J. Phys. Chem. 1986, 90,4438-4442
4438
Solvent Effect on the Hydrogen-Bonding Interaction between Adenlne and Uracil Yoshiisa Ohta, Hidetsugu Tanaka, Yoshihiro Baba, Akihiro Kagemoto,* Department of Chemistry, Osaka Institute of Technology, Asahi-ku, Osaka 535, Japan
and Kichisuke Nishimoto Department of Chemistry, Faculty of Science, Osaka City University, Sumiyoshi- ku, Osaka 558. Japan (Received: November 8, 1985; In Final Form: April 1 , 1986)
The stability of the adenine-uracil hydrogen-bonded systems of the Watson-Crick and the Hoogsteen pairs in vacuo and in aqueous solution is investigated by means of ab initio MO calculations and calorimetry. The calculated hydrogen-bonding energies of the Watson-Crick and the Hoogsteen pairs in vacuo are -58.8 and -51.4 kJ mol-’, respectively. The heat of mixing of adenine and uracil in aqueous solution is measured at 298.15 K and the enthalpy change obtained is -12 kJ mol-’. The calculated formation energies of the hydrated Watson-Crick pair and Hoogsteen one from the hydrated adenine and uracil by means of ab initio MO calculationsare -8.3 and +5.5 kJ mol-’, respectively. These calculated values may be reasonable compared with the experimental ones.
1. Introduction
It is well-known that the deoxyribonucleic acid (DNA) is a macromolecule with a double-stranded helical structure formed by the complemental interaction between purine and pyrimidine bases1 and brings about the helix-coil transition by a change of environmental conditions such as pH, ionic strength, temperature, and so on.2 To understand the biological function of the DNA molecule, it seems to be important to obtain quantitative information about the stability and about the relationship between structure and property of the D N A molecule. In the previous paper,3 while obtaining information about an intermolecular force between different chains of biopolymer systems, we reported that the heats of mixing of an equimolar mixture of poly(riboadeny1icacid) (poly(A)) and poly(ribouridy1ic acid) (poly(U)) solutions with 0.1 mol dm-3 Tris-HC1 buffer solution at pH 7.60 were measured by LKB batch type microcalorimeter at 298.15 K and also that the enthalpy change accompanying the duplex formation from an equimolar mixture of poly(A) and poly(U) was about -21 kJ (mol base pair)-’. Sarai et aL4 have calculated the hydrogen-bonding energy in vacuo between adenine and uracil for the Watson-Crick pair by means of a b initio MO calculations with the STO-3G minimal basis set by using the structure determined from experiment. But this result does not agree with that determined by our calorimetric experi m e n t ~demonstrating ,~ that this is mainly due to the difference between the hydrogen-bond formation in aqueous solution and that in vacuo. In this paper, in order to obtain further information about the hydrogen-bonding interaction, the hydrogen-bonding energies between adenine and uracil for the possible base pair configurations such as the Watson-Crick5 and the Hoogsteen6*’pairs in vacuo are calculated by ab initio MO calculations, and the solvent effect of water molecule on the hydrated adenine, uracil, and adenine-uracil hydrogen-bonded system is also studied by the same method. Furthermore, in order to confirm the hydrogen-bonding energies obtained by calculations, the heat of mixing of an equimolar mixture of adenine and uracil at pH 7.0 and 298.150 i 0.005 K is measured. From the results obtained by ab initio (1) Watson, J. D.;Crick, F. H. C. Nature (London) 1953, 171, 737. (2) Saenger, W. Principles of Nucleic Acid Structure; Cantor, C . R., Ed.; Springer-Verlag: New York, 1984; Chapter 8. (3) Tanaka, S.; Baba, Y.; Kagemoto, A. Polym. J . (Tokyo) 1976,8, 325. (4) Sarai, A.; Saito, M. Int. J . Quantum Chem. 1984, 25, 527. (5) Seeman, N. C.; Romberg, J. M.; Suddath, F. L.; Kim, J. J. P.; Rich, A. J . Mol. Biol. 1976, 104, 109.
(6) Frey, M. N.; Koetzle, T. F.; Lehmann, M. S . ; Hamilton, W. C. J . Chem. Phys. 1973, 59, 915. (7) Hoogsteen, K. Acta Crystallogr. 1963, 16, 907.
0022-3654/86/2090-4438$01.50/0
MO calculations and by calorimetric experiment, we will discuss the hydrogen-bonding energies between adenine and uracil in vacuo obtained by calculation and the solvent effect based on the calculated and experimental results for the Watson-Crick and the Hoogsteen pairs. 2. Experiment Adenine (Ade) and uracil (Ura) samples used in this study were purchased from Sigma Chemical Co. and used without further purification. Water as a solvent was purified by the ordinary method* and finally distilled by the use of a long column. The buffer solution used to adjust pH was 0.1 mol dm-3 Tris-HC1 (trishydroxymethylaminomethane-hydrochloric acid) solution (pH 7.0). The calorimeter used in this study was the LKB batch type microcalorimeter, whose procedure was qescribed in the previous paper,9 and the measured temperature was 298.150 f 0.005 K. For the measurement of the heat of mixing, equal volumes of 5 X mol dm-3 Ade and 5 X IO” mol dm-3 Ura were mixed. 3. Calculations Ab initio MO calculations were carried out with the IMSPACKIO and GAUSSIAN 80” programs. The structure of Ade was optimized with the STO-3G minimal basis set and that of Ura was referred to the calculated value with the same basis set as reported by Nishimura et a1.I2 The structure of water was referred to the experimental value. For the structure of the nonhydrated and hydrated hydrogenbonded systems, only the intermolecular geometric parameters were optimized. The hydrogen-bonding energy, EHB,was calculated as EHB = E(x-Y) - (E(X) E(Y)) (1)
+
where E(X-Y), E ( X ) , and E(Y)are the total energies of the X-Y hydrogen-bonded system and the X and Y molecules, respectively. 4. Hydrogen-Bonding Interaction between Ade and Ura Determination of the Structures of Ade and Ade-Ura Hy-
drogen-BondedSystems. The optimized structure of Ade is shown (8) Weissberger, A.; Proskauer, E. S. Organic Solvents: Interscience: New York, 1955. (9) Baba, Y.; Tanaka, S . ; Kagemoto, A. Makromol. Chem. 1977, 178, 2117.
(IO) Morokuma, K.; Kato, S.; Kitaura, K.; Ohmine, I.; Sakai, S . ; Obara, S . IMSPACK, IMS Computer Center Program Library, The Institute for Molecular Science, 1980, Program No. 372. (11) Binkley, J. S.;Whiteside, R. A.; Krishnan, R.; Seeger, R.; DeFrees, P. J.; Schlegel, H. B.; Topiol, S . ; Kahn, L. R.; Pople, J. A. Quantum Chemistry Program Exchange 1981, 13, 406. (12) Nishimura, Y.; Tsuboi, M.; Kato, S.; Morokuma, K. J . Am. Chem. SOC.1981, 103, 1354. (13) Hoy, A. R.; Bunker, P. R. J . Mol. Spectrosc. 1979, 74, 1.
0 1986 American Chemical Society
The Journal of Physical Chemistry, Vol. 90, No. 18, 1986 4439
Solvent Effect on Adenine and Uracil
TABLE I: Calculated Hydrogen-Bonding Energies, Em, the Experimental Enthalpy Change of Association, AHo, between Ade and Ura, and Calculated Dipole Moments of X and Y Components and Their Total Values for the W-C and the HG Pairs
W-C pair H G pair
EHB/kJ mo1-I this work -58.8" (-60.9)c
-51.4"
AHo/kJ moP
-60.7' -60.7'
dipole moment/debye Xc Y e totald 0.59 0.37 0.70
4.60
1.85
4.96
"This work. bReference 16. eRefer to Figure 3. dTotal value of X and Y components. eReference 4.
TABLE II: Calculated Hydrogen-Bonding Energies and Their Components for Ade-Ura Hydrogen-Bonded Systems of the W-C and the HC Pairs W-C pair/ H G pair/
H
Y
119.9
121.9
EHB EES EEX
EPL ECT
ECT(A-U) ECT(U-A)
Figure 1. The optimized structure of Ade. The values in parenthesis are the structure parameters of 9-methyladenine determined by e~periment.'~ Units are angstroms and degrees.
kJ mol-'
kJ mol-'
-58.8 -82.5 130.9 -5.3 -87.3 -41.3 -45.6
-51.4 -72.7 106.4 -4.3 -72.5 -37.7 -34.5
agreement with experimental ones of 9-methyladenine. The calculated net charges of Ade and Ura are also shown in Figure 2, parts a and b, respectively. From these figures, it may be possible for the N, and the N7 of Ade and the O7 and the O8of Ura to become the proton acceptor due to an increase of the and the NloH15of Ade and the electron charge, while the NIOH14 N3HIoof Ura become the proton donor. Thus, the following four configurations are possible for Ade-Ura hydrogen-bonded systems:
(a)
@3
I
Figure 2. The net charges of (a) Ade and (b) Ura. The open and shaded circles represent the positive and negative net charges, respectively. The area of the circle shows the relative magnitude of the net charge.
in Figure 1, together with the experimental values14in parenthesis. As seen in Figure 1, the calculated values are in fairly good
1
2
3
4
Since 1 and 2, which are called the Watson-Crick (W-C) and the Hoogsteen (HG) pairs, respectively, are known experimentall^,^-^ we calculated these two pairs. The optimized intermolecular geometric parameters of Ade-Ura hydrogen-bonded systems for the W-C and the H G pairs are shown in Figure 3, parts a and b, respectively, together with the experimental values of 9-N-methyladenine and 1-N-methyluracil by X-ray diffraction crystall~graphy'~ in parenthesis. As seen in Figure 3, the intermolecular distances are somewhat underestimated because of the use of the STO-3G minimal basis set. Stability of the W-C and HG Pairs. The calculated hydrogen-bonding energies and the dipole moments for the W-C and the H G pairs were calculated, respectively, and the results obtained are summarized in Table I, together with the experimental hydrogen-bonding energy estimated by mass spectrometric techniquet6 and that calculated by Sarai et aL4 As seen in Table I, the results of ab initio MO calculations are in fairly good agreement with the experimental values. According to our ab initio MO calculations, it is indicated that the W-C pair is more stable than the H G pair in vacuo. However, the dipole moment of the H G pair is 7 times as large as that of the W-C pair. When the effect of dipole-dipole interaction between solute and solvent is taken into consideration, the present results suggest that the H G pair becomes preferable in the solution because of the stabilization based on this interaction. Energy Decomposition for the Estimated Ade-Ura Hydrogen-Bonded Systems. In order to obtain information about the (14)Stewart, R. F.;Jensen, L. H. J. Chem. Phys. 1964,40, 2071. (15) Arnott, S.;Wilkins, H. F.; Hamilton, L. D.; Langridge, R. J . Mol. Biol. 1965, 11, 391. (16) Yanson, I. K.;Teplitsky, A. B.; Sukhodub, L. F. Biopolymers 1979, 18, 1149.
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The Journal of Physical Chemistry, Vol. 90, No. 18, 1986
i
(a)
Ohta et al. TABLE III: Experimental Enthalpy Changes of the Hydrogen-Bond Formation between Ade and Ura AH'lkJ environ (mol base uair)-' ref ~
H2O CHC1," CHC1," CCI, gas phase
-12
-25.9 f 2.5 -25.9 h 1.3 -30.1 -60.7
this work
19 20 21 16
9-Ethyladenine and 1-cyclohexyluracil. is H 2 0 > CHCI, > CCI, > gas phase, which coincides with the polarity of solvents, demonstrating that this tendency of the AHo value may be the influence of a long-range dipole-dipole interaction between solute and solvent. Water molecules might form the hydrogen bond with the base and/or base pair, suggesting that water molecules bound to the base and base pair may play an important role along with the formation of hydrogen bond between bases. Unfortunately, it is very difficult to estimate experimentally the hydrogen-bonding energy between them because of the lack of information on such quantities as the energy of the hydration of Ade and/or Ura and the dehydration energy due to the hydrogen-bond formation.
H
(b)
H
\
c, =c
/" \
6. Solvent (Water) Effect on the Hydrogen Bond between Ade and Ura
Y
L
H Figure 3. The optimized intermolecular geometric parameters of (a) the
W-C and (b) the HG pairs. Units are angstroms and degrees. energy contribution to stabilize the hydrogen bond formed by interaction between Ade and Ura, the hydrogen-bonding energy was decomposed into the components such as the electrostatic (EES),the exchange repulsion (EEX),the polarization (EPL),and the charge-transfer (ECT)energies by means of the KitauraMorokuma method.17 The results obtained are listed in Table 11, where ECT(AdmUra) and Ea(um-.Ade) refer to the chargetransfer interaction energies from Ade to Ura and vice versa, respectively. As seen in Table 11, it may be suggested that E M and Ecr play an important role in the stabilization of the hydrogen bond formed between Ade and Ura, as well as the usual hydrogen-bonded systems.18
5. Heat of Mixing of Ade and Ura Aqueous Solutions The heat of mixing of Ade and Ura aqueous solutions was measured at 298.150 f 0.005 K by using a calorimeter as described previously. This system was exothermic, demonstrating that the heat of mixing may correspond to the enthalpy change (AHo)due to the hydrogen-bond formation between Ade and Ura, under the assumption that the heat of dilution may be negligible small. The result obtained is summarized in Table 111, together with AHo values reported by other investigator^.^^,^^-^^ As seen in Table 111, it is of interest to note that the order of AHo values (17) Kitaura, K.; Morokuma, K. Int. J . Quantum Chem. 1976, 10, 325. (18) Morokuma, K.; Kitaura, K. Chemical Applications ofAtomic and Moleculur Electrostatic Potentials; Politzer, P., Truhlar, D. G., a s . ;Plenum: New York, 1981; p 215-242. (19) Kyogoku, Y.; Lord, R. C.; Rich, A. J . Am. Chem. SOC.1967,89,496. (20) Binford, J. S.,Jr.; Holloway, D. M. J . 'fd.Bioi. 1968, 31, 91. (21) Kuechler, E.; Derkosch, J. 2. Naturforsch, E: Anorg. Chem. Org. Chem. 1966, 21B, 209.
In section 5, we suggested that the small value of the enthalpy change in aqueous solution was due to the long-range dipoledipole interaction and the short-range hydrogen-bonding interaction between solute and water molecule. In order to obtain information about the solvent effect, we carried out ab initio MO calculations of the hydrated Ade, Ura, and Ade-Ura hydrogen-bonded systems and will discuss the solvent (water) effect on the hydrogen-bonding interactions between bases and also the dehydration process for forming the hydrogen-bonded systems. Structure of the Hydrated Ade, Ura, and Ade-Ura Hydrogen-Bonded Systems. The calculated geometries of the hydrated Ade and Ura are shown in Figure 4, where the numerical indices 1-8 indicate the positions of the binding sites of water molecules. As seen in Figure 4, the configurations of Ade and Ura binding with four water molecules are in good agreement with those obtained by Pullman et aLZ2 But they did not determine the optimized structures for these hydrogen-bonded complexes. On the other hand, although Del Bene2, reported that three water molecules only coordinated to sites 5,6,and 8 of Ura, our configuration suggests that it is possible for Ura to form a linear hydrogen bond with the fourth water molecule at site 7 as shown in Figure 4b. To obtain information about the structures for possible hydration of Ade-Ura hydrogen-bonded systems, the electron density changes for the W-C and the HG pairs are calculated and shown in Figure 5, parts a and b, respectively. As seen in Figure 5, the electron densities of the H l l atom of Ade in the W-C pair (see Figure 5a) and the HI, atom of Ade in the H G pair (see Figure 5b) decrease significantly, demonstrating that the H 2 0 bound to site 7 forms an unusual C-H6+-0 hydrogen bond with the C2-Hl, in the W-C pair and the Cs-H13 in the H G pair. This type of hydrogen bond will be also expected in the hydration scheme of the Ade-Tymine system by Goldblum et al.24 The other binding sites of H 2 0 to Ade-Ura hydrogen-bonded systems are similar to those of Ade and Ura, but only the intermolecular geometric parameter of site 7 hydration was optimized. The schematic structures of hydrated Ade-Ura hydrogen-bonded systems can also be seen in Figure 5 , parts a' and b', corresponding to Figure 5 , parts a and b, respectively. (22) Pullman, B.; Niertus, S.; Perahia, D. Theor. Chim. Acta 1979, 50, 317. (23) Del Bene, J . E. J . Comput. Chem. 1981, 2, 188. (24) Goldblum, A,; Perahia, D.; Pullman, A. FEBS Lett. 1978, 91, 213.
Solvent Effect on Adenine and Uracil
The Journal of Physical Chemistry, Vol. 90, No. 18, 1986 4441
(a)
(b)
(3) N HO-H
520.1
1.596
Figure 4. The optimized intermolecular geometric parameters of (a) hydrated Ade and (b) hydrated Ura. Units are angstroms and degrees. TABLE I V Calculated Hydrogen-Bonding Energies between Hydrated Ade and Ura W-C pair HG Dair
site no.'
Od 1
UHB'I
-EHBI kJ mol-'
kJ mol-'
58.8 58.5 58.5 51.6
+0.3 +0.3 +7.2
57.4 58.9 64.Oe 59.5'
+1.4 -0.1 -5.2 -0.7
- E H B ~ UHB'I kJ mol-I kJ mol-' 51.4 51.5 52.8
-0.1 -1.4
46.1 50.1 50.7 71.lC
+5.3 +1.3 +0.7 -19.7
63.lC
-11.7
"Refer to Figure 5, parts a' and b'. 'UHB = EHB - (-58.8). ' A E H B - (-51.4). dNonhydrated Ade-Ura hydrogen-bonded systems. CThevalues contain the C-H6+--0 hydrogen-bonding energies. = EHB
TABLE V Calculated Energies of Hydrogen-Bond Formation between Hydrated Ade and Ura and the Experimental Enthalpy Change in Aqueous Solution W-C pair HG pair AE3fkJ mol-l -8.3 +5.5 AHo "/kJ mol-' -12 -12
" Data from calorimetric experiment (see Table 111). From the hydrogen-bonding processes as mentioned above, the following enthalpy (internal energy) cycle can be written: Ade t 4 H 2 0 t Ura t
/.E5 Ade-Ura
4H20
AE2
Ura-4HpO AE3
f 8Hp0
3HzO-Ade-Ura-2HpO
AE4
Hydrogen-Bonding Energies of Hydrated Ade and Ura. The calculated hydrogen-bonding energies of the hydrated Ade-Ura hydrogen-bonded systems are summarized in Table IV, together with the values of the Ad-Ura hydrogen-bonded systems in vacuo. As seen in Table IV, each water molecule bound to sites 3 , 4 , and 7 in the Ade-Ura hydrogen-bonded system seems to cause a significant influence on the hydrogen-bonding energy between Ade and Ura. It is indicated that the hydrogen bonding between Ade and Ura becomes more stable when H 2 0 is bound to site 7 for both the W-C and the H G pairs; on the other hand, that of sites 3 and 4 becomes rather unstable. When six water molecules are simultaneously hydrated to Ade-Ura hydrogen-bonded systems, the hydrogen-bonding energy between bases for the W - C pair does not change too much, while the hydrogen bond for the H G pair becomes stable. Stability of the Hydrated W-C and HG Pairs. In order to estimate the stability of the hydrated W-C and H G pairs, the following hydrogen-bonding processes may be considered: each Ade and Ura forms a hydrogen bond with four water molecules (see Figure 4). In order to form the W-C pair between Ade and Ura, the water molecules bound to sites 4 and 8 must be removed. While, for the formation of the H G pair, the water molecules bound to sites 3 and 8 should be taken away. From the results, it is considered that the hydrated Ade-Ura systems both of the W-C and H G pairs form hydrogen-bonded systems with six water molecules, where it should be noted that the water molecule bound to site 7 of Ura forms a hydrogen bond with Ade as shown in Figure 5.
Ade-4HpO
- + 1 A €1
/
t (Hp0)2
/
H20
where AE, and AE2 are the total hydration energies of Ade and Ura, and the calculated values are AEl = -181.3 and AE2 = -1 16.5 kJ mol-', respectively. AE4 is the total hydration energy of the hydrated Ade-Ura system, and was evaluated as -247.3 kJ mol-' for the W-C pair and -240.9 kJ mol-' for the HG pair. AE5 is the hydrogen-bonding energy, EHB,between Ade and Ura in vacuo given in Table I. AE3 is the energy difference between E(hydrated Ade-Ura) and (E(hydrated Ade) E(hydrated Ura)) and may correspond to the mixing process from the calorimetric experiment as described in section 5. AE3 will be written as a combination of the energies in the processes mentioned above as follows:
+
+ AE2 + AE3 = AEa + AES Therefore, AE3 can be estimated as AE4 + AE5 - (AEl + AEJ. AEl
The AE3 value obtained in such a way is -8.3 kJ mol-' for the W-C pair and 5.5 kJ mol-I for the H G pair, respectively. From these results, it may be concluded that the hydrated W-C pair is more stable than the hydrated H G pair, demonstrating that the W-C pair rather than the H G pair is liable to form in the aqueous solution. The results obtained are summarized in Table V, together with the A" value determined from calorimetric experiment. As seen in Table V, the value of AE3 for the W-C pair is in fairly good agreement with the AHo. But, the sign of the AE3 value for the H G pair is opposite compared with AHo. This is destabilization due to the dehydration. As pointed out in section 4, however, some
4442
The Journal of Physical Chemistry, Vol. 90, No. 18, 1986
Ohta et al.
H -,
H.
P... .. H H,
w
.--o\c/
I
I C\ H, C
I
H
,
n
Figure 5. The electron density changes due to the hydrogen-bonding in (a) the W-C and (b) the HG pairs. Full and dotted lines indicate the density increases and decreases, respectively. The values of these lines are fO.0001,*0.0005, and fO.001 (bohr)-', successively. The hydration schemes and reoptimized intermolecular geometric parameters between base pair and water for the case of hydration to site 7 of (a') the W-C and (b') the HG pairs. The other intermolecular geometric parameters are same as those shown in Figure 4. Units are angstroms and degrees.
amount of stabilization for this pair will be expected, taking dipole-dipole interaction between the H G pair and the solvent into consideration. In conclusion, water molecules play an important role in the solvent effect on the hydrogen-bonding interaction between Ade and Ura.
7. Conclusions The stability of the Ade-Ura hydrogen-bonded system in vacuo and in aqueous solution has been investigated by means of ab initio M O calculations and solution calorimetry. The calculated hydrogen-bonding energies in vacuo were determined to be -58.8 kJ mol-' for the W - C pair and -51.4 kJ mol-' for the H G one, respectively. We concluded that the electrostatic and the charge-transfer interactions played an important role in the stabilization of hydrogen-bonding interaction between bases, and the dipole moment of the H G pair was 7 times as large as that of the W-C one, demonstrating that the HG pair would be expected to become more stable than the W-C one in a polar solvent because of the stabilization based on the dipole-dipole interaction between solute and solvent.
On the other hand, the enthalpy change of association between Ade and Ura in aqueous solution was estimated to be -12 kJ mol-' by using the microcalorimeter. As shown in Table 111, this value was the largest of the enthalpy changes in various environments such as CHC13, CC14, and gas phase, suggesting that the effect of water molecules on hydrogen-bond formation between bases has to be considered. In order to confirm the fact as mentioned above, the hydrogen-bond formation energies between hydrated Ade and Ura were also calculated and the results obtained were -8.3 kJ mol-' for the W-C pair and 5.5 kJ mol-' for the H G one. We concluded that these calculated results might be reasonable compared with our present experiments, demonstrating that water molecules played an important role in the contributions such as hydration and dehydration to form the hydrogen bond between bases in aqueous solution. Acknowledgment. We are grateful t o the Computer Center of the Institute for Molecular Science and the Data Processing Center of Kyoto University for the use of the HITAC M-200H and FACOM M380/382 computers.
