thymine* base pairs - ACS Publications - American Chemical Society

1542

J. Phys. Chem. 1993,97, 1542-1551

Structure, Energetics, and Harmonic Vibrational Spectra of the Adenine-Thymine and Adenine*-Thymine* Base Pairs: Gradient Nonempirical and Semiempirical Study Vojtkh Hrouda,+Jan FloriBn,* and Pave1 Hobza‘J The Heyrovskj Institute of Physical Chemistry and Electrochemistry, Czechoslovak Academy of Sciences, DolejJkova 3, 182 23, Prague 8, Czechoslovakia, and Institute of Physics, Charles University, Ke Karlovu 5, 121 16, Prague 2, Czechoslovakia Received: August 24, 1992

The structure, interaction energies, and harmonic vibrational spectra of adenine-thymine and adenine*-thymine* (iminwnol tautomers) base pairs werestudied by the ab initioand semiempirical methods. Gradient optimization at the SCF/MINI-1 level has shown that the former complex is only about 10 kcal/mol more stable than the latter. We have demonstrated that single-point calculations with a larger basis set performed for the reference geometry optimized in the minimal basis set (SCF/MIDI-1 //SCF/MINI-1) and those taking the correlation energy into account can lead to unrealistic interaction energy values. Hence, single-point calculations of this kind should be taken with great care for AT and A*T* complexes. The results obtained by the semiempirical PM3 method agree reasonably well with the ab initio values; this is not true of the AM1 method. In addition to the interaction energy, reorganization energy and basis set superposition error were also determined; both the latter terms (which are positive) are important and should not be neglected. The theoretical interaction enthalpy of the AT formation agrees fairly well with the corresponding experimental value. Knowledge of the harmonic vibrational spectra of isolated A, T, A*, and T* bases and the AT and A*T* base pairs enabled us to determine the frequency and intensity changes induced by the Watson-Crick type of hydrogen bonding, tautomeric transitions, and double proton transfer in the AT base pair.

1. Introduction The specific pairing of adenine (A) with thymine (T) and guanine (G) with cytosine (C) in the DNAdouble helix is essential for the transfer and expression of genetic information. As early as 1963 LBwdin’ suggested that simultaneous double proton transfer in these base pairs (leading to the pairs formed by the unusual imino-enol tautomers) could represent one possible step in a process of spontaneous point mutagenesis. Since then, an enormous amount of theoretical (semiempiricaland nonempirical) work has been done to support this attractive idea (only several representative papers are cited2-6). For rigorous evaluation of the probability of double proton transfer, the complete potential energy surfaceshould be available. The energies of both minima and of a transition state are required for the qualitative estimationof this probability. Reliablerelative energies for complexes formed by usual and unusual tautomers can be obtained only from nonempirical ab initio calculations utilizing gradient optimization. Any attempts to calculate real systems at nonempirical and semiempirical levels without geometry optimization or to model these systems should be taken with care. The formation of the molecular complex is connected with changes in the intrasystem coordinates: the stronger the binding, themore pronounced thechanges that occur. While thesechanges are usually negligible for vdW molecules formed by nonpolar systems and the use of the frozen subsystem approximation is justified for these systems, thechange in the intrasystemgeometry may be important and the use of the frozen subsystem approximation is not recommended for H-bonded complexes. In our particular case, the AT as well as A*T* complexes have an interaction energy larger than 10 kcal/mol (SCF/MINI-1). Consequently, significant changes in the geometry of these subsystems can be expected. The aim of this paper is to investigate the structure and energetics of the AT and A*T* base pairs as well as the isolated ~~

+

Heyrovskf Institute. of Physics.

1 Institute

0022-3654/93/2091- 1542304.00/0

subsystems at the ab initio SCF and correlated levels and also at the semiempirical level (A* and T* are the iminwnol tautomers of A and T; cf. Figure 1). The complete gradient optimization has been performed at the ab initio SCF and semiempirical levels. The beyond-SCF calculations have been carried out for the SCFgeometry. Having the gradient optimized structures of both AT and A*T* complexes and isolated monomers, we have extended our study to the calculation of the harmonic force fields, vibrational frequencies, and in-plane normal vibrations, permitting us to determine the effects of WatsonCrick type hydrogen bonding and of tautomeric transitions on the vibrational spectra of the nucleic acid (NA) bases adenine and thymine. Although general, experimentally based knowledge of the effects of hydrogen-bond formation on the NA bases vibrational spectra (involving a marked loweringof the frequencies of the N-H stretching modes and an increaseof their IR intensities, a red shift of the C = O stretching frequencies, and upshift of frequencies of N-H bending vibrations) has long been available,’a more quantitative theoretical studies have so far been missing. A great deal of experimental as well as theoretical work has been carried out to investigate the rare tautomers of NA bases for their presumed crucial role in mutagenesis (cf. ref 6 and references therein). Early Raman measurements indicated the prevailing presence of normal tautomeric forms of NA bases in a aqueous s~lution.~a Indirect arguments involving a comparison of ~ K v a l u e s have ’ ~ led to the conclusion that in solution adenine predominates adenine* by a factor of 105. Because of such a small number of rare tautomers in solution or in gas phase, the theoretical calculations of the respective vibrational spectra can provide a valuable tool for the rare tautomers detection.

2. Computational Strategy 2.1. Selection of Computational Method. Reliable values of various properties of vdW molecules are obtained only if a nonempirical ab initio method is employed. The size of the complex and the applicationof a gradient optimizationtechnique prevent the use of larger than the minimal basis set. We have shown8 that, among minimal and medium basis sets, Huzinaga’s 0 1993 American Chemical Society

The Journal of Physical Chemistry, Vol. 97, No. 8, 1993 1543

Adenine-Thymine and Adenine*-Thymine' Base Pairs

a

/ l4

d

,11.12

e

a

Figure 1. SCF/MINI-I optimized structures (gradient norm O.OO0 15) and dipole moments of isolated adenine (a) and thymine (c), their rare tautomers (b, d) and both the adenine-thymine (e) and adenine*-thymine* (f) complexes. d+ represents the sum of the dipole moments of the two subsystems(for subsystems in the same position as in the complex but with the hydrogene bonds lengthened to infinity). The orientation of the coordinate system is indicated (x axes parallel with the N I X 2 bond in adenine and with the C 4 N 3 bond in thymine).

minimal MINI- 1 basis set9 yields surprisinglygood characteristics for H-bonded complexes. This basis set was successfully used laterloto evaluate the stabilization energies for all the 29 possible pairs formed by G, C, T, and A. We demonstrated that the dispersion energy represents an important part of the interaction energy for all the base pairs. Later" we pointed out that the intrasystem correlation energy for these pairs is not negligible. The rigorous treatment would therefore require the use of the gradient optimiziation technique in combination with methods including the correlation energy. Such a treatment for the complexes under study is, however, highly time and memory consuming, even if a minimal basis set is used. The following strategy was therefore employed. First, the geometry of the complexes and of the subsystems was optimized at the SCF/ MINI-1 level. Assuming that planar structures of all systems under study represent real minima, the C,symmetry constraint was introduced. Later, higher level calculations were performed for this geometry. The following levels were considered: MP2/ MINI-1, SCF/MIDI-1, and MPZ/MIDI-l (MIDI-llois a split-

valence basis set (3,2/2) obtained from the MINI-1 basis set). It should be mentioned here, however, that the use of higher level calculations for geometries obtained at a lower level is questionable, especially for molecular complexes. The nonempirical gradient optimization of the systems under study (therequired toleranceon theenergy gradient wasO.OO0 15) isenormouslytimeconsuming. The applicabilityof semiempirical methods was therefore tested. We have frequently had the opportunity to warn against the use of these methods for vdW systems.l*J3 The recently introduced AM1 and PM3 semiempirical methods14 are, however, better suited for theoretical treatment of some types of vdW molecules. These methods were parametrized, among other characteristics, also with respect to the H-bonded molecules. The AM1 and PM3 methods were used as described above. 2.2. InteractionEnergy .adEnthalpy. The interaction energy should be corrected for the effect of the basis set extension and the effect of geometry reorganization of the interacting subsystems. The correction of the interaction energy for the basis

1544 The Journal of Physical Chemistry, Vol. 97, No. 8, 1993

set superposition error (BSSE) is now widely a ~ c e p t e d . ~The ~-l~ BSSE is usually evaluated according to the Boys and Bernardi correction scheme using the function counterpoise correction15

+

BSSE = E(R) E(?")- E[R(T)]- E[T(R)]

(1) where E(R) and E [ R ( T ) ] are the energies of subsystem R evaluated in its own basis set and in the basis set of the whole complex. On the other hand, the reorganization energy is believed to be rather small and is neglected in a majority of intermolecular energy calculations. The reorganization energy (ErwrE), Le., the energy accompanying the transition from optimal subsystem geometries to the geometries which these subsystems have in the complex, is evaluated in the following way:

+

Erwrg = E(R) E(?")- E(R? - E(T? (2) where E(R7 and E(R) are the energies of subsystem R in its optimal geometry and in the geometry it has in the optimized complex, respectively. The reorganization energy defined in this way is positive. We did not call this energy 3elaxation" because the term ++elaxation energy" is understand to be the relaxed, Le., liberated energy which is negative. In accordance with ref 16, the reorganization energy is evaluated in the basis of free subsystems. Interaction energy (AE)taking both effects mentioned into account is determined as follows:

+

h E = E ( R...?")-E[R(T)]- E [ T ( R ) ] Erwrg (3) where E(R ...T) is the energy of the optimized complex. For definition of remaining symbols, see eqs 1 and 2. The interaction energy can also be rewritten in a different way:

AE = AE'+ BSSE

(4)

where

hE'= E(R...?")- E(R9 - E(T? AE'is now the interaction energy evaluated as the difference in the energies of the optimized supersystem and subsystems. This energy contains the reorganization energy and does not contain the BSSE. Only in very special cases can the interaction energy be deduced from experiment; the interaction enthalpy ( M O O ) is usually measured. M o o differs from AE by the changes in the zeropoint energy (ZPE):

+

AHo" = AE AZPE (6) AZPE is evaluated as one-half of the difference between the sum of the harmonic vibrational frequencies of the supersystem and of the subsystems. Because AZPE is positive, M o o is smaller in absolute value than AE. 2.3. Geometry. The geometry and vibrational frequencies of the subsystems and supersystems were evaluated at the energy minima found by the gradient optimization technique. We are aware of the fact that the complete potential energy surface and not only the minimum should be corrected for the BSSE. This procedure would lead to a slightly different geometry. Such a procedure is, however, feasible only for the optimization of a few coordinates. The error mentioned is reduced by using basis sets with as small BSSE as possible. The MINI-1 basis set is characterized* by a relatively small BSSE value. 2.4. Vlbmtionrrl Spectra. The harmonic force fields and vibrational frequencies have been calculated for the optimized planar structures of adenine, thymine, their imino-cnol tautomeric forms, and both normal and tautomeric AT base pairs by the ab initio (SCF/MINI-1) and semiempirical (PM3) methods. Only the SCF/MINI-1 IR intensities are given, since a routine for calculating the IR intensities in the MOPAC program (version 5.0). which we used for the PM3 calculations, gives values in error by about 30%'' The existence of two minima on the potential energy surface for the double proton transfer has been

Hrouda et al. demonstrated by the positive values of all the SCF/MINI-1 frequencies. One imaginary frequency due to an out-of-plane vibration of the amino group has been encountered for adeninecontaining systems when the PM3 or AM1 methods and the planarity constraint on the geometry are used. The AM1 and PM3 methods are also knownlE to put the N-H bond of the a-amino group in proteins out of the plane of the peptide bond. The nonplanar geometry has also been calculated for adenine, guanine, andcytosine aminogroups using the STO-3G basisset.I9 Surprisingly, a nonplanar geometry was also found for thymine at the PM3 level. Nevertheless, the PM3 in-plane frequencies and normal modes calculated under the assumption of the planarity of adenine and thymine are in good agreement with both the MINI-1 and experimental results. Cartesian PM3 and MINI- 1 harmonic force fields, calculated as the second analytical derivatives of the total energy, have been transformed into standard sets of in-plane local symmetry coordinates,20J as proposed by Fogarassi and Pulay,22~~~ using the generalized inverse (pseudoinverse) B matrix f o r m a l i ~ m . ~ ~ * ~ ~ The redundant set of two stretching and two bending internal coordinates was introduced for the description of the intermolecular vibrational modes (cf. Table I). The spectroscopic program MOLVIB 626 was employed for evaluation of the B matrixes and scale factors and to perform normal-coordinate analysis. Instead of using the well-known GF method,27diagonalizationis performed by the MOLVIB program in mass-weighted Cartesian coordinates. The redundancies are most conveniently treatedZEusing this algorithm. All quantum chemicalcalculations of harmonic force constants at the SCF level are affected by various, partly systematic errors arising from neglect of the electron correlation and molecular environmentand from the finitenessof the basis set. These errors as well as the effect of the harmonic approximation can be corrected, at least to a certain extent, by the widely used scaling in which force constants of a similar type are multiplied by scale factors close to 1.O, obtained by fitting to the experimental vibrational frequencies. Since the influence of hydrogen bonding and tautomeric transitions on the vibrational spectra of isolated molecules is to be established in our paper, a set of scale factors determined from the gas-phase experimental data should ideally be used. However, only IR data (and no Raman spectra) of adenine and thymine embedded in lowtemperature inert-gas matrices are available,3*32 so that it is difficult to obtain the complete set of fundamental frequencies needed for fitting the scale factors. The values of scale factors18,20,2i determined from the vibrational spectra of solidstate adenine and thymine, on the other hand, already include the mean effects of intermolecular interactions. If this set of scale factors were used for the calculation of the vibrational spectra of AT base pairs, the intermolecular interactions would be taken into account twice. Therefore, we have used the single scale factor of 1.0 (no scaling) for all the intramolecular MINI-I and PM3 force constants. Two scale factors for the force constants of hydrogen bonds were adjusted to give frequencies of intermolecular vibrational modes in agreement with experimentaldata (56, 69, 106 cm-I for in-plane modes) obtained by polarized IR and Raman spectroscopieson the Hoogsten-typemethyladeninemethylthymine 1:l single crystal.33 Their values are given in Table I. As can be seen from Table I, both MINI-1 and PM3 methods strongly overestimate all the interaction force constants involving hydrogen bonds and also all the interaction force constants coupling adenine and thymine intramolecular coordinates. Consequently, a tentative scale factor of 0.2 was used for all the above-mentioned interaction force constants.

3.1. Isolated Subsystems. Optimal geometries of adenine and thymine, as well as those of A+ and T* are given in Table 11. For A and T, also the experimental geometries,taken from the crystal

Adenine-Thymine and Adenine*-Thymine* Base Pairs

The Journal of Physical Chemistry, Vol. 97, No. 8, 1993 1545

TABLE I: Internal Coordinrtes and Unscaled In-Plane Force Constants of Both Normal and Tautomeric (*) Form of A W and Tbymiae M Isolated Molecules (A, T, A*, T*) and Their Complexes (AT, A*T*) Calculated at the ab Initio SCF/MINI-l rad Semiempirid PM3 Levels (Diagonal Intermolecular Force Constants and a List of Some Significant Intermokculu Interaction Force Constants in the Last Continuation of the Table) Adenine unscaled diagonal force constants' internal coordinatesb descriDtion

MINI-1

PM3

symbol

AT

A*T*

A

A*

AT

A

N 1C2A C2N3A N3C4A C4C5A C5C6A C6N 1A CNlOA C5N7A N7C8A C8N9A N9C4A NHllA NHl2A C2HA C8HA N9HA NlHA* C6TrA D6ElA D6E2A D5R=A D5RIA DC6NA DNHSA DNHRA CD2HA DC8HA DN9HA DNlOHA* DNlHA*

7.114 8.035 6.687 7.643 6.475 7.321 7.209 6.186 9.352 6.969 7.743 8.395 6.71 1 6.004 6.264 8.230

7.370 9.033 6.097 8.016 5.886 5.837 10.013 6.359 9.189 7.061 7.881 7.889

6.903 7.843 6.874 7.592 6.621 7.344 7.877 6.143 9.351 6.984 7.682 8.450 8.487 6.165 6.252 8.25 1

7.256 9.644 6.100 8.347 5.664 6.591 10.992 6.436 9.017 7.179 7.872 7.596

7.853 9.453 8.093 8.703 8.419 7.864 7.777 7.484 9.892 6.926 7.877 6.881 5.815 4.816 5.106 6.636

7.951 9.264 8.212 8.610 8.546 8.302 8.402 7.442 9.918 6.925 7.810 6.897 6.859 4.886 5.100 6.637

1.329 1.397 1.329 1.614 1.797 0.940 0.517 0.774 0.373 0.380 0.409

1.335 1.416 1.319 1.610 1.791 0.753 0.454 0.526 0.372 0.380 0.409

~~~

stretching

bending of the 6- and 5-membered rings

C6-N 10 bending NH2 scissoring NH2 rocking C-H, N-H bending

1SO4 1.565 1.353 2.104 2.121 0.990 0.529 0.863 0.604 0.493 0.453

5.947 6.293 8.198 5.179 1.542 1.589 1.332 2.119 2.145 1.024 0.580 0.491 0.453 1.086 0.71 1

1SO6 1.573 1.368 2.102 2.1 14 0.834 0.489 0.594 0.601 0.495 0.452

6.074 6.299 8.206 8.250 1.547 1.556 1.278 2.127 2.152 0.803 0.585 0.490 0.45 1 1.011 0.540

Thymine unscaled diagonal force constants MINI-1

internal coordinates description stretching

symbol

AT

A*T*

T

NlC2T 6.608 6.326 6.751 C2N3T 6.738 5.956 6.75 1 N3C4T 5.526 8.297 6.460 C4C5T 5.098 5.318 5.090 C5C6T 9.7 15 9.436 9.862 C6NlT 7.195 7.418 7.198 1 1.059 1 1.098 11.184 C70T C80T 11.074 6.926 11.883 C5C9T 5.400 5.414 5.381 MeST 6.255 6.256 6.252 MeAT 6.354 6.352 6.352 O8HT* 4.632 C6HT 6.233 6.215 6.239 N3HT 5.747 8.207 NlHT 8.332 8.275 8.323 ring bending D6TrT 1.479 1.431 1.476 D6ElT 1.207 1.234 1.179 D6E2T 1.372 1.385 1.353 0.920 0.955 0.985 C==O bending DC7OT 0.921 DCIOT 1.007 1.154 0.666 0.669 0.676 C5-C9 bending DC5CT 0.677 0.677 0.678 CH3 sym bending DMeST 0.639 0.640 0.631 CH3 antisym bending DMeAT 0.756 0.755 0.760 CH3 rocking DMeRT 0.538 0.536 0.530 C-H, N-H, 0-H bending DC6HT DN3HT 0.515 0.684 0.543 0.539 0.529 DN 1HT D08HT* 0.953 MINI-1 internal coordinates description symbol AT Diagonal Intermolecular Force Constantsd NI(A)-H14(T) stretchr ATS 1 0.609 (0.6) 08(T)-H12(A) stretche ATS2 0.396 (0.6)

PM3

T*

AT

T

6.136 5.496 9.380 5.5 13 9.344 7.440 11.504 7.040 5.395 6.252 6.342 8.699 6.208

6.323 6.653 5.299 6.774 1 1.272 7.445 14.264 14.233 6.645 5.812 5.115

6.431 6.672 6.167 6.742 1 1.384 7.440 14.327 15.018 6.631 5.812 5.117

4.962 4.689 6.3% 1.145 1.183 1.205 0.703 0.888 0.870 0.547 0.545 0.658 0.447 0.683 0.456

4.959 6.287 6.394 1.128 1.156 1.182 0.688 0.832 0.866 0.547

8.243 1.429 1.262 1.357 0.966 1.033 0.656 0.677 0.641 0.763 0.527 0.533 1.042 A'T' 0.870 (0.6) 1.046 (0.6)

0.544

0.657 0.447 0.472 0.456 PM3 AT 0.967 (0.4) 0.871 (0.4)

1546 The Journal of Physical Chemistry, Vol. 97, No. 8, 1993

TABLE I:

Hrouda et al.

(Continued) internal coordinates description

N1 (A)-H 14(T)-N3(T) bending 08(T)-Hl2(A)-NlO(A) bending

MINI-1 symbol AT Diagonal Intermolecular Force Constantsd ATBl 0.543 (0.2) ATB2 0.444 (0.2)

Some Significant Intermolecular Interaction Force Constantd C8OT-CN 1OA 0.354 N3C4T-CSC6A 0.162 N3C4T-DNHRA 0.601 C2N3A-DN3HT 0.111 DN3HT-DNHRA 0.208 0.156 C6N 1 A-ATS 1 NH 12A-ATS2 0.297 08HT*-ATS2 C80T-ATS2 0.256 N3C4A-ATB 1 -0.095 N 3C4T-ATB2 0.501 ATS1-ATS2 -0.059 ATBl-ATB2 -0.128

A*T*

PM3 AT

0.582 (0.2) 0.695 (0.2)

0.421 (0.3) 0.395 (0.3)

0.288 0.059

0.344 0.245 0.6 IO 0.135 0.128 0.305 0.146

-0.545 1.322 -0.817 0.066 0.286 -0.115 0.023

0.324 -0,095 0.506 -0.026 -0,172

a A list of all interaction force constants and PM3 force constants for A*, TI, and A*T* is not, for the sake of brevity, given here. They can be obtained on request from the authors. For internal coordinates definitions see refs 20 and 23; for atom numbering see Figure I . All intramolecular diagonal stretching and bending (the first letter is D) force constants are given in mdyn/A and mdyn A, respectively. Scale factors used are given in parentheses. e Definition of internal coordinates pertinent to the A*T* base pair: ATSI: N3(T*)-H12(A*). ATS2: NlO(A*)-H14(T*). /All SCF/MINI-1 and PM3 interaction force constants except intramolecular ones (cf. section 2) have been multiplied by the scale factor 0.2 for the calculatioin of the AT and A*T* vibrational spectra.

structures, are presented.19 Table I1 summarizes the results obtained by the SCF/MINI-1, AM1, and PM3 procedures; for comparison, the results obtained by the SCF/3-21G procedure34 are also included. The 3-21G and experimental bond lengths are in good agreement. The semiempirical and especiallythe MINI- 1 values are larger than the experimentalvalues. The SCF/MINI- 1 procedure is known8 to overestimate the bond lengths. The bond angles calculated nonempirically as well as semiempirically (cf. Table 11) coincide fairly well with those obtained from the experiment (the differences are not larger than 4'). One strange result of AM1 for adenine should be mentioned here: the C4-CS bond becomes larger than the CS-C6 one. Let us recall that CS-C6 is considered to be a single bond while C M 5 is a double bond. This incorrect prediction has an unpleasant consequence the force constants evaluated for these bonds are qualitatively wrong. The PM3 method and the nonempirical procedure give the proper relative values for these bonds (cf. Table 11). The dipole moments of A, A*, T, and T* calculated at the SCF/MINI-1 and PM3 levels are summarized in Table 11; only thosecalculated at theSCF/MINI-1 level are depicted in Figure 1. For comparison,the dipole moments obtained e~perimentally~~ and calculated at the SCF/3-21G leveP5 are given in Table 11. Both tautomeric transitions are accompanied by a considerable change in the direction of the dipole moment, which indicates considerable reorganization of the electronic system within the molecules. In this respect, the MINI-1 and PM3 methods yield qualitatively similar results. We havealsostudied theinfluenceof the rotationofthe thymine methyl group on the energy of both the isolated thymine molecules (T,T*)and the complex. The position of the methyl group depicted in Figure 1 is energetically preferred at the nonempirical as well as semiempirical levels. The heats of formation of adenine, thymine, guanine, cytosine, and uracil (U) calculated by the PM3 and AM1 methods were compared with the experimental~ a l u e sto 3 ~estimate the reliability of these semiempirical methods in evaluating various properties of the NA basis (Table 111). From Table 111, the priority of PM3 over AM1 is clearly evident. The heats of formation were also calculatedat theSCF/MINI-1 level;becauseof the considerable discrepancy between the calculated and experimental values, which is probably caused by the extension of the minimal basis set, we postponed further discussion to an independent note. While STO-3G, 3-21G, and 4-21G ab initio calculations of adenine vibrational spectra have been p~blished,~~.32,3~.3* no

theoreticalcalculationof thymine vibrational spectra has appeared since the empirical analysis of Susi and Ard.39 Our unscaled MINI-1 and PM3 in-plane vibrational frequencies and distributions of the potential energy of isolated adenine and thymine are given in Tables IV and V. The diagonal MINI-1 and PM3 force constants are compared in Table I. The MINI-1 and PM3 methods have been found to yield similar results-they slightly overestimate the frequenciesof the ring-stretching vibrations and underestimate the in-plane bending modes. For the lowest frequency DC6N and DCSC vibrations of adenine and thymine, respectively, and the three thymine bands in the 1600-1900-~m-~ region, the PM3 results agree even better with the experimental data30-32J9,40 than the MINI-1 results. The changes in the vibrationalspectra and force fieldsof adenine and thymine induced by tautomeric transitions can be estimated by comparing the calculated results presented in Figure 2 and in Tables IV and VI (MINI-1 spectra), Tables V and VI (PM3 spectra), and Table I (force constants). From the structural point of view, the NH12 bond of adenine and N3H bond of thymine are removed and new N1 H and 08H bonds are formed in A* and T*, respectively, in the process of the tautomeric transition. For the followingdiscussion of the positions of new vibrational bands, we have considered the approximate scale factor of 0.9 for the C=N stretching force constants. This helped us to approach possible experimental findings more closely. For the sake of clarity, it should be noted that no intrasystem scaling is considered in Figure 2 and Tables IV-VI. The best utilizable experimental markers for the presence of rare tautomers might be observed in the 3000-4000- and 1500-1800-cm-' parts of the vibrational spectra. In the former, the 3-20-cm-1 frequency downshift of the stretching modes of C-H and N-H bonds, the hydrogens of which do not directly participate in the tautomeric transition, have been predicted. In the latter, the new strongvibrationalbandsdue to thecharacteristic stretching vibrations of N 3 4 4 (rare tautomer of thymine) and C6-N 10 (rare tautomer of adenine) double bonds can be predicted to appear, both in the spectral region without the presence of any fundamental band of normal tautomeric forms, Le., for thymine31J2J9 in the 1500-1630-~m-~gap and for adenine in the 1700-1800-~m-~region.30.M In addition to the CNlO bond of adenine, a significant increase of the bond order is also calculated for the C2N3 bond of adenine. The band corresponding to the stretchingvibrationof this bond has high IR intensity (high Raman

The Journal of Physical Chemistry, Vol. 97, No. 8, 1993 1547

Adenine-Thymine and Adenine*-Thymine. Base Pairs

TABLE II: Bond Lengths, Bond Angles, and Dipole Moments for A, T, A*, T*, AT, and A*T* Determined by Different Procedures and Experiment

adenine

bond, dipole momenta 1-2 2-3 3-4 4-5

5-6 6-1

thymine

5-7 7-8 8-9 9-4 6-10 10-1 1 10-12 8-14 9-15 2-13 dx dY d 1-2 2-3 3-4 4-5 5-6

AT

adenine*

thymine*

6- 1 2-7 4-8 5-9 9-10 9-1 1 1-13 3-14 6-15 dx dY d 8-12 1-14 dx (dx+) dv (dv+) d(d/)

MINI-I 1.424 1.401 1.422 1.444 1.474 1.408 1.465 1.368 1.452 1.431 1.422 1.044 1.044 1.141 1.050 1.146 0.223 2.327 2.338 1.463 1.462 1.472 1.553 1.388 1.45 1 1.300 1.295 1.569 1.134 1.138 1.047 1.049 1.141 -1.403 -3.795 4.046

A,T (single molecules) 3-2 1Gb PM3 1.337 1.371 1.347 1.325 1.378 1.332 1.414 1.381 1.420 1.395 1.334 1.371 1.407 1.395 1.339 1.292 1.414 1.389 1.401 1.367 1.371 1.339 0.988 0.996 0.989 0.996 1.093 1.063 0.988 0.995 1.098 1.068 -0.324 2.170 2.4 2.194 1.374 1.424 1.374 1.417 1.390 1.432 1.463 1.473 1.325 1.355 1.381 1.403 1.212 1.226 1.213 1.220 1.503 1.483 1.083 1.098 1.083 1.099 0.998 0.995 1.001 0.999 1.070 1.099 -1.466 -3.693 4.7 3.973

(-1.180) (-1.467) (1.883)

AM 1 1.360 1.353 1.368 1.459 1.436 1.376 1.402 1.342 1.413 1.399 1.368 0.989 0.989 1.096 0.985 1.112

1.412 1.402 1.407 1.477 1.363 1.380 1.249 1.242 1.475 1.117 1.120 0.994 0.997 1.106

exv

MINI-I

1.338 1.332 1.342 1.382 1.409 1.349 1.385 1.312 I .367 1.376 1.337

3.0 1.314 1.345 1.413 1.476 1.369 1.408 1.246 1.193 1.522

MINI-I

1-2 2-3 3-4 4-5 5-6 6-1 5-7 7-8 8-9 9-4 6-10 10-1 1 1-12 8-14 9-1 5 2-1 3 dx dY d 1-2 2-3 3-4 4-5 5-6 6-1 2-7 4-8 5-9 9-10 9-1 1 1-13 8-14

1.440 1.361 1.469 1.424 1.529 1.478 1.451 1.375 1.446 1.426 1.335 1.068 1.048 1.139 1.051 1.149 3.357 -0.037 3.358 1.483 1.492 1.360 1.524 1.397 1.437 1.298 1.434 1 S68 1.134 1.138 1.048 1.018

A*,T* (single molecules) PM3 1.398 1.322 1.404 1.402 1.448 1.444 1.394 1.349 1.406 1.396 1.293 0.988 0.995 1.093 0.987 1.100 3.181 0.1 18 3.184 1.444 1.420 1.328 1.447 1.368 1.391 1.218 1.346 1.482 1.098 1.099 0.995 0.953

AM 1

1.422 1.396 1.429 1.442 1.480 1.410 1.463 1.368 1.453 1.429 1.409 1.045 1.071 1.141 1.050 1.151

1.376 1.343 1.382 1.412 1.424 1.380 1.406 1.340 1.414 1.400 1.362 0.988 1.006 1.093 0.988 1.100

1.360 1.352 1.370 1.458 1.438 1.377 1.402 1.342 1.413 1.398 1.364 0.989 0.995 1.096 0.985 1.113

1.467 1.457 1.452 1.551 1.389 1.447 1.302 1.307 1.568 1.134 1.138 1.046 1.095 1.141

1.427 1.417 1.420 1.472 1.356 1.401 1.226 1.231 1.483 1.098 1.099 0.995 1.036 1.099

1.415 1.401 1.402 1.476 1.364 1.379 1.249 1.246 1.475 1.117 1.119 0.994 1.005 1.106

1.729 1.647 -0,883 -0.877 1.245

1.812 1.776 -1.329 -1.034 1.684

2.101 2.134

4.2

(-1.790) (-1.524) (2.351)

bond, dipole moment

AT (complex) PM3

A*T* (complex) PM3

AM 1

MINI-I

1.383 1.322 1.395 1.437 1.469 1.430 1.392 1.351 1.408 1.395 1.297 0.997 0.995 1.095 0.986 1.113

1.429 1.373 1.458 1.430 1.514 1.449 1.455 1.371 1.450 1.424 1.354 1.058 1.112 1.139 1.OS 1 1.153

1.395 1.326 1.400 1.403 1.443 1.432 1.397 1.346 1.409 1.395 1.308 0.990 1.027 1.093 0.987 1.102

AM 1 1.380 1.326 1.393 1.439 1.467 1.424 1.394 1.349 1.410 1.394 1.302 0.996 1.005 1.095 0.985

1.436 1.410 1.329 1.456 1.378 1.368 1.245 1.367 1.472 1.117 1.119 0.995 0.974

1.475 1.470 1.383 1.535 1.395 1.439 1.304 1.385 1.567 1.134 1.138 1.048 1.107

1.436 1.416 1.343 1.453 1.366 1.392 1.222 1.324 1.482 1.098 1.099 0.995 0.985

1.430 1.404 1.333 1.459 1.378 1.371 1.249 1.355 1.472 1.117 1.120 0.994 0.990

1.115

Hrouda et al.

1548 The Journal of Physical Chemistry, Vol. 97, No. 8, 1993

TABLE II: (Continued) bond, dipole moment 6-15 dx A*T*

MINI-1

A*,T* (single molecules) PM3

1.142 4.104 -2.454 4.782

d 14-10 3-1 2 dx (dx+) dY (dY+) d (d+)

1.099 -3.974 -2.439 4.663

-0.747 -2.49 1 2.600

A*T* (complex) PM3

MINI-I

1.107

1.142

1.099

1.106

1.474 1.568 -0.557 -1.610 1.704

1.741 1.788 -0.763 -2.380 2.499

1.988 2.044

-0.793 -2.321 2.453 A,T (single molecules)

angle adenine

1-2-3 2-34 3 4 5 4-5-6 5-6-1 6-1-2 4-5-7 5-7-8 7-8-9 8-9-4 9 4 5 5-6-10 6-10-1 1

thymine

AT

6-10-12 3-2-1 3 7-8-14 8-9- 15 1-2-3 2-3-4 3 4 5 4-5-6 5-6-1 6- 1-2 1-2-7 3 4 8 4-5-9 5-9-10 5-9- 1 1 6-1-13 2-3-14 5-6-1 5 4-5-9-1 1 10-12-8 4-8-12 3-14-1 14-16

AT (complex)

MINI-I

3-2 1G

PM3

AM 1

131.13 109.64 126.99 116.31 120.47 115.45 111.53 103.23 113.57 106.34 105.33 121.16 1 18.44 117.98 114.88 124.77 128.07 114.36 126.04 1 15.00 118.93 123.10 122.57 122.51 120.45 116.45 110.10 109.35 121.24 116.04 121.38 59.17

126.48 113.42 125.04 117.29 117.90 119.87 110.11 105.40 112.16 106.86 105.47 122.71 120.87 118.88 117.18 125.84 127.65 113.21 127.88 114.46 118.48 122.81 123.16 123.24 120.87 117.06 110.50 111.01 120.70 115.71 121.91 59.55

125.52 114.70 123.93 117.51 118.26 120.09 108.67 107.67 110.11 107.28 106.28 124.43 119.72 120.94 117.92 124.77 126.16 118.03 121.71 117.03 120.58 121.57 121.08 120.13 115.56 117.86 112.17 110.74 119.70 118.13 122.20 59.52

130.31 1 12.44 123.82 117.1 1 118.74 117.58 109.92 105.03 113.59 106.20 105.26 120.25 119.02 120.89 115.22 125.27 127.51 118.05 122.83 116.49 119.67 122.09 120.88 120.09 1 18.53 117.12 111.33 109.95 121.61 117.30 122.28 59.22

exP 129.0 110.8 126.9 116.9 117.6 118.8 110.7 103.9 113.8 105.9 105.7 123.4

118 126 114 119 120 123 122 121 119

MINI-1

PM3

AM 1

130.29 109.38 127.46 116.80 118.40 1 17.67 111.55 103.30 113.38 106.42 105.35 122.19 116.01 120.35 1 15.94 124.94 128.20 115.44 124.44 116.76 118.45 122.57 122.34 121.48 121.01 116.75 110.18 109.34 121.33 116.44 121.60 59.14 177.3 1122.49 178.4 I + 121.91

125.57 114.75 123.97 117.87 1 17.70 120.14 108.68 107.67 110.00 107.29 106.35 124.69 118.84 121.42 118.16 124.81 126.15 118.56 120.78 118.11 120.27 121.28 121.00 119.30 116.19 118.24 112.17 110.75 119.65 118.61 122.23 59.53 175.99128.42 176.98+ 122.77

130.09 112.47 123.87 117.23 118.31 1 18.03 109.92 105.06 113.53 106.20 105.29 120.57 118.78 121.42 115.50 125.32 127.50 118.20 122.53 116.90 119.58 121.92 120.87 119.60 118.87 117.29 111.33 109.91 121.60 117.38 122.28 59.22 174.44127.45 176.09+ 120.53

A*,T* (single molecules) adenine*

thymine.

angle 1-2-3 2-34 3 4 5 4-5-6 5-6-1 6-1-2 4-5-7 5-7-8 7-8-9 8-94 9 4 5 5-6-10 6-10-1 1 6-1-12 3-2-1 3 7-8-14 8-9-1 5 1-2-3 2-3-4 3 4 5 4-5-6 5-6-1 6-1-2 1-2-7 3 4 8

MINI-I 127.64 109.31 128.96 119.89 109.53 124.67 11 1.43 103.81 112.41 106.45 105.88 131.95 107.15 115.62 1 17.47 125.35 128.26 117.47 1 15.69 128.58 114.42 120.75 123.08 119.21 116.25

PM3 124.33 115.48 124.59 119.95 113.10 122.55 108.76 107.79 109.47 107.34 106.64 131.44 116.73 119.1 1 117.07 124.76 126.26 117.84 118.86 124.52 117.05 120.74 120.99 118.01 116.28

AM 1

AMI

A*T* (complex) AMI 128.22 113.32 124.06 120.26 112.26 121.88 110.20 104.98 112.96 105.96 105.91 127.95 114.49 118.39 116.51 125.32 127.64 119.33 117.72 124.98 1 15.87 121.52 120.58 116.81 120.01

MINI-1 128.33 108.91 128.86 1 18.69 111.95 123.26 111.55 103.66 112.61 106.58 105.60 128.71 108.97 1 15.66 118.15 125.33 128.26 117.80 118.82 123.79 116.32 121.23 122.04 120.02 120.48

PM3 124.64 115.28 124.49 119.61 113.96 122.02 108.73 107.78 109.54 107.34 106.61 129.51 114.69 118.89 117.54 124.83 126.20 118.73 119.02 123.02 117.89 120.80 120.54 118.70 118.18

AM 1 128.24 113.19 124.11 120.02 112.63 121.82 110.17 104.99 113.00 105.98 105.86 127.03 114.34 118.60 116.86 125.38 127.61 119.63 118.40 123.83 116.30 121.59 120.25 117.62 120.88

The Journal of Physical Chemistry, Vol. 97, No. 8, 1993 1549

Adenine-Thymine and Adenine*-Thymine* Base Pairs

TABLE II: (Continued)

A*T*

angle

MINI-I

4-5-9 5-9-10 5-9-1 1 6-1-13 4-8-14 5-6-15 4-5-9-1 1 8-14-10 14-10-6 3-12-1 2-3-1 2

120.10 109.64 109.64 120.83 105.00 122.31 59.46

A*.T* (single molecules) PM3 121.02 111.90 110.92 119.04 109.19 121.82 59.71

A*T* (complex) AM 1

MINI-I

PM3

AM 1

120.74 111.30 110.07 121.11 109.96 121.40 59.30

118.73 109.83 109.44 121.25 113.22 122.04 59.22 177.05td 127.30 173.70+ 113.81

120.49 1 1 1.98 110.86 119.36 113.10 121.89 59.64 17 1 . W 124.45 172.87+ 114.12

120.40 1 1 1.34 110.00 121.19 111.10 121.50 59.23 176.60+ 127.43 168.22+ 1 1 1.58

For atom numbering see Figure I . Orientation of dipole moments (debye); x axis oriented in the N I X 2 direction for A and in C 4 N 3 direction for T, y axis perpendicular to x as indicated in Figure 1 . For definition of d+ see section 3.2.1. References 34 (geometries) and 35 (dipole moments), t (-) mean that the torsion angles (C6-N10-H12-08 and CZ-N3-H14-N1, CReference~19 (geometries) and 35 (dimle . . moments).I dSvmbols . respectively) are'i80O ( O O ) . '

TABLE IIk Heats of Formation (kcal/mol) for Adenine, Thymine, Guanine, Cytosine, and Uracil Determined by Two Semiempirical Methods and Experiment' adenine thymine guanine cytosine

ArH(298 K) PM3 AMI exp

57 -76 87 -61 4 9 f 2 -79h 1

10 49 0.5

uracil

-12 -67 3 -54 - 1 4 f 2 -72f0.5

Reference 36.

intensity can also be expected for this mode) and it should appear in the 16W1650-cm-' region in the experimental vibrational spectra. 3.2. Base Pairing. 3.2.1. Geometries and Dipole Moments. The geometries of AT and A*T* complexes evaluatedby gradient optimization using the SCF/MINI-1, AMI, and PM3 methods are summarized in Table 11, while the atom numbering and the optimal SCF/MINI-1 structures are depicted in Figure 1. The shortest intermolecular distances were found using the SCF/MINI-1 procedure, while PM3 and especially AM1 yield larger values. It is well-known*that the lengths of the hydrogen bonds are underestimated by the SCF/MINI-1 method. This is probably also true for the AT and A*T* complexes. The AM1 values are, on the other hand, clearly too large. The intramolecular geometry changes due to the complex formation can be easily deduced from the entries in Table 11. In the following discussion, we will focus our attention mainly on the SCF/MINI-1 values. The AT complex will be discussed first. The intrasystem geometry reorganization of both subsystems is rather small but should not be, in general, neglected. It is not surprising, that the geometry characteristics alter considerably mainly in the region of the hydrogen bonds. As expected, the most pronounced shift in the bond length can be found for the N-H bonds which directly participate in the hydrogen bonds. The N10-Hl2 bond of adenine and N3-Hl4 bond of thymine are len thened by 0.027 and 0.046 A (SCF/MINI-I), 0.017 and 0.037 (PM3) and 0.006 and 0.008 A (AM1). Evidently, the PM3 relative geometries are closer to the SCF/MINI-1 values. Further, the N10-Hl2 bond of adenine is modified more than the N3-Hl4 bond of thymine. On the other hand, the bond angles of thymine are distorted less than those of adenine. These distortions are smaller than 1.5O (except the C2-N3-C4 and N 3 - C K 5 angles) for thymine and larger than 2O not only for angles of the NH2 group (angles C6-Nl0-Hll and C6-Nl0H12) but also for the ring angles (angles C 5 4 6 - N l and C6Nl-C2) in adenine. The intrasystem geometry changes in A*T* are moresignificant than those calculated for the AT complex. In the A* molecule (further discussion concerns the MINI-1 values), the C b N l and C6-N10 bond lengths are shifted by 0.029 and 0.019 A, respectively, and the N1-H12 bond length by 0.064 A. The N 3 4 4 and C4-08 bond lengths of the T* molecule are changed

f

by 0.023 and 0.049 A, respectively, and the 08-H14 bond length is increased by as much as 0.089 A. The bond angles are distorted even more than those in the AT complex; this is especially true of the T* molecule. While the C5-C6-N1 and CS-C6-N10 angles in A* are changed by 2' and 3O, respectively, the C2N3-C4 and N3-C4-C5 ring angles in T* are changed by 3O and So, respectively, and the N3-C-8 and C4-08-Hl4 angles increase by 4O and 8O, respectively. The PM3 and AM1 bond length and bond angle changes were found to be smaller but relatively corresponding with the SCF/MINI-1 values. The dipole moments of all the subsystems and complexes calculated at the SCF/MINI-1 and PM3 levels are depicted in Figure 1 and Table 11. Considering the large dipole moments of A and T, the dipole moment of the AT complex is rather small. The explanation is obviousfrom Figure 1;since the dipole moments of A and T are almost antiparallel (when the subsystems are considered to be in the same position as in the complex but with the hydrogen bonds lengthened to infinity) and do not differ significantly in length one from another, their vector sum (in Figure 1 denoted.by is a relatively small vector. Vector is further diminished in process of AT base-pairing. 3.2.2. Interaction Energy. Interaction energies AE' (eq 5 ) evaluated by the SCF/MINI-1, PM3, and AM1 methods are given in Table VII. It should be emphasized again that the interaction energy for each complex is evaluated with respect to its free subsystems (see section 2.2). Hence, the larger value of AE'obtained for A*T* does not mean that the A*T* complex is more stable than the AT one. From the A values (cf. Table VII) it is evident that AT is more stable than A*T* at all the computational levels. The geometry relaxation calculated at the SCF/MINI- 1level is surprisinglylarge; it incream the interaction energy (understand in absolutevalue)from-12.88 kcal/mol (only intermolecular modes 0ptimized)'O to -17.03 kcal/mol (32%). The energy differenceA between the AT and A*T* pairs is rather small, about 9.5 kcal/mol. This is considerably less than the valueof 5 1.5 kcal/molobtained previously by Kong et ala2without complete geometry optimizationat the SCF/STO-3G level. Such a strong overestimationof A is caused partly by the choice of the basis set but mainly it is due to the use of the frozen subsystem approximation. The semiempiricalinteraction energy values are considerably smaller than the nonempirical values; this is especially true of the AM1 values. The relative stability of both pairs is, however, predicted correctly by the semiempiricalmethods. Here, again, the PM3 values are closer to the nonempirical results. Table VI1 contains the interaction energies which are not corrected for the BSSE. This correction is, however, rather important for the base pairs.10 Table VI11 gives the values of the real interaction energy ( M )evaluated by eq 3, as well as other energy characteristics (reorganization energy, BSSE)calculated at the SCF and MP2 levels with the MINI-1 and MIDI-1 basis sets.

a)

Hrouda et al.

lSS0 The Journal of Physical Chemistry, Vol. 97, No. 8, 1993

TABLE IV: Calculated (SCF/MINI-1) Influence of the Watson-Crick Type of Hydrogen Bondihg on the In-Plane Gas-Phase Vibrational Spectra of Adenine and Thymine (Three Intermolecular Modes Included)’ freq

int

adenine main contributions to the PED (%)*

239 476 506 592 691

13.2 3.7 3.8 2.0 0.5

DC6N (56), D6E2 (16), DNHR (10) D6E2 (30), DC6N (28), DNHR (9) D6E1 (77) D5RI (35), D6E2 (25), C5C6 (19) N3C4 (25), D5RI (12), C5C6 (10)

854 927 1004 1075

13.2 8.0 6.5 28.0

D6Tr (53), D6E2 (12) DSR= (69) DNHR(42),C6NI (28) DC8H (33), C8N9 (27), DN9H (21)

1134 1195 1213

2.9 127.9 30.5

DN9H (23), C8N9 (17), DC8H (12) N l C 2 (35). N3C4 (15), C6N1 (13) DC2H (21), DC8H (17), DNHR (17), D5RI (10)

1256 1323 1373 1417 1531 1550 1579 1628 1711 1719

31.7 1.8 34.0 30.1 4.2 29.5 35.0 65.6 463.6 157.3

C2N3 (45), DNHR (15), C6N1 (9) DC2H (41), C5C6 (9) C5N7 (41), D6Tr ( l l ) , N1C2 (lo), C6N1 (9) C8N9 (32), DN9H (31), DC2H (10) N9C4 (30), C4C5 (15), N7C8 (13), DNHS (11) DNHS (29), C6N1 (17), N9C4 (13), C2N3 (9) N7C8 (52), DC8H (9) DNHS (37),CNlO (19),C4C5 (11) CNlO (21), C4C5 (20), CSC6 (lo), N3C4 (9) C5C6 (27), N3C4 (14), D5RI (9), N9C4 (9)

3379 3409 3826 3885 4025

269.1 327.6 582.9 500.8 227.4

C2H (98) C8H (98) N H l l (52), N H l 2 (48) N9H (99) NH12 (52), N H l l (48)

freq

int

main contributions to the PED (56)

233 343 414 504 546 703 772 937 1021 1145 1224 1287 1379 1431 1456 1483 1529 I550

4.5 19.3 16.1 2.9 0.3 1.0 1.7 0.7 6.6 49.7 36.9 5.3 3.2 44.4 22.6 20.0 21.5 140.1

DCSC (62), D C 8 0 (16), D6E1 (9) DC70 (44), D C 8 0 (22), D6E1 (13) D6E2 (70), D C 7 0 (9) D6E1 (36), DC8O (25), DC70 (13) D6E1 (27). DC70 (20). DC8O (16), DC5C (12) C4C5 (38), C5C9 (1 5 ) D6Tr (53), C5C9 (13) N1C2 (31), C2N3 (IS), D6Tr (13) DMeR (59), C5C6 (9) DC6H (28), D N l H (18), C6N1 (15), DMeR (10) N3C4 (25), DC6H (21), DN3H (20), C5C9 (1 1) C5C9 (22), C6N1 (21), DC6H (21), D N l H (14) DN3H (46). DC6H (1 3) D N l H (36), DMeS (15), N3C4 (10) DMeS (56), C5C9 (IO), C2N3 (9) C2N3 (20), N l C 2 (15), N3C4 (14), DMeS (14) DMeA (66), N1C2 (7) DMeA (20), C6N1 (14), C4C5 ( l l ) , D N l H (9)

1793 1819 1854

30.3 259.0 457.9

C 8 0 (54). C5C6 (22) C 7 0 (56), N l C 2 (9) C5C6 (42), C 8 0 (16)

3306 3402 3459 3868 3898

85.3 233.1 84.5 320.3 405.6

MeST (99) C6H (99) MeAT (99) N3H (99) N1H (99)

freq

int

57 61 116 29 1 486 504 600 678

3.2 0.6 1.o 38.2 7.1 18.1 21.7 1.5

859 932

21.8 13.2

1070 1103 1122 1191 1243

24.9 12.0 8.8 49.5 142.7

1273 1346 1365 1422 1519 1563 1578

10.0 9.9 22.2 62.4 8.5 90.8 14.4

1677 1707 1782 3338 3412 3525 3880 3931

55.7 169.9 506.5 261.7 636.6 2864.0 519.1 363.6

complex main contributions to the PED (%) ATBl (39), ATSl (20), ATSZ (14), ATBZ ( 5 ) ATBZ (39), ATBl (16), ATSZ (12), ATSl (9) ATSl (41), ATSZ (39) DC6NA (30), D6E2A (16), ATSZ (14) DC6NA (25), D6E2A (18), D6ElA (14) D6EIA (48), D6TrA (9) DSRIA (27), D6E2A (19), CSC6A (18) N3C4A (23), D5R;A (IS), D6E2A (9), CNlOA (9) N9C4A (9) D6TrA (48), D6E2A ( 1 1) DSR=A (71) DCIHA (32), C8N9A (22), DN9HA (16), D5RIA (11) C6NIA (28), DNHRA (17), NlC2A (9) DN9HA (21), C8N9A (20), DNHRA (10)

DCsHA(35),DN9HA(9),DNHRA(9) NlC2A (25), DNHRA (1 l), DC2HA (IO), CSN7A (9) N3C4A (9) DC2HA (30), C2N3A (23), DNHRA (20) C3N3A (18). DC2HA (17), DNHRA (13), CSC6A (9) CSN7A (35), NlC2A (14), D6TrA (I]), C6NIA (9) DN9HA (29), C8N9A (27), DC2HA (lo), NlC2A (10) N9C4A (31), C4CSA (17), DNHSA (IO), N7C8A (9) C6NlA (19), DNHSA(14).N9C4A(12),CNlOA(II) N7C8A (52), DCIHA (9) C4CSA (26), C5C6A (12), C2N3A (12), DNHSA (12) N3C4A (18), C5C6A (15), N9C4A (12), C6NlA (10) DNHSA (43), CNlOA (31) C2HA (99) C8HA (98) NHl2A (91), N H l l A (6) N9HA (99) N H l l A (95)

thymine

complex

freq 247 347 431 563 699 779 925 1017 I128 1198 1288

int 1.4 111.6 19.9 13.0 45.8 32.4 11.2 23.8 31.4 30.2 27.7 25.5

1402 1441 1464 1530 1548 1618

25.4 14.6 32.6 8.4 136.2 5.2

1764 1809 1855 3285 3307 3400 3459

52.3 83.7 585.1 3468.0 80.3 634.2 571.6

3900

476.0

505

main contributions to the PED (96) DCSCT (58) DC7OT (30), DC8OT (23), N3C4T (10) D6E2T (74) D6EIT (27), DC8OT (18), DC70T (17) D6ElT (24), DC7OT (21), DC8OT (16), DCSCT (10) C4C5T (36), C5C9T (I]), N3C4T (IO), D6EIT (9) D6TrT (56), CSC9T (14) NlC2T (28), C2N3T (13) DMeRT (46), D6TrT (12), C5C6T (9) DMeRT(19), DNlHT(1l),N3C4T(10),C6NIT(10) DC6HT (39), N3C4T (16), DN3HT (12) C5C9T (25), C6NlT (21), DC6HT (17), D N l H T (13) C4C5T (20). D N l H T (20), DC6HT (10) C2N3T (32), NlC2T (22), D N l H T (12), DC7OT (10) DMcST (74), C5C9T (15) DMeAT ( 5 5 ) , NlC2T (lo), D N l H T (9) DMeAT (30), C 6 N l T (la), D N l H T ( l l ) , NIC2T (9) DN3HT (27), C 7 0 T (18), C8OT (la), C4CST (13) N3C4T (10) C 8 0 T (53), C5C6T (14), N3C4T (9). DN3HT (9) C 7 0 T (43), C5C6T (17), NlC2T (9) CSC6T ( 3 9 , DN3HT (IO), C 7 0 T (9) N3HT (92), ATSl ( 5 ) MeST (97) C6HT (99) MeAT (99) N 1 H T (99)

For pertinent force fields and scale factors see Table I. * The frequencies are given in cm-I, IR intensities (absolute integrated molar absorption coefficients) in km/mol. Only contributions greater than 8% for the potential energy distributions (PED) are included (in several special cases, when it seems significant, contributions smaller than 8% are given). a

Let us first analyze the SCF/MINI- 1 results. T h e reorganization energy (AErMrg) is relatively small for t h e A T complex; t h e opposite is true, however, for A*T*. This is in agreement

with t h e pronounced changes in the geometry of A* and T* when passing from the isolated subsystems to A*T* (see above). The BSSE for A*T* is relatively larger than that of AT; in both cases,

Adenine-Thymine and Adenine*-Thymine* Base Pairs

The Journal of Physical Chemistry, Vo1.97, No. 8, 1993 1551

TABLE V: Calculated (PM3) Influence of the Watson-Crick Type of Hydrogen Bonding on the In-Plane Gas-Phase Vibrational Spectra of Adenine and Thymine (Three Intermolecular Modes Included)' frep

277 493 509 600 744 848 918 995 1049 1063 1164 I201 1293 1339 1395

adenine main contributions to the PED (%)b

DC6N (68), D6E2 (la), D5RI (7) D6E2 (42), DC6N (29), D6Tr (10) D6E1 (76), D5RI (6), CNlO (6) D5R; (47), D6E2 (26), C5C6 (IO), D6E1 ( 5 ) D5R= (39). N3C4 (11). . . C5C6 (10). CNlO (9) N9C4(9) . D6Tr (44), D5R= (22), D6E2 (10) D5R=(30), C5N7 (13), D6Tr ( I l ) , C4C5 (10) C5C6 (9) DC2H'(40), DNHR (36), C6N1 (11) DC8H (47). DNHR (18) DC2H (33), DC8H (25), DNHR (24) DN9H (32), C8N9 (31) N1C2 (22), N3C4 (22), DN9H (14), C6N1 (10) N9C4 (18), N1C2 (13), CNlO (11). C8N9 (10) C5C6 19) C2N3 i44), C6N1 (17) C8N9 (37), DN9H (26), N1C2 (16)

freq

62 68 130 329 494 510 614 73 1 846 920 1023 1055

1141 1162 1197 1290 1356 1394

complex main contributions to the PED (7%) ATBl (51), ATBZ (16), ATSl (13) ATBZ (32), ATSl (26), ATSZ (13), ATBl (7) ATS2 (45), ATSl (34), DC6NA (7) DC2OT (26), DC6NA (15), DC5CT (12) D6ElA (32), DC6NA (18), D6E2A (13), DNlOA (9) D6ElA (33), D6E2A (22), DC6NA (17), D6TrA (9) D5RIA (40), D6E2A (20), D6ElA (9) D5R=A (30), CNlOA ( l l ) , N3C4A (lo), C5C6A (10) N9C4A (9) D5R=A (34), D6TrA (33), D6ElA (8) D5R=A (24), D6TrA (17), C5N7A (12), C5C6A (9) C4C5A (9) DC2HA (74) DC8HA (70) DNHRA (48) DNHRA (18), C8N9A (IS), C6NlA (13), DN9HA (12) DN9HA (26), N3C4A (19), NlC2A (17), C6NlA (11) NlC2A (21), C8N9A (13), N9C4A ( l l ) , C5N7A (11) C2N3A (33), DNHRA (15), C6NlA (12) NlC2A (24). C8N9A (13). . . DN9HA (13). . . C6NlA (12) C5N7A (9) ' C5N7A (31), C8N9A (21), DN9HA (12) N9C4A (34), C4C5A (25), DNHSA (lo), CNlOA (9)

1409 1490

1563

C5N7 (39), C4C5 (15), N1C2 (IO) N9C4 (33), C4C5 (23), CNlO (12), DNHS (1 1) D6Tr (11) DNHS (26), C6N1 (24), C2N3 (13)

1588 1637 1709 1767

N7C8 (69), C2N3 (9) DNHS (49), CNlO (29), C6N1 (9) N3C4 (33). C4C5 (24), N9C4 (9) C5C6 (45), C2N3 (9)

1587

C6NlA (25), C2N3A (18), CNlOA (14), C4C5A (9) N7C8A (9) N7C8A (65), C2N3A (1 1)

3001 3069

C2H (99) C8H (99)

3476 3501 3557

N9H (99) NH12 (59), N H l l (41) N H l l (60), NH12 (40)

1702 1749 1852 298 1 3071 3345 3475

N3C4A (31), C4C5A (17), N9C4A (11) C5C6A (34), C4C5A (14). C2N3A (1 1) DNHSA (50), CNlOA (24) C2HA (99) C8HA (99) NHl2A (93) N9HA (99)

3533

N H l l A (99)

1422 1509

1564

thymine freq 304 346 429 499 554 749 822 963 999 1132 1207 1267 1339

main contributions to,the PED (7%) DC5C (71), DC80 (13) DC70 ( 5 5 ) , DC80 (29)

freq 308 359

D6E2 (83) D6E1 (41), DC80 (27), D C 7 0 (15) D6E1 (32), DC80 (22), DC5C (18), DC70 (15) D6Tr (76), C5C9 (9) C4C5 (39),CSC9(11),N3C4(1l),NlC2(9) C2N3 (9) N l C 2 (35), C2N3 (19), C4C5 (12), DC6H (9) DMeR (78) DC6H(54),C6Nl ( l l ) , D N l H ( l O )

438 50 1 567 754 813

1402 1436 1509

N3C4 (40). DN3H (14), DC6H (13) D N l H (34), C5C9 (18), DMeS (17), C6N1 (15) N l C 2 (22), C4C5 (14). DMeS (12), D N l H (11) C2N3 (9) DN3H'(41), N3C4 (la), D N l H (14), C6N1 (9) C2N3 (28), DN3H (17), DMeS (16), N1C2 (14) DMeA (11) DMe (74). C2N3 (6) DMe (33), C5C9 (25), C6N1 (17) C4C (23), C6N1 (16), C5C9 (1 1). N3C4 (10)

1816 1898 1941

C5C6 (74) C 7 0 (78) C 8 0 (80), C4C5 (9)

302 1 3087 3179 3378 3409

C6H (99) MeAT (99) MeST (99) N3H (99) N l H (99)

1362 1380

complex

954 999 1122 1166 1266 1343

main contributions to the PED (96) DC5CT (47), DC6NA (19) DC80T (21), DC70T (18), ATSZ (la), DC5CT (10) DC6NA (9) D6E2T (82) DC8OT (27), D6ElT (26), DC7OT (25) D6ElT (38), DC80T (14), D C 7 0 T ( l l ) , DCSCT (11) D6TrT (76), C5C9T (9) C4C5T (38), N3C4T (13), C5C9T (9) NlC2T (33), C2N3T (16), DMeRT (13) DMeRT (66) DC6HT (18), C6NlT (15), N3C4T(11), D N l H T (11) DN3HT (9) DC6HT (39), N3C4T (22), DN3HT (10) D N l H T (33), C5C9T (19), DMeST (18), C 6 N l T (14) NlC2T (21), D N l H T (IS), DMeST (14), C4C5T (13) C2N3T (12)

1367

C2N3T(32), DMeST(19), NlC2T(l5), DNlHT(11)

1401 1437 1502 1864 1890 1909 2999 3021 3087 3179

DMeAT (82) DMeST (351, C5C9T (27), C6NlT (17). D N l H T (9) C4C5T (25), C6NlT (13), C5C9T (12), D N l H T (8) NlC2T (9) DN3HT (61), N3C4T (13), ATBl (12) C5C6T (46), C 7 0 T (24), C 8 0 T (10) C 8 0 T (44), C5C6T (19), C4C5T (9) C 7 0 T (51). C 8 0 T (24) N3HT (92). ATSl (7) C6HT (99) MeAT (99) MeST (99)

3410

N 1HT (99)

1667

For pertinent force fields and scale factors see Table I. The frequencies are given in cm-I. Only contributions greater than 8% for the potential energy distributions (PED) are involved (in several special cases, when it seems significant, contributions smaller than 8% are given).

Hrouda et al.

1552 The Journal of Physical Chemistry, Vol. 97, No. 8, 1993 IR Intensity (logaritmic scale)

3 676

i678

I691

DSR: 1076

DSH=

DCBH

DCBH

1075

1070

&llJz 1176 ,

1191

m

N9C4 1628

DNHS

\

- 233

-343 -414

D6E2

''----) CEO

1793 C5C6

I

t

Q

thy minec (isolated)

-

1819 --'Io 1854 C5C6

thymine (isolated)

17641809 1855 thymine (complex)

Figure 2. Influence of the Watson-Crick hydrogen bonding and the tautomeric transition on the in-plane vibrational spectra of adenine and thymine calculated at the SCF/MINI-1 level (cf. Tables IV and VI). All the characteristic vibrations are denoted by the symbol of the dominant internal coordinate (we have considered the vibration which involves at least one internal (dominant) coordinate contributing more than 30% to the PED as characteristic). Two vibrational bands corresponding to the same characteristic vibration are interconnected (-). The symbols of the remaining characteristic vibrations are given in frames. Arrows point to the vibrational bands into which a significant part (contribution greater than 20%to the PED) of the respective internal coordinate was transferred (cf. Tables IV and VI).

Adenine-Thymine and Adenine*-Thymine* Base Pairs

The Journal of Physical Chemistry, Vol. 97, No. 8,1993 1553

TABLE VI: Calculated SCF/MINI-l and PM3 In-Plane Gas-Phase Vibrational Spectra of A*, T*, and A*T* Adenine. MINI-1

frtx

int

258 478 489 575 676 880 944 1043 1076 1132 1176 1246 1311 1346 1411 1474 1513 1545 1610

3.1 23.4 3.6 1.o 0.3 8.4 8.8 12.2 23.2 5.7 72.9 71.7 5.9 60.0 13.4 67.7 61.3 32.4 0.0

1672 1694 1838 3355 342 1 3717 3873 388 1

16.6 269.4 263.6 309.4 359.6 275.3 754.7 186.2

PM3

main contributions to the PED DC6N (49). D6E2 (24), C5C6 (7) D6E2 (28), DC6N (25), D6E1 (lo), N9C4 (9) D6E1 (70), D6Tr (8), DC6N (6) D5Rl (36), D6E2 (23), C5C6 (20), DC6N (6) N3C4 (26), C5C6 (1 l), C6N1 (9), N9C4 (7) D6Tr (57), D6E2 (9), D6E1 (7) D5R= (80) C6N1 (25), N1C2 (IS), DNlOH (15), DC2H (11) DC8H (30), DN9H (21), C8N9 (20), D5RI (7) DN9H (22), C8N9 (19), N l C 2 (9), D N l H (8) DC8H (29), D N l H (18), N l C 2 ( l l ) , DN9H (10) DC2H (29), DNlOH (26), DC8H (9), D N l H (6) DC2H (48), N3C4 (8), DC8H (3,C2N3 ( 5 ) C5N7 (36), DNlOH (24), N3C4 ( 5 ) C8N9 (34), DN9H (22), C5N7 (lo), DNlOH (5)

frcq

main contributions to the PED (%)

296 479 494 590 732

D66N (61), D6E2 (19) D6E2 (32), D6E1 (27), DC6N (20) D6E1 (sa), D6E2 ( l l ) , DC6N (lo), D6Tr (10) D5Rl (46), D6E2 (25), C5C6 (1 1) D5R= (31), N3C4 (12), C5C6 (12), D6Tr (10) C6N1 (9), N9C4 (9) D6Tr (49), D5R= (21) D5R= (40), D6Tr (9), C4C5 (9) DC2H (30), DNlOH (28), C6N1 (20) DC8H (78) DC2H (49), DNlOH (35) N1C2 (24), C8N9 (21), DN9H (15), D N l H (15) DN9H (42), N1C2 (16), D N l H (15), C8N9 (10) N3C4 (21), DC2H (12), DNlOH (lo), N9C4 (10) C5N7 (27), D N l H (14), DNlOH (12), C6N1 (11) C8N9 (IO) C8N9 (25), C5C6 (9), N9C4 (9) D N l H (28), N1C2 (27), C5N7 (1 l), C6N1 (1 1) C8N9 (15), N9C4 (14), C5N7 (12), DN9H (1 1) N7C8 (49), N9C4 (18), D5Rl (10) C2N3 (21), C5N7 (15). C5C6 (13), N7C8 (12) N9C4 (11) C2N3 (44), N3C4 (18) C4C5 ( 4 9 , N3C4 (16), C2N3 (12) CNlO (63), C5C6 (24) C2H (99) C8H (99) N l H (99) N9H (99) N H l l (99)

84 1 908 101 1 1051 1113 1165 1189 1269 1319

DNlH(39),NlC2(12),DNlOH(ll),C5N7(7) N7C8 (41), N1C2 (9), D5RI (8), C6N1 (8) N9C4 (26), N7C8 (14), C8N9 (9), C6N1 (8) N9C4 (16), C4C5 (14), C2N3 (12), C5C6 (12) N7C8 (9) C4C5 (40), N3C4 (21), CNlO (9), DN9H (7) C2N3 (50), N1C2 (9), DC2H (8), D6E2 (6) CNlO (57), C5C6 (14), C6N1 (7), C4C5 (6) C2H (99) C8H (99) N H l l (99) N9H (86), N l H (13) N l H (86), N9H (13)

1375 1420 1455 1551 1618 1669 1717 1875 2986 3074 3403 3478 3490

Thymine* MINI-1

PM3

freq

int

main contributions to the PED (5%)

234 335 437 497 54 1 705 759 912 1024 1130 1266 1277

3.8 14.6 5.6 4.0 3.8 2.6 3.4 12.0 12.3 85.8 52.4 11.4

1320 1358 1460 1488 1531 1554 1666 1800 1821 3 306 3395 3456 3879 3960

114.4 29.8 9.9 10.3 3.5 124.6 160.9 162.1 414.9 81.9 234.4 82.5 426.9 201.6

DC5C (62), DC80 (18), D6E1 (9) DC80 (33), DC70 (28), D6E1 (9), DC5C (8) D6E2 (76), DC70 (9) DC70 (31), DC80 (30), D6E1 (18) D6E1 ( 4 9 , C 8 0 (1 l), DC70 (lo), DC5C (8) C4C5 (32), C5C9 (14), D6E1 ( l l ) , C2N3 (10) D6Tr (51), C5C9 (14), C 7 0 (6) N1C2 (28), C2N3 (21), D6Tr (12), C4C5 (10) DMeR (as), C5C6 (10) DC6H (37), D N l H (14), C6N1 (12). C2N3 (9) C 8 0 (20), D08H (14), DC6H (lo), D6Tr (10) D N l H (18), DC6H (17), C6N1 (17). C2N3 (12) N1C2 (9), C 8 0 (9) D08H (32), C5C9 (18), C4C5 (12) NlC2(19),C2N3 (l6),DC6H(14),D04H (13) DMeS (82), C5C9 (14) D N l H (35), C6N1 (33), C 7 0 (8) DMeA (74), C 8 0 (8) C 8 0 (30), N3C4 (20), DMeA (17), C4C5 (8) N3C4 (33), C4C5 (20), C5C6 (19), D08H (1 1) C 7 0 ( 5 9 , C5C6 (14), N l C 2 (6) CSC6(32),C70(17),N3C4(11),C6Nl (11) McS(99) C6H (99) MeA(99) NlH(99) 0 8 H (99)

freq 284 323 441 486 557 746 838 959 999 1141 1243 1264 1302 1332 1399 1437 1443 1590 1691 1800 1935 3022 3086 3180 3409 3851

main contributions to the PED (%) DC80 (48), DC5C (40) DC70 (44), DC5C (26), DC80 (15) D6E2 (80), DC70 (10) DC70 (31), DC80 (30), D6E1 (la), DC5C (16) D6E1 (58), DC5C (1 1) D6Tr(70) C4C5 (32), C5C9 (18), C2N3 ( l l ) , N1C2 (10) N1C2 (41), C4C5 (13), C2N3 ( l l ) , DC6H (10) DMeR(82) DC6H (60), D N l H (10) C2N3 (24), D N l H (19), C6N1 (18), NlC2 (13) D08H (56), C 8 0 (11) D N l H ( 2 3 , N1C2 (14), D08H (13), C2N3 (11) DC6H (10) DMeS (44), C2N3 (IS), C 8 0 (10) DMeA (84) DMeS (37), C5C9 (27) C6N1 (47), D N l H (21) C 8 0 (43), C4C5 (18), N3C4 (17) C5C6 (29), C4C5 (26), N3C4 (25) C5C6 (42), N3C4 (23) C70(84) C6H(99) MeA(99) MeS (99) NlH(99) 08H(99)

Adenine*-Thymine.

frca 68 82 147 259 335 378 44 1

MINI-1 main contributions to the PED (4%) . . ATSl (22), ATBZ (20), DC40T (lo), D6ElT (8) ATBl (34), ATSl (14), ATB2 (lo), DC6NA (10) ATSl (33), ATSZ (28), DC5CT (13) DC5CT (53). DC6NA (9) D6E2A (20), ATSZ (16), DC6NA (14), DC70T (10) DC5CT (9) DC7OT (28). DC8OT (la), ATSZ (lo), ATBZ (9) D6E2T (71). DC7OT (8)

frcu 60 76 138 309 338 36 1 444

PM3 main contributions to the PED (%) ATBZ (&O), ATSl (17), ATBl (16), DC80T (6) ATBl (36), ATSl (25), ATSZ (lo), ATBZ (7) ATSZ (44), ATSl (32), DC6NA (8) DC5CT (56), DC6NA (12) DC70T (38), DC8OT (15), DC6NA (1 1) ATSZ (19), DC8OT (IS), DC6NA (13), DC7OT (10) D6E2A (9) D6E2T (79)

Hrouda et al.

1554 The Journal of Physical Chemistry, Vol. 97, No. 8,1993

TABLE M: (Continued) Adenine*-Thymine. freq 493 504 514 572 586 683 724 770 888 915 94 1 1024 1034 1081 1142 1146 1188 1243 1250 1282 1315 1360 1373 1410 1417 1450 1464 1492 1515 1524 1550 1584 1608 1613 1667 1716 1785 1803 1814 2917 3135 3307 3325 3396 3419 3459 3787 3872

MINI-1 main contributions to the PED (%) DC6NA (32), D6E2A (14), C6NIA ( 1 1) D6ElA (45), D6EIT (21) D6ElA (21), D6ElT (16), DC70T (16), DC80T (15) DC8OT (19), DC70T (17), D6ElT (14), DC5CT (10) DSRIA (29), D6E2A (26), C5C6A (14) N3C4A (24), C5C6A ( l l ) , C6NlA (IO) C4C5T (34), D6ElT (15), C5C9T (9) D6TrT (57), C5C9T (18), C 7 0 T (6) D6TrA (54), D6E2A (1 l), D6ElA (6) NlC2T (29), C2N3T (21), DC8OT (6) D5R=A (78) DMeRT (6l), C5C6T (9) C6NlA (22), D5R:A (15), DNlHA (12), DNlOHA (9) DC6NA (9) C8N9A (29), DCSHA (26), DN9HA (26) DC6HT (32), D N l H T (17), C6NlT (12) DC8HA (18), DN9HA (16), C8N9A (12), C5N7A (8) NlC2A (35), DC8HA (16), D N l H A (9) DC2HA (46), DC8HA (6) DC6HT (19), DO8HT (18), DC2HA (7) C5C9T (26), C6NlT (20), D N l H T (16). D6TrT (9) DC2HA (19), N3C4A (13), DC8HA (9), C5N7A (9) NlC2T (22), DC6HT (16), C2N3T (14), DO8HT (13) C5N7A (19), DNlOHA (15), C8N9A (14), DN9HA (11) C5C6A (9) DO8HT (16), C8N9A (14), C2N3T (9), DNlOHA (9) DO8HT (18), DNlOHA (15). C8N9A (lo), C5N7A (9) DMeST (27), D N l H T (23), N3C4T (17), C6NlT (12) DMeST (53), CSC9T (12), C6NlT (12), D N l H T (9) DNlOHA (23), C2N3A (lo), C5C6A (8), D N l H A (8) N7C8A (31), C4C5A (13), N9C4A (13), NlC2A (8) DMeAT (54), C8OT (18), C4C5T (8) DMeAT (33), C 8 0 T (29), C4C5T (9), N3C4T (6) N7C8A (29). C2N3A (18), NlC2A (12), C4C5A (11) N9C4A (19), CNlOA (17), DNlHA (1 l), C4C5A (8) N3C4T (30), C4C5T (12) C4C5A (25), N3C4A (21), N9C4A (12), DN9HA (8) C2N3A (22), C5C6A (19), DNlHA (9), C6NlA (8) C 7 0 T (59), C5C6T (9), NlC2T (8), D N l H T (6) C5C6T (38), C6NlT (9), CNlOA (9) CNlOA (26), D N l H A (15), C5C6T ( l l ) , C6NlA (10) 0 8 H T (86), ATSZ (10) N l H A (88). ATSl (8) MeST (99) C2HA (98) C6HT (99) C8HA (99) MeAT (99) N H l l A (99) N9HA (99)

freq 484 506 509 572 595 735 750 841 850 907 958 lo00 1008 1053 1114 1144 1174 1212 1244 1292 1305 1326 1340 1373 1391 1414 1434 1442 1485 1525 1589 1627 1634 1663 1706 1742 1783 1836 1914 2967 3021 3075 3084 3086 3179 3410 3442

PM3 main contributions to the PED (%) C6NA(31),D6EZA (25),C6NlA(11),D6ElA(ll) D6ElA (49). D6ElT (12) DC8OT(28), DC7OT(lb), D6ElT (16). D6ElA (11) D6EIT (35), DC5CT (12), DC8OT (12) D5RIA (35). D6E2A (26), C5C6A (9) D5R=A (32), N3C4A (12), C5C6A ( l l ) , C6NlA (9) N9C4A (9) D6TrT (69) C4C5T (27), D6TrA (14), C5C9T (13) D6TrA (36), D5R=A (22) D5R=A (34), D6TrA ( l l ) , D5RiA (9), C6NIA (9) NlC2T (42). C2N3T (16), DC6HT (9) DMeRT (83) DC2HA (29). C6NlA (17). . . DNlOHA (13) . . DC8HA (78) DC2HA (52). DNlOHA (17). C6NlA (12) DCLHT(6l),’DNlHT(l2) DN9HA (38), C8N9A (32) NIC2A (28), DN9HA (19), DNlOHA (12), N3C4A (11) D N l H T (27), C6NlT (20), C2N3T (14), DC6HT (1 1) DMeST (17), C5C9T (14), DO8HT (12). D6TrT (9) NlC2A (28), DNlOHA (27) NlC2T (28), C2N3T (28), D N l H T (1 l), DMeST (9) C5N7A (25), NlC2A (1 l), N7C8A (9), N3C4A (9) C8N9A (28), N9C4A (lo), C5C6A (9) DMeAT (53), DMeST (18) DMeAT (35), DMeST (22), D N l H T (12) C6NlT (36), DMeST (15), D N l H T (13), C5C9T (10) N9C4A (21), C5N7A (20), C8N9A (15), C4C5A (12) Dn9HA (11) DO8HT (28), N3C4T (25). C5C9T (18) C2N3A (23), N7C8A (23), C4C5A (lo), DNlHA (9) N7C8A (35), C2N3A (29), N3C4A (9) C 8 0 T (37), C4C5T (30) N9C4A (17), C5N7A (13), CNlOA (13), N3C4A (9) N3C4T (34), C4C5T (14), DO8HT (13), C5C6T (13) C 8 0 T (9) C4C5A (43), N3C4A (22) DNlHA (36), C2N3A (28), C6NlA (9) C5C6T (59) CNlOA (53), C5C6A (26) C 7 0 T (83) C2HA (98) C6HT (99) C8HA (98) N l H A (91), ATSl (6) MeAT (99) MeST (99) N l H T (99) 0 8 H T (94), ATSZ (6) .

I

”

0 For pertinent force fields and scale factors see Table 1. * The frequencies are given in cm-I, IR intensities (absolute integrated molar absorption coefficients) in km/mol. Only contributions greater than 8% for the potential energy distributions (PED) are involved (in several special cases, when it seems significant, contributions smaller than 8% are given).

it attains the expected values (2G-304 of the pertinent M). All the valuesdiscussed in the previous paragraph were obtained consistently, i.e., the geometry and energy were determined at the same computational level without including the contribution from the electron correlation. However, the dispersion energy has been often shownI0Jl to be an important part of the total interaction energy. In the papers mentioned, thedispersion energy was evaluated using the London-type expression and the change in the intramolecular correlation energy was approximated by a simple electrostatic term. To solve these problems exactly, the geometry should be optimized for the complex (and also the subsystems) not only at the SCF level but also at the beyondSCFlevel. Let us recall that such a calculation requiresI2.’3larger basis sets including the polarization functions. Unfortunately, the size of the system under study excludes the gradient optimization at the beyond-SCF level. The single-point calculations with the MINI-1 and MIDI-1 basissets (for thegeometry optimized at the SCF/MINI-1 level) werecarried out employing

the second-order Maller-Plesset perturbation theory. We are certainly aware of the problems connected with the use of a small basis set for evaluation of the correlation interaction energy and have warned against it repeatedly.’*J3 Thus, the respectivevalues given in Table VI11 should be used with care. The M’values for both the complexes calculated with MINI-1 become larger in the absolute value at the MP2 level. This is the expected tendency. However, when the BSSEs are taken into account, the M‘values calculated at the MP2 level become smaller than the SCF values. Thus, the sum of the correlation energies of both subsystemshas a greater absolutevalue, than that for thecomplex. Such an evidentlyincorrect result can be attributed to the following facts: (i) the use of the minimal basis set for evaluation of the correlation interaction energy which results in strong underestimation of this energy; (ii) geometry optimizations were performed at the SCF level and not at the MP2 level, which again leads to underestimation of the correlation part of the interaction

The Journal of Physical Chemistry, Vol. 97, No. 8, 1993

Adenine-Thymine and Adenine*-Thymine* Base Pairs

TABLE VII: Interaction Energies (AE', kcal/mol) for AT and A*T* Complexes Evaluated by Gradient Optimization Techniques at Different Levels. A Is the Total Energy Mfference between Both Complexes level

"(AT)' -17.03' -6.57 -4.88

SCF/MINI-I PM3 AM 1

AE'(A*T*)" -27.81 -12.21 -6.63

Ab -9.5 1 -12.67 -24.55

*

Equation5. A = E(AT)-E(A*T*). AE'=-12.88 kcal/molwhen the subsystems are frozen at their optimized energies (cf. ref 10).

TABLE VIII: Interaction Energies (AE, Cf. Eqs 3 and 4; AE; Cf. Eq 5), the Reorganization Ener (ADO-, Cf. Eq 2), the Basis Set Superposition ErrorykSE, Cf. Eq 1) and the Interaction Enthalpy (AHiO, Cf. Eq 6) for the AT and A*T* Complexes Evaluated at Different Levels (AU Quantities in kcal/mol) AT basis set MINI-1

MIDI-1

SCF

2.80 AE' -17.03 BSSE 3.88 AE -13.15 MH," -11.32 AErsorg 5.33 AE' -20.45 BSSE 6.85 AE -13.60 AErsorg

A*T* MP2 5.59 -19.74 8.41 -11.33 24.38 -4.09 11.41 7.32

SCF

MP2

133.78 -27.81 9.17 -18.64 -18.16 124.75 -35.58 10.67 -24.91

115.00 -32.03 22.18 -9.85 125.56 -15.68 17.68 2.00

energy. Inclusion of the correlation energy changes the energy difference between AT and A*T* from -9.51 to -14.71 kcal/ mol. The effect of basis set extension was investigated again for geometriesdeterminedat theSCF/MINI-1 level (cf. TableVIII). The AE'values become larger in absolute value when passing to MIDI-1 and the same is true for the AI3 values. At the SCF/ MIDI-1 //SCF/MINI-1 level, the energy difference between AT and A*T* increases (in comparison with SCF/MINI-l//SCF/ MINI-1 level) to 20.12 kcal/mol. Inclusion of the correlation energy leads to unrealistic values of the AE' as well as AE interaction energies for both complexes (cf. Table VIII). This is certainly caused by the fact that the geometry was obtained at the SCF/MINI-1 level. The strategy for the higher level, single-point calculations for the geometry obtained at a lower level is successfully utilized for small systems. Clearly, it is of limited use for larger complexes and the respective conclusions should be accepted with caution. 3.2.3. InteractionEnthalpy and Comparison with Experiment. The AZPE (SCF/MINI-1) accompanying the formation of AT is larger than that for A*T* (1.83,0.48 kcal/mol). The M o o (cf. eq 6) for the formation of AT and A*T* amounts to -1 1.32 and -18.16 kcal/mol, respectively (cf. Table VIII). Using field mass spectrometry, AHo was determined4' for the formation of AT in the gas phase. The value of -12.9 kcal/mol found agrees fairly well with our result. The agreement is, in fact, even better because the experimental data were measured at 300 K. The temperature dependence of the interaction enthalpy is always negative,I3 which makes our theoretical M o o closer to the experimental value. Let us mention that inclusion of the zero-point energy for both the AT and A*T* complexes only slightly influences the energy difference A, which is then -9.88 kcai/mol. 3.2.4. Vibrational Spectra. The results of MINI- 1 and PM3 harmonic vibrational analysis of the hydrogen-bonded base pair in both the AT and A*T* tautomeric forms are compared with the calculations performed for isolated bases in Tables IV-VI. Intermolecular modes: The highest frequency in-plane intermolecular vibrational mode near 120 cm-' was calculated by both the MINI-1 and PM3 methods to be in-phase symmetric stretching of hydrogen bonds (ATS1 + ATSZ). The remaining two in-plane intermolecular vibrational modes lying close each

1555

other near 60 cm-I have been determined to be coupled bending and out-of-phase stretching vibrations of hydrogen bonds. All three mentioned intermolecular modes are shifted to higher frequencies as a consequence of the double proton transfer. The values of the ATS1, ATS2, ATB1, and ATB2 diagonal force constants of the A*T* base pair in MINI-1, Le., 0.870 mdyn/A, 1.046 mdyn/A, 0.582 mdyn A, and 0.695 mdyn A, respectively, have also been computed to be substantially higher than their normal tautomer counterparts (cf. Table I). A similar trend can be observed for the three out-of-plane intermolecular vibrations. Because we have not performed the normal-coordinate analysis in internal coordinates for the out-of-plane vibrations, the three unscaled frequencies obtained directly from the output of the ab initio program are given without detailed interpretation. For AT: 27 (o.P.), 35 (o.P.), 68 (i.p.), 80 (o.P.), 101 (i.p,), 129 cm-1 (i.p.). For A*T*: 33 (o.P.), 40 (o.P.), 83 (Lp.), 104 (o.P.), 115 (i.p.), 132 cm-I (i.p.). For comparison and clarity, the unscaled intermolecular planar vibrations (i.p.) are given along with the nonplanar modes (0.p.). All six intermolecular modes of the A*T* complex exhibit higher frequencies in comparison with those of the AT complex. The higher values of the corresponding force constants imply the somewhat surprising conclusion that the potential energy surface as a function of the in-plane intermolecular coordinates is more flat for the AT complex than for the A*T* complex in the region of the energy minimum. Undoubtedly, this effect is associated with greater interaction and reorganization energies (in absolute value) of the A*T* complex. Intramolecular modes: The vibrational modes of the isolated monomers remain largely recognizable as intramolecular modes in the ATcomplex (cf. Table IV), whereas a pronounced coupling between the A* and T* vibrations occurs for the A*T* base pair (cf. TableVI). Our attempt todetermine thevibrational spectrum of the AT complex using the scale factorsl8JI refined on the experimental data from crystalline adenine and thymine resulted in the much larger mutual coupling of vibrations of the individual subsystems. The three main effects, Le., the changes in the geometry and force fields of the subsystems and the presence of the intermolecular force constants, are responsible for the extent of the frequency shifts upon formation of the hydrogen bonds. Due to the general tendency of the SCF calculations in the minimal basis sets to overestimate the interaction energy and to underestimate the hydrogen bond lengths, all these three effects can also be assumed to be overestimated. As a result, too large shifts of the intramolecular vibrations of adenine and thymine can be expected to be obtained at the SCF/MINI-1 level.13 We have attempted to decrease the predicted frequency shift by scaling the calculated diagonal and interaction intermolecular force constants and force constants coupling adenine and thymine intramolecular vibrations by scale factors in the range 0 . 2 4 6 (see Table I). The choice of such extremely low-scale factors was made to mimic the experimentally determined frequencies of the intermolecular vibrational modes of the methyladeninemethylthymine Hoogsteen-type base pair in a single crystal.33 In addition, the mutual coupling of the adenine and thymine vibrational modes is reduced by these low-scale factors. Consequently, thecalculated spectrum ofthecomplex can be discussed simply in terms of shifts of the normal modes of the isolated subsystems. This is especially advantageous for use of our results as a tool for interpretation of spectral information obtained in experimental studies of biochemical systemsin which base pairing plays a crucial role. Nevertheless, there are some obstacles to the direct comparison of our calculated results with the experimentally determined changes in the NA bases vibrational spectra caused by hydrogen bonding. The experimental data from NA bases in argon or nitrogen matrixes are available over a wide range of concentrations, making it possible to study the spectral change induced by self-association of the studied molecules." However, the geometry of these associates usually remains

1556 The Journal of Physical Chemistry. Vol. 97, NO. 8, 1993

Hrouda et al.

adenine N1C2 and C6N1 diagonal stretching force constants, unknown, Moreover, the matrix site effects cannot, in general, which have been found to undergo significant changes with be neglected. The presence of plausible structural information opposite signs. is a major advantage of vibrational studies on NA bases in single 3.3. Proton Trmsfer. For the full description of the proton crystals. The spectra of the base molecules embedded in different transfer in the AT base pair it is not sufficient to know only the types of single crystals, which differ in the local net of hydrogen optimized structures andenergies of the ATand A*T* complexes. bonds (e.g., adenine hemisulfate hydrate compared with adenine At least one saddle point for the simultaneous double proton hydrobromide hemihydrate), can then be recorded.2'J.42,4sUsing transfer is needed when the dynamics of both protons which form this procedure and spectroscopic much less prominent two hydrogen bonds in the Watson-Crick AT base pair is to be spectral changes can be observed compared with our results studied. For anharmonic vibrational analysis, a suitable set of relating the spectra of isolated and hydrogen-bonded molecules. intermolecular internal coordinates must be selected and the The influence of the Watson-Crick type of base pairing on the potential energy surface (PES) of the pertinent dimension vibrational spectra of adenine and thymine will be discussed in constructed. In spite of great effort, we have not localized any this paragraph for the SCF/MINI-1 results (cf. Table IV and transition states at the SCF/MINI-1 level for the double proton Figure 2). For adenine, the amino group bending vibration transfer. As a first step, a four-dimensional PES at the (DC6N) calculated at 239 cm-1 exhibits a 52-cm-' blue-shift semiempirical (PM3) level is therefore c o n ~ t r u c t e d .This ~ ~ PES upon complex formation. This may be the main reason why the should enable us to localize not only the transition state for the unscaled quantum chemical calculations for cytosine, adenine, double proton transfer but also other appropriate saddle points. and guanine tend to strongly underestimate this frequency The dipole moment of the AT complex obtainednonempirically compared with the spectra of solid samples. Only a slight upshift as well as semiempirically is not greatly affected by the double of 5-10 cm-1 is predicted for the ring-bendingvibrational modes, proton transfer, mainly because of the parallel orientation of the with theexceptionof the 506-cm-I linecorrespondingto the D6El dipole moment and the hydrogen bonds. mode, which is lowered to 504 cm-1. A frequency decrease has been predicted for the adenine breathing vibration calculated at 4. CO~ClUSiOIM 691 cm-1. The well-localized ring-stretching vibrational modes at 1373 (C5N7) and 1531 cm-I (N9C4) are downshifted by 8 The adenine-thyminecomplex is more stable than the adenine*and 12 cm-I, respectively, one mode at 1195 cm-I (NlC2) is thymine* complex at any theoretical level; the energy difference upshifted by 48 cm-1. Two other modes, C4C5 and C5C6, between the AT and A*T* complexes at the SCF/MINI-1 level contribute to the bands with lower frequency, modes C6N1 and is -9.5 kcal/mol, which is considerably less than can be deduced C2N3 to the bands with higher frequency (cf. Table IV). The from previous calculations. amino group rocking mode (DNHR), which appears for the The semiempiricalPM3 and AM1 methods correctly predict isolated moleculeof adenineat 1004cm-1, is shifted in thecomplex that both the AT and A*T* structures are stable. The PM3 to 1103 cm-I and is found to be largely delocalized, influencing results are in better agreement with the SCF/MINI-1 results all the normal modes in the 1100-1350-cm-~ range. This is not than the AM 1ones. This is true of the subsystem and supersystem the case of the amino group scissoring vibration which remains geometries,harmonic force fields, heats of formation, interaction fairly characteristic (localized) in the complex. It is upshifted energies and the energy difference between AT and A*T* from 1628 to 1782 cm-I, and its IR intensity is greatly increased complexes. upon complexation. The expected intensification and red-shift The geometry changes when passing from the subsystems to by about 300 and 100 cm-I were obtained for the stretching the supersystem are much larger for the A*T* complex, which vibrations of the amino group. On the other hand, the C2H is reflected in the larger reorganization energy of A*T*. stretching mode downshift is rather unexpected. The gradient optimizationof H-bonded complexes is essential The low-frequency in-plane vibrations of thymine calculated if the characteristics of various stationary points are to be at 233, 343, 414, and 546 cm-1, which include a significant compared. This was demonstrated for energy minima (AT and contribution from the C 8 4 bending vibration (DC80), are A*T*), and it is expected that the same is true for comparison upshifted in the complex by about 10 cm-I. The thymine ring of minima and saddle points. stretchingvibrationscalculated at 937 and 1483cm-1exhibit 12The theoretical value of the interaction enthalpy (-1 1.32 kcall and 42-cm-1 downshifts upon complexation, respectively, as a mol) describing the AT formation agrees well with the correresult of weakening of the N1C2 and C2N3 bonds, respectively. sponding experimental value (-12.9 kcal/mol). A large change due to the complex formation from 1379 to 1618 The vibrational spectra of A and T remain recognizable in the cm-I has been calculated for the frequency of the N3H in-plane AT base pair. Consequently, the frequency shifts and intensity bending vibration (DN3H), whereas the downshifts of 600 and changes in the A and T vibrational spectra due to base pairing 30 cm-1 together with an intensity increase are predicted for the could be predicted. This is not true of the A*T* complex, where N3H and C 8 0 stretching vibrations, respectively. significant coupling of the normal vibrations between A* and T* Although the ability of ab initio computations in a minimal occurs. basis set to reproduce the experimentallyobserved IR intensities A trend to intensification of the in-planering vibrationalmodes is not good enough, they can be expected to successfully predict of isolated bases and N-H bending modes of adenine upon the relative intensity alterations caused by formationof hydrogen formation of hydrogen bonds has been found. bonds. The calculated intensification of the N-H stretching The appearance of new intensive bands corresponding to the vibrations, which is in accordancewith theexperimental findings, stretching modes of the N 3 4 4 and C6-NlO double bonds of can serve as an example. A general tendency of the WatsonT* and A*, respectively, in the spectral regions with no thymine Crick type of hydrogen bonding to increase the IR intensities of and adenine vibrational bands is proposed as a clear marker for thevibrational modes below 1000 cm-1, corresponding to the ring the spectroscopic detection of the presence of A* and T* rare deformation vibrations, has been calculated for the vibrational tautomers in solutions. The same spectral bands are also decisive spectra of both adenine and thymine. Indeed, the comparison of for experimentalindicationsof the existence of the double protonthe IR spectra of adenineand thymine measured in the crystalline transfer phenomenon. state, where a net of hydrogen bond exists, and measurement in inert-gas matrices confirm this intensity b e h a v i o ~ r . 3 0 ~ ~ ' , ~ ~ * ~References ~ and Notes The intramolecular force constants and the changes in the (1) (a) Lbwdin, P. 0. Rev. Mod. Phys. 1963, 35,724. 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