionsregions for for the the highest highest fluence fluence measurement. measurement.

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(a)(a) (b)(b)

−−11 1 FigureFigure 7.7. ((aa)) Valine Valine IR IR spectrumspectrum aroundaround around thethe the 21092109 2109 cmcm cm− band.band.band. TheThe The threethree three regionsregions regions selectedselected selected correspondcorrespond correspond to:to: −−11 1 to:(I)(I) the (I)the the 21092109 2109 cmcm cm band,−band,band, (II)(II) (II) backgroundbackground background belowbelow below thisthis this band,band, band, andand and (III)(III) (III) backgroundbackground background nextnext next toto it. it. ( (bb))) TheTheThe integratedintegrated absorbanceabsorbance evolutionevolutionevolution withwithwith projectileprojectileprojectile fluencefluencefluence forforfor thesethesethese three threethree spectrum spectrumspectrum regions. regions.regions.

1 FigureFigure8 88 depicts depictsdepicts the thethe same samesame data datadata as asas in inin Figure FigureFigure6 6but6 butbut zooming zoomingzooming into intointo the thethe 3200–2400 3200–24003200–2400 and andand 1340–1315 1340–13151340–1315 cm cmcm−−−11 regions;regions; intermediateintermediate fluences fluencesfluences are areare now nownow included.included.included. NoteNote that:that: (a) (a) nono significantsignificant significant peakpeak shiftsshifts areare observed;observed; 12 2 (b)(b) peakspeakspeaks becomebecomebecome moderately moderatelymoderately broader broaderbroader at atat high highhigh fluences fluencesfluences (the (the(the thicker thickerthicker line lineline for forfor fluence fluencefluence ~2 ~2~2 ××10 10101212ions ionsions cm cmcm−−−22 1 × maymay bebe takentaken asas aa reference);reference); (c)(c)(c) some somesome peaks peakspeaks (e.g., (e.g.,(e.g., at atat 1329 13291329 cm cmcm−−−11)) disappear disappear at at high high fluences fluencesfluences but but others others 1 (e.g.,(e.g., atatat 296129612961 cmcmcm−−−11)) do do not, not, which which provides provides evidenceevidence thatthat thesethese areareare residues.residues.residues. TheThe peakpeak broadeningbroadeningbroadening causescauses thethe disappearancedisappearance ofof minimaminima betweenbetween somesome bands.bands.bands.

1 −1 FigureFigure 8.8.8. Absorbance AbsorbanceAbsorbance decrease decreasedecrease for forfor the the 3200–2400the 3200–24003200–2400 and 1340–1315andand 1340–13151340–1315 cm− regions, cmcm−1 regions,regions, as a function asas aa offunctionfunction projectile ofof fluence.projectileprojectile The fluence.fluence. first spectrum TheThe firstfirst (top) spectrumspectrum and the (top)(top) one and markedand thethe byoneone the markedmarked thicker byby line thethe correspond thickerthicker lineline to thecorrespondcorrespond non-irradiated toto thethe 12 1 samplenon-irradiatednon-irradiated and to a samplesample fluence andand of 2 toto a10a fluencefluenceions cmofof 2−2 ××, respectively.10101212 ionsions cmcm−− Note11,, respectively.respectively. the disappearance NoteNote thethe of disappearancedisappearance minima at high ofof × 2 fluences.minimaminima atat The highhigh legend fluences.fluences. at the TheThe right legendlegend side at expressesat thethe rightright fluence sideside expressesexpresses in ions cm fluencefluence− . inin ionsions cmcm−−22..

TheThe dependencesdependencesdependences of ofof the thethe integrated integratedintegrated absorbances absorbancesabsorbances on onon fluence fluencefluence for for thefor the 3300–2400,the 3300–2400,3300–2400, 1335–1304, 1335–1304,1335–1304, 1279–1261, 1279–1279– 1 957–937,1261,1261, 957–937,957–937, and 726–705 andand 726–705726–705 cm− bands cmcm−−11 bandsbands are depicted areare depicteddepicted in Figure inin 9 FigureFigure for (a) 99 high forfor fluences(a)(a) highhigh andfluencesfluences (b) low andand fluences. (b)(b) lowlow Clearly,fluences.fluences. the Clearly,Clearly, slopes thethe are slopesslopes close but areare not closeclose identical. butbut notnot Fouridentical.identical. possible FourFour reasons possiblepossible are: reasonsreasons (i) compaction, are:are: (i)(i) compaction,compaction, (ii) growth (ii)(ii) of products,growthgrowth ofof (iii) products,products, uncertainty (iii)(iii) uncertaintyuncertainty of the baseline ofof thethe selected baselinebaseline for selected theselected absorbance forfor thethe calculation,absorbanceabsorbance andcalculation,calculation, (iv) dependence andand (iv)(iv) ofdependencedependence A-values on ofof fluence.A-valuesA-values In onon detail: fluence.fluence. InIn detail:detail: 1.1. CompactionCompaction eeffectseffectsffects have havehave been beenbeen observed observedobserved to occurtoto occuroccur at low atat lowlow fluences fluencesfluences and diandandfferently differentlydifferently for distinct forfor distinctdistinct bands. bands.bands.However, However,However, since this sincesince is a thisthis property isis aa propertyproperty of the material, ofof thethe material,material, the different thethe differentdifferent absorbance absorbanceabsorbance evolutions evolutionsevolutions are expected areare expectedexpectedto be similar toto bebe for similarsimilar any ionforfor any beam.any ionion Indeed, beam.beam. Indeed,Indeed, comparing comparingcomparing Figure 3FigureFigureb with 3b3b Figure withwith 9FigureFigureb, it can 9b,9b, be itit cancan seen bebe 1 seenseenthat—for that—forthat—for both both irradiations—theboth irradiations—theirradiations—the 948 cm 948948− cmcmband−−11 bandband absorbance absorbanceabsorbance is the isis one thethe that oneone decreases thatthat decreasesdecreases the most, thethe 1 most,whilemost, while thosewhile ofthosethose the 2900ofof thethe and 29002900 1329 andand cm 13291329− bands cmcm−−11 decrease bandsbands decreasedecrease much less. muchmuch The less.less. compaction TheThe compactioncompaction effect modifies effecteffect modifiesmodifiesabsorbances absorbancesabsorbances up to 20%. upup toto 20%.20%. 2.2. ProductProduct bands:bands: ForFor lowlow fluences,fluences, thethe concentrationconcentration ofof daughterdaughter moleculesmolecules isis stillstill tootoo lowlow forfor disturbingdisturbing thethe chemicalchemical environmentenvironment inin suchsuch aa wayway toto modifymodify precursor’sprecursor’s absorbancesabsorbances (this(this effecteffect isis neverthelessnevertheless expectedexpected toto bebe seenseen atat highhigh fluences).fluences). Furthermore,Furthermore, thethe absorbanceabsorbance slopesslopes

Int. J. Mol. Sci. 2020, 21, 1893 9 of 21

2. Product bands: For low fluences, the concentration of daughter molecules is still too low for disturbing the chemical environment in such a way to modify precursor’s absorbances (this effect Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 9 of 21 is nevertheless expected to be seen at high fluences). Furthermore, the absorbance slopes do not seem to be correlated with product formation. Figures8 and6b show that the 1271, 948, and do not seem to be correlated with product formation. Figures 8 and 6b show that the 1271, 948, 716 cm 1 bands are due only to valine and, consequently, their absorbances decrease to zero at and 716− cm−1 bands are due only to valine and, consequently, their absorbances decrease to zero the end of irradiation; the 3300–2400 and 1700–1300 cm 1 (large) regions contain contributions at the end of irradiation; the 3300–2400 and 1700–1300 cm− −1 (large) regions contain contributions of daughter molecules and their absorbances decrease more slower. The 716 cm 1 band is well of daughter molecules and their absorbances decrease more slower. The 716 cm− −1 band is well seen in the non-irradiated valine spectrum, but contrarily to what happens with H+ irradiation, seen in the non-irradiated valine spectrum, but contrarily to what happens with H+ irradiation, this band is not observed at the last fluence (Figure6a). This may be explained by the fact this band is not observed at the last fluence (Figure 6a). This may be explained by the fact that that thickness of the sample irradiated by the S15+ beam was half of that irradiated by the H+ thickness of the sample irradiated by the S15+ beam was half of that irradiated by the H+ beam, beam, preventing small (valine or product) peaks to be observed in the highest fluence spectrum. preventing small (valine or product) peaks to be observed in the highest fluence spectrum. The The large background in the 1700–1200 cm 1 region is probably due to amide compounds. large background in the 1700–1200 cm−1 −region is probably due to amide compounds. Consistently, Figure9a shows that the 2900 and 716 cm 1 bands have a lower slope at high Consistently, Figure 9a shows that the 2900 and 716 cm−−1 bands have a lower slope at high fluences, indicating overlapping with product’s bands. fluences, indicating overlapping with product’s bands. 3.3. BaselineBaseline selection:selection: FigureFigures7a,b 7a,b show show that that the the baseline baseline is is not not critical, critical, since since the the baseline baseline and and peak peak evolutionsevolutions are are similar. similar. However, However, once once baseline baseline is generated is generated by very by very large large vibrational vibrational bands, bands, these maythese have may distinct have distinct sensitivities sensitivities to compaction. to compaction. 4.4. ChemicalChemical environmentenvironment changes:changes: Irradiation modifiesmodifies thethe crystallinecrystalline structurestructure (compaction,(compaction, amorphizationamorphization and and crystallization).crystallization). Therefore,Therefore, a a moderatemoderate dependence dependence of of A-value A-value on on constituent constituent concentrationsconcentrations isis expected.expected. AnAn overviewoverview ofof thethe A-valueA-value variation,variation, beforebefore andand afterafter compaction,compaction, isis presentedpresented inin TableTable2 2for for the the four four di differentfferent ion ion beams. beams. Inspection of the data presented in Table2 reveals that: Inspection of the data presented in Table 2 reveals that: 1. For non-irradiated samples, the dispersion of the relative A-values are about 20%. This is probably 1. For non-irradiated samples, the dispersion of the relative A-values are about 20%. This is due to non-homogeneous samples. Porosities may be different. No particular correlation between probably due to non-homogeneous samples. Porosities may be different. No particular the relative A-values with sample thickness is observed. correlation between the relative A-values with sample thickness is observed. 2. For non-irradiated samples, the relative A-value variations are band-dependent. For the H+ 2. For non-irradiated samples, the relative A-value variations are band-dependent. For the H+ beam, the relative A-values for the 2900 and 716 cm 1 bands have increased by a factor ~2 from beam, the relative A-values for the 2900 and 716 cm−−1 bands have increased by a factor ~2 from F = 0 to F = Fref; these two bands are compaction sensitive (Figure3b); for the other bands, the F = 0 to F = Fref; these two bands are compaction sensitive (Figure 3b); for the other bands, the relative A-values are close. relative A-values are close. 3. Relative A-value variations are lower for the N+ and S15+ beams. A possible explanation is that 3. Relative A-value variations are lower for the N+ and S15+ beams. A possible explanation is that these beams have larger stopping power than the two others. these beams have larger stopping power than the two others.

(a) (b)

FigureFigure 9.9. ((aa)) IntegratedIntegrated absorbanceabsorbance decreasedecrease ofof fivefive valinevaline bandsbands asas a a function function of of 230 230 MeV MeV S 15S+15+ projectileprojectile fluence. fluence. Data Data have have been been normalized normalized to unity to forunity the virginfor the sample. virgin Thesample. dashed The line dashed represents line degradationrepresents degradation with the average with crossthe average section .( sectionb) Zoom <σ of>. the (b) same Zoom data of forthe thesame low data fluence for the region. low (*)fluence means region. overlapping (*) means with overlapping product’s band. with product’s band.

Int.Int. J. Mol. Sci. 2020, 21, x 1893 FOR PEER REVIEW 10 ofof 2121

Table 2. Relative A-values (integrated absorbance ratios), before and during irradiation. Ratios refer Tableto the 2.948Relative cm−1 band, A-values taken (integrated as reference. absorbance F = 0 means ratios), non before irradiated and duringsample irradiation. and Fref is the Ratios fluence refer for to 1 thewhich 948 the cm absorbance− band, taken ratios as were reference. measured F = 0 (4th means line). non Sample irradiated thickness sample values and are Fref alsois the shown. fluence for which the absorbance ratios were measured (4th line). Sample thickness values are also shown. A-Value/A-Value (Fref) Ion Beam: + A-Value+ /A-Value (F+ ) 15+ Ion Beam: H 1.5 MeV He 1.5 MeV N ref1.5 MeV S 230 MeV Sample thickness:H + 1.5 2.4 MeV μm He+ 1.50.96 MeV μm N+ 1.50.23 MeV μm S15+ 2300.58 MeV μm Band (cm−1) (interval) Sample FrefThickness (ions cm-2): 2.4 5.8µm × 1014 0.961.1µm × 1013 0.234.39µm × 1012 0.583.2µ m× 1011 Band (cm 1) 0 273 282 235 246 2900* (3300–2400)− F (ions cm 2) 5.8 1014 1.1 1013 4.39 1012 3.2 1011 (interval) ref Fref− × 768 × 602 × 270 × 303 00 2733.94 2823.07 2359.51 24610.8 13292900* (1335–1301) (3300–2400) Fref Fref 7685.23 6026.34 27010.5 30313.8 00 3.940.876 3.071.16 9.510.981 10.80.984 12711329 (1279–1261) (1335–1301) Fref Fref 5.230.955 6.341.70 10.50.997 13.81.22 0 0.876 1.16 0.981 0.984 1271 (1279–1261) reference 1 1 1 1 948 (957–937) Fref 0.955 1.70 0.997 1.22 referencereference 11 1 1 1 1 1 1 948 (957–937) reference0 12.80 12.70 12.35 1 3.39 716* (726–705) 0 2.80 2.70 2.35 3.39 716* (726–705) Fref 5.05 3.31 2.54 3.85 Fref 5.05 3.31 2.54 3.85 This analysis confirms that a procedure to separate compaction effects from radiolysis/sputtering degradation is to analyze absorbance at different fluences. At the beginning of This analysis confirms that a procedure to separate compaction effects from radiolysis/sputtering irradiation, effects due to all three processes are observable; after a certain fluence, which depends degradation is to analyze absorbance at different fluences. At the beginning of irradiation, effects due on the beam stopping power, the compaction process is over. Annealing would be another procedure to all three processes are observable; after a certain fluence, which depends on the beam stopping to promote compaction and inducing crystallization. power, the compaction process is over. Annealing would be another procedure to promote compaction and inducing crystallization. 2.3. Cross Section Measurements

2.3. CrossFigure Section 10 illustrates Measurements the concepts presented in Section 4.1 for the S15+ and He+ ion beam −1 irradiations,Figure 10 using illustrates absorbances the concepts of the presented 775 cm in Section band. 4.1The for measured the S15+ and apparent He+ ion beamdestruction irradiations, cross sections are quite distinct, σdap(S)/1 σdap(He) = 8.5, while the compaction ones are close to each other, using absorbances of the 775 cm− band. The measured apparent destruction cross sections are quite σc(S)/σc(He)ap = 0.60.ap The relative porosities of the two samples used for irradiation with the S15+ and distinct, σd (S)/σd (He) = 8.5, while the compaction ones are close to each other, σc(S)/σc(He) = 0.60. + TheHe relativeion beams porosities are ζ = of0.32 the and two ζ samples = 0.12, respectively. used for irradiation Note that, with for the both S15+ irradiations,and He+ ion the beams sample are −1 ζporosity= 0.32 and hasζ =the0.12, effect respectively. to decrease Note the that, absorbances for both irradiations, at wavenumbers the sample around porosity 775 has thecm e.ff ectOnce to compaction starts to remove pores at the beginning of irradiation,1 the absorbance increases even if decrease the absorbances at wavenumbers around 775 cm− . Once compaction starts to remove pores + atthe the real beginning column ofdensity irradiation, decreases the absorbance due to radiolysis increases and even sputtering. if the real For column low fluence density He decreases beam, duethe tocompaction radiolysis effect and sputtering. dominates Forover low those fluence of the He other+ beam, processes, the compaction so that S(F)/S effectp remains dominates greater over than those 1 up to F ~ 2/σc = 2.4 × 1012 ions cm−2. For much higher fluences, the S(F) evolution is dominated12 by the2 of the other processes, so that S(F)/Sp remains greater than 1 up to F ~ 2/σc = 2.4 10 ions cm . × − Forradiolysis much higherand sputtering. fluences, the S(F) evolution is dominated by the radiolysis and sputtering.

1 Figure 10.10. IntegratedIntegrated absorbance absorbance decrease decrease for for the the 775 775 cm −cmband−1 band as aas function a function of fluence of fluence for the for 1.5 the MeV 1.5 HeMeV+ and He+ theand 230 the MeV 230 MeV S15+ beams.S15+ beams. Fittings Fittings are performedare performed with with Equations Equations (7) and (7) and (8) (Section (8) (section 4.2). 4.2).

Table3 3o offersffers an overview overview of of the the measured measured apparent apparent destruction destruction cross cross sections sections for forthe theall the all theion 1 ionbeams, beams, based based on five on five selected selected bands; bands; as illustration, as illustration, one one extra extra band band (782–763 (782–763 cm cm−1) −was) was analyzed analyzed for the He+ and S15+ ion beams to extract σc. The conclusion, already anticipated by the results exhibited

Int. J. Mol. Sci. 2020, 21, 1893 11 of 21

+ 15+ for the He and S ion beams to extract σc. The conclusion, already anticipated by the results exhibited in Figures3–5, is that cross sections vary according the selected band. These variations should not be attributed to statistical fluctuations since distinct irradiations yield similar discrepancies. For describing this systematic variation supported by experimental data, the parameter ∆σj, defined in Equation (9) (Section 4.2), is introduced.

Table 3. Band interval used for the integrated absorbance calculation. Apparent destruction cross sections obtained from individual fittings for 1.5 MeV, H+, He+ and N+, and 230 MeV S15+ ion 15+ ap irradiations. For S , ∆σj is the discrepancy between the mean value and each individual σd . (*) Overlapping with product’s band.

1 Ion Beam Band (cm− ) 1.5 MeV 230 MeV H+ He+ N+ S15+ Band Band ap ∆σj = (σd )mean Interval Maximum ap 14 2 σ ap σd (10− cm ) ( d )j Observations − 14 2 (10− cm ) 3300–2400 2900* 14 3.3 7.2 29 4.7 no compaction, tholins at the end 1335–1304 1329 16 3.8 7.6 30 3.7 no compaction 1279–1261 1271 33 4.9 11 39 5.3 disappears at the end − 957–937 948 27 7.8 13 37 3.3 − 14 2 σc(S) = 50 10 cm σc(He) = 782–763 775 - 4.0 - 34 -0.3 × − 82 10 14 cm2 × − no compaction, tholins peaks too 726–705 716 * 42 7.2 15 33 0.7 small Mean σ ap ∆σ 26 16 5.4 2.1 11 4 33.7 4 0 12% rms error value d,j ± j ± ± ± ±

The 230 MeV S15+ beam data were analyzed in the same way. In order to evaluate the influence of ap 15+ the chemical environment on absorbance for each vibration mode, σd was determined for the S irradiation, based on data plotted in Figure9a. Results are presented in Table3. The mean value is ap 14 2 σd = (33.7 4) 10− cm . Data presented in Figure9a are evidence that absorbance evolutions ± × ap of bands are not equal to each other but similar, so that the σd extracted from them are distinct. Futhermore, since compaction and product formation are not responsible for such discrepancies, the conclusion is that A-values of band j should depend on constituent concentrations. For the S15+ irradiation, ∆σj was determined by fitting data with Equation (9) and the obtained values are also shown in Table3. According to this model, ∆σj should be a characteristic of the band and, therefore, the evolution pattern of the bands should be the same for all ion beams. A comparison of Figure9a with Figure3a, Figure4, and Figure5a shows that this is indeed the case.

2.4. Summary of the Experimental Results The methodology used to obtain the results of Figure 10 and Table3 (see Section 4.2) was also applied to the other measurements. The corresponding cross sections and relevant experimental characteristics of the ion beams interacting with valine are summarized in Table4. Average values of the initial column density, N0, and of the thickness, Tk, are obtained from analysis of 1 18 1 18 the 716 cm− (Aν = 3.37 10− cm/molec) and the 948 cm− (Aν = 1.04 10− cm/molec) bands; ap × × σd is determined by the average behavior of several bands. Int. J. Mol. Sci. 2020, 21, 1893 12 of 21

Table 4. Relevant characteristics of the four irradiations: beam energy, electronic and nuclear stopping 1 powers for valine, initial absorbances for the 716 and 948 cm− bands, initial column density, initial sample thickness, maximum beam penetration (range) and measured apparent destruction cross section.

Ion Beam H+ He+ N+ S15+ Energy (MeV) 1.5 1.5 1.5 230 1 Se (keV µm− ) 26.7 252 998 1690 1 Sn (keV µm− ) 0.0187 0.256 7.84 1.03 1 1 Sp 716 cm− (cm− ) 1.82 0.903 0.20 0.688 1 1 Sp 948 cm− (cm− ) 0.173 0.345 0.0849 0.151 Valine sample N (1017 0 8.12 6.56 1.61 4.00 molec/cm2) Tk (µm) 2.4 0.96 0.23 0.58 Range (µm) 35 5.8 2.4 97 σ ap (10 14 cm2) 26 16 5.4 2.1 11 4 34 4 d − ± ± ± ±

3. Discussion As fluence increases, three evident characteristics can be seen in the spectra presented in Figures1 and2: (i) the overall spectrum shape remains approximately the same, (ii) the spectral resolution deteriorates, and (iii) there is an exponential decrease of absorbance. In general spectrum shapes are preserved during irradiation, evidence that the absorbance decrease on fluence is quite uniform over the analyzed spectrum range. Comparing the spectrum of the virgin sample with the one obtained at F = 1.4 1015 ions/cm2 for H+ ions, small differences can be × recognized: in the irradiated sample spectrum, peaks are larger and peak/baseline ratio is lower. The 1 15 2 shoulder at ~3200 cm− visible in the virgin sample spectrum disappears at F = 1.4 10 ions/cm . 1 × The same occurs for the 2109 cm− band, which is clearly seen in the former but is well reduced in the 1 latter. Features visible around 2300 cm− are due to CO2 contamination outside the chamber, but inside the spectrometer. Figures3–5 and9, drawn in a semi-log plot, show that the trend of the integrated absorbance decrease is exponential. Discrepancies from this function are due to compaction (at low doses) and overlapping with daughter molecule bands (mainly at high fluences). With different ion beams, for already compacted samples and for pure precursor bands, slopes for distinct bands are systematically different from each other. Since this fact happens for precursor bands that do not overlap with product ones, it strongly suggests that A-values are not constant during irradiation. We propose that A-values have a weak exponential dependence on fluence, which has to be taken into account due to the exponential decrease of the precursor concentration and, consequently, due to the exponential increase of the concentration of products. Literature data on amino acid radiolysis by MeV ions are poor. Two similar works on glycine bombarded by MeV H+ are available: Gerakines et al., 2012 and Pilling et al., 2013 [16,17]. In the former, for glycine at 140 K irradiated by 0.8 MeV H+, destruction cross section was determined to be 0.12 10 14 cm2; it is expected that at 300 K this value be slightly higher. In the latter, for glycine at × − 300 K irradiated by 1.0 MeV H+, the cross sections 0.1 to 0.5 10 14 cm2 were determined for β-Gly × − and 2 to 3 10 14 cm2 for α-Gly, respectively; cross sections for α-Gly are higher, but they may be × − affected by compaction, a process better understood nowadays. These results are in good agreement with the values 0.14 to 0.42 10 14 cm2 obtained for valine in the current work for 1.5 MeV H+. × − 3.1. Dependence of Cross Sections on the Electronic Stopping Power The dissociation of a molecule in a highly excited electronic state is very likely and therefore the dependence of its destruction cross section on the electronic stopping power Se is expected. Figure 11 depicts the evolution of Se with the projectile energy for the four beams used. A pertinent question is whether this dependence is linear or not, revealing if dose is the relevant quantity in degradation Int. J. Mol. Sci. 2020, 21, 1893 13 of 21 Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 13 of 21

Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 13 of 21 by radiolysis. This analysisanalysis maymay bebe performed performed dividing dividing absorbance absorbance values values by by Se Sande and comparing comparing the the normalizednormalized integrated integrated absorbance absorbance evolution evolution with with fluence fluence for thefor the diff erentdifferent ion ion beams. beams. radiolysis. This analysis may be performed dividing absorbance values by Se and comparing the normalized integrated absorbance evolution with fluence for the different ion beams.

Figure 11. Dependence of electronic stopping power on projectile (H, He, N and S) energy. Dash lines Figure 11. Dependence of electronic stopping power on projectile (H, He, N and S) energy. Dash lines indicate the two ion beam energies used in the current work. indicate the two ion beam energies used in the current work. Figure 11. Dependence of electronic stopping power on projectile (H, He,−1 N and S) energy. Dash lines Figure 12a shows how the integrated absorbance of the 948 cm 1 band varies with fluence for Figureindicate 12 thea showstwo ion howbeam the energies integrated used in absorbance the current work. of the 948 cm− band varies with fluence for each irradiation;Figure 12a all shows data are how divided the integrated by the initial absorbance integrated of theabsorbance, 948 cm−1 Sband0, which varies means with that fluence they for each irradiation; all data are divided by the initial integrated absorbance, S0, which means that they areeach normalized irradiation; to unityall data for are the divided virgin bysample. the initial The integratedexponential absorbance, decrease isS0 ,evident which meansfor the that four they are normalized to unity for the virgin sample. The exponential decrease is evident for the four measurements.are normalized It isto alsounity clear for thethat virgin the higher sample. the The stopping exponential power decrease the steeper is evident the absorbance for the four measurements. It is also clear that the higher the stopping power the steeper the absorbance decrease. decrease.measurements. In order toIt iscompensate also clear that this the effect, higher absorbance the stopping is plotted power as the a functionsteeper the of absorbanceabsorbed dose, decrease. D, In order to compensate this effect, absorbance is plotted as a function of absorbed dose, D, defined as definedIn order as theto compensate projectile energy, this effect, deposited absorbance in a given is plotted volume as a of function the sample, of absorbed divided dose, by the D, massdefined in as the projectile energy, deposited in a given volume of the sample, divided by the mass in that volume: thatthe volume: projectile D energy,= Se F/U deposited, where U inis amass given density. volume Figure of the sample,12b presents divided the by same the massdata inexhibited that volume: in D = Se F/ρ, where ρ is mass density. Figure 12b presents the same data exhibited in Figure 12a but FigureD = S12ae F/ butU, where now Uas is a massfunction density. of D. Figure The span12b presentsin the evolution the same duedata to exhibited the different in Figure beams 12a is but now as a function of D. The span in the evolution due to the different beams is strongly reduced: stronglynow as reduced: a function except of D. for The the spanHe beam, in the data evolution fluctuate due around to the thedifferent dashed beams line, iscorresponding strongly reduced: to except for the He beam, data fluctuate around the dashed line, corresponding to the average function theexcept average for function the He beam, S/S0 = dataexp( −σfluctuatedap F) = aroundexp(−D/D themean dashed), where line, D meancorresponding = Se/(U σdap) to is thethe averagemean dose function to S/S = exp( σ ap F) = exp( D/D ), where D = S /(ρ σ ap) is the mean dose to destroy valine. 0 d mean mean+ e apd −14 2 19 destroyS/S0 = valine.exp(− −σ Fordap F) instance, = exp(−− D/Dfor meanthe ),1.5 where MeV D Nmean beam, = Se/( U< σσddap>=) is (11 the r mean4) 10 dose cm to, D destroymean = 6.9 valine. × 10 For For instance, for the 1.5 MeV N+ beam, <σ ap>= (11 4) 10 14 cm2,D = 6.9 1019 keV/g = 7 d − mean keV/ginstance, = 1.1 × for 10 the Gy. 1.5 MeV N+ beam, <σdap>= (11 r 4) 10±−14 cm2, Dmean = 6.9 × 1019 keV/g× = 1.1 × 107 Gy. 1.1 107 Gy. ×

(a) (b)

Figure 12. (a) Evolution(a) of the 948 cm−1 band integrated absorbance on( bfluence) for H, He, N and S ion beams. In semi-log plot, angular coefficients1 represent cross sections. Integrated absorbances have FigureFigure 12.12. ((a)) EvolutionEvolution ofof thethe 948948 cmcm−−1 bandband integrated integrated absorbance on fluencefluence for H,H, He,He, NN andand SS ionion been normalized to 1 at F = 0. (b) Same data, but plotted as a function of the absorbed dose. beams.beams. In semi-logsemi-log plot,plot, angularangular coecoefficientsfficients representrepresent crosscross sections.sections. IntegratedIntegrated absorbancesabsorbances havehave beenbeen normalizednormalized toto 11 atat FF == 0. ( b) Same data, but plotted as a function of the absorbed dose. As discussed before, radiolysis and sputtering are supposed to have the same dependence on fluenceAsAs discusseddiscussed and cannot before,before, be (easily) radiolysisradiolysis determined andand sputteringsputtering individually: areare supposedsupposed what is toto experimentally havehave thethe samesame determined dependencedependence by onon this fluencefluencemethodology andand cannotcannot is thebebe (easily)(easily)sum of determinedthedetermined two effects, individually:individually: namely the whatwhat apparent isis experimentallyexperimentally destruction cross determineddetermined section bybyof thisvaline.this ap ap methodologymethodologyThis quantity, isis the the σ sum dsum, ofis of thedisplayed the two two eff effects,ects, in namelyFigure namely the13. the apparentThe apparent current destruction destructionmeasurements cross cross section indicate section of valine. ofthat valine. Thisσd is approximately proportional to the electronic stopping power: This quantity, σdap, is displayed in Figure 13. The current measurements indicate that σdap is

approximately proportional to the electronicσd apstopping = a (Se)n power: (1)

σdap = a (Se)n (1)

Int. J. Mol. Sci. 2020, 21, 1893 14 of 21

ap ap quantity, σd , is displayed in Figure 13. The current measurements indicate that σd is approximately proportional to the electronic stopping power:

ap n Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW σd = a (Se) 14 of(1) 21

−20 20 2.9362.936 0.936 0.936 ap ap 2 wherewhere the best fitting fitting yields a a == 1.81.8 ×1010 cmcm /keV/keV and andn = 0.936;n = 0.936; σd andσ Seand are expressed Se are expressed in cm × − d inand cm keV/2 andμm, keV respectively./µm, respectively. This result This is result equivalent is equivalent to the statement to the statement that the that destruction the destruction cross section cross sectionand the and sputtering the sputtering yield of yield valine of valineare approximately are approximately proportional proportional to the to deposited the deposited dose dose in the in thematerial. material.

Figure 13. Dependence of the apparent destruction cross section on electronic stoppingstopping power.power. Dash apap ap ap 2 lineline corresponds to to σσdd proportionalproportional to toSe. SFore. Forthe thefitting fitting parameters, parameters, σd andσd Sande are Sexpressede are expressed in cm inand cm keV/2 andμm, keV respectively./µm, respectively. 90 MeV 90 127 MeVI projectile127I projectile data were data obtained were obtained with secondary with secondary ion mass ion massspectrometry. spectrometry.

In thethe datadata shownshown inin FigureFigure 1313,, oneone extraextra crosscross sectionsection isis thethe valuevalue correspondingcorresponding toto valinevaline irradiatedirradiated byby 9090 MeVMeV 127127I14+14+ projectiles.projectiles. This This result result was was obtained obtained by by Salehpour Salehpour et et al. al. [23], [23], using low fluxflux projectilesprojectiles (1000(1000 ionsions/s)/s) andand acquiringacquiring thethe time-of-flighttime-of-flight spectrumspectrum ofof thethe desorbeddesorbed ions.ions. TheThe electronic stoppingstopping powerpower of of 90 90 MeV MeV127 127II++1414 ionsions in in valine valine is 1.04 × 1044 keV/keV/μµm. Besides Besides the desorption × valine products,products, thethe ejectedejected ionsions werewere composedcomposed by by protonatedprotonated valine valine (M (M+ +H) H)++ and by the cluster ion + 11 series (Mn ++ H)H)+, where, where n runsn runs up up to to~20. ~20. During During the theirradiation irradiation with with up to up 2 to× 10 2 11 projectiles,10 projectiles, the yield the × yieldof emitted of emitted cluster cluster ions ionsis exponentially is exponentially quenched. quenched. The The damage damage (destruction) (destruction) cross cross sections sections of of the + 14 2 protonated (M + H)H)+ andand deprotonated deprotonated (M-H) (M-H)− −speciesspecies were were determined determined to tobe be 68 68 (±18) ( 18) × 10−1014 cm− 2 cmand 14 2 ± × and44 (±15) 44 ( ×15) 10−1410 cm− 2, cmrespectively., respectively. We Wenote note that that this this is a is direct a direct sputtering sputtering measurement measurement of of charged ± × particles. Although neutral neutral particles are dominant in the induced desorption, the measured cross section corresponds to radiolysisradiolysis,, thatthat is,is, onlyonly toto thethe destructiondestruction crosscross section.section. Indeed,Indeed, thethe sputteringsputtering yield (of ion species) reflectsreflects thethe evolution ofof the valine concentration on the sample surface which is ruled byby itsits radiolysis.radiolysis. Therefore,Therefore, thethe radiolysisradiolysis crosscross sectionsection forfor the the 90 90 MeV MeV127 127II1414++ beam shown in Figure 13 appears below the line which represent values produced by both sputtering and radiolysis. radiolysis.

3.2. Astrophysical Implications The assumption that Equation (1) holds for the destruction of solid valine by all cosmiccosmic raysrays regardless ofof theirtheir energyenergy allowsallows evaluatingevaluating itsits absoluteabsolute destructiondestruction rate.rate. For each cosmic ray constituent, j, thethe correspondingcorresponding partialpartial destructiondestruction raterate is:is: ஶ ݀ߔ Z∞௝ ௔௣ ܴ௝ ൌ  න ሺdܧΦሻjߪ ሺܧapሻ݀ܧ (2) R = ݀ܧ (ௗEǡ௝)σ (E)dE (2) j଴ dE d,j 0 where E is the kinetic energy of species j, )j(E) is its flux density and σd,j(E) its apparent destruction cross section given by Equation (1); for the current calculations, we have considered a = 1.0 × 10−20 cm3/keV and n = 1.0. Shen et al. [37] proposed a model in which the galactic cosmic ray (GCR) flux densities present the analytical expression: ଴Ǥଷ ݀ߔ௝ ܧ ሺܧሻ ൌ ܥ௝ ଷ (3) ݀ܧ ሺܧ ൅ ܧ଴ሻ

where E is the GCR energy per nucleon, E0 is a parameter considered here as equal to 400 MeV, and Cj is determined from the GCR abundances. For the current calculations, we considered abundances

Int. J. Mol. Sci. 2020, 21, 1893 15 of 21

where E is the kinetic energy of species j, Φj(E) is its flux density and σd,j(E) its apparent destruction cross section given by Equation (1); for the current calculations, we have considered a = 1.0 10 20 cm3/keV × − and n = 1.0. Shen et al. [37] proposed a model in which the galactic cosmic ray (GCR) flux densities present the analytical expression: dΦj E0.3 (E) = C (3) dE j 3 (E + E0) Int. J. Mol. Sci. 2020, 21, x FOR PEER REVIEW 15 of 21 where E is the GCR energy per nucleon, E0 is a parameter considered here as equal to 400 MeV, and Cj is determined from the GCR abundances. For the current calculations, we considered abundances and and fluxes presented in Table 1 and Figure 2 of ref. Shen et al. [37]; the fluxes are multiplied by 2π sr, fluxes presented in Table1 and Figure2 of ref. Shen et al. [ 37]; the fluxes are multiplied by 2π sr, for for taking into account the isotropic GCR incidence on a spot located in a flat surface. The flux density taking into account the isotropic GCR incidence on a spot located in a flat surface. The flux density dependence on E/m (Equation (3)) is presented in Figure 14a and the destruction rate dependence on dependence on E/m (Equation (3)) is presented in Figure 14a and the destruction rate dependence on E/m (Equation (2)) is shown in Figure 14b. The dominant effect of H and He ions at low GCR energy E/m (Equation (2)) is shown in Figure 14b. The dominant effect of H and He ions at low GCR energy (and of Fe ions at high energy) is evident. The integral in Equation (2) was performed from 10 keV (and of Fe ions at high energy) is evident. The integral in Equation (2) was performed from 10 keV up up to 10 GeV/u. Table 5 presents the Cj values (integrated over 2π sr) used, the Rj results for j = H. He, to 10 GeV/u. Table5 presents the C j values (integrated over 2π sr) used, the Rj results for j = H. He, C, C, O, Ne and Fe, as well as the respective partial half-lives, defined as ln(2)/Rj , the total destruction O, Ne and Fe, as well as the respective partial half-lives, defined as ln(2)/R , the total destruction rate rate and total half-life. j and total half-life. The valine radiolysis and sputtering by GCR are ruled by their iron constituents. The half-life of The valine radiolysis and sputtering by GCR are ruled by their iron constituents. The half-life of valine in the ISM (InterStellar Medium) is estimated to be about one million years. Therefore, since valine in the ISM (InterStellar Medium) is estimated to be about one million years. Therefore, since no no IR (infrared) signal of valine has been detected yet, we would like to encourage observations of IR (infrared) signal of valine has been detected yet, we would like to encourage observations of valine valine rotational features by radio spectroscopy. rotational features by radio spectroscopy.

(a) (b)

Figure 14. (a) Galactic cosmic ray (GCR) flux densities as predicted by Shen et al. [37]. (b) Valine Figure 14. (a) Galactic cosmic ray (GCR) flux densities as predicted by Shen et al. [37]. (b) Valine destruction rate dependence on cosmic ray energy. destruction rate dependence on cosmic ray energy. 1 1 Table 5. The Cj flux parameter, the destruction rate Rj (in second− and in million-year− ), and the Tablehalf-live 5. The (in million-year)Cj flux parameter, for each the GCRdestruction species rate j. Rj (in second−1 and in million-year−1), and the half- live (in million-year) for each GCR species j. 2 1 1.7 16 1 1 j Cj Ions cm− s− MeV− Rj (10− s− ) Rj (Ma− ) τ1/2 = ln(2)/Rj (Ma) j Cj Ions cm−2 s−1 MeV−1.7 Rj (10−16 s−1) Rj (Ma−1) τ1/2 = ln(2)/Rj (Ma) H 5.96 105 7.1 0.022 31 × 5 HHe 5.964.11 × 10104 7.17.5 0.022 0.024 2931 × HeC 4.111.79 × 10104 3 7.58.8 0.024 0.028 2529 × C O 1.792.22 × 10103 3 8.828 0.028 0.088 7.9 25 × ONe 2.22 438× 103 28 12 0.088 0.038 7.9 18 Fe 425 170 0.54 1.2 Ne 438 12 0.038 18 Total 6.42 105 230 0.74 0.94 Fe 425× 170 0.54 1.2 Total 6.42 × 105 230 0.74 0.94

4. Materials and Methods

4.1. Ion Beam Irradiation of Valine

Irradiations using 1.5 MeV H+, He+, and N+ ion beams were performed at PUC-Rio and those with 230 MeV S15+ projectiles were carried out at GANIL. Pilling et al. [17] and Vignoli Muniz et al. [30] published detailed descriptions of the experimental set-ups, respectively. Chamber pressure was lower than 10−6 mbar. Samples were irradiated at room temperature (~300 K) and effects for lower temperature (40–300 K) on shape and integrated absorbance of valine vibrational bands were reported recently by da Costa and da Silveira [33]. Samples were prepared as follows: D-Valine (99.5% of purity, delivered by Sigma Aldrich, São Paulo, Brazil) was dissolved in a solution of water (40% v/v) and ethanol (60% v/v). The mixture was

Int. J. Mol. Sci. 2020, 21, 1893 16 of 21

4. Materials and Methods

4.1. Ion Beam Irradiation of Valine Irradiations using 1.5 MeV H+, He+, and N+ ion beams were performed at PUC-Rio and those with 230 MeV S15+ projectiles were carried out at GANIL. Pilling et al. [17] and Vignoli Muniz et al. [30] published detailed descriptions of the experimental set-ups, respectively. Chamber pressure was 6 lower than 10− mbar. Samples were irradiated at room temperature (~300 K) and effects for lower temperature (40–300 K) on shape and integrated absorbance of valine vibrational bands were reported recently by da Costa and da Silveira [33]. Samples were prepared as follows: d-Valine (99.5% of purity, delivered by Sigma Aldrich, São Paulo, Brazil) was dissolved in a solution of water (40% v/v) and ethanol (60% v/v). The mixture was shaken in ultrasound machine up to a complete and homogeneous solution has been obtained. For the experiments at the Van de Graaff Laboratory, this solution was sprayed onto a ZnSe window, a 2 mm thick and 13 mm diameter disk. For the GANIL experiment, drops of this solution were deposited onto the ZnSe window. Substrate and solution were heated at 100 ◦C for enhancing the solvent evaporation. Sample thicknesses, Tk, were determined from Tk = S ln(10) M/ρ NA Aν, where S is the integrated absorbance of a given band, Aν is its A-value (band strength), ln(10) = 2.303, M = 117.15 g/mol the 3 valine molecular weight, ρ = 1.32 g/cm the valine mass density and NA the Avogadro number. Two 1 18 bands have been used for this calculation: the one at 948 cm− with Aν = 1.04 10− cm/molec, and 1 18 × the one at 716 cm with Aν = 3.37 10 cm/molec. The results agree within 50% for several samples. − × − At the Van de Graaff Laboratory, the samples were kept inside the analytical chamber on a stainless 6 steel sample-holder at room temperature (pressure below 10− mbar). Ion beam fluence was determined from current measurements via two nanoampere meters connected to a beam collimator and to a Faraday cup, respectively; both electrodes were biased to +90 V, for minimizing secondary electron emission. Infrared spectra were acquired in transmission mode by a JASCO FTIR-4100 spectrometer. 1 1 The 4000–600 cm− spectral region was inspected by averaging 70 scans with 2.0 cm− resolution. Absorbances were measured by integrating areas after subtracting a linear background defined within the band limits. At GANIL, the Casimir chamber was installed at the SME irradiation beamline. This is a dedicated beamline for sample irradiation with homogeneous irradiation field (xy-scanning of the 9 2 1 15+ ion beam) and permanent control of the beam flux, which was about 1 10 cm− s− for MeV S . 6 × · projectiles The residual pressure was about 2 10− mbar; FTIR acquisition was done by a Nicolet ×1 1 Magna 550 spectrometer over the 4000–600 cm− range with 1-cm− resolution. The observed CO2 bands are produced by molecules outside the chamber and do not interfere with the valine radiolysis. The ion beam electronic (Se) and nuclear (Sn) stopping powers for valine were determined through the software SRIM [38]; Se >> Sn for all used ion beams, ion–atom collisions occurred in the electronic energy loss regime.

4.2. Cross Sections from Modelling of Fluence Dependent Absorption Determination of molecular destruction and formation cross sections requires monitoring abundance rates of molecular species. This can be done by infrared spectroscopy, using the Beer–Lambert law, N = ln10 S/Aν, which connects the integrated absorbance S with the molecular column density N for each substance in the sample—provided that the A-value parameter, Aν, is known. A major concern is that this parameter varies with the chemical environment of the molecule, which in turn depends on temperature, solid state phase (crystallization/amorphization) and relative abundance of molecular constituents of the sample, quantities that change with irradiation. Common models describing the dependence of integrated absorbance on projectile fluence consider that S(F) variation is due to sputtering (ejection of valine or fragments), radiolysis (chemical reactions) and—sometimes—by beam induced phase transition (molecular rearrangement in the sample, such as crystallization, amorphization, and compaction). Since molecular rearrangement processes are accomplished faster than the sample destruction, data analysis may be separated in two Int. J. Mol. Sci. 2020, 21, 1893 17 of 21 parts: a first one, when absorption changes by the rearrangement and by other processes, and a second one, when only sputtering and radiolysis proceed. Since the compaction process does not alter the column density N of a molecular film (although its thickness may vary), absorbance changes due to A-value variations are considered in the current model to avoid misinterpretation of destruction cross sections. Inside the material (where there is no sputtering), the decrease rate of the precursor concentration is proportional to the concentration itself and, therefore, this concentration decreases as exp( σ F) with fluence. Accordingly, at the material surface, the precursor sputtering yield, Y, also − d decreases exponentially for the same reason: the radiolysis dictates the reduction of the precursor concentration (Sundqvist et al. [25]). Infrared spectroscopy in transmission mode measures the precursor column density as a function of fluence. Hereby, radiolysis and sputtering effects are simultaneously monitored:

dN = σ N Y (4) dF − d − Considering the precursor sputtering yield Y = Y (C/C ) Y (N/N ), where Y ,C and N 0 0 ≈ 0 0 0 0 0 are the sputtering yield, the concentration at surface and the column density of the virgin sample. For fluences that are not too high, Equation (4) can be rewritten as:

dN N ap σdN Y0 σd N (5) dF ≈ − − N0 ≡ − with the solution:  ap N(F) N exp σ F) (6) ≈ 0 − d ap = + Equation (6) shows that the apparent destruction cross section σd σd Y0/N0 is the quantity actually determined in FTIR measurements [29]. This experimental inability should not be regarded as a methodological deficiency. Rather, it reveals that the laboratorial simulation mimics correctly the combined effect of molecular dissociation and molecular sputtering that occurs when swift heavy ions impinge on a material surface in space. In order to describe Equation (6) in terms of absorbance, the Beer–Lambert law is applied: N(F) = ln10 S(F)/Av(F) and, N0 = ln10 Sp/Av(0):

S(F) A (F)   = v ap exp σd F (7) Sp Av(0) − where Sp is the “porous” initial absorbance, that is, the absorbance for the fresh sample as prepared. The ratio Av(0)/Av(F) describes compaction effects, and also explains why the different precursor bands do not evolve proportionally to each other as fluence increases. For compaction, it was found empirically that [39,40]: Av(F) 1 ζ exp( σcF) = − − (8) A (0) 1 ζ v − where ζ = (S0–Sp)/S0 is the relative porosity, understood as a (beam-dependent) parameter able to quantify the effect of porosity on the absorbance evolution of a given band. S0 is interpreted as being the initial integrated absorbance of a compacted sample; for non-compac ted materials, this value is obtained by extrapolating the integrated absorbance decay to F = 0, but using absorbances for an already compacted sample. Equation (8) takes into account the infrared spectrum change of a porous sample when it suffers compaction either by irradiation or by annealing (before irradiation); each band shows this absorbance change differently, reason why each band has its own ζ for a specific ion beam. The parameter σc is called compaction cross section; for σc F << 1, Equation (8) writes Av(F)/Av(0) ~ 1 + (ζ/1 ζ) σcF, another way of seeing that absorbance may increase or decrease with fluence depending − whether ζ is positive or negative, respectively. Int. J. Mol. Sci. 2020, 21, 1893 18 of 21

Independently of compaction or other phase changes, Av(F) may also have a dependence on fluence due to the persistent increase of daughter molecules in the sample. Since concentrations vary j j exponentially, it is reasonable to assume in first order approximation that Av (F) = Av (0) exp( ∆σ F) − j for each vibrational band j. In this case, Equation (7) writes, excluding compaction:

j       Sj(F) Av (F) ap ap = exp σ F = exp σ + ∆σ F (9) j d,j d,j j Sp,j Av (0) − −

ap The prediction is that absorbances decrease exponentially but not with the same σd for all bands; ap the dispersion is nevertheless small, once ∆σj << σd,j . Again, comparison among different systems should be made with caution, comparing cross sections for the same band or mean values.

5. Conclusions Thin films of D-valine were irradiated by four MeV ion beams. Compaction, radiolysis and sputtering processes were analyzed by FTIR spectroscopy at room temperature. The main conclusions are: 1. Compaction effects are seen via absorption modification, which means band strength modification. This process is due to the destruction of pores and to phase changes in the solid sample. 2. The chemical effects of the irradiation by distinct ion beams on valine are similar except for their molecular destruction rates (or destruction cross sections), which vary according to the deposited dose. 3. The elimination of valine molecules from the irradiated sample proceeds by radiolysis and by sputtering. Radiolysis imposes that the sample column density decreases exponentially with beam fluence. Another consequence is that the precursor concentration on the sample surface varies also exponentially and, in turn, the precursor sputtering yield decreases accordingly. 4. Strong evidence that the sputtering yield decays exponentially during irradiation is given by mass spectrometry measurements. Indeed, Salehpour et al. [23] found this behavior for valine bombarded by 127I14+ ions. Furthermore, Ferreira-Rodrigues et al. reported similar results analyzing the sample surface by TOF-252Cf–PDMS for glycine radiolysis [22]. FTIR spectroscopy determines the loss rate of precursors: the technique cannot distinguish those sputtered from those ap dissociated. Accordingly, the apparent destruction cross section, σd , is measured: it quantifies ap the combined effect of both processes. It is found that σd is approximately proportional to the electronic stopping power and, therefore, to the absorbed dose. This is an unexpected finding, ap n since for condensed gases the literature indicates σd proportional to Se , where n ~ 3/2 [28]. 5. At the end of irradiation, valine was destroyed and their bands vanished. The still visible bands are due to valine’s daughter molecules. Structural attributions are attempted. 6. Band strengths evolve with fluence but not linearly; moreover, some A-values are more sensitive to fluence than others. This feature does not depend on the processing ion and is attributed to compaction and to the increase of product concentrations. 7. Concerning Astrophysics, using theoretical GCR flux distribution, the solid valine half-life is predicted to be about one million years. Recent work estimated solid adenine half-life to be 10 8 million years (Vignoli Muniz et al. [30]). These results suggest that the search for valine by ± radio astronomy should be envisaged. 8. Concerning Astrobiology, 1.1 107 Gy is the mean dose to destroy solid valine. This is a huge × value for Biology standards. For human beings, 50 Gy is a typical lethal dose. 9. Concerning radiotherapy, the current results, obtained for valine, are actually typical for amino acids in general and even for biological material. Stopping powers are calculated for ion-atom interactions and biological materials are mostly formed by carbon, oxygen, nitrogen and hydrogen—the same atoms of the molecular structure of valine; biological material mass densities are close to 1 g/cm3, so that penetration depths are similar to valine. Therefore, the findings of Int. J. Mol. Sci. 2020, 21, 1893 19 of 21

this work may be a useful contribution for the understanding of microscopic processes in the damage of biological targets, and in particular, radiation protection and ion beam therapy.

Author Contributions: Conceptualization, C.A.P.d.C., G.S.V.M., P.B. and H.R.; Data curation, C.A.P.d.C. and E.F.d.S.; Formal analysis, C.A.P.d.C. and G.S.V.M.; Funding acquisition, P.B. and E.F.d.S.; Investigation, C.A.P.d.C., G.S.V.M., P.B., H.R. and E.F.d.S.; Methodology, C.A.P.d.C., G.S.V.M., P.B., H.R. and E.F.d.S.; Project administration, E.F.d.S.; Resources, P.B.; Supervision, P.B. and H.R.; Visualization, C.A.P.d.C. and H.R.; Writing—original draft, C.A.P.d.C., H.R. and E.F.d.S.; Writing—review & editing, H.R. All authors have read and agreed to the published version of the manuscript. Funding: The authors would like to acknowledge the partial support by the Brazilian agencies CNPq (INEspaço and Science without Borders) and FAPERJ (E-26/202.843/2018), as well as the CAPES-COFECUB French-Brazilian exchange program. Acknowledgments: We thank the staff of Van de Graaff Laboratory at PUC-Rio, CIMAP and GANIL. Conflicts of Interest: The authors declare no conflict of interest.

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