J. Phys. Chem. 1983, 87,1730- 1732
1730
Na-Y confirms the suggestion made earlier1 that there is no opportunity for oxidation of molybdenum in a zeolite that does not contain protons. Dehydrated Na-Y contains Na+ cations in site I, site 1', and all available sites II.39 Zerovalent molybdenum produced by decomposition of Mo(CO), at 200 "C may be blocked from entering hidden sites by Na+ cations in site I1 and is therefore readily accessible to gaseous oxygen in the supercage. Immediate oxidation, largely to Mo6+,then occurs on exposure of the activated material to air. The greater resistance to oxidation of samples activated above 200 "C may be due to migration of zerovalent molybdenum into sites inaccessible to O2 at higher temperatures (@-cageor D6R). Alternatively, sintering may occur above 200 "C; larger clusters of molybdenum metal may be formed in the supercages or on the external surface of the zeolite which resist bulk oxidation. Further study of the MoNa-Y system is needed to distinguish between these possibilities. This system may however resemble the alumina-supported molybdenum
catalysts prepared by decomposition of Mo(CO), on a fully dehydroxylated alumina s ~ p p o r t , ~ which ' - ~ ~ are thought to consist of clusters of zerovalent molybdenum anchored on Mo'+ cations. Similar anchoring of zerovalent clusters to Na+ cations may be occurring in the zeolite, and interesting catalytic properties for these materials may be anticipated. Acknowledgment. Acknowledgment is made to the donors of the Petroleum Research Fund, administered by the American Chemical Society, for support of this research. We thank Professor A. P. Hagen for preparation of the 95Mo(CO)6. Registry No. Mo, 7439-98-7; Mo(CO),, 13939-06-5; 02, 7782-44-7; NH,, 7664-41-7; pyridine, 110-86-1. (42) R. G. Bowman and R. L. Burwell, J. Catal., 63, 463 (1980). (43) C. Defosse, M. Laniecki, and R. L. Burwell, Proc. Int. Congr. Catal., 7th, 1980, 1331 (1981). (44) R. Nakamura, R. G. Bowman, and R. L. Burwell, J . Am. Chem. Soc., 103, 673 (1981).
Bond and Molecular Polarizabilities in the Structural Studies of Thymine and I t s Derivatives D. V. Subbalah,'
M. Sreentha Sastry, and V. Rama Murthyt
Department of Physics, S.K. University Col/ege.Anantapur 515 003, India (Received: May 24, 1982; I n Final Form: October 26, 1982)
Bond and molecular polarizabilities of thymine and a few of its derivatives are determined by the molecular vibration method and the Lippincott 6-function model method. Interestingly the longitudinal bond polarizabilities of C4-C5 and C5-CH3 bonds are consistent with the earlier view-based on X-ray diffraction data, chemical reactions, photoelectron data, and quantum chemical calculations-that position 5 of the pyrimdine nucleus is aromatic while position 4 is aliphatic in nature.
Introduction Though Pullman1 has used molecular polarizabilities for estimating the electrostatic induction forces prevailing among the pyrimidine bases of the nucleic acids, polarizability has not so far been used to investigate the structural aspects of the nucleic acid bases. With an interest to find how polarizability can be used to understand the reactivity of carbon atoms in certain molecules, we determined bond and molecular polarizabilities of a few halogenated pyrimidine2 and successfully confirmed the aliphatic nature of positions 2, 4, and 6 of the pyrimidine nucleus in our latest communication.2 The present work concentrates mainly on the confirmation of the aromatic character of the carbon atom at position 5 of the pyrimidine nucleus of thymine and a few of its derivatives.
Met hods The bond and molecular polarizabilities of the cited molecules are determined by (i) the molecular vibration method3 and (ii) the Lippincott &function potential model4 method. Molecular Vibration Method. Based on the theory of the Kerr effect, this method was developed in this laboratory by Rao and M ~ r t h y .They ~ have derived equations relating longitudinal (bL) and transverse (bT) bond polarizability coefficients to the stretching force constant ( K ) of the bond, and its mean amplitude of stretching vibration (#). The meaning of various terms in these expressions is given in our recent paper.2 The details of the derivation and sample calculations are given in the literature cited.3 The appropriate relations are
From these equations bL and bT values of each bond can
THYMINE Maitre de Conference, Department de Physique, University d'Oron, Oron, Algeria.
(1) B. Pullman, 'Molecular Biophysics", B. Pullman and Mitchel Weissbluth, Eds., Academic Press, New York, 1965, 117. (2) D. V. Subbaiah, M. S. Sastry, and V. R. Murthy, J . Mol. Struct. Theochem., 87, 105 (1982). (3) B. P. Rao and V. R. Murthy, Indian Chem. J., 13, 17 (1979). (4)E. R. Lippincott and J. M. Stutman, J. Phys. Chem., 68, 2926 (1964).
0022-3654/83/2087-1730$01.50/00 1983 American Chemical Society
The Journal of Physical Chemistry, Vol. 87, No. 10, 1983
Structural Studies of Thymine and Its Derivatives
TABLE I: Bond Polarizability Coefficients ba bond
c-c C-N C= N
c=c C-H N-N N-H C-H(Me in C - C H , ) C-H(Me in N - C H , ) C*-CH, N-CH,
2c=0 4C= 0
c=s
Units:
b I,
bT
0.143 0.157 0.170 0.130 0.076 0.136 0.094 0.077 0.078 0.227 0.195 0.169 0.168 0.285
0.046 0.042 0.075 0.045 0.063 0.050 0.084 0.064 0.065 0.139 0.091
0.041 0.042 0.063
(bL + 2b~)/3 0.078 0,080 0.107 0.073 0.067 0.079 0.087 0.068 0.069 0.168 0.126 0.084 0.084 0.137
cm3.
be obtained. Molecular polarizability of the molecule is given by a~
C(ni(bL + 2 b ~ ) i / 3 ) i
(3)
where ni is the number of bonds of the type i. bL - bT of each bond is evaluated by utilizing the force field data for thymine., The K value of the N-N bond is estimated from the bond length data6 by the Decius’ method. For the C=S bond it is evaluated from the frequency data8 of 5,6-dihydro-2-thiouracil.Mean amplitudes of vibration required in the calculations are evaluated with the help of the well-known secular matrix 1CG-l- EA1 = 0, and the IR and Raman frequency The b L and bT values are reported in Table I, while the mean molecular polarizabilities are presented in Table 11. Lippincott &Function Potential Model Method. This method is based on determining (a) the parallel component of polarizability, (b) the nonbond region electron contribution to the parallel component, ( c ) the perpendicular components of polarizability, and (d) the mean molecular polarizability. The appropriate relations are given below. The details are available in our recent paper2 and in the literature4v9cited.
(5)
The data on internuclear distances are taken from Singh and Hodgson,6 Ozeki et a1.,I0 Hoogsteen,l’ Furberg and Jensen,12 and Camerman and Camerman.’, Pauling’s (5)H.Susi and J. S. Ard, Spectrochim. Acta Part A, 30,1843(1974). (6)Phirtu Singh and Derek J. Hodgson, Acta Crystallogr., Sect. E , 30, 1430 (1970). (7)J. C. Decius, J. Chem. Phys., 45,1069 (1966). (8) H. M. Randall, R. G. Fowler, N. Fuson, and J. R. Dangl, ‘Infrared Determination of Organic Structures”. Van Nostrand, New York, 1949. and J. M. Stutman, J. Phys. (9)E. R. Lippincott, G. Nagarajan, . Chem., 70,78 (1966). (10)K. Ozeki, N. Sakabe, and J. Tanaka, Acta Crystallogr., Sect. B , 25, 1038 (1969). (11)Karst Hoogsteen, Acta Crystallogr., 16,28 (1963). (12)S. Furberg and L. M. Jensen, J. Am. Chem. Soc., 90,470(1968).
1731
electronegativitiesand Lippincott’s4atomic polarizabilities are also used in these calculations. The polarity correction has been used for all the molecules, and the results are presented in Table 11.
Discussion In connection with the reactivity of various carbon atoms in the pyrimidine ring, interesting facts arise from an examination of the data in Table I. The longitudinal bond polarizability coefficients (bL values; all the bL and bT values are given in cm3 units) of the C4-C5 and C6CH, bonds offer a clue to understanding the reactivity of the carbon atoms in the pyrimidine nucleus of thymine. bLC4-c5 (= 0.143) of the present work falls in between the aliphatic bLCC (0.099 in C6H12) and aromatic bLCC (= 0.224 in C6H6)values of Le Fevre14and suggests that the C4-C5 bond is a hybrid aliphatic-aromatic linkage. To resolve which of the two carbon atoms (C, or C,) is aromatic, the bond polarizability of CS-CH3 can be examined. The bLCdCH3(= 0.227) of the present work agrees well with the bLCary~-Calw (= 0.225 in C6H5CH3)value of Le Fevre and Rao15 and disagrees with their Cdkyl-Cdkyl(0.30 in CH,CH,) value and thus suggests that C5-CH3is an aryl-alkyl linkage and not an alkyl-alkyl linkage. This result necessitates C5t~ be aromatic in character which in turn fixes the aliphatic character for the C4 atom. The latter result is in conformity with our work on the halogenated pyrimidines,2 where we have proved that positions 2,4, and 6 in pyrimidine are aliphatic in nature. The above results can be corroborated by the conclusions from X-ray diffraction studies, chemical reaction studies, photoelectron data, and quantum chemical calculations. Shortening of single bonds is a characteristic property of aromaticity. In thymine and its derivatives considered here, the C4-C, internuclear distance varies between 1.476 and 1.429 A and is shorter than the normal value (1.54 A). Once again, Clews and Cochran16 have measured C-C1 internuclear distances a t positions 2,4, and 6 of chloropyrimdines as 1.77, 1.79, and 1.78 A,which compare well with the aliphatic value (C-C1 = 1.77 A in CH3C1). But Sternglanz and Bugg,17 Young and Morris,18 and Stuart and Coulterlg have measured the C-C1 bond length at position 5 in 5-chlorouracil(5-chloropyrimidine-2,4-dione) and its nucleosides as 1.715, 1.716, and 1.722 A, which compare well with the aromatic value (1.70 f 0.01 A in C,&C1). Thus, one can observe the shortening of single bonds around the fifth carbon atom of the pyrimidine nucleus. This confirms the aromatic property of that position. According to Kenner and Todd,20 chlorine atoms in positions 2,4, and 6 of pyrimidine resemble chlorine in aliphatic compounds in undergoing a variety of replacement reactions, and this behaviour is in contrast to that of chlorine a t position 5, which resembles that of chlorobenzene in its low reactivity. Badgerz1and Shepherd and (13)N. Camerman and A. C. Camerman, J . Am. Chem. Soc., 92,2523 (1970). (14)R. J. W. Le Fevre, Adu. Phys. Org. Chem., 3, 1 (1965). (15)R. J. W. Le Fevre and B. P. Rao, J. Chem. Soc., 1465 (1958). (16)C. J. B.Clews and W. Cochran, Acta Crystallogr., 1,4(1948);2, 46 (1949). (17)Helene Sternglanz and Charles E. Bugg, Biochim. Biophys. Acta, 378,1 (1975). (18)D.W.Young, and E. M. Morris, Acta Crystallogr., Sect. E , 29, 1259 (1973). (19)W. H.Stuart and Charles L. Coulter, Acta Crystallogr., Sect. E , 27,34 (1971). (20)G. W. Kenner and Sir Alexander Todd, “Heterocyclic Compounds”, Vol. 6, R. C. Elderfield, Ed., Wiley, New York, 1957, Chapter 7,p 234. (21)G.M. Badger, ‘The Chemistry of Heterocyclic Compounds”,L. F. Fieser and Mary Fieser, Eds., Academic Press, New York, 1961,p 377.
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Subbaiah et at.
The Journal of Physical Chemistry, Vol. 87,No. 10, 1983
TABLE 11: -_
Molecular Polarizabilities __-
ea
OM
molecule thymine 1-meth y1t h y m in e 4-thiothymine 1,3-dimethylthymine 5,6-dihydrothymine 6-azathymine uracil a
Units:
em3.
CoIIn
'O1llD
1.8149 2.1068 2.2448 2.5224 1.9383 1.7032 1.5071
0.1384 0.1384 0.2202 0.1384 0.1381 0.1681 0.1384
2011
1.1832 1.3341 1.3285 1.5590 1.2368 1.0969 0.9585
Lippincott 1.0455 1.1931 1.2645 1.4066 1.1045 0.9894 0.8680
MVM~ 1.252 1.498 1.305 1.744 1.391 1.218 0.950
Le Fevre 1.426 1.672 1.425 1.918 1.512 1.373 1.052
Molecular vibration method
Fedrickz2have also observed that position 5 of the pyrimidine nucleus facilitates electrophilic reaction and retards nucleophilic reaction. The converse is the case with positions 2,4, and 6. These observations are true, in general, among pyrimidine and its derivatives; but, of course, a few exceptions have been noticed in the l i t e r a t ~ r e . ~These ~ results are by and large in consonance with our conclusions. The photoelectron dataz4of methyl-substituted uracils, including thymine, stand as yet more evidence in support of our conclusion. Padva et al.24have observed that the a1orbital is most strongly destabilized by substitution in the 1- and 5-positions and is relatively unperturbed by substitutions in the 3- and 6-positions. The azorbital, on the other hand, is most sensitive to substitution in the 3-position. Their theoretical and spectroscopic results point out the high sensitivity of the ionization potential of uracil to substitution a t the 1- and 5-positions. Their electron density maps indicate that the upper (al) and lower (a2)orbitals have high electron density at the 1,5 and 3-positions, respectively. Thus, among the carbon atoms C5 has high electron density. Their work on 5-halouracilsZ5 indicated that there is significant interaction of the K system with C1-atom lone-pair orbitals in 5-chlorouracil. These are in conformity with the chemical reaction studies and the bond polarizabilities are able to predict these facts. The estimated values of the net a and cr charges by Geissner and Pullmanz6for positions 2,4, 6, and 5 of thymine are 0.466+, 0.366+, and 0.149+, and 0.119-. The quotedzi free valence indices for these carbon atoms are 0.245, 0.255, 0.536, and 0.496, respectively. According to Denis and Pullman,28among the structural characteristics of thymine worth understanding is the high electron density of its C5 atom. With a comprehensive knowledge of electron densities, free valence indices, and localization energies of pyrimidine bases of nucleic acids, Kochetkov and BudovskiiZ7concluded that C5 is the most reactive atom in pyrimidines relative to electrophilic reactions and C2, C6, C,* are most reactive relative to nucleophilic reac(22) Robert G. Shepherd and James L. Fedrick, "Advances in Heterocyclic Chemistry", Vol. 4, A. R. Katritzky, Ed., Academic Press, New York, 1965, p 145. (23) G. S. Rork and Ian H. Pitman, J. Am. Chem. Soc., 97,5559 (1975). (24) A. Padva, T. J. O'Donnell, and P. R. Lebreton, Chem. Phys., Lett.. 41. 278 (1976). (25) A. Padva, S. Peng, J. Lin, M. Shahbaz, and P. R. Lebreton, Biopolymers, 17, 1523 (1978). (26) C. Giessner-Prettre and A. Pullman, Theor. Chzm. Acta 9, 279 (1968). (27) N. K. Kochetkov and E. I. Budovskii, "Organic Chemistry of Nucleic Acids", Plenum Press, London, 1971, p 170. (28) Armelle Denis and Albert Pullman, Theor. Chim. Acta 7, 110 (1967).
tions. Brown and HeffernanZ9have observed from molecular orbital calculations that electrophilic localization energies follow the order 4 > 2 > 5 in pyrimidines. All the above experimental and theoretical studies lend satisfactory support to our conclusion that, in thymine, C5 is aromatic and C4is aliphatic in character. Similar results have been obtained in the case of uracil and a few of its derivatives. CYMvalues of uracil are given in Table I1 for comparison, and other results have been communicated for publication. The mean molecular polarizabilities from both methods (Table 11) agree well with the Le Fevrel4J5B0values. The latter predicts experimental results with f470 error. The present study indicates that the &function model has fallen short a little in accurately predicting the CYMvalues. This, perhaps, may be due to the presence of the highly polar nitrogen atoms in the ring. The CY^ of thymine estimated from atomic refractions3I and bond p~larizabilities~~ (of Denbigh33)are 1.10 and 1.20 X cm3, respectively. The aMof uracil from bond polarizabilitie~~~ is 1.02 x cm3. These values agree with the values of the molecular vibration method in Table 11. According to Le Fevre14 the C-H bond is isotropically polarizable in all cases. But in the present work bLC-H # bTC-H confirms ourMearlier view that the C-H bond is also anisotropically polarized and finds support from the work of Denbigh33 (bL = 0.079 and bT = 0.058), Amos and C r i ~ p i n and , ~ ~ Chantry and Plane.36 From the present work it is concluded that position 5 in thymine is aromatic while position 4 is aliphatic in nature, with reference to reactivity. The bond polarizability, which is a measure of the instantaneous deformation of the electron cloud around the bond, is in a position to reflect the reactivity of the carbon atoms very well.
Acknowledgment. M.S.S. is grateful to the Council of Scientific and Industrial Research, India, for awarding a Senior Research Fellowship. Registry No. Thymine, 65-71-4; 1-methylthymine, 4160-72-9; 4-thiothymine, 35455-79-9; 1,3-dimethylthymine, 4401-71-2; 5,6dihydrothymine, 696-04-8; 6-azathymine, 932-53-6; uracil, 66-22-8. (29) R. D. Brown and M. L. Heffernan, Aust. J. Chem., 9,83 (1956). (30) R. J. W. Le Fevre, Proc. Chem. Soc., 363 (1959). (31) Howard De Voe and Ignacio Tinoco, Jr., J. Mol. Biol., 4, 500 (1962). (32) B. Pullman, Pierre Claverie, and Jacqueline Caillet, Science, 147, 1305 (1965). (33) K. G. Denbigh, Trans. Faraday SOC.,36, 936 (1940). (34) D. V. Subbaiah, Ph. D. Thesis, S. V. University, Tirupati, India, 1978. (35) A. T. Amos and R. J. Crispin, J. Chem. Phys., 63, 1890 (1975). (36) G. W. Chantry and R. A. Plane, J. Chem. Phys., 33,634 (1960).
