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A simple experimental arrangement for measuring the vapour pressures and sublimation enthalpies by the Knudsen effusion method: Application to DNA and RNA bases
ARTICLE IN PRESS
Nuclear Instruments and Methods in Physics Research A 560 (2006) 219–223 www.elsevier.com/locate/nima
A simple experimental arrangement for measuring the vapour pressures and sublimation enthalpies by the Knudsen effusion method: Application to DNA and RNA bases A.L.F. de Barros, A. Medina, F. Zappa, J.M. Pereira, E. Bessa, M.H.P. Martins, L.F.S. Coelho, W. Wolff, N.V. de Castro Faria Instituto de Fı´sica, Universidade Federal do Rio de Janeiro, Cx. Postal 68528, Rio de Janeiro 21941-972, RJ, Brazil Received 16 November 2005; received in revised form 10 January 2006; accepted 10 January 2006 Available online 9 February 2006
Abstract We measured the vapour pressure of several DNA and RNA bases—uracil, adenine, guanine, thymine and cytosine—in the 300–450 K range. In each case the sample mass loss rate was measured as function of temperature with a simple setup consisting of a commercial film deposition system and a homemade oven. Afterwards vapour pressure values were extracted from these data using the Knudsen effusion method. Sublimation enthalpy values, obtained from vapour pressure data by applying the Clausius–Clapeyron equation, are in very good agreement with literature values. The results suggest that crystal-based film thickness monitors may be useful in on-line crosssection measurements, monitoring the gas target thickness. They also show the viability of using this oven for producing a biomolecular gas target. r 2006 Elsevier B.V. All rights reserved. PACS: 82.39.Pj; 64.70.Hz; 82.60.Cx Keywords: Vapour pressure; Enthalpy of sublimation; Uracil; Adenine; Guanine; Thymine; Cytosine
1. Introduction The discovery of X-rays by Roentgen in 1895 and the subsequent works of Becquerel and Curie completely changed many medical and biological specialties [1]. This importance was clear right from the beginning, not only due to the use of X-rays and g-rays in diagnostics but also with radiation dermatitis and cancer affecting some of these pioneering researchers. Since then more than a century of studies of clinical and other uses of radiation followed, employing an increasing diversity of natural and artificial radiation sources—radioactive materials, accelerators, and reactors—yielding photons, electrons, neutrons, ions and pions and leading to the accumulation of a wealth of radiobiological data. Even so much basic data is Corresponding author. Tel.: +55 21 25627732; fax: +55 21 25627368.
E-mail address: [email protected] (L.F.S. Coelho). 0168-9002/$ - see front matter r 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.nima.2006.01.026
still needed, due to the variety of radiations used, the diversity and complexity of biological systems, and the difficulty for describing the interaction of projectiles with them [2,3]. For example, the projectile-organism interaction may be modelled as a succession of binary encounters between the projectile and the living cell molecules, where free electrons with typical energies below 20 eV are generated in the collision process [4]. This approach—usual for atomic collisions in solids—is hindered however by the scarcity of experimental cross-section data for both processes, the direct projectile–molecule and the posterior electron–molecule collisions. As examples of these processes, which started being studied only recently, one has: electron attachment to uracil, thymine and cytosine [5–8], electronic and vibrational excitation of thymine by electrons [9] and electron scattering from DNA and RNA bases [10]. These molecules must be in the gas phase and the thermodynamic
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properties of these materials, in particular their vapour pressures and sublimation enthalpies, then become of primordial experimental relevance. Active clinical research is pursued worldwide in hadronic radiotherapy, where high-energy heavy particles are used (hadrons include protons, neutrons and pions). Beams of fast protons, in particular, are ideal to treat deeply located tumors as they are easily produced in accelerators [11]. These ions present a large Linear Energy Transfer (LET) near the end of their range. This effect, associated to nuclear stopping and nominated the Bragg peak, turns this treatment more efficient than the conventional photon and electron radiotherapy. Other ions have also been clinically tested: light ones—such as carbon and neon ions—as well as heavier ones—like silicon, argon and even uranium. Recently other types of radiation have also been tested, particularly negative pions. Measurements of binary collisions of all these projectiles with organic molecules, the direct kinematics processes, are important steps for understanding the much more complex projectile–tissue interaction. Nevertheless collisions of high-energy ions with DNA and RNA bases—uracil, adenine, guanine, thymine and cytosine—in the gas phase have only been studied when biomolecular ions are accelerated towards a gas target, the inverse kinematics case [12]. In order to study systematically the fragmentation of DNA and RNA bases under the impact of a projectile, the direct kinematics case, the vapour pressures of these bases must be known, with sublimation enthalpies being relevant parameters. Our interest in sublimation enthalpies was then prompted by the necessity to establish the suitable temperature range to evaporate the DNA and RNA bases, generating a gas flow or gas jet with a constant density, as only then it will be possible to measure ion— (DNA and RNA bases) collision cross-sections. Examination of the data available in literature reveals a general agreement in the reported experimental sublimation enthalpies for a given organic substance (see, for instance, a recent review [13]), although some discrepancies are present. This article, in short, describes a simple procedure for measuring vapour pressures and molar enthalpies, without the need of a dedicated measuring setup [14]. A straightforward consequence of these measurements is to test the regularity of the gas flow from the oven, ensuring the viability of a gas target based on the present setup. The present procedure is employed to study DNA and RNA bases—uracil, adenine, guanine, thymine and cytosine— with a good agreement with literature data. We have already developed a system useful for the study of direct kinematics processes [15,16]: fast ions collided with molecular targets and were afterwards detected in different charge states in coincidence with charged molecule fragments. The target could be a gas jet, as in these experiments, or a vapour coming from an oven if the material is in a condensed phase at room temperature. The results obtained agree very well with literature values,
showing the viability of this simple method for accurate measurement of sublimation enthalpies. The pressure values obtained also point to the feasibility of a gas target derived from the present oven setup, which may be employed for future hadrontherapy data measurements. 2. Experimental setup and data analysis methods The measurements used basically as apparatus a standard thin-film evaporator system (Fig. 1a) provided with a homemade oven (Fig. 1b). The thin film evaporator system E306A includes a water-cooled quartz digital film thickness monitor (Edwards model FTM3). The vapour pressure values were obtained by the Knudsen effusion method [17] while the subsequent determination of the sublimation enthalpies was carried out using the Clausius–Clapeyron equations [18,19]. The molecules studied in this work were uracil, adenine, guanine, thymine and cytosine. They were purchased from Sigma Aldrich and present purities ranging from 98.6% to 99%. 2.1. Oven The oven is 5.3 cm long cylinder made of electrolytic copper. The employment of pure copper, with high thermal conductivity, satisfies two requirements: the oven temperature must be well defined and must be easy to monitor. The oven is filled with the chosen substance in powder form, in a previously weighed quantity. Afterwards this sample is manually compressed. The oven is placed inside a container with 6 cm in length, 2.5 cm of external diameter and 0.5 cm wall thickness. The internal resistance, protected by an isolating coil around the pipe, delivers a maximum power of 70 W. 2.2. Quartz crystal The quartz setup is placed inside of the evaporator chamber. The flow of sublimated molecules, coming from the oven, is directed towards a piezoelectric rocking quartz
Fig. 1. General view of the experimental setup.
ARTICLE IN PRESS A.L.F. de Barros et al. / Nuclear Instruments and Methods in Physics Research A 560 (2006) 219–223
crystal, which has holes on its surface. The molecules condense on the crystal surface, as the crystal is watercooled. The oscillating frequency of the crystal changes proportionally to the mass deposited on the quartz sensor [20], and is recorded as a function of time. The sensitivity of the quartz setup is 300 Hz to 106 g, allowing fast measurement runs.
221
2.3. Data analysis As below described the vapour pressures were directly obtained from the experimental data, using the Knudsen method. Afterwards, using the Clausius–Clapeyron equation, the value of the sublimation enthalpy was extracted from the vapour pressure data [18,19]. The basis of the Knudsen method is relating the sample mass loss rate, dm=dt, to the vapour pressure PV ðTÞ, where T is the sample temperature. In the present case this mass loss rate is assumed identical to the mass deposition rate on the crystal, as the crystal is kept at room temperature while the oven temperature ranges from 300 to 450 K. A straightforward thermodynamics calculation, assuming (a) perfect gas behaviour, (b) low gas density inside the oven and (c) the oven orifice has a length much smaller than its diameter, leads to 1 dm 2pN A kT 1=2 1 dm 2pRT 1=2 PV ðTÞ ¼ ¼ , S dt M S dt M
(1)
Fig. 2. Oven.
where S is the orifice area and M is the molecular weight of the substance under study. R ¼ N A k is the gas constant, Table 1 Sublimation enthalpy values: present data and literature values reviewed by Chickos and Acree [13] Substance
T min –T max (K)
hDH sub i (kJ/mol)
T measure (K)
Methoda
Reference
Adenine ðC5 H5 N5 Þ
305–360 400–438 448–473 – – – 315–435 394–494 452–587 452–587 378–428 – 500–545 – 393–458 – – 305–355 383–438 – 378–428 – – – 320–410 505–525 423–483 – – 450–470 325–405 –
130 2 140.4 109.2 126.3 127.2 108.7 125:3 0:2 127:0 2:0 130:6 4:0 131 5 120:5 1:3 121.7 133:9 8 126:5 2:2 120:5 5:2 115:5 2:1 83.7 135:8 0:4 125:7 3:6 131:3 4:0 124:4 1:3 138 10 134:1 4:2 124.3 167:7 0:5 151:7 0:7 147:2 2:6 155:0 3:0 167 10 176 10 168:3 0:6 186.2
330 – 460.5 – – – 425 439 519 298 403 425 523 440 426 – 485 330 411 298 403 298 298 – 365 – 453 298 298 298 365 –
QR,ME ME – LE QR ME QR,ME TE ME,TE TE,GS QR MS HSA C LE ME MS QR,ME ME – QR TE C LE QR,ME GS ME – TE C QR,ME LE
Present [21] [22] [23] [21,24] [25,26] Present [27] [28] [28] [29] [30] [31] [32] [23] [33] [25] Present [34] [34] [29] [35] [32] [23] Present [36] [34] [34] [35] [23] Present [23]
Uracil ðC4 H4 N2 O2 Þ
Thymine ðC5 H6 N2 O2 Þ
Cytosine ðC4 H5 N3 O2 Þ
Guanine ðC5 H5 N5 OÞ
work
work
work
work
work
Methodsa : C—calorimetric determination; GS—gas saturation; HSA—head space analysis; LE—Langmuir evaporation; ME—mass effusion; QR— quartz resonator; TE—torsion effusion.
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with N A being the Avogadro number and k the Boltzmann constant. This pressure is related to the enthalpy of sublimation, DH sub , by the Clausius–Clapeyron equation:
where the first term on the right-hand-side of the equation is a constant and a plot of T 1=2 dm=dt against 1=T yields DH sub .
dðln PÞ DH sub ¼ dT RT 2
3. Experimental results of the enthalpy
(2)
which, upon integration from T 0 to T, yields: DH sub DH sub PðTÞ ¼ PðT 0 Þ exp exp RT 0 RT DH sub ¼ A exp RT
ð3Þ
where A is a constant and DH sub is assumed to present a negligible temperature dependence. From these equations one finally has an expression relating the directly measured quantities, dm=dt and T, to DH sub : ! dm 1=2 ASM1=2 DH sub T (4) ¼ ln ln 1=2 dt RT ð2pRÞ
The measurements of the sublimation enthalpy were made for the 5 nitrogenated bases: uracil, guanine, cytosine, adenine and thymine. The lnðPV Þ versus 1=T plots, together with straight line fittings, are displayed in Fig. 2. The good linearity of these fittings over the whole temperature ranges show the validity of the assumption of total condensation of the molecules, and henceforth eliminates a possible source of error for the vapour pressure values. From these angular coefficients we obtained the sublimation enthalpies of these five molecules, DH sub , shown at Table 1, together with all literature data values reviewed by Chickos and Acree [13]. We calculated the average and the standard deviation of the literature values for each substance and compared them with the present work respective measured value. They are,
Fig. 3. Vapour pressure as function of 1=T for (a) uracil, (b) guanine, (c) thymine and (d) cytosine.
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Fig. 4. Sublimation enthalpies for (a) uracil and (b) thymine.
respectively, equal to, in kJ/mol: 122:4 14:4 and 130 2 for adenine; 125:2 7:1 and 125:3 0:2 for uracil; 129:6 7:2 and 135:8 0:4 for thymine; 157:9 12:1 and 167:7 0:5 for cytosine and 186.2 and 168:3 0:6. Except for guanine (which presents a single literature without standard deviation) the present data agrees very well with the literature averages. The quality of this agreement may also be seen at Fig. 3, where we display our measured values for uracil and thymine, together with the literature data values (Fig. 4). 4. Conclusions The simple setup proposed allowed the measurement of vapour pressures for uracil, guanine, thymine, cytosine and adenine as function of temperature, for the 300–450 K. From these vapour pressure data we extracted the respective sublimation enthalpy values, agreeing very well with the previously measured data reported in literature [13]. This agreement suggests that crystal-based film thickness monitors may be useful in on-line cross-section measurements, monitoring the gas target thickness. It also points to the viability of using this oven to produce a gas target, in future experiments. Acknowledgements This work was partially supported by the Brazilian agencies CAPES, CNPq and FAPERJ. References [1] K.N. Prasad, CRC Handbook of Radiobiology, second ed., CRC, Boca Raton, FL, 1995. [2] B. Coupier, B. Farizon, M. Farizon, M.J. Gaillard, F. Gobet, N.V. de Castro Faria, G. Jalbert, S. Ouaskit, M. Carre´, B. Gstir, G. Hanel, S. Denifl, L. Feketeova, P. Scheier, T.D. Ma¨rk, Eur. Phys. J. D 20 (2002) 459.
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[3] J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlatho¨lter, J. Phys. B 35 (2002) 4373; J. de Vries, R. Hoekstra, R. Morgenstern, T. Schlatho¨lter, Eur. Phys. J. D 24 (2003) 161. [4] B. Boudaiffa, P. Cloutier, D. Hunting, M.A. Hues, L. Sanche, Science 287 (2000) 1658. [5] S. Denifl, S. Matejcik, B. Gstir, G. Hanel, M. Probst, P. Scheier, T.D. Ma¨rk, J. Chem. Phys. 118 (2003) 4107. [6] G. Hanel, B. Gstir, S. Denifl, P. Scheier, M. Probst, B. Farizon, M. Farizon, E. Illenberger, T.D. Ma¨rk, Phys. Rev. Lett. 90 (2003) 188104. [7] S. Denifl, S. Ptasinska, M. Cingel, S. Matejcik, P. Scheier, T.D. Ma¨rk, Chem. Phys. Lett. 377 (2003) 74. [8] R. Abouaf, J. Pommier, H. Dunet, Int. J. Mass Spectrom. 226 (2003) 397. [9] R. Abouaf, J. Pommier, H. Dunet, Chem. Phys. Lett. 381 (2003) 486. [10] P. Mozejko, L. Sanche, Radiat. Envirom. Biophys. 42 (2003) 201. [11] W. Wieszczycka, W.H. Scharf, Proton Radiotherapy Accelerators, World Scientific Publishing, Singapore, 2001. [12] F. Gobet, B. Farizon, M. Farizon, M.J. Gaillard, M. Carre´, M. Lezius, P. Scheier, T.D. Ma¨rk, Phys. Rev. Lett. 86 (2001) 3751. [13] J.S. Chickos, W.E. Acree, J. Phys. Chem. Ref. Data 31 (2002) 537. [14] L.A. Torres, I. Herna´ndez-Contreras, J.A. Guardado, M.G. Gonza´lez, Meas. Sci. Technol. 5 (1994) 51. [15] F. Zappa, S.D. Maga˜lhaes, J.C. Acquadro, T.S. Cabral, G. Jalbert, L.F.S. Coelho, N.V. de Castro Faria, Phys.Rev. A 64 (2001) 032701. [16] F. Zappa F, L.F.S. Coelho, S.D. Maga˜lhaes, W.M.S. Santos, A.M. Luiz, M.H.P. Martins, A.L.F. de Barros, J.A.M. Pereira, N.V. de Castro Faria, Phys. Rev. A 67 (2003) 012702. [17] M. Knudsen, Ann. Phys. 28 (1909) 75. [18] R.E. Honig, D.A. Kramer, RCA Lab. Rev. 30 (1969) 285. [19] R.C. Reid, J.M. Prausnitz, B.E. Poling, The Properties of Gases and Liquids, McGraw-Hill, Singapore, 1988. [20] Edwards High Vacuum Instructions, 1976, M18042/3. [21] W. Zielenkiewicz, J. Chem. Eng. Data 45 (2000) 626. [22] R.M. Stephenson, S. Malanowski, Handbook of the Thermodynamics of Organic Compounds, Elsevier, New York, 1987. [23] I.K. Yanson, B.I. Verkin, O.I. Shlyarevskii, A.B. Teplitskii, Stud. Biophys. 32 (1974) 29; I.K. Yanson, A.B. Teplitskii, Russ. J. Phys. Chem. 49 (1975) 428. [24] A. Zielenkiewicz, W. Zielenkiewicz, L.F. Sukhodub, O.T. Glukhova, A.B. Teplitskii, K.L. Wierzchowski, J. Solution Chem. 13 (1984) 757. [25] L.B. Clark, G.G. Peschel, I. Tinoco, J. Phys. Chem. 69 (1965) 3615. [26] J.D. Cox, G. Pilcher, Thermochemistry of Organic and Organometallic Compounds, Academic Press, New York, 1970. [27] B. Brunetti, G. Della Gatta, V. Piacente, J. Chem. Eng. Data 45 (2000) 237. [28] G. Bardi, L. Bencivenni, D. Ferro, B. Martini, C.S. Nunziante, R. Teghil, Thermochim. Acta 40 (1980) 275. [29] A.B. Teplitskii, I.K. Yanson, O.T. Glukhova, A. Zielenkiewicz, W. Zielenkiewicz, K.L. Wierzchowski, Biophys. Chem. 11 (1980) 17. [30] I.K. Yanson, A.B. Teplitskii, L.F. Sukhodub, Biopolymers 18 (1979) 1149. [31] M.J. Nowak, K. Szczepaniak, A. Barski, D. Shugar, Z. Natureforsch. C: Biosci. 33C (1978) 876. [32] M. Nabavian, R. Sabbah, R. Chastel, M. Laffitte, J. Chim. Phys. Phys-Chi. Biol. 74 (1977) 115. [33] B.C. Romanov, B.I. Sukkhorukov, E.A. Miroshnichenko, Yu. A. Lebedev, 1972, Fourth International Biophysical Congress, Abstract E7, (a4/7)b (as quoted in Reference 27). [34] P.M. Burkinshaw, C.T. Mortimer, J. Chem. Soc. Dalton Trans. 1 (1984) 75. [35] D. Ferro, L. Bencivenni, R. Teghil, R. Mastromarino, Thermochim. Acta 42 (1980) 75. [36] A. Zielenkiewicz, M. Wszelaka-Rylik, J. Poznanski, W. Zielenkiewicz, J. Solution Chem. 27 (1998) 235.
Nuclear Instruments and Methods in Physics Research A 560 (2006) 219–223 www.elsevier.com/locate/nima
A simple experimental arrangement for measuring the vapour pressures and sublimation enthalpies by the Knudsen effusion method: Application to DNA and RNA bases A.L.F. de Barros, A. Medina, F. Zappa, J.M. Pereira, E. Bessa, M.H.P. Martins, L.F.S. Coelho, W. Wolff, N.V. de Castro Faria Instituto de Fı´sica, Universidade Federal do Rio de Janeiro, Cx. Postal 68528, Rio de Janeiro 21941-972, RJ, Brazil Received 16 November 2005; received in revised form 10 January 2006; accepted 10 January 2006 Available online 9 February 2006
Abstract We measured the vapour pressure of several DNA and RNA bases—uracil, adenine, guanine, thymine and cytosine—in the 300–450 K range. In each case the sample mass loss rate was measured as function of temperature with a simple setup consisting of a commercial film deposition system and a homemade oven. Afterwards vapour pressure values were extracted from these data using the Knudsen effusion method. Sublimation enthalpy values, obtained from vapour pressure data by applying the Clausius–Clapeyron equation, are in very good agreement with literature values. The results suggest that crystal-based film thickness monitors may be useful in on-line crosssection measurements, monitoring the gas target thickness. They also show the viability of using this oven for producing a biomolecular gas target. r 2006 Elsevier B.V. All rights reserved. PACS: 82.39.Pj; 64.70.Hz; 82.60.Cx Keywords: Vapour pressure; Enthalpy of sublimation; Uracil; Adenine; Guanine; Thymine; Cytosine
1. Introduction The discovery of X-rays by Roentgen in 1895 and the subsequent works of Becquerel and Curie completely changed many medical and biological specialties [1]. This importance was clear right from the beginning, not only due to the use of X-rays and g-rays in diagnostics but also with radiation dermatitis and cancer affecting some of these pioneering researchers. Since then more than a century of studies of clinical and other uses of radiation followed, employing an increasing diversity of natural and artificial radiation sources—radioactive materials, accelerators, and reactors—yielding photons, electrons, neutrons, ions and pions and leading to the accumulation of a wealth of radiobiological data. Even so much basic data is Corresponding author. Tel.: +55 21 25627732; fax: +55 21 25627368.
E-mail address: [email protected] (L.F.S. Coelho). 0168-9002/$ - see front matter r 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.nima.2006.01.026
still needed, due to the variety of radiations used, the diversity and complexity of biological systems, and the difficulty for describing the interaction of projectiles with them [2,3]. For example, the projectile-organism interaction may be modelled as a succession of binary encounters between the projectile and the living cell molecules, where free electrons with typical energies below 20 eV are generated in the collision process [4]. This approach—usual for atomic collisions in solids—is hindered however by the scarcity of experimental cross-section data for both processes, the direct projectile–molecule and the posterior electron–molecule collisions. As examples of these processes, which started being studied only recently, one has: electron attachment to uracil, thymine and cytosine [5–8], electronic and vibrational excitation of thymine by electrons [9] and electron scattering from DNA and RNA bases [10]. These molecules must be in the gas phase and the thermodynamic
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properties of these materials, in particular their vapour pressures and sublimation enthalpies, then become of primordial experimental relevance. Active clinical research is pursued worldwide in hadronic radiotherapy, where high-energy heavy particles are used (hadrons include protons, neutrons and pions). Beams of fast protons, in particular, are ideal to treat deeply located tumors as they are easily produced in accelerators [11]. These ions present a large Linear Energy Transfer (LET) near the end of their range. This effect, associated to nuclear stopping and nominated the Bragg peak, turns this treatment more efficient than the conventional photon and electron radiotherapy. Other ions have also been clinically tested: light ones—such as carbon and neon ions—as well as heavier ones—like silicon, argon and even uranium. Recently other types of radiation have also been tested, particularly negative pions. Measurements of binary collisions of all these projectiles with organic molecules, the direct kinematics processes, are important steps for understanding the much more complex projectile–tissue interaction. Nevertheless collisions of high-energy ions with DNA and RNA bases—uracil, adenine, guanine, thymine and cytosine—in the gas phase have only been studied when biomolecular ions are accelerated towards a gas target, the inverse kinematics case [12]. In order to study systematically the fragmentation of DNA and RNA bases under the impact of a projectile, the direct kinematics case, the vapour pressures of these bases must be known, with sublimation enthalpies being relevant parameters. Our interest in sublimation enthalpies was then prompted by the necessity to establish the suitable temperature range to evaporate the DNA and RNA bases, generating a gas flow or gas jet with a constant density, as only then it will be possible to measure ion— (DNA and RNA bases) collision cross-sections. Examination of the data available in literature reveals a general agreement in the reported experimental sublimation enthalpies for a given organic substance (see, for instance, a recent review [13]), although some discrepancies are present. This article, in short, describes a simple procedure for measuring vapour pressures and molar enthalpies, without the need of a dedicated measuring setup [14]. A straightforward consequence of these measurements is to test the regularity of the gas flow from the oven, ensuring the viability of a gas target based on the present setup. The present procedure is employed to study DNA and RNA bases—uracil, adenine, guanine, thymine and cytosine— with a good agreement with literature data. We have already developed a system useful for the study of direct kinematics processes [15,16]: fast ions collided with molecular targets and were afterwards detected in different charge states in coincidence with charged molecule fragments. The target could be a gas jet, as in these experiments, or a vapour coming from an oven if the material is in a condensed phase at room temperature. The results obtained agree very well with literature values,
showing the viability of this simple method for accurate measurement of sublimation enthalpies. The pressure values obtained also point to the feasibility of a gas target derived from the present oven setup, which may be employed for future hadrontherapy data measurements. 2. Experimental setup and data analysis methods The measurements used basically as apparatus a standard thin-film evaporator system (Fig. 1a) provided with a homemade oven (Fig. 1b). The thin film evaporator system E306A includes a water-cooled quartz digital film thickness monitor (Edwards model FTM3). The vapour pressure values were obtained by the Knudsen effusion method [17] while the subsequent determination of the sublimation enthalpies was carried out using the Clausius–Clapeyron equations [18,19]. The molecules studied in this work were uracil, adenine, guanine, thymine and cytosine. They were purchased from Sigma Aldrich and present purities ranging from 98.6% to 99%. 2.1. Oven The oven is 5.3 cm long cylinder made of electrolytic copper. The employment of pure copper, with high thermal conductivity, satisfies two requirements: the oven temperature must be well defined and must be easy to monitor. The oven is filled with the chosen substance in powder form, in a previously weighed quantity. Afterwards this sample is manually compressed. The oven is placed inside a container with 6 cm in length, 2.5 cm of external diameter and 0.5 cm wall thickness. The internal resistance, protected by an isolating coil around the pipe, delivers a maximum power of 70 W. 2.2. Quartz crystal The quartz setup is placed inside of the evaporator chamber. The flow of sublimated molecules, coming from the oven, is directed towards a piezoelectric rocking quartz
Fig. 1. General view of the experimental setup.
ARTICLE IN PRESS A.L.F. de Barros et al. / Nuclear Instruments and Methods in Physics Research A 560 (2006) 219–223
crystal, which has holes on its surface. The molecules condense on the crystal surface, as the crystal is watercooled. The oscillating frequency of the crystal changes proportionally to the mass deposited on the quartz sensor [20], and is recorded as a function of time. The sensitivity of the quartz setup is 300 Hz to 106 g, allowing fast measurement runs.
221
2.3. Data analysis As below described the vapour pressures were directly obtained from the experimental data, using the Knudsen method. Afterwards, using the Clausius–Clapeyron equation, the value of the sublimation enthalpy was extracted from the vapour pressure data [18,19]. The basis of the Knudsen method is relating the sample mass loss rate, dm=dt, to the vapour pressure PV ðTÞ, where T is the sample temperature. In the present case this mass loss rate is assumed identical to the mass deposition rate on the crystal, as the crystal is kept at room temperature while the oven temperature ranges from 300 to 450 K. A straightforward thermodynamics calculation, assuming (a) perfect gas behaviour, (b) low gas density inside the oven and (c) the oven orifice has a length much smaller than its diameter, leads to 1 dm 2pN A kT 1=2 1 dm 2pRT 1=2 PV ðTÞ ¼ ¼ , S dt M S dt M
(1)
Fig. 2. Oven.
where S is the orifice area and M is the molecular weight of the substance under study. R ¼ N A k is the gas constant, Table 1 Sublimation enthalpy values: present data and literature values reviewed by Chickos and Acree [13] Substance
T min –T max (K)
hDH sub i (kJ/mol)
T measure (K)
Methoda
Reference
Adenine ðC5 H5 N5 Þ
305–360 400–438 448–473 – – – 315–435 394–494 452–587 452–587 378–428 – 500–545 – 393–458 – – 305–355 383–438 – 378–428 – – – 320–410 505–525 423–483 – – 450–470 325–405 –
130 2 140.4 109.2 126.3 127.2 108.7 125:3 0:2 127:0 2:0 130:6 4:0 131 5 120:5 1:3 121.7 133:9 8 126:5 2:2 120:5 5:2 115:5 2:1 83.7 135:8 0:4 125:7 3:6 131:3 4:0 124:4 1:3 138 10 134:1 4:2 124.3 167:7 0:5 151:7 0:7 147:2 2:6 155:0 3:0 167 10 176 10 168:3 0:6 186.2
330 – 460.5 – – – 425 439 519 298 403 425 523 440 426 – 485 330 411 298 403 298 298 – 365 – 453 298 298 298 365 –
QR,ME ME – LE QR ME QR,ME TE ME,TE TE,GS QR MS HSA C LE ME MS QR,ME ME – QR TE C LE QR,ME GS ME – TE C QR,ME LE
Present [21] [22] [23] [21,24] [25,26] Present [27] [28] [28] [29] [30] [31] [32] [23] [33] [25] Present [34] [34] [29] [35] [32] [23] Present [36] [34] [34] [35] [23] Present [23]
Uracil ðC4 H4 N2 O2 Þ
Thymine ðC5 H6 N2 O2 Þ
Cytosine ðC4 H5 N3 O2 Þ
Guanine ðC5 H5 N5 OÞ
work
work
work
work
work
Methodsa : C—calorimetric determination; GS—gas saturation; HSA—head space analysis; LE—Langmuir evaporation; ME—mass effusion; QR— quartz resonator; TE—torsion effusion.
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with N A being the Avogadro number and k the Boltzmann constant. This pressure is related to the enthalpy of sublimation, DH sub , by the Clausius–Clapeyron equation:
where the first term on the right-hand-side of the equation is a constant and a plot of T 1=2 dm=dt against 1=T yields DH sub .
dðln PÞ DH sub ¼ dT RT 2
3. Experimental results of the enthalpy
(2)
which, upon integration from T 0 to T, yields: DH sub DH sub PðTÞ ¼ PðT 0 Þ exp exp RT 0 RT DH sub ¼ A exp RT
ð3Þ
where A is a constant and DH sub is assumed to present a negligible temperature dependence. From these equations one finally has an expression relating the directly measured quantities, dm=dt and T, to DH sub : ! dm 1=2 ASM1=2 DH sub T (4) ¼ ln ln 1=2 dt RT ð2pRÞ
The measurements of the sublimation enthalpy were made for the 5 nitrogenated bases: uracil, guanine, cytosine, adenine and thymine. The lnðPV Þ versus 1=T plots, together with straight line fittings, are displayed in Fig. 2. The good linearity of these fittings over the whole temperature ranges show the validity of the assumption of total condensation of the molecules, and henceforth eliminates a possible source of error for the vapour pressure values. From these angular coefficients we obtained the sublimation enthalpies of these five molecules, DH sub , shown at Table 1, together with all literature data values reviewed by Chickos and Acree [13]. We calculated the average and the standard deviation of the literature values for each substance and compared them with the present work respective measured value. They are,
Fig. 3. Vapour pressure as function of 1=T for (a) uracil, (b) guanine, (c) thymine and (d) cytosine.
ARTICLE IN PRESS A.L.F. de Barros et al. / Nuclear Instruments and Methods in Physics Research A 560 (2006) 219–223
Fig. 4. Sublimation enthalpies for (a) uracil and (b) thymine.
respectively, equal to, in kJ/mol: 122:4 14:4 and 130 2 for adenine; 125:2 7:1 and 125:3 0:2 for uracil; 129:6 7:2 and 135:8 0:4 for thymine; 157:9 12:1 and 167:7 0:5 for cytosine and 186.2 and 168:3 0:6. Except for guanine (which presents a single literature without standard deviation) the present data agrees very well with the literature averages. The quality of this agreement may also be seen at Fig. 3, where we display our measured values for uracil and thymine, together with the literature data values (Fig. 4). 4. Conclusions The simple setup proposed allowed the measurement of vapour pressures for uracil, guanine, thymine, cytosine and adenine as function of temperature, for the 300–450 K. From these vapour pressure data we extracted the respective sublimation enthalpy values, agreeing very well with the previously measured data reported in literature [13]. This agreement suggests that crystal-based film thickness monitors may be useful in on-line cross-section measurements, monitoring the gas target thickness. It also points to the viability of using this oven to produce a gas target, in future experiments. Acknowledgements This work was partially supported by the Brazilian agencies CAPES, CNPq and FAPERJ. References [1] K.N. Prasad, CRC Handbook of Radiobiology, second ed., CRC, Boca Raton, FL, 1995. [2] B. Coupier, B. Farizon, M. Farizon, M.J. Gaillard, F. Gobet, N.V. de Castro Faria, G. Jalbert, S. Ouaskit, M. Carre´, B. Gstir, G. Hanel, S. Denifl, L. Feketeova, P. Scheier, T.D. Ma¨rk, Eur. Phys. J. D 20 (2002) 459.
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