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Ab Initio Prediction of the Geometry and
IR Frequencies of the Mono- and
Dihydrated Complexes of the
Oxo-amino-Tautomers of Guanine
LEONID GORB,U JERZY LESZCZYNSKI
Department of Chemistry, Jackson State University P.O. Box 17910, 1325 J. R. L. Lynch Street,
Jackson, Mississippi 39217
Received 29 March 1997; revised 3 June 1997; accepted 3 June 1997
ABSTRACT: The results of ab initio post-Hartree]Fock study of the molecular
structures, relative stabilities, and Hartree]Fock level calculations of IR frequencies and
intensities for mono- and dihydrated oxo-amino-tautomers of guanine are reported. The
geometries of the local minima were optimized without symmetry restrictions at the
second-order Mller]Plesset perturbation theory. The standard 6-31 G d . basis set was
used. Local minima were verified by calculations of the matrix of energy second
derivatives w Hessian at the HFr6-31 G d . levelx . The single-point calculations were also
performed at the MP4SDQ.r6-31G d .rrMP2r6]31G d . and MP2r6-31qq
Gd, p.rrMP2r6-31G d . levels of theory. The total energies were corrected for the
zero-point energy contributions scaled by a factor of 0.9. The structural parameters of
mono- and dihydrated complexes were analyzed and related to the characteristics of
hydrogen bonds. We found that the interaction of guanine tautomers with two water
molecules changes the order of the gas-phase stability: 7GUA f 9GUA into the order
which corresponds to the stability of the guanine tautomers in the polar solvent:
9GUA 4 7GUA. The predicted IR HFr6-31G d . level frequencies and intensities are
presented. Q 1997 John Wiley & Sons, Inc. Int J Quant Chem 65: 759]765, 1997
Correspondence to: J. Leszczynski.
address: Institute of Water and Colloid Chemistry of the National Academy of Sciences, 42 Vernadsky av.,
Kiev-142, 252680 Ukraine.
Contract grant sponsor: NSF.
Contract grant number: OSR-945285.
U Permanent
International Journal of Quantum Chemistry, Vol. 65, 759]765 (1997)
Q 1997 John Wiley & Sons, Inc.
Contract grant sponsor: Office of Naval Research.
Contract grant number: N00014-95-0049.
Contract grant sponsor: Army Research Office and the University of Minnesota.
Contract grant numbers: DAAH04-95-2-003; DAAH94-95-C008.
CCC 0020-7608 / 97 / 050759-07
GORB AND LESZCZYNSKI
Introduction
he structural characteristics of the isolated
DNA and RNA bases and the prototypic
molecules have been the subject of extensive spectroscopic studies in recent years. Most of the structural characteristics have been obtained using
infrared spectroscopy and high-resolution microwave studies. These investigations are always
more relevant if they are performed in parallel
with ab initio quantum chemical calculations,
which, at the correlated level with sufficiently large
basis sets, are able to reproduce such structural
characteristics as geometry and IR frequencies with
the same accuracy as those of experiments see
e.g., w 1x. . Examples of such spectroscopic investigations coupled with ab initio quantum chemical
calculations can be found in w 2x .
Currently, the focus of these combined investigations is strongly shifted toward the study of
isolated intermolecular complexes with water
molecules. It is so natural because the hydration of
the DNA and RNA bases plays a special role in
determining the three-dimensional structure of
these kinds of biopolymers. The available literature on this subject consists of investigations of
only the pyrimidine type of DNA bases and their
prototypic molecules w 3x . To fill the gap formed by
a lack of investigations of hydrated puring bases,
we initiated ab initio calculations of the two tautomers of guanine: the oxo-amino form of the
N9.H tautomer 9GUA. and the oxo-amino form
of the N7.H tautomer 7GUA., which are the
lowest minima on the potential surface of isolated
guanine tautomers w 4x .
Before discussing the objective of this article,
justification for considering the mono- and dihydrated species of guanine tautomers is in order.
We are interested only in the cyclic forms of these
complexes because of the existence of both experimental and theoretical data which support the idea
that similar structures are the most important minima on the potential surface of the water]DNA
base complexes:
(i) According to the X-ray data of guanidine
monohydrate w 5x , the water molecule is
located in the vicinity of the carbonyl
oxygen;
(ii) according to the calculations of formamide
and acetamide]water complexes w 6, 7x , the
760
)C O ? ? H 2 O ? ? HN- bifurcated structure is really the global minimum; and
(iii) recently, it was concluded from the studies
of rotationally resolved fluorescence excitation spectrum w 3a, bx that the mono- and
dihydrated complexes of pyridone have the
same geometrical structure as that assumed for the 79.GUA ? H 2 O and the
79.GUA ?2H 2 O species in this study.
The purpose of this article was to provide accurate theoretical data for the studied species. The
following properties of the mono- and dihydrated
guanine species are predicted: 1. the geometry
and rotational constants of the mono- and dihydrated 79.GUA species; 2. the stability of these
complexes and a comparison with the stability of
isolated species; and 3. IR frequencies of monoand dihydrated 79.GUA species and a comparison with the spectra of isolated components.
Computational Methods
The ab initio LCAO-MO method w 8x was used to
study the interaction of guanine tautomers with
water molecules. The calculations were carried out
with the Gaussian-92 program w 9x . The standard
6-31G d . basis set was used. All the geometries
were optimized without symmetry restrictions C1
symmetry was assumed. by the gradient procedure w 10x initially at the HF level and subsequently
at the second-order Mller]Plesset perturbation
theory w 11x . Local minima were verified by establishing that the matrix of energy second derivatives Hessian. w at the HFr6-31G d . levelx has only
positive eigenvalues. The single-point calculations
w ere p erform ed at th e M P 4 SD Q . r 631G d .rrMP2r6-31G d . and MP2r6-31 q q
Gd, p.rrMP2r6-31G d . levels of theory. The total
energies were corrected for the HFr6-31G d . level
with a zero-point energy contribution scaled by a
factor of 0.9.
Results
The calculated geometrical parameters for
mono- and dihydrated complexes of 79.GUA are
presented in Figure 1. Tables I and II present the
computed rotational constants along with selected
intermolecular parameters for 79.GUA ? H 2 O and
79.GUA ? 2H 2 O. The data corresponding to the
VOL. 65, NO. 5
GEOMETRY OF OXO-AMINO-TAUTOMERS OF GUANINE
FIGURE 1. Structural parameters of mono- and dihydrated oxo-amino-guanine complexes. (A) Up indexes:
monohydrated oxo-amino-N(9)H guanine; down indexes: monohydrated oxo-amino-N(7)H guanine. (B) Up indexes:
dihydrated oxo-amino-N(9)H guanine; down indexes: dihydrated oxo-amino-N(7)H guanine.
relative stability of isolated and hydrated guanine
species together with computed dipole moments
are collected in Table III. The computed IR frequencies are given in Tables IV and V.
Discussion
GEOMETRY OF 7(9)GUA ? H 2 O AND
7(9)GUA ? 2 H 2 O SPECIES
An analysis of the structural parameters in hydrogen-bonded systems AH ??? B, where A and
TABLE I
MP2 / 6-31G( d ) rotational constant (A, B, C, GHz)
) for the
and selected intermolecular parameters (A
monohydrated 7(9)-guanine complexes.
A
B
C
RN10 O17
RO14 O17
9GUA ? H 2 O
7GUA ? H 2 O
1.47278
0.74504
0.49581
2.822
2.818
1.46761
0.74764
0.49647
2.811
2.820
B are heavy atoms which are involved in hydrogen
bonding, is crucial for an understanding of the
reasons for proton transfer in DNA bases. According to the classification of nearly linear hydrogen
bonds w 12x AHB more than 1658., the very low
values of the proton-transfer barriers take place
A and
when the AB distance is less than 2.5 A
B are oxygens andror nitrogens atoms.. In this
case, the two heavy atoms are so close to each
TABLE II
MP2 / 6-31G( d ) rotational constant (A, B, C, GHz)
) for the
and selected intermolecular parameters (A
dihydrated 7(9)-guanine complexes.
A
B
C
RN10 O17
RO17 O120
RO14 O 20
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
9GUA ? H 2 O
7GUA ? H 2 O
1.23260
0.524809
0.37245
2.868
2.719
2.794
1.22306
0.52490
0.37073
2.845
2.752
2.804
at the MP2 /
The O } O distance in (H 2 O) 2 is 2.915 A
6-31G( d ) level of theory.
761
GORB AND LESZCZYNSKI
TABLE III
Relative stability (kJ mol y1) and dipole moments (D) of guanine tautomers and their mono- and dihydrated
species.
Species
9GUA
7GUA
9GUA ? H 2 O
7GUA ? H 2 O
9GUA ? 2H 2 O
7GUA ? 2H 2 O
a
MP4(SDQ)/
6-31G( d )//
MP2/
6-31G( d )
MP2/
6-31++G( d )//
MP2/
6-31G( d )
MP2/
G-31G( d )//
MP2/
6-31G( d )
ma
0.0
1.6
0.0
y4.1
0.0
6.8
0.0
1.8
0.0
0.5
0.0
2.7
0.0
y0.2
0.0
y2.3
0.0
4.8
7.0
1.6
5.7
1.6
4.9
2.8
Evaluated from MP2-optimized geometry using HF density.
other that the zero-point energy level could appear
even under the barrier. In the case of the AB
the value of the
distance between 2.8 and 3.0 A,
proton-transfer barrier is much higher. This observation is the reference point for our analysis of the
structural data Fig. 1 and Tables I and II. of
mono- and dihydrated tautomers of 97. guanine.
According to the data of previous theoretical
studies and experimental observations w 3a, bx , the
influence of the interaction with one andror two
water molecules on the bond distances and bond
angles of prototypic molecules manifests itself
mainly in the region of intermolecular hydrogen
bonding. Our data see Fig. 1 and Tables I and II.
completely confirm this point. All other structural
parameters of the heterocyclic rings are vitually
the same w except for the N1 C 6 single bond of
97.GUA tautomers which is also under the influence of hydrogen bondingx and depend only on
the chemical structure of tautomers.
The addition of the second water molecule
makes a noticeable change in the geometrical
structure of the hydrogen-bonded complexes. All
of them become much more linear compared to
the monohydrated complexes; the distance between O14 and O 20 of dihydrated complexes is
much shorter than the corresponding distance
O14 O17 of the monohydrated complexes. Also,
the distance between O17 and O 20 is much shorter
than the interatomic distance in a free water dimer
see data in Tables I and II.. All the observed
trends for the 97.GUA ? H 2 O and 97.GUA ? 2H 2 O
complexes are congruous with the available experimental and calculated w 3a, bx data of the monoand dihydrated complexes of pyridone. Thus,
762
based on geometrical characteristics, one might
expect that the participation of two water
molecules in a proton-transfer reaction between
the N1 and O14 atoms of the guanine molecule
could be more favorable than is the participation
of only one water molecule.
RELATIVE STABILITIES
The relative stabilities of the isolated and solvated guanine tautomers have been predicted by
different levels of theory up to an MP4SDQ.r6311 q q G d, p .rrMP2r6-31G d . approximation
w 13x . In Table III, the calculated stabilities of isolated tautomers are in complete agreement with
the data in w 13x .
Our present discussion will concentrate on an
evaluation of the relative stability of the hydrated
complexes. For the isolated tautomers of guanine,
the following stability pattern is established:
7GUA f 9GUA.
1.
This relationship 1. corresponds well with the
available experimental data for the species in the
gas phase w 4x . According to the data of experimental IR studies, 7GUA is probably the most stable
tautomer. The tendency for the 7GUA form of
guanine monohydrates to stabilize exists. Based on
the data presented in Table III, the same stability
pattern in obtained for complexes of guanine with
one water molecule:
7GUA ? H 2 O f 9GUA ? H 2 O.
2.
The described peculiarity of monohydrated complexes is changed for the dihydrated isolated com-
VOL. 65, NO. 5
GEOMETRY OF OXO-AMINO-TAUTOMERS OF GUANINE
TABLE IV
TABLE IV
(Continued)
Calculated IR frequences (FREQ, in cm y1)
and absolute intensities (INT, km mol y1) for
9-guanine species.
9-Guanine
FREQ
INT
9-Guanine
FREQ
INT
9GUA ? H 2 O
FREQ
INT
9GUA ? 2H 2 O
FREQ
INT
152
180
218
339
355
366
392
522
573
576
608
654
679
721
729
790
823
871
908
969
1033
1147
1162
1192
1251
1282
1425
1457
1478
1535
1577
1687
1736
1781
1792
1842
1999
3452
3814
3849
3909
3927
50
110
153
167
186
218
247
351
370
381
387
398
526
562
576
581
676
690
719
735
771
815
865
894
909
970
1032
1158
1162
1206
1262
1288
1428
1466
1513
1536
1578
1702
1743
1787
1797
1840
1854
1959
3451
3732
3820
3908
3937
34
57
59
147
157
164
192
199
220
237
315
356
367
385
391
430
496
533
550
575
584
680
700
719
736
777
819
830
870
905
922
969
1032
1158
1162
1219
1266
1295
1430
1465
1505
1536
1572
1704
1745
1786
1804
1838
1856
6
2
10
17
93
7
1
7
43
109
293
109
8
10
30
60
13
90
15
4
11
13
12
22
21
59
5
54
62
22
8
26
112
464
111
536
901
4
69
76
112
56
6
18
2
1
6
25
90
6
38
63
73
59
57
256
196
57
256
196
2
31
2
48
6
202
40
5
13
15
7
10
10
70
11
11
189
16
9
45
76
305
148
638
111
1001
5
305
90
114
61
4
1
4
18
4
1
4
100
12
4
129
9
11
1
7
27
349
9
91
168
6
176
142
6
54
9
22
353
63
26
180
5
15
17
6
7
5
71
17
11
151
26
16
44
59
304
144
796
89
9GUA ? H 2 O
FREQ
INT
9GUA ? 2H 2 O
FREQ
INT
3968
4144
1866
1938
3450
3761
3811
3887
3909
3930
3944
4132
4145
217
125
99
1073
5
278
168
379
125
637
71
110
135
plexes which display the quite usual tendency to
approach the stability of fully hydrated species:
9GUA ? 2H 2 O ) 7GUA ? 2H 2 O.
IR FREQUENCIES
The present IR frequencies are intended to guide
experimental investigators in the study of the title
species. As can be expected from the calculated
data, it is clear that the major differences between
the spectra of isolated species and complexes are
the intermolecular vibration modes 50]300 cmy1 .
and the valence sym and antisym OH and NH
vibrations 3400]4100 cmy1 .. The predicted shifts
of vibrational frequencies upon the complexation
can be applied to an identification of these species
in the isolated-matrix experiments. Although the
HFr6-31G d . level harmonic frequencies overestimate the experimentally observed unharmonic
spectrum by approximately 10%, the differences
between predicted and observed shifts are usually
not larger than 10]20 cmy1 .
Conclusion
In this article, the stability, the harmonic IR
frequencies, and the structural parameters at the
post-Hartree]Fock level are revealed. The principal conclusions from this study are the following:
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY
1. The structural parameters of mono- and dihydrated oxo-amino-guanine tautomers calculated at the MP2r6-31G* level permits the
763
GORB AND LESZCZYNSKI
TABLE V
TABLE V
Calculated IR frequences (FREQ, in cm y1) and
absolute intensities (INT, km mol )1) for
7-guanine species.
(Continued)
7-Guanine
FREQ
INT
7-Guanine
FREQ
INT
7GUA ? H 2 O
FREQ
INT
7GUA ? 2H 2 O
FREQ
INT
160
169
213
324
344
366
406
509
523
586
644
669
685
702
733
814
824
869
907
1027
1041
1135
1203
1223
1259
1306
1408
1452
1482
1547
1607
1650
1710
1755
1804
1854
1970
3450
3799
3851
3908
3913
49
111
158
174
192
251
287
333
352
387
394
422
451
544
583
608
665
680
694
746
778
832
848
896
908
1027
1050
1143
1194
1229
1259
1336
1369
1461
1504
1551
1591
1619
1673
1702
1787
1812
1832
1871
3443
3825
3835
3922
3944
33
57
59
147
160
167
180
202
219
235
317
345
365
385
399
433
484
508
526
553
594
678
691
699
741
798
811
836
869
905
925
1033
1038
1151
1211
1234
1265
1319
1410
1469
1502
1547
1608
1661
1720
1756
1811
1849
1855
764
22
6
3
1
110
1
1
133
3
5
84
205
56
44
21
51
49
100
14
4
1
19
5
40
14
85
25
19
83
233
64
3
1
304
72
602
1003
6
56
79
49
142
2
11
20
1
5
59
74
41
24
31
53
118
71
16
276
30
172
1
150
25
1
21
161
87
43
6
3
41
57
17
28
78
65
113
186
208
251
84
169
60
618
128
156
508
7
51
608
135
46
1
2
1
10
7
11
4
114
7
3
134
33
4
4
1
43
138
74
104
294
13
197
2
104
41
9
10
346
63
14
187
3
1
20
21
16
13
67
45
5
192
191
74
66
29
166
46
843
129
7GUA ? H 2 O
FREQ
INT
7GUA ? 2H 2 O
FREQ
INT
3987
4144
1864
1917
3447
3734
3811
3893
3917
3934
3937
4134
4146
311
156
67
1132
7
381
116
348
131
711
10
111
136
classification of the intermolecular hydrogen
bonds as rather weak.
2. It is found that the interaction of guanine
tautomers with two water molecules changes
the order of gas-phase stability 7GUA 9GUA.
into the order which corresponds to the stability of the guanine tautomers in a polar
solvent 9GUA 4 7GUA..
3. The main difference in the calculated IR frequences of isolated, monohydrated, and dihydrated species are found in the region of
valence sym and antisym vibrations of OH
and NH bonds and in the region related to
the intermolecular vibrations.
ACKNOWLEDGMENTS
The authors thank the Mississippi Center for
Supercomputing Research for computational facilities. This work was facilitated by NSF Grant No.
OSR-945285, by the Office of Naval Research Grant
No. N00014-95-1-0049, 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 under
the auspices of the Department of the Army, Army
Research Laboratory cooperative agreement No.
DAAH04-95-2-0003rcontract no. DAAH04-95-C008. The policy of the government and no official
endorsement should be inferred.
VOL. 65, NO. 5
GEOMETRY OF OXO-AMINO-TAUTOMERS OF GUANINE
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