J. Phys. Chem. l!J92,96,9278-9282
9278
Further studies of a-donor systems of this type must be done in order to validate or invalidate the correlation in Figure 2.
Conclusion Ab initio calculations of Lewis acid-base complexes of AIC13 yielded the followihg order for the binding energies with these t#ises: H2C0 (26 kcal/mol) > HClCO (0bound) (21 kcal/mol) > C2H4 (15 kcal/mol), H,CCI, CzHz(14kcal/mol) > HClCO (Cl bound) (9 kcal/mol). Vibrational frequency calculations indicated red shifts of from -35 to 150 cm-I for the bonds immediately adjacent to the coordinated center@). Attempts to correlate binding energy with charge transfer as gauged by Mulliken populations was unsuccessful; however, a possible correlation of the binding energy with the A1 out of plane distance for complexes with lone pair donor molecules may exist. Acknowledgment. I would like to thank the San Diego Supercomputer Center for an allocation of computer time without which this work could not have been performed. I would also like to thank the ACS-PRF (Grant No. 26276-GB6) for supporting this work and Dr. Shi-yi Liu for helpful discussions. References d Notes (1) Cotton, F. A.; Wilkinson, G. Advanced Inorganic Chemistry, 5th ed.; Wiley: New York, 1988; p 217 ff.
(2) Carey, F. A.; Sundberg, R. J. Advanced Organic Chemistry, Part A: Structure and Mechanisms, 3rd ed.; Plenum: New York, 1990; p 229. (3) Reference 2, pp 570-576. (4) Lewis, N.; Morgan, I. Synth. Commun. 1988, 18, 1783. ( 5 ) Coppi, L.; Ricci, A.; Taddei, M. J . Org. Chem. 1988,53, 911. (6) Reference 1, pp 1257 ff. (7) Bock, C. W.; Trachtman, M.; Murphy, C.; Muschert, B.; Mains, G. J. J. Phvs. Chem. 1991. 95. 2339. (8) v'an der Woerd, M. J:;Lmmertsma, K.; Duke, B. J.; Schaefer, H. F., I11 J . Chem. Phys. 1991, 95, 1160. (9) Shen, M.; Schaeffer, H. F., I11 J . Chem. Phys. 1992, 96, 2868. (10) Marsh. C. M. B.: Hamilton. T. P.:. Xie.. Y.:. Schaeffer. H. F.. 111 J . Chem.'Phys. 1992, 96, 5310. (11) Sakai, S.J . Phys. Chem. 1991, 95, 175. (12) Sakai, S.J . Phys. Chem. 1991, 95, 7089. (13) LePage, T. J.; Wiberg, K. B. J . Am. Chem. Soc. 1988, 110,6642. (14) Wilson, M.; Coolidge, M. B.; Mains, G. J. J . Phys. Chem. 1992,96, 4851.
(15) Szabo, A.; Ostlund, N. S. Modern Quantum Chemistry, 1st ed.; MacMillan: New York, 1982. (16) Frisch, M. J.; Head-Gordon, M.; Schlegel, H. B.; Raghavachari, K.; Binkley, J. S.;Gonzalez, C.; Defrecs, D. J.; Fox, D. J.; Whiteside, R. A,; Seeger, R.; Melius, C. F.; Baker, J.; Martin, R. L.; Kahn, L. R.; Stewart, J. J. P.; Fluder, E. M.; Topiol, S.;Pople, J. A. Gaussian Inc., Pittsburg, PA. (17) Stevens, W. J.; Basch, H.; Krauss, M. J. Chem. Phys. 1984,81,6026. (18) Krauss, M.; Stevens, W. J. Annu. Rev. Phys. Chem. 1984, 35, 357. (19) Jasien, P. G. Chem. Phys. Lett. 1992, 188, 135. (20) Jasien, P. G.; Stevens, W. J. J. Chem. Phys. 1986,84, 3271. (21) Weast, R. C., Ed. CRC Handbook of Chemistry and Physics, 57th ed.;CRC Press: Cleveland, 1976.
Scaled Quantum Mechanical Force Fields and Vibrational Spectra of Solid-state Nucleic Acid Constituents. 3. 2-Aminoadenine Jan Florih,* Peter Mojzei, and Josef Stepinek Institute of Physics, Charles University, Ke Karlova 5, I21 16 Prague, Czechoslovakia (Received: March 9, 1992)
Raman and IR spectra of the polycrystalline rare nucleic acid base 2-aminoadenine were measured in the 100-1800- and 28W35OO-m-l region. The vibrational assignment of the in-plane normal vibrational modes of 2-aminoadenine was performed using scaled ab initio STO-3G force field. The scale factors have been obtained by the least-squares fit to the experimental vibrational frequencies. The 1.5% agreement between calculated and experimental frequencies has been obtained. The changes of geometry, Mulliken atomic populations, protonation energy, and force constants caused by adding the amino group to the C2 atom of adenine have been evaluated at the STO-3G and 4-31G HF SCF levels.
Introduction 2-Aminoadenine (Figure l), the only modified purine base which was evidenced in natural DNAs, has been observed in the DNA of cyanophage S-2L where it completely replaces the molecules of adenine.'J Owing to the presence of two amino groups 2-aminoadenine is structurally similar to both adenine and guanine. The presence of the second amino group at the C2 positionin 2-aminoadcninc permits formation of the third hydrogen bond in the 2-aminoadenine-thymine and 2-aminoadenine-uracil base pairs. It aecms to account for the higher melting temperature for the cyanophage S-2L DNA compared with the adenine-containing DNA.' The 2-amino group not only changes the thermal stability of DNA but also alters the external appearance of the helix minor groove. The substitution of 2-aminoadenine for adenine in the T7 DNA promoter site was shown to prevent utilization of this promoter by the T7 RNA polymerase3which interprets the 2-amino group in the minor groove as belonging to guanine. However, within a transcribed region the 2-aminadenine is recognized and transcribed as adenine due to Watson-Crick pairing specificity. Further biological interest in 2-aminoadenine stems from the influence of the 2-amino group on conformational Corresponding address: Institute of Physics, Charles University, Ke Karlovu 5 , 121 16 Prague, Czechoslovakia. E-mail: FLORIAN@CSPUNIlZ; Fax: (00422)299272.
0022-3654/92/2096-9278$03.00/0
i" 4,
\ H,,
Figure 1. Atom numbering of 2-aminoadenine.
stability of poly(d2-aminoadeninedT). As was shown by various experimental methods,"5 poly (d2-aminoadenine-dT) undergoes a cooperative transition to a different helical structure under the conditions which are otherwise insufficient to change the conformation of normal poly(dA-dT). To characterize the structural, energetic, and conformational consequences of 2-aminadenine substitution, the variety of riboand deoxyribopolynucleotides containing 2-aminoadenine has extensively been examined by the UV absorption and CD,69 'H 2D NOE NMR,5*7J0 NMR? and IR4v8spectroscopies as well as X-ray diffraction.' I Nevertheless, neither the experimental vibrational data nor the theoretical vibrational analysis of 2aminadenine single base and its derivatives, neceSSary for a correct 0 1992 American Chemical Society
2-Aminoadenine interpretation of vibrational spectra of the 2-aminoadenine containing polynucleotides, has been published yet. The above mentioned biological significance of 2-aminoadenine promoted us to investigate Raman and IR spectra of polycrystalline 2-aminoadenine. Our vibrational assignment of 2aminoadenine has been based on a combination of empirical and ab initio approach proposed by Blom and Altona12and further developed by Fogarasi and The scaled quantum mechanical (SQM) force field is evidently the best suited for the calculation of vibrational spectra of molecules embedded in solid state or aqueous solution because it can implicitly involve in the scale factors the effects of electron correlation and finiteness of basis set and anharmonicity as well as the influence of weak intermolecular interaction^'^ which can play an important role just in crystalline samples and polar solutions. Intermolecular interactions and anharmonicity can, of course, be partly involved also in the classical empirical normal coordinate treatment, where, however, the number of fitted parameters greatly exceeds the number of observables which result in ambiguity of refined force parameters. The STO-3G basis has widely been used for interpretation of nucleic acids bases.16 In our papers on molecules of adenine,I7guanine and guanine-residue,l8N1 and Nl,N7 protonated adenine,17 N3-protonated adenine,19 N7-protonated guanine208and N3-protonated cytosine,20bwe have shown that the minimal STO-3G basis set, if properly scaled, can provide vibrational spectra with better than 2% accuracy, the force constants being well transferable between similar molecules. We present in this paper the results of ab initio HF-SCF/STO-3G calculations of the geometry and harmonic force constants of 2-aminoadenine, followed by the least-squares fit of the set of scale factors to the experimentally determined frequencies. To assess the proton affinity and probability for forming imino tautomers we have evaluated also the ab initio HF-SCF/4-31G Mulliken atomic charges and protonation energy of 2-aminoadenine and compared it with the 4-31G results for other NA bases published previously. 21
Methods 2-Aminoadenine was recrystallized from aqueous solution and
dried at a temperature of 40 OC under vacuum. The IR absorption spectra were obtained from a KBr pellet using a Bruker IFS-85 spectrometer. Spectral resolution of 2 cm-' was used in both the 300-1800- and 2800-3500-~m-~ regions. Raman measurements were carried out on a homemade modular UV-vis spectrometer based on a Jobin-Yvon THR-1500 monochromator.z The central line was cut off with a POC Raman holographic edge filter. The polycrystalline powder was pressed in a rotating cell. The Raman spectra excited by the 514.5-nm argon laser line were recorded with a spectral resolution of 2 cm-'. The ab initio HF SCF force constants of 2-aminoadenine were obtained as second analytical derivatives of the total energy13at the STO-3G optimized geometry (Table I) with the GAMESS programqz3The planar symmetry was supposed for the molecule during the optimization of geometry. In the subsequent normal coordinate analysis, performed in the standard set of symmetrized internal coordinates13(Table 11), only the in-plane normal vibrations were considered. The modified Gauss least-squares methodz4as included in the program MOLVIB625,26was used for fitting the scale constantsof the STO-3G force field to the in-plane vibrational spectra of 2-aminoadenine. To decrease the number of fitted parameters and consequently to support plausibility of the calculated force field we have introduced as low a number as possible of different scale factors. Hence, only the 10 scale factors have been fitted to the 25 in-plane experimental frequencies in the 300-1800-~m-~ frequency region. The scale factor for the NH2 scissoring force constants was not refmed but was fmed at its value obtained for adenine for which also experimental data from deuterated derivatives were available. Three different scale factors were needed for the correction of the C-N diagonal stretching force constants in order to reach an acceptable agreement with the experimental frequencies. For this purpose the C-N stretches were divided into three groups in dependence
The Journal of Physical Chemistry, Vol. 96, No. 23, 1992 9279 TABLE I: Comparison of ST0-N Geometries of Adenine,2' 2-Amiwrdeaiw, rad Nl-Prot-ted Z A ~ ~ i ~ ~ ~ d(AA) enine
2-aminoadenine adenine Distances (A) N1C2 C2-N3 N3C4 C4C5 C5C6 C6-N 1 C6-N 10 C2-N 1 1 C5-N7 N7C8 C8-N9 N9C4 C8-H N9-H NlO-Hl2 NlO-Hl3 Nll-H14 Nll-H15 Nl-H
1.368 1.342 1.370 1.386 1.415 1.357 1.383
C6-NlC2 NlC2-N3 C2-N3-C4 N3C4C5 C4C5C6 C5C6-Nl C4C5-N7 C5-N7-C8 N7C8-N9 C8-N9-C4 N9C4-CS C5C6-NlO NlC2-Nl1 C6-Nl O-H 12 C6-Nl O-H 13 C2-N 1 1-H 14 C2-Nll-H15 N7C8-H C8-N9-H C6-N 1-H
115.9 130.4 110.5 126.4 116.6 120.2 1 1 1.4 103.4 113.8 106.2 105.2 121.8
1.424 1.309 1.400 1.392 1.085 1.020 1.014 1.014
H+ at N1 of AA
1.382 1.356 1.368 1.386 1.417 1.348 1.383 1.392 1.424 1.307 1.404 1.391 1.084 1.020 1.015 1.014 1.013 1.013
1.415 1.333 1.382 1.401 1.399 1.389 1.354 1.371 1.422 1.307 1.412 1.370 1.087 1.025 1.021 1.020 1.017 1.018 1.025
115.5 130.4 109.8 127.1 116.4 120.8 111.6 103.4 113.6 106.4 105.0 121.5 113.5 120.3 119.7 119.4 120.4 125.6 126.9
122.5 124.7 111.5 128.1 118.3 114.9 111.5 103.3 113.3 107.0 104.8 125.1 115.9 118.5 122.7 122.8 118.0 125.9 127.0 119.0
Angles (dcg)
120.4 119.7 125.4 127.1
on their magnitudes. This is in accordance with the experience For that the stronger bonds tend to have smaller scale f~ctors.~~J* the same reason the scaling of interaction force constants was done independently on the values of the scale factors of corresponding diagonal force constants, unlike the widely used scaling procedure proposed by h l a y et al.I4 in which the interaction scale factors are calculated as geometric mean values of the product of the two scale factors belonging to the corresponding diagonal force constants. The more flexible scaling scheme used by us is required especially for empirical correctionsof force fields calcdated using minimal basis sets." As a natural basis for grouping of interaction force constants we have chosen their stretch/bend origin giving rise to the three, stretch-stretch, stretch-bend, and bend-bend groups, each of them scaled by a common scale factor.I7 The 4-3 1G HF SCF single point energy, Mulliken populations, and dipole moments of adenine, 2-aminoadenine, and N1protonated 2-aminoadenine were computed at the STO-3G reference geometry. The energy of protonation has been obtained as a difference between the 4-3 lG/STO-3G energies of neutral and N1-protonated molecules without any correction for the basis set superposition error (BSSE) and the zero point vibrational energy. The same approach applied to the other NA bases by Del Benez1turned out to give the order of their proton affinities in agreement with the experimental pK, values.27
Results Structure of 2 - A m i w p m . The calculated STO-3G geometries of neutral and N1-protonated 2-aminoadenine are presented
9280 The Journal of Physical Chemistry, Vol. 96, No. 23, 1992
Florifin et al.
TABLE Ik Detinitioa of In-phw Ietenul Coordiartea of 2-AQiaordwiw description C-N stretching
symbol NlC2. N3C4. C6N10 C5N7; C8N9; N9C4 C2Nl1, C2N3, C6N1 N7C8 C4C5, C5C6 NH12, NH13, NH14 NH15, C8H, N9H D6RTr
-
C C stretching C-H, N-H stretching six-memb ring in-plane deformations
D6REl D6RE2
C6N10 bending C 2 N l l bending five-memb ring in-plane deformations
DC6N DC2N D5R=
SNlOH SNllH RN 1OH RNllH DC8H DN9H
NH2 rocking C8-H 14 bending N9-Hl5 bending
+
+
+
D5R NH2 scissoring
definition" N l C 2 . N 3 C 4 . C6-NlO C5-N7; C8-N9; N 9 C 4 C2-Nl1, C2-N3, C6-N1 N7C8 C4C5, C5C6 NlO-Hl2, N10-Hl3, Nll-H14 N11-Hl5, C8-Hl6, N9-Hl7 ( C 6 - N l C 2 ) + (C2-N3-C4) + ( C M 5 C 6 ) (Nl-C2-N3) - ( N 3 C M 5 ) - (CS-C&Nl) 2[(C2-N3-C4) + (C5*6-Nl)] [(C6-N1C2) + ( N l C 2 - N 3 ) + ( N 3 C 4 C 5 ) (C4-C5-C6)] (C6-NlC2) + ( N 3 4 4 C 5 ) (NlC2-N3) - ( C 4 C 5 C 6 ) (C5C6-NlO) - (NlC6-NlO) (NlC2-Nll) - (N3C2-Nll) OS63245(N7C8-N9) (-0.51 167)[(CS-N7
