3 January 1997

CHEMICAL
PHYSICS
LETTERS
ELSEVIER Chemical Physics Letters 264 (1997) 92-100

Comparative study on the vibrational IR spectra of cytosine and

thiocytosine by various semi-empirical quantum mechanical
methods
V. Subramanian a, K. Chitra b, K. Venkatesh a, S. Sanker c, T. Ramasami a
a Central Leather Research Institute, Adyar, Madras 600 020, India
b Queen Mary's College, Madras 600 005, India
c Department of Physics, Anna University, Madras 600 020, India

Received 20 September 1996; in final form 1 November 1996

Abstract

The vibrational 1R spectra of two tautomers of cytosine (amino-hydroxy and amino-oxo forms) and thiocytosine
(amino-thiol and amino-thione forms) and their dipole moments have been calculated using the MNDO, AMI and PM3
methods and the results are compared with those calculated from ab initio and density functional theory (DFT) calculations.
The ability of the semi-empirical methods to predict the vibrational frequencies have been probed.

1. Introduction molecules have been determined using both local

The understanding of the physico-chemical prop-
erties and spectra of nucleic acid bases and various
tautomers are important due to their possible role in
base pairing and 'rare' tautomers in mutagenesis [ 1].
The possible presence of one or more of the DNA
bases in an unusual form can increase the mispairing
of purines with pyrimidines and hence may lead to
point mutation [2]. This stimulated a significant
amount of research towards an understanding of
tautomerism in nucleic acids and their spectra [3-12].
The thiocytosine and several derivatives are of spe-
cial importance due to their unusual biological prop-
erties [13]. This base has also been found in tRNA
[14]. The structure and relative energies of all possi-
ble tautomeric forms of the uracil and cytosine
and gradient-corrected density functional methods by
Corongu and coworkers [15]. They have also ex-
tended the density functional calculations on cyto-
sine and uracil by including the solvent effect using
Onsager's reaction field model [16]. Recently, the
molecular structure and spectra of cytosine and its
thio and seleno analogues have been predicted using
the conventional ab initio calculations and density
functional methods [17].
Since the ab initio calculation of large biological
macromolecules is computationally tedious, the test-
ing of semi-empirical methods in the calculation of
spectra of biological macromolecules is necessary.
The aim of the present investigation is to analyze the
reliability of MNDO [18,19], AMI [20] and PM3
[21] methods in predicting the molecular parameters

0009-2614/97/$17.00 Copyright © 1997 Elsevier Science B.V. All rights reserved.

PII S0009-261 4(96)01307-3
 V. Subramanian et a l . / Chemical Physics Letters 264 (1997) 92-100 93

Table 1
Comparison of PM3, AM1 and MNDO vibrational frequencies with DVI" and HF values for the amino-hydroxy form of cytosine
No. Description DFT a HF a PM3 AM 1 MNDO Experimental
of vibration
1 ,-,(OH) 3782 4162 3860 3410 3952 3618,3592
2 ua~(NH2) 3741 3992 3535 3518 3590 3575,3592
3 vs(NH ~) 3607 3853 3431 3494 3568 3461,3461
4 v(C5H) 3217 3389 3085 3228 3437
5 v(C6H) 3170 3349 3036 3143 3389
6 v(C5C6) 1672 1826 1749 1783 1817 1625,1622
13sc(NH2)
7 13sc(N H 2) 1645 1795 1707 1686 1797 1592,1589
8 v(C4C5) 1620 1783 1669 1734 1776 1569,1570
v(N3C4) 1563,1561
v(NIC2)
9 13sc(NHz) 1538 1664 1595 1727 1734 1495,1496
~(C5H)
10 [3(C6H) 1488 1621 1549 1606 1659 1441,1439
v(C20) 1430,1427
v(N 1C2)
11 v(C5C6) 1416 1530 1449 1539 1520 1380
13(Rl)
v(C4Nam )
12 [3(C6H) 1358 1464 1347 146 1 1467 1338, 1333
1324,1329
13 v(C6Nl) 1312 1368 1208 1325 1381 1257,1258
13(C6H)
14 13(COH) 1254 1318 1166 1287 1299 1198,1196
v(C2N3)
15 13(C5H) 1136 1222 1131 1221 1249 1113,1110
[3ro(NH2)
16 ~ro(NH2) 1105 1204 1074 1189 1238 1083,1085
17 v(C4C5) 1008 1132 1135 1056 1129 984,980
[3ro(NH2)
[3(RI)
18 !3(R 1) 994 1088 1015 1092 1095 948
v(N 1C2)
v(C2N3)
19 v(C6H) 992 1081 964 977 1039 948, 955
20 'y(C5H) 811 913 856 887 914 809, 807
"y(C4Nam)
'r(R1)
~(C20)
21 13(R3) 798 877 818 869 857 781,796
-dc4c5)
22 ~/(C5H) 795 858 779 764 793 784,751
"r(R1)
,y(c2o)
23 ~,(C4N~ ) 719 800 712 679 747 711,710
-dC20)
24 [3(R2) 602 652 611 638 65 I 600,601,569
~/(C20)
25 -fro(OH) 570 607 560 589 596 525,520
26 13(R3) 563 583 519 507 549 553, 557
[3(R2)
94 I/. Subramanian et a L / Chemical Physics Letters 264 (1997) 92-100

Table 1 (continued)
27 13(C20) 513 556 443 459 511 511,507
"rto(NH 2)
~3(C4N~n)
28 'rto(NH 2) 495 545 424 436 441 498, 498
[3(C20)
29 "r(R3) 451 492 408 376 414 443, 443
'y(C4Nam )
~(RI)
"rto(NH2)
30 13(C4Nam ) 344 374 338 341 345 342, 343,350
13(c2o)
31 'rinv(NH 2) 326 248 283 294 287 297
32 'r(R3) 220 237 199 205 208 -

~(R1)
33 "r(R2) 190 215 186 187 190 -

a From Ref. [15].

Table 2
Comparison of PM3, AM 1 and MNDO vibrational frequencies with DFT and HF values for the amino-oxo form of cytosine
No. Description DF-'T a HF a PM3 AM 1 MNDO Experimental
of vibration
1 Vas(NH2) 3744 4002 3534 3534 3594 3564, 3575
2 v(N 1H) 3635 3892 3431 3505 3583 3474, 3472
3 vs(NH 2) 3607 3857 3398 3473 3570 3457, 3441
4 v(C5H) 3236 3406 3081 3230 3436 -
5 v(C6H) 3208 3380 3021 3132 3393 -
6 v(C20) 1818 1982 1930 2007 2118 -
7 v(C5C6) 1705 1855 1760 1804 1839 1730, 1733
v(N3C4)
8 13sc(NH2) 1641 1789 1670 1720 1797 1602, 1598
9 v(N3C4) 1577 1730 1663 1689 1717 1539, 1540
v(C4C5)
10 v(N3C4) 1517 1636 1510 1650 1645 1475, 1475
v(C4Nam )
[3(C6H)
11 13(N 1H) 1446 1577 1429 1564 1598 1423, 1423
12 13(C6H) 1363 1479 1296 1407 1441 1340, 1337
v(C4Nam )
13(C5H)
13 v(C2N3) 1263 1391 1271 1385 1421 1237, 1244
14 13(C6H) 1217 1310 1358 1299 1169 1198, 1196
f3(N 1H)
v(C6N 1)
15 [3(C5H) 1129 1219 1125 1230 1259 1130, 1109
v(C6N 1)
v(C5C6)
16 I3~o(NH2) 1095 1209 1100 1186 1242 1088
17 13(R1) 989 1108 1099 1087 1023 -
v(c4c5)
18 "y(C6H) 958 1071 953 1061 1042 -
19 v(N 1C2) 923 1012 943 959 1022 -
v(C4C5)
 V. Subramanian et a l , / Chemical Physics Letters 264 (1997) 92-100 95

Table 2 (continued)
20 v(C20) 771 882 839 877 900 784, 818
"r(R1)
21 ~'(C20) 770 854 795 860 841 767, 747
22 ~/(C5H) 762 832 759 751 770 749, 747
'y(C4Nam )
23 "y(C5H) 732 801 678 679 727 717, 716
-r(Rl)
3'(C4Nam )
24 ~(N 1H) 630 665 611 628 646 614, 614
25 13(R2) 577 626 544 571 585 571,575
26 [3(R3) 547 589 491 566 536 53 l, 535
"rto(NH ~)
27 13(R3) 534 584 452 523 524 53 I, 535
"rto(NH 2)
p(c2o)
28 "5o(NH 2) 526 581 452 461 512 531,535
"rto(NH 2)
[3(C20)
29 'r(R2) 395 433 353 381 364 397,400
'r(Rl)
30 13(C4N~) 358 391 314 368 350 330
13(C20)
31 "rinv(NH2) 275 221 275 232 303 220, 235,232
32 'r(R3) 203 158 184 166 196 -
"r(Rl)
33 "r(R2) 139 93 119 145 132 270 (197), 235

a From Ref. [15].

Table 3
Comparison of PM3, AMI and MNDO vibrational frequencies with DF/" and HF values for the amino-thiol form of thiocytosine
No. Description DFT a HF a PM3 AM I MNDO Experimental
of vibration
1 Vas(NH2) 3740 3989 3535 3514 3588 3561, 3559
2 vs(NH 2) 3608 3851 3430 3490 3566 3444, 3444
3 v(C5H) 3213 3387 3084 3227 3435
4 v(C6H) 3170 3351 3034 3144 3390 -
5 v(SH) 2706 2924 1717 2008 2977 26 l 7, 2615
6 [3~(NH 2) 1662 1805 1709 1753 1816 1611, 1619
v(C4Nam )
7 13sc(NH 2) 1625 1783 1671 1724 1766 1575, 1579
v(C5C6)
8 v(C4C5) 1604 1766 1661 1710 1746 1562, 1558
9 v(N3C4) 1498 1635 1531 1674 1658 1458, 1463
v(C4Nam )
13(C6H)
10 v(C2C3) 1408 1531 1457 1526 1535 1364, 1366
11 [3(C6H) 1383 1491 1378 1452 1492 1348, 1350
v(C4Nam )
12 v(NIC2) 1297 1376 1188 1314 1322 1241, 1245
v(C6N 1)
13 13(C6H) 1251 1287 1134 1253 1307 1216, ! 217
v(C6N 1)
14 [3(C5H1) 1124 1217 1115 1215 1240 1098, I100
v(C5C6)
15 {3ro(NH 2) 1079 1164 1062 1157 1205 1058, 1058
96 V. Subramanian et aL / Chemical Physics Letters 264 (1997) 92-100

Table 3 (continued)
16 ~(C6H) 993 1086 1057 1135 1133 -
g(RI)
17 ~(C6H) 994 1131 981 1049 1048 979, 977
~(RI)
18 ~(C5H) 958 1045 967 1005 1040 946, 941
v(C4C5)
19 B(C5H) 912 1003 938 978 1001 891,888
20 ~(C5H) 817 903 855 874 918 807,811
~(C4Nam)
21 ~(R1) 788 873 805 782 825 -
22 ~(R2) 735 794 728 773 764 724,724
23 ~(C4Nam) 673 746 712 657 747 660, 663
~(c2s)
24 ~(R3) 561 606 592 622 630 556, 560
25 %o(NH2) 498 536 542 485 567 515, 560
26 ~(R2)
~(R3) 440 481 428 469 482 446,446
27 v(C2S) 435 476 414 453 445 427, 432
~(a2)
28 ~(C4Nam) 421 458 400 432 423 412,413
v(C2S)
v(C2S)
~(c2s)
29 r~(SH) 435 476 414 453 445 427, 432
30 rm~(NHz) 318 263 275 282 252 307, 300
31 B(C2S) 238 258 216 253 240 239, 222
32 r(R3) 204 223 191 194 198 -
x(R1)
33 ~(R2) 161 184 154 163 165 -

a From Ref. [15].

and vibrational spectra o f cytosine and thiocytosine
in comparison with ab initio and density functional
methods.
2. Computational details
The standard M O P A C package version 5.0 [22]
has been used for the calculation. The precise option
has been used for all the calculations. The geome-
tries of the various bases have been taken from the
standard values available for the bases [23]. The
vibrational frequencies have been calculated for both
tautomers of cytosine (amino-hydroxy and amino-oxo
forms) and thiocytosine (amino-thioi and amino-
thione forms). Complete optimisations have been
carried out for the starting geometry and using the
force option the spectral frequencies have been cal-
culated. Since the scaling factor differs for each
method, only unscaled frequencies have been calcu-
lated and compared with unscaled values obtained
from ab initio and D F T calculations [17]. All the
calculations have been performed on an IBM 486
computer.
3. Results and discussion
The unscaled vibrational spectral frequencies cal-
culated for cytosine (amino-hydroxy form) using
M N D O , AM1 and PM3 calculations have been pre-
sented in Table 1 along with the ab initio and density
functional values [17]. Generally, it can be seen from
the table that the frequencies calculated using the
PM3 method are in close agreement with the experi-
ment [24-28] and those calculated from D F T [17].
The M N D O method always overestimates the vibra-
tional frequencies compared to the AM1 method.
The frequencies calculated in the range between
 V. Subramanian et al. / Chemical Physics Letters 264 (1997) 92-100 97

Table 4
Comparison of PM3, AMI and MNDO vibrational frequencies with DFT and HF values for the amino-thione form of thiocytosine
No. Description DFT a HF a PM3 AM 1 MNDO Experimental
of vibration
I Va~(NH2) 3759 3998 3534 3540 3594 3334,3319
2 vs(NH 2) 3617 3878 3437 3510 3570 3312,3293
v(NIH)
3 v(NIH) 3614 3851 3358 3414 3568 3110,3103
vs(NH2)
4 v(C5H) 3239 3410 3083 3226 3436
v(C6H)
5 v(C6H) 3218 3388 3018 3133 3396
~(C5H)
6 v(C5C6) 1691 1836 1738 1781 1825 1645,1651,
1635
7 13sc(NH 2) 1647 1796 1665 1729 1788 1580,1574
8 13(NIH) 1588 1738 1649 1683 1715 1545,1552
1522,1527
1504,1512
9 v(C4Nam) 1512 1631 1516 1660 1662 1460,1459
v(N3C4)
13(C6H)
10 13(NIH) 1471 1622 1451 1562 1611 1460,1459
v(c4c5)
v(N3C4)
11 v(C4Nam ) 1384 1497 1332 1484 1513 1368,1369
13(C6H)
13(C5H)
12 v(C2N3) 1335 1425 1269 1394 1436 1302, 1306
13 13(C6H) 1235 1323 1173 1302 1388 1200, 1181,
13(N1H) 1202
v(C6N 1)
14 v(NlC2) 1148 1265 1118 1227 1316 1098,1099
13(Rl)
15 13(C5H) 1116 1204 1098 1205 1254 1087,1093
v(C6N 1)
16 y(C6H) 1074 1172 1071 1158 1234 1011,1093
17 13(R1) 978 1111 1022 1089 1083 940, 988
18 y(C6H) 963 1058 957 1030 1030 930,966
19 v(C4C5) 927 998 919 960 1021 859,874
20 y(C5H) 774 874 831 864 901 812, 806, 752
"y(C4Nam)
21 'r(R 1) 742 827 732 791 786 724,751
y(C5H)
22 13(R2) 717 772 708 725 749
v(NIC2)
23 *y(N1H) 690 760 673 663 686 652,650
y(C2S)
24 ~/(C2S) 659 726 596 605 621 594,650
"y(C4Nam)
25 13(R3) 556 605 553 603 559 542,551,550
26 "rto(NH2 ) 548 598 523 499 525 527
27 v(R2) 469 498 438 479 481 498
v(c2s)
98 V. Subramanian et al. / Chemical Physics Letters 264 (1997) 92-100
Table 4 (continued)
28 ]3(C4Nam ) 438 475
v(C2S)
29 "r(R2) 409 450
"r(R3)
30 13(C2S) 270 291
13(C4Nam)
31 "r(R3) 191 216
"r(R1)
32 "rinv(NHz) 131 206
33 "r(R2) 122 147
"r(R1)
a From Ref. [15].
1800 and 200 c m - ~ are predicted reasonably well by
the MNDO and AM1 methods and are in better
agreement with the HF calculation [17]. The higher
frequencies (3500-3000 cm - l ) calculated by the
PM3 method are found to be in good agreement with
the experimental [24-28] and DFT values [17].
In the case of the amino-hydroxy form of cyto-
sine, the bands observed in the high-frequency re-
gion (3700-3400 cm -~) originate from the stretch-
ing of the OH, NH 2 and NH groups. The recent DFI"
calculation [17] also gave the incorrect sequence for
v(OH) and Va~(NH2). In the present calculation, the
MNDO and PM3 methods predicted the correct or-
der whereas the AMI method gave a reversed se-
quence of v(OH), vs(NH 2) and vas(NH2). In the
lower-frequency regions, 1800-900 cm -~, most of
the bands are due to stretching vibrations of the ring
mixed with the CH bending and scissoring of the
amino groups. Such bands are predicted in the re-
gions 1749-964 cm -1 by the PM3 method, 1783-
977 cm -~ by the AM1 method and 1817-1039
cm-~ by the MNDO method. It can be seen that the
MNDO method overestimates these frequencies. The
ordering of the levels is in agreement with ab initio
and DFT calculations [17]. In the regions below 900
cm -~, the bands are due to in-plane and out-of-plane
bending vibrations. Such bands are reasonably pre-
dicted by the semi-empirical methods. A recent DFT
calculation predicted intense bands of about 300
c m - 1 due to torsional inversion of the amino group
[17]. The same is observed around 290 cm -I by our
semi-empirical calculations.
The vibrational frequencies calculated for the
amino-oxo form of cytosine are presented in Table 2.
401 466 446 456, 423
385 389 359 434, 422, 423
344 274 305 -
236 208 160 225
177 140 186 142
122 75 121 -
In the case of the amino-oxo tautomer, the stretching
frequency due to the CO group is predicted to be at
1930, 2007 and 2118 cm -~ by PM3, AM1 and
MNDO calculations, respectively. The band due to
inversional torsion of the amino group can be seen at
275, 232 and 303 cm -~ by the PM3, AM1 and
MNDO methods.
The vibrational frequencies calculated using
semi-empirical, ab initio and DFF calculations for
thiocytosine in the amino-thiol form are presented in
Table 3. Infrared matrix isolation studies on thiocy-
tosine shows the existence of thiocytosine in the
amino-thiol form [29,30]. In this study, we observed
3500-3050 cm -1 bands which originate due to
stretching vibrations of the NH 2 and CH groups. The
same bands have been predicted at 3700-3300 c m -
by the infrared matrix isolation study [29,30]. Ab
initio and DFT calculations [17] have predicted the
same bands in the region 3900-3100 c m - I . It can be
observed from the results that our semi-empirical
calculations underestimate the frequencies of the
v(NH 2) and v(CH) vibrations. On substitution of
sulfur by oxygen, the SH stretching vibration is
predicted to be at 1717 c m - t by PM3, 2088 c m - i
by AMI and 2977 cm -~ by MNDO. This band is
predicted at 980-1000 c m - t in the infrared matrix
isolation study [29,30]. The respective band is pre-
dicted at 1114 cm-~ by ab initio (HF/6-31G(d,p))
and 1044 cm -l by DFT calculations [17]. It can be
seen from the frequency calculated for the v(SH)
vibration that the semi-empirical methods overesti-
mates the experimental value [29,30] when compared
with the ab initio and DFT calculations [17]. The
scissoring vibrations of the NH 2 group are overesti-
 V. Subramanian et a l . / Chemical Physics Letters 264 (1997) 92-100
Table 5
Comparison of PM3, AMI and MNDO dipole moments of two tautomers of cytosine and thiocytosine with DFT and HF values
Tautomer DFT a HF a
cytosine
amino-hydroxy form 3.16 3.39
amino-oxo form 6.29 7.12
thio-cytosine
amino-thiol form 3.91 4.09
amino-thione form 8.06 9.28
a From Ref. [15].
mated by our semi-empirical calculations compared
to experiment [29,30]. The rocking mode of the
amino group, predicted at 1062 cm -t by the PM3
calculation, is in close agreement with the experi-
mental value at 1058 c m - t [29,30]. The band due to
inversion of the torsion of the amino group is found
to be around 275 cm -~ by the AM1 and PM3
calculations. The same band is underestimated by the
MNDO calculation performed in this investigation.
The experimental frequency corresponding to this
band is observed at 300 c m - ~ by the nitrogen matrix
spectrum [29] with a characteristic 'blue-shift'. The
SH torsional vibrational frequency is also overesti-
mated by the present semi-empirical calculations
when compared with the experimental values [29,30]
and values obtained in the ab initio and DFT calcula-
tions [ 17].
The vibrational frequencies calculated for thiocy-
tosine in the thione form are presented in Table 4.
Comparison of the ab initio and DFT results [17]
with our present semi-empirical calculations show
that the semi-empirical results are in better agree-
ment with the experimental values in the region
3300-3100 cm -t In the other regions, semi-em-
pirical calculations overestimate the frequencies. The
calculated dipole moments for the cytosine and thio-
cytosine tautomers using semi-empirical methods are
presented in Table 5 along with the values from ab
initio and DFT calculations [17]. It can be seen from
the data presented in Table 5 that the semi-empirical
methods underestimate the dipole moments when
compared to the ab initio and DFT calculations [17]
except for a closer agreement of the PM3 value with
DFT [17] in the case of the amino-oxo form of
cytosine and an overestimation by MNDO in the
case of the amino-thione form of thiocytosine.
99
PM3 AM1 MNDO Experimental
4.17 2.66 2.55
5.67 6.24 5.57 (6.0-6.5)
3.18 2.91 2.73
7.84 7.64 8.62
In summary, the PM3 method predicts unscaled
vibrational frequencies of cytosine and thiocytosine
reasonably well when compared to other semi-em-
pirical methods included in this study. The dipole
moments are not predicted well by the three semi-
empirical methods used in this study. For a large
biomolecular system for which exact ab initio calcu-
lations are not possible, the PM3 method can be
employed to predict the vibrational spectral frequen-
cies. A proper scaling of the vibrational frequencies
obtained from PM3 calculations may help further to
improve the quality of prediction.
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