J. Phys. Chem. 1993,97, 12193-12196
12193
Theoretical Evaluation of Nonclassical Nucleic Acid Bases. 3.’ Structures and Properties of Wye Tautomers Jerzy Leszczyhski Department of Chemistry, Jackson State University, 1400 Lynch Street, Jackson, Mississippi 3921 7 Received: April 13, 1993; In Final Form: July 12, 1993’
Three tautomers of the prototype of tricyclic minor tRNA base Wye were studied by theoretical methods. H F and MP2 techniques were used in conjunction with 3-21G, 6-31G, 6-31G*, and 6-31G** basis sets. The molecular geometries of the tautomers were optimized at the HF/3-2 1G and HF/6-3 1G** levels, and harmonic vibrational frequencies were evaluated at the HF/3-21G approximation. N(7)H tautomer 1 is the global minimum at all levels of theory. Our best gas-phase estimate (MP2/6-31G**//HF/6-31G** ZPE) is that it lies about 36 (79) kJ mol-’ lower than N(9)H tautomer 2 (hydroxy tautomer 3). The magnitude of dipole moments were calculated for all species at the electron correlated level with 6-31G** basis set. Relatively large dipole moment predicted for 2 indicates that the computed tautomeric equilibria should be shifted toward this form in the polar solvents. This prediction is supported via the results of a single-point self-consistent reaction field (SCRF) MP2/6-3 1** level calculations. Calculated molecular parameters of Wye and the relative stability of the tautomers were compared to those of the corresponding guanine forms.
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guanine which is caused by closing amino group in guanine to the N1 with an ethylene bridge. Comparison of molecular structure Transfer RNA (tRNA) are relatively small nucleic acids. They and tautomeric properties of Wye with those of guanine could play a key role in the cell by interpreting the genetic code. Each lighten a shadow on function of Wye in tRNA species. tRNA molecule is able to carry a specific amino acid and A remarkable feature of Wye is its absorption and fluorescence recognizes the corresponding condons on the messenger RNA. The recorded UV spectra of Wye consist of four Thus, there are many different types of tRNA.2 A striking aspect electronictransitions located at significantlylonger wavenumbers of all tRNA sequences is their high content of unusual bases. (320, 300,265, and 235 nm) than for the normal DNA bases.10 Many of these unusual bases differ from normal bases by the The characteristic fluorescence of Wye was used to study the presence of one or more methyl groups. The others are anticodon loop of tRNAPhcand also to characterize the binding characterized by substitution of the normal element by their of Mg2+ and its influence on the loop conformation.11 heavier analogous like sulfur or bromine.’ In addition to In this paper we present ab initio study on the molecular monocyclic pyrimidinesand bicyclic purines somespecies of tRNA geometries and the relative energies of three tautomers of the contain tricyclic minor bases such as Wye. Although the function Wye prototype where two methyl groups were replaced by of most of the unusual base is not yet clear, some have been hydrogen atoms. As far as we are aware these molecules have shown to play important regulatory roles in tRNA function. not been investigated yet by theoretical calculations. We shall Among others, the fluorescent base Wye was found in the explore the tautomeric properties of Wye and also the differences anticodon loop of yeast phenylamine tRNAPhca4 of molecular parameters and properties of the studied species Tricyclic base Wye ( 1,4-dihydro-4,6-dimethyl-9H-imidazo- and corresponding guanine tautomers. [1,2-a]purin-9-one, I) can be considered as a modification of
Introduction
Method
&
I
*Abstract published in Advance ACS Absrracrs. October 15, 1993.
0022-3654/93/2097- 12193$04.00/0
The geometries of tautomers were fully optimized at the C, symmetry, using standard gradient optimization techniques.lZ Theclosed-shellrestricted Hartree-Fock 3-2 1G level” was applied to find stationary points on the potential energy surface (PES). At these geometries harmonic vibrational frequencies were evaluated from analytical second derivatives. The predicted 3-21G molecular parameters were used as a input data for the further optimizations performed for all tautomers at the 6-31G** level. The basis set dependence of the calculated relative energies was studied at the HF/3-21G geometries using 6-31G, 6-31G*, and 6-3 1G** basis sets. The electron-correlation contributions were determined by Moller-Plesset perturbation theoryI4through single-point second-order (MP2) calculations at the HF/3-2 1G and HF/6-3 1G** geometries using the frozen-core approximation. Our best (MP2/6-3 lG**) relative energies were corrected for HF/3-21G zero-point energy (ZPE) differences scaled by the recommended factor of 0.9.15 All calculations reported here were performed using standard ab initio LCAO-MO method with the GAUSSIAN90 and GAUSSIAN92 series of programs.I6 0 1993 American Chemical Society
Leszczyhski
12194 The Journal of Physical Chemistry, Vol. 97, No. 47, 1993
TABLE I: Total Energies (-au) of Wye Tautomers HF/3-21G//HF/3-21G HF/6-3 1G//HF/3-21G HF/6-3lG*//HF/3-2lG HF/6-31GS*//HF/3-21G HF/6-31G**//HF/6-31G** MP2/6-31G//HF/3-21G MP2/6-31G1//HF/6-3lG** MP2/6-31GS*//HF/6-31G** ZPEa a
1
2
3
611.65744 614.818 93 615.113 49 615.127 50 615.130 52 616.067 54 616.964 14 617.006 70 -0.140 98
611.64664 614.805 70 615.099 67 615.113 75 615.1 16 85 616.054 05 616.949 65 616.992 47 -0.140 41
611.61374 614.775 32 615.078 04 615.094 44 615.099 44 616.023 87 616.930 47 616.975 10 -0.139 49
Zero-point energies (uncorrected) at the HF/3-21G level.
TABLE 11: Relative Energies (kJ mol-') of Wye Tautomers
Figure 1. HF/6-31G** (bold)andHF/3-21G (inparentheses) optimized C, geometries of tautomer 1. Bond lengths are in angstroms, and bond angles are in degrees.
HF/3-21G//HF/3-21G HF/6-3lG//HF/3-2lG HF/6-3 lG*//HF/3-21G HF/6-31GS*//HF/3-21G HF/6-3lG**//HF/6-3lG** MP2/6-31G//HF/3-21G MP2/6-3 lG*//HF/6-3 1G** MP2/6-31G**//HF/6-31G**
TOTa
1
2
3
0 0 0 0 0 0 0 0 0
28.4 34.7 36.3 36.1 35.9 35.4 38.0 37.4 36.1
114.7 111.5 93.1 86.8 81.6 114.6 88.4 83.0 79.4
MP2/6-3 1GS*//HF/6-31G** energiescorrectedfor 0.9 scaled ZPE (HF/3-21G). a
Figure2. HF/6-31G** (bold) andHF/3-21G (in parentheses) optimized C, geometries of tautomer 2. Bond lengths are in angstroms, and bond angles are in degrees.
Figure3. HF/6-31G** (bold) andHF/3-21G (inparentheses)optimiztd C,geometries of tautomer 3. Bond lengths are in angstroms, and bond angles are in degrees.
Results and Discussion In a biological environment and in the polar solvents Wye occurs as oxo N(7)H tautomer 1 (for the convenient reference we adopted here the atomic numbering scheme of guanine" in Figure 1). To predict tautomeric equilibria two other forms 2 (oxo N(9)H) (Figure 2) and 3 (hydroxy) (Figure 3) were also studied by us. All three tautomers are minimum structures,
indicated by only positive harmonic vibrational frequencies predicted for these forms. Calculated HF/3-21G and HF/631G** levels molecular parameters of the studied species are shown in Figures 1-3. Overall a good agreement between these two sets of bond distances and bond angles should be noticed. The largest observed discrepancy is in order of 0.02 A for 0-H, (2-0, and some of the C-N bond lengths. Also generally bond angles predicted at these levels differ not more than by 1O, except two angles in hydroxy form 3 ( H a - C angle by 3.3O and N7C8-N9 angle by 2S0, respectively). Interestingly, the calculated geometrical parameters of the Wye tautomers are very similar to those of the corresponding guanine species.l* The observed differences are caused by the addition of the ethylene bridge to the six member ring of guanine. As a consequence, a single carbon-amino nitrogen bond (C2N12) in guanine becomes a double bond in Wye, which shrinks by about 0.07 A. Contrary, C2-N3 double bond of guanine turns into a single bond in Wye and increases its length by approximately 0.07 A. In Table I the basis set dependenceof the HF and MP2 energies are reported as well as the ZPE energies calculated at the HF/ 3-21G level. The relative energies of the tautomers and their basis set dependence are summarized in Table 11. Figure 4 visualized the trends in the relative energies upon the basis set improvementand inclusion of the electron correlation contribution. Clearly, 1 is the most stable species at all applied levels of theory, being slightly stabilized relatively to the second tautomer (2) by improvement of the basis set quality and reference geometry and by inclusion of the electron correlation effects. Though ZPE contributions decrease somewhat the relative energy of 2, the relative stability of this tautomer is rather unvarying and differs only by less than 8 kJ mol-I between the lowest (HF/3-21G// + HF/3-21G) and the highest (MP2/6-31G**//HF/6-3lG** ZPE) theory level applied. The relative energies of the hydroxy tautomer 3 depend noticeably on the basis set employed. The inclusion of the d-polarization functions on the second-rowelements significantly stabilize this form (by 21.6 kJ mol-'). The effect of the augmenting basis sets by p-polarization functions on hydrogens, which stabilize 3 by additional 6.3 kJ mol-' follows general basis set dependence noticed recently for the oxo-hydroxy eq~i1ibria.I~
The Journal of Physical Chemistry, Vol. 97, No. 47, 1993 12195
Nonclassical Nucleic Acid Bases
TABLE III: Dipole Moments (debye) of Wye Tautomers 1101
HF/3-2 lG//HF/3-2 1 G HF/6-3 lG**//HF/3-21G HF/6-31G**//HF/6-31G** MP2/6-31G**//HF/6-3 lG**
1
2
3
3.72 3.71 3.72 3.3 1
7.03 7.27 7.11 6.42
3.23 2.91 2.9 1 3.01
TABLE I V SCRF Energies Predicted via Single-Point MP2/6-31C** Calculations total energy (-au) re1 energy (kJ mol-')
f
1 2 3
-n
+tpl
um#
W l
YIP
YIP
Lyosna
uy m( ule-u1Dl.na-
-#
my.
YY
#a#
Figurel Plot of the tautomers' relative energiesversus theoretical levels. All energies are relative to that of 1. TOT are the MP2/6-31GS*// HF/6-31G** + 0.9 ZPE(HF/3-21G) relative energies.
Improvementof the reference geometry decreases relative energy of 3 by 5.2 kJ mol-'. The electron correlation energy contributions destabilize both forms 2 and 3 relatively to 1 but this effect is in order of 2 kJ mol-'. ZPE contributions play minor role in stabilization of the both minor tautomers lowering their relative energies by 1.3 (2) and 3.6 (3) kJ mol-'. At the MP2/6-31G** 0.9 ZPE level relative energy of the these forms amounts to 36.1 and 79.4 kJ mol-' for 2 and 3, respectively. Presumably, the strong basis set and electron correlation effects dependenceof the relative energy of 3 is due to a different type of bonds than in other forms. A conservation of the number of bonds of each type in 1 and 2 allows for cancellation of these contributions. Generally, there are virtually no differences between relative energies of Wye tautomers calculated at the HF/3-21G and HF/ 6-31G levels. Also their relativestabilitiesat the HF/6-31Gand MP2/6-3 1G approximations are practically the same indicating essential role of the polarization functions for the appropriate account of the electron correlation effects. Substantial relative energy of N(9)H tautomer of Wye should be noticed. The predicted relative energy of the corresponding guanine conformer amounts to 0.5 kJ mol-'; that of the form 3 is smaller than 5 kJ mol-l. The relative stability order of guanine tautomers depends noticeably on the level of calculations.'8a At the HF/3-21G//HF/3-21G approximation N(7)H tautomer is a local minimum species characterized by relative energy of 10.5 kJ mol-', while at the electron-correlated MP2/6-31G**//HF/ 6-31G level it becomes the global minimum form. However, the dependence of the relative energies of the forms 2 upon the level of calculations are similar for Wye and guanine. In both cases the relative destabilization of these tautomers upon improvement of the basis sets, inclusion of the electron correlation effects and ZPE contributions amounts to ca. 10 kJ mol-'. A chemical model of factors governing stability of Wye and the parent guanine tautomers can be reveal. On the basis of this model also qualitative explanations of different relative stabilities of 1 and 2 in these two systems can be given. An apparent reason for stabilization of the form 1 of Wye is that only this structure could be stabilized by oxygen interaction with two hydrogens: from N7 (major effect) and C10 (minor component). In case of the analogous tautomer of guanine, C 10 is replaced by a hydrogen. As a consequence, much stronger interaction with oxygen is observed from the hydrogen connected to N1, and this is a dominating stabilization effect for the form 1 in guanine. When
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HF 615.132 000 615.122 237 615.100 569
MP2 617.008 193 616.997 843 616.976 227
HF 0 25.6 82.5
MP2 0 21.2 83.9
oxo tautomer N(7)H 1 shifts into N(9)H form 2 in Wye a major stabilization of the oxo form is lost, while in guanine, the N(9)H oxo tautomer is still stabilized by a relatively strong interaction with hydrogen from N( 1). From our calculations seems that this effect accounts for about 32 kJ mol-' difference between stabilization of forms 2 in Wye and in guanine. The magnitude of tautomers' dipole moments is necessary to predict the interaction between different forms and biological environment. Table I11 shows dipole moments of the studied species calculated at the H F and MP2 levels. The predicted dipole moments of 2 and 3 change with the improvement of the basis set (by 3 and lo%, respectively) though the reference geometry govern only the magnitude of dipole moment of 2 (difference of 2% was noticed upon the improvement of the tautomer's geometryfromthe3-21G to 6-31G** level). Inclusion of the electron correlation decrease the dipole moments of 1 and 2 by 11% and lo%, respectively, while that of 3 increases by 3%. As it was discussed recently, dipole moments of the nucleic acid bases calculated at the electron correlated level with the 6-31G* or 6-3 1G** basis sets approximate well experimental data.20 At all levels the calculated dipole moment of 2 is almost 2 times larger than thoseof the other species,which strongly suggest that this tautomer is stabilized by the polar solutions. We predict increase of its relative concentration in biological environment with comparison to the gas phase equilibria. To test this prediction and quantitatively account for the tautomers' interaction with a polar solvent, a single-point selfconsistent reaction field (SCRF) calculations at the MP2/631G** level were carried out. The solvent's dielectric constant was chosen to be 40.0 and the cavity radius 4.65 A, respectively. The computed total and relative HF/SCRF and MP2/SCRF energies are presented in Table IV. As predicted on the basis of magnitude of tautomers' dipole moments, 2 is strongly stabilized by interaction with the polar solvents and its relative MP2/SCRF level energy amounts to 21 kJ mol-', while that of 3 is equal to 84 kJ mol-l. Conclusions The important conclusions from the present study can be summarized as follows: The N(7)H tautomer of Wye is predicted to be the global minimum species. This form exists in a biological environment. Our calculations predict significant enhancement of its relative stability in comparison with the corresponding equilibria for guanine tautomers. All studied tautomers are minimum structures on the HF/ 3-21G potential energy surface. The relative energies of 2 and 3 amount to 36 and 79 kJ mol-l, respectively (at the MP2/631G**//HF/6-31G** ZPE level). While the relative energy of 2 is almost independent of the theory level, the stability of 3 depends significantly on the basis set, electron correlation contributions, and ZPE.
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12196 The Journal of Physical Chemistry, Vol. 97, No. 47, 1993
An overall good agreement has been noticed between ab initio HF/3-21G* and HF/6-31G** bond distances and angles for forms 1 and 2. Improvement of the reference geometry effects more noticeably some of the predicted molecular parameters of 3.
Calculated molecular parameters of Wye tautomers are very similar to those of the corresponding guanine forms. However, the relative energies of local minimum tautomers are much higher for Wye than those predicted for guanine tautomers. Due toa largedifferencesin magnitudesof the predicted dipole moments between tautomer 2 and forms 1 and 3,2 is predicted to be stabilized in the polar solvents. This prediction is confirmed by the results of MP2/SCRF calculations.
Acknowledgment. This study was supported in part by NIH Grant 332090 and by a contract (DAAL 03-89-0038) between the Army Research Office and the University of Minnesota for the Army High Performance Computing Research Center. The Mississippi Center for SupercomputingResearch is acknowledged for generous allotment of computer time. We appreciate the referees’ valuable comments.
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