J. Phys. Chem. 1993,97, 9081-9086
9081
ARTICLES FTIR Study of the Symmetric v , ( P O ~ ~Mode -) of 5‘-CMP in 2H20 Solution. Molecular Relaxation Processes R. Navarro, I. Bratu,? and A. Hemanz’ Departamento de QuImica Fisica, Universidad Nacional de Educacibn a Distancia, Senda del Rey s/n, 28040-Madrid, Spain Received: December 8 , 1992; In Final Form: June 2, 1993
FTIR measurements on the V,(PO~~-) band shape of 5’-CMP in 2H20 solution at different concentrations, 0.002-0.58 mol dm-3, and temperatures, 10-55 OC, have been interpreted in terms of the dynamics of the POs2group and the self-association processes of this mononucleotide. A possible aggreation process of 5’-CMP a t -0.3 mol dm-3 has been detected from the second derivative and the integrated intensity of the band. Vibrational relaxation seems to be the main relaxation pathway for this mode, and vibrational dephasing appears as the fastest process among the different relaxation channels. An intermediate modulation regime for the vibrational frequency is obtained. Introduction The phosphate groups play an important role in the structure, dynamics, and interactions of mono- and polynucleotides. In 5’-mononucleotides, the presence of the phosphate group at the 05’ position restricts the conformational flexibility of the remainder of the molecule.1 Therefore, the study of the dynamics of the POS2-group can give information on the mononucleotide mobility and interactions. In previous works,Z-4the concentration and temperature effects on the dynamics of the P032-group of guanosine 5’-monophoshate, 5’-GMP, in 2H2O and H20 solutions have been studied by infrared and Raman band profile analysis. Now we extend this study to cytidine 5/-monophosphate, 5/-CMP. The 5‘-GMP forms ordered aggregates in aqueous solution with the P032-groups acting as bridges (ribose OH OP bonds) between tetrameric rings,%’ a function that obviously hinders the reorientational motion of these groups. Until now, however, there was no evidenceof a similar behavior for its complementary mononucleotide 5’-CMP or of a self-association process of this mononucleotide in aqueous solution. We have detected interactions of this type. Motivations of our work are to ascertain if the P032- group takes part in this process and to study possible changes in the POP2-dynamics. The symmetric stretching mode of this group, v,(P032-), in 5’-GMP and 5’-CMP gives rise to an infrared band of medium intensity at -974 cm-1 in 2H20 that appears reasonably isolated from other bands of the spectrum. A study on the v,(P032-) FTIR band profile of 5’-CMP in 2H20 solutions, 0.002-0.58 mol dm-3, within the temperature range 10-55 OC is done in this work. Vibrational and reorientational contributions to the relaxation of the vs(P032-) mode cannot be separated using infrared data only. However, the v,(POS2-)mode is a weak Raman scatterer that generates a weak Raman band at -976 cm-’ in 2H20, making a profile analysis difficult,’ especially at low concentrations, 10-LlO-3 mol dm-3, i.e., when approaching physiological conditions. Taking into account the results obtained for Y-GMP, the considerable molecular weight and moments of inertia of 5’-CMP, the high densityof vibrational states (96 normal modes of vibration), and the fact that POS2-
-
Present address: Institute of Isotopic and Molecular Technology, Laboratory of Molecular Physics, R-3400 Cluj-Napoca 5, P.O. Box 700, Romania. Author to whom correspondence should be addressed.
is a polar group surrounded by a polar solvent and probably involved in intermolecular hydrogen bonding interactions, a predominant vibrational contribution to the infrared correlation function must be expected. Application of Kubo-Rothschild’sa and Oxtoby’s9 vibrational dephasing theoriesto these results could give an insight into these points, and it would also supply additional information on the modulation regime of the Y,(PO~~-) oscillator.
Experimental Section Materials and instrumentation. Previously desiccatedsamples of cytidine 5’-monophosphatedisodiumsalt from Sigma Chemical Co., purity 99% according to the manufacturer, were solved in deuterium oxide from Scharlau, deuteration degree higher than 99.8% checked by its infrared spectra. Their FTIR spectra were immediately recorded in a Specac Ltd. vacuum-tight heatable cell with BaF2 windows and 41-pm path length, 1, measured from its interferencefringes. The cell was placed in a thermocirculating water jacket connected to a thermostat through a vacuum accessory for circulating fluids designed by the authors. A thermocouplejunction was introduced into one cell window for temperature monitoring. The temperature stability of the system was f0.05 OC, and the spectra were recorded between 10 and 55 OC. The spectra were recorded under vacuum, pressure 1133.3 Pa, using a Bomem DA3 FTIR interferometer equipped with a MCT detector. Working under vacuum, a very stable base line free from water absorptions is achieved, and thereforereproducible spectral data for the v,(P032-) region up to mol dm-3 of mononucleotide in 2H20 are obtained. The nominal resolution was 2.Ocm-l, but the resultingspectralresolutionafter apodization (Hamming’s apodizing function) was s = 2.5 cm-1. The digital resolution of the recorded spectra was 0.964 cm-1. In order to reach a good signal-to-noise ratio, SIN, the number of interferograms coadded for each spectrum were as follows: 1000 for 0.58-0.3 mol dm-3 solutions, 2000 for 0.3-0.2 mol dm-’, 4000 for 0.2-0.08 mol dm-3,7500 for 0.08-0.05 mol dm-3, and 15 000 for 0.05-0.002 mol dm-3, this last concentrationbeing in thedetection limit of the instrument. Data Treatment. A linear base line correction of the band was done by using its lower absorbance points at each temperature
0022-365419312097-908 1%04.00/0 0 1993 American Chemical Society
Navarro et al.
9082 The Journal of Physical Chemistry, Vol. 97,No. 36, 1993
0.58
0.32 0.23
2
--d
0.10
2 0.04 1 ’ 1 1 1 1 1 1 1 1 1 1 1 ( 1 1 1 / 1 1 1 ( 1 1 1 1 1 1 ‘
800
1000
;/cm-l Figure 1. u,(PO3”) FT’IRband of 5’-CMP in
2H20 at
the indicated concentrationsin mol dm-3. The spectra have been base line corrected, and the flat ends of each spectrum correspond to zero absorbance.
-
and concentration, 1006915 cm-1. This integration range corresponds to an average number of 8.8 f 1.4 full-widths at half-height, fwhh, over 36 base-line-corrected spectra. Peak position and fwhh of the band were determined using Bomem Calc software. fwhh were evaluated from the half-maximum absorbances. The ratio of the apodized resolution to fwhh of the band was below 0.26. Despite this low ratio, the instrument line shape distortion on the observed FTIR bands was corrected by applying Dijkman’s equation:’*
where is the true fwhh and A%/2isthe observed or apparent fwhh. Measurements of the band moments and time correlation functions, CFs, as well as fittings to Kubo-Rothschild’s8 and Oxtoby’s9 equations were performed using programs written by the authors. The Fourier transformation was computed by direct numerical integration of the transform integral at each time point. The spectral range considered for moment and CF evaluation was from seven to nine times the fwhh of the band. According to Turrell et al.,” this spectral range involves an average time resolution for the correlation functions of 0.27 ps. From the apodized resolution, 2.5 cm-I, these authors” predict that the resulting CFs are reliable up to 6.7 ps. The relaxation time was evaluated by integration of the C F over the time range from 0 to 4 ps, where the CF approaches zero. The modulation time was obtained from the fittings of K u b Rothschild’s and Oxtoby’s equations to the experimental CF.
Results and Discussion The v,(P032-) FTIR band shows a fairly symmetric profile without shoulders or splittings, Figure 1, in the concentration range, c = 0.002-0.58 mol dm-3, and temperatures, 10-55 OC, studied. But an analysis of its second derivative reveals that there are more than one component under the band contour for concentrations higher than -0.32 mol dm-3, see Figure 2. The separation between components, -4-8 cm-1, is larger than the
11
900
/
/
l
I
t
l
/
I
I
f
/
l
I
0.23 I
I
/
I
I
I
I
I I
I
I
I
I
I
I
I
I
I
I
I
I
l
I
/
I
1000
Glcm-1 Figure 2. Second derivative (sign changed) of the U,(PO~~-) FTIR band of 5’-CMP in *HzO at the indicated concentrations in mol dm-3. Nine convolution points have been used in the evaluationof the second derivative for all spectra.
spectral resolution. These components could be attributed to the presence of different Y,(PO~~-) oscillators associated with the formation of 5’-CMP aggregates at high concentration, the POSzgroups being involved in the intermolecular bonding and the concentration at which self-associationoccurs being the same as that for 5’-GMPa2Therefore,a band shapeanalysis beyond -0.32 mol dm-3 does not make sense, and the analysis of the band done in this work is limited to the concentration interval 0.002432 mol dm-3. A study on the relative intensities of the band components between 0.32-0.58 mol dm-3 using curve-fitting procedures is in progress. Band Parameters. Wavenumber of the band maximum, ;-; apparent integrated intensity, B; band shape parameters as moments; and the Cauchy-Gauss, CG, index at different concentrations are given in Table I. The wavenumber of the maximum does not undergo significant changes with concentration, and theobserved variations are of the order of thespectral resolution. The apparent integrated intensity appears to be independent of the cl product; therefore, the absolute intensity of the band has been evaluated from the mean value of B, 104 km mol-’, instead of from application of Wilson and Well’s method,l2 i.e., extrapolating B a t cl 0. The absolute intensity of the infrared v,(PO~~-) band of 5’-CMP in 2Hz0 is only slightly lower than the absolute intensity for its complementary mononucleotide 5’-GMP,Z 112 km mol-’, indicating that the change of the purine base by the pyrimidine base in the mononucleotide involves a small decrease of the derivative of the electric dipole moment with respect to the normal coordinate v,(P032-), d p / aQk. The reduction in the size of the base, and in its electronic r system, could be associated with this effect. The second band moment, M2, exhibits a weak increase with concentration, the same result as observed for the truncated second moment,13 p&) = b-2M2 where b = A;: ,/2 and j = (; - imaX)/b,in Figure 3. behavior of p2(j) in this kgure suggests that the CG index of the band fluctuates around 0.5, as is shown in Table I, with the higher Gaussian contribution to the band profile corresponding to the lowest concentration. The values of the third moment reveal that the band has a very symmetric profile in the concentration interval 0.0024.3 mol dm-3, in which the second derivative exhibits only one component. The integrated absorbance of the band, A, divided by the path length of the cell, 1, presents an inflection at -0.3 mol dm-3, Figure 4, that corresponds to the
-
Symmetric V,(PO~~-) Mode of 5’-CMP
The Journal of Physical Chemistry, Vol. 97, No.36, 1993 9083
TABLE I: Parameters of the v, (Po3%) FTIR Band of 5’-CMP in 2 H ~ for 0 Different Concentrations at 25 “C* clmol dm-3 0.0023 0.0035 0.0060 0.0070 0.0080 0.0090 0.0150 0.0175 0.0300 0.0350 0.0500 0.0600 0.0700 0.0875 0.1000 0.1200 0.1350 0.1500 0.1613 0.1650 0.1800 0.1900 0.2000 0.2010 0.2150 0.2300 0.2500 0.2700 0.2800 0.2950 0.3225 0.3600 0.3800 0.4300 0.4400 0.4600 0.5400 0.5800
B/10 km
;-/cm-l 974.8 974.8 972.9 974.3 973.9 974.1 973.9 973.9 975.1 973.9 973.9 973.9 973.9 973.9 973.9 974.8 974.8 974.8 974.8 974.8 974.8 974.8 974.8 974.8 974.8 974.8 975.8 974.8 975.8 974.8 974.8 914.8 974.7 974.8 975.8 974.8 974.8 975.8
mol-‘ 7.9 9.9
-
11.1
-
8.1 16.5 15.2 10.7 9.8 13.0 10.7 10.3 12.3 9.9 11.7 8.6 9.7 11.5 11.2 10.7 11.0 13.9 11.5 10.7 8.6 7 .O 8.6 8.5 12.0 11.2 10.4 10.8 10.4 7.6 7.1 7.1 7.3
CG Mz/cm-2 Ms/Mz3/2 index 31 38 42 39 40 35 37 53 35 43 43 46 43 45 53 46 48 48 50 47 49 50 62 52 49 50 51 59 51 55 56
-
-
-
0.76 0.46 -0.86 -0.64 -0.60
-
-0.76 -0.87 -0.91 -0.93 -1.13 -1.50 -0.26 -0.56 -0.96 -0.93 -0.81 -0.64 -0.99 -0.79 -0.96 -0.32 -0.47 -0.66 -0.91 -0.65 -0.81 -0.43 -1.05 -0.80 461
-
-
0.25
0.40 0.54 0.60 0.66 0.75 0.46 0.78 0.25 0.40 0.52 0.60 0.51 0.41 0.49 0.48 0.44 0.38 0.49 0.41 0.46 0.42 0.39 0.44 0.46 0.42 0.42 0.36 0.45
0.44 0.40
-
-
-
2.50
3
~120) ( w 2 ) l&c&
1.11 1.11 1.04 0.97 1.44 0.51 0.68 0.69 1.18 0.87 0.84 0.79 1.02 0.98 0.83 1.03 0.96 1.08 1.16 1.04 0.85 0.93 1.19 1.06 0.96 1.10 1.00 0.71 0.94 1.08 1.10
-
2.00
1.00
i 1
/
0.00 , , I I I , I I I , I I I I I , I I I I I I I I I , I , , I I I J 0.00 1.00 2.00 3.00
‘ I I / l I , 8 1 8 # t
8IIIIIIl
4.00
5.00
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1
6.00
j Figure 3. Truncated second moment of the U , ( P O ~band ~ - ) at different concentrations (in mol dm-3): ( 0 )0.0023, (+) 0.007, (A)0.035, ( 0 ) 0.12. Truncated second moments for Cauchy’s (solid line) and Gauss’ (dashed line) band shapes. 5.00 1 3
I
E
54
4.00 1
1 3
I
?
3.00 -
* Baseline correction is difficult to estimate for spectra recorded at c < 10-2 mol dm-3, and band shape analysis does not make sense when the
second derivative of the band exhibits more than one component, Le.,
when c > -0.32 mol dm-3. These are the reasons for the lack of some computed parameters in the table.
concentration at which aggregation of the mononucleotidewould occur. This result supports the idea suggested from the results of the second derivative that self-associationof the mononucleotide takes place at concentrations higher than -0.3 mol dm-3. The observed increase of the true fwhh with concentration suggests that the main contribution to the infrared C F is of vibrational type.14J5 The linear relationship between the true fwhh and 6,Figure 5 , and the fwhh value extrapolated at 6 0, 8.5 cm-1, indicate that vibrational dephasing is probably the most efficient relaxation mechanism.16 In order to study the dependence of the band shape on temperature, a concentration of 0.23 mol dm-3 has been selected. Effects of mononucleotide aggregation on the band shape are avoided, and spectra with a high SIN ratio are recorded at this concentration. Small changesof the band parameters are observed from 10 to 55 “C, Table 11. The wavenumber of the band maximum and the apparent integrated intensity decrease slowly, but the second band moment increases, Figure 6. The temperature dependenceof the true fwhh exhibitsa small negative slope, Figure 7,an additional indication that thevibrational relaxation process seems to be dominant.17-lg Correlation Functions and Relaxation Times. The infrared CFs, Gi,(t), of the V,(PO~~-) mode have been determined from the FTIR spectra recorded at the indicated concentrations. Two limiting profiles are shown in Figure 8, for 0.009and 0.3225 mol dm-3 solutions. The decay of Gb(t) is faster with the increasing
-
0.00 l . O O0.00 ~
0.10
0.20
0.30
0.40
0.50
0.60
c/mol dm-3 Figure 4. Integrated absorbance of the V,(PO~~-) band divided by the path length of the cell vs concentration of 5’-CMP.
concentration; the same result was observed for the vS(POp2-) mode of 5’-GMP2 and for other oscillators.20.21 At low concentration, c I 10-2, the experimental CF approaches well to a Gaussian C F until 1 ps, but the decay becomes of Cauchy’s C F type at longer times. At higher concentrations, an intermediate profile is obtained until 2 ps, Figure 8. From this time on, Cauchy’s CF fits better to the experimental CF. The faster decay of the infrared C F with increasing concentration is also evident in the infrared relaxation time, 7ir,obtained by integrating the infrared CF, Figure 9. 7ir tends to decrease. For the complementary mononucleotide, 5’-GMP, a similar tendency has been observed, but qrvalues are slightly shortera2An interesting result for 5’GMP is that the vibrational relaxation time, T”, obtained from the Raman Zb spectra of 5’-GMP is of the same order of magnitude of q r . 3 This is a clear evidence that vibrational relaxation is the main broadening factor of the infrared V,(PO~~-) band in 5’GMP.3 Hence, a similar behavior for this mode of 5’-CMP should be expected.
Navarro et al.
9084 The Journal of Physical Chemistry, Vol. 97, No. 36, 1993 3
20‘oo
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1
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cv 16.00 7
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8.00
0.20
0.40
0.60
0.0
10.0
20.0
30.0
40.0
, , G / ~ ~ dm-3i2 I~I~ Figure 5. True fwhh of the v,(PO~~-) band vs square root of the mononucleotide concentration.
50.0
60.0
t/OC Figure 7. True fwhh of the v,(PO~Z-)band vs temperature for a 0.23mol dm-3 solution of 5’-CMP. 1.00
*,
/ 6
1.50 :
A
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0
1.00
0.50
0.40
-
0.20
j, p /
0.00 0.00
I , I , I , I ,
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,,,,/,,,,,,, I 4.00 5.00
0.00
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tlps
j Figure 6. Second moment of the v,(PO~~-) band of 5’-CMP in 2Hz0, 0.23 mol dm-3 at different temperatures: (*) 10, (0)34,and (A)55 OC. Second moments for Cauchy’s (solid line) and Gauss’ (dashed line) band shapes.
The increase of temperature tends to slow the decay of the infrared CF, Figure 10, as has been observed for the u3 mode of chloroform.22 Accordingly, the relaxation time, qr, becomes slightly longer with increasing temperature, Table 11. The intermediate character of the experimental CF between the Cauchy and Gaussian CF is not significantly affected by temperatureCG index values of -0.5 can be observed in Table 11. Nevertheless,the Gaussian character is more pronounced at high temperature in the short time range of the CF. KubRotbschiId’s and Oxtoby’s Models. Modulation Times. Some important evidence supporting that vibrational relaxation is the fastest process in the relaxation of the v ~ ( P O ~mode ~ - ) has been presented previously: the concentration dependence of the true fwhh14J5and of 7w20.23J4 and the behavior of the fwhh with temperat~re,’~-’~ Figure 7. From various vibrational relaxation mechanism, energy r e laxation, resonant energy transfer, and vibrational dephasing, the last one seems to be the most important. Energy relaxation
5.00
4.00
Figure 8. Infrared correlation function for the V,(Po32-) band at (*) 0.009 and (0)0.3225 mol dm-3. Computed correlation functions for Cauchy’s (solid line) and Gauss’ (dashed line) bands with fwhh and absorbance at the maximum equal to those observed for the band at 0.3225 mol dm-3. The inflections of the correlation function for the Cauchy band are caused by the slow decay of this type of band and by theuseofafinitespectralrange(1003.7-912.17cm-~)forcomputingits Fourier transform.
-
-
to translational and rotational bath degrees of freedom (v t,r) or to other vibrational degrees (v v’), intra- or intermolecular processes, cannot be considered so efficient due to the high frequency gap (>lo0 cm-1) between v,(POP2-)and the closest vibrational mode (centered at 1100cm-l) or regarding the low concentrationsused. The observed concentration dependence of the fwhh, Figure 5 , and the dilution of the mononucleotide in 2H20 suggest that vibrational dephasing is the most efficient mechanism in the relaxation of the v,(PO~~-) mode. Its contribution to the average fwhh, 10 cm-l, determined as stated previously, Figure 5 , is 8.5 cm-1; Le., the main broadening effect is due to this mechanism. Different models on vibrational dephasing have been proposed to describe the experimental CF. In the theory developed by Kubo and Rothschild,* the logarithm
-
Symmetric v,(P032-) Mode of 5’-CMP
The Journal of Physical Chemistry, Vol. 97, No. 36, 1993 9085
TABLE Ik Parameters of the v,(PO$) FTIR Band of 5’-CMP (0.23 mol dm-9 in 2H~0 at Different Temperatures
li
t/OC ;-/cm-l
1
0.80 0.00 I
10 15 20 22 24 26 28 30 32 34 35 36 38 40 45 50 55 /
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c/mol dm-3 Figure 9. Infrared correlation time obtained by integration of the correlation function for the V,(Po32-) band vs mononucleotide concen-
tration.
-0.00
1nGir(t)
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-1.00
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-3.00
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-7.00 0.00
1.00
2.00
3.00
4.00
5.00
tlw Figure 10. Natural logarithm of the infrared correlation function for the v,(FQ,~-) band of 5’-CMP in 2H20,0.23 mol dm-3, at (X) 10 OC and ( 0 ) 50 o c .
of the vibrational CF is expressed by
In GJt) = -(02)(T:[eXp(-t/Tc)
- 11 + 7;)
(2)
where T~ is the modulation time and (02)= 4m2M2is the average frequency fluctuation or modulation amplitude. However, OxtobyQproposed another equation for this CF:
In G,(t) = - ( w ~ ) T : In cosh(-t/T,)
bf3/bf23/2
9.2 9.1 8.8 8.6 8.5 8.6 8.5 8.8 8.8 8.7 8.6 8.7 8.7 8.7 8.7 8.9 8.5
-0.94 -1.02 -0.66 -0.66 -0.51 -0.71 -0.75 -0.58 -0.56 -0.52 -0.48 -0.65 -0.68 -0.77 -0.70 -0.84 -0.83
index ~l,/ps 0.46 0.47 0.44 0.45 0.42 0.43 0.45 0.45 0.46 0.49 0.45 0.47 0.50 0.49 0.55 0.48 0.51
1.06 1.09 1.06 1.05 1.05 1.06 1.06 1.06 1.06 1.06 1.06 1.07 1.06 1.05 1.05 1.05 1.05
(~~)*/2~~2fox
0.97 1.10 1.02 1.03 1.12 1.00 1.11 1.03 1.06 1.06 1.08 1.03 1.04 0.96 1.02 0.98 0.93
.
0.40
0.30
975.8 975.8 975.7 975.7 975.7 975.6 975.6 975.1 975.1 975.1 975.1 975.1 975.1 975.1 975.1 974.9 914.8
CG
B/10
km mol-’
(3) These equations behave at long times as straight lines with slope equal to - ( O ~ ) T * Both equations have been fitted to the experimental CF using the observed values of M Zto determine (02). Values of T~ corresponding to the best fit to each model were evaluated, as well as the modulation speed, ( w ~ ) ~ / % , .In general, Oxtoby’s model fits better the experimental CF than Kubo-Rothschild’s model, but at very low concentrations, c I 0.009 mol dm-3, there is a significant deviation of both models at long times, Figure 11. The observed CF relaxes more rapidly than eqs 2 and 3 predict. This additional relaxation could be
interpreted as an indication of the contribution of other relaxation mechanisms. Nevertheless, it might also be considered that at these low concentrations, and the corresponding small absorbances, difficulties in the base line estimation appear. By studying the concentration and temperature effects on the theoretical CF, one can obtain some additional information. The modulation time increases very slowly with concentration, and the modulation speed remains nearly constant, Table I. Despite the increase of M2 with temperature, Figure 6, the decrease of T~ obtained for both models, Figure 12, results in a slow decrease of the modulation speed on increasing temperature, Table 11. Similar results were obtained in the analysis of the VI mode of nitr~methane.~~ This behavior excludes dissipation to the thermal bath as the prevailing relaxation process. The temperature behavior of T~ shows that kinetic and not distance effects are governing the dynamics of the P032-group. The values of the modulation speed, close to 1, indicate an intermediate modulation regime. The parameters 7ir and T~ decrease while Mz increases on increasing temperature, indicating that vibrational dephasing takes place through interactions controlled by repulsive potentials.26 The concentration effect on themodulation timeconfirms this interpretation.2’ A deeper insight into the vibrational dephasing mechanism consideringthe hydrodynamic28and Lynden-Bell’sB theories could be obtained by studying the dependence of the true fwhh with viscosity at different temperatures. However, the short temperature interval with biological significance for this molecule and the relatively small change detected for ~ i Table ~ , 11,between 10 and 55 OC put difficulties on the analysis of the adequacy of both theories. In biological molecules like mononucleotides with a large molecular weight, the contribution of an intramolecular nearresonant energy-transfer process can, in principle, appear.22From this point of view, vibrational relaxation cannot be due to the dephasing mechanism exclusively.
Conclusions The analysis of the v,(P032-) FTIR band shape of 5’-CMP in 2H20 solutions at different concentrations and temperatures, approaching physiological conditions, has been done in terms of molecular dynamics and self-associationprocesses of this mononucleotide. Second derivative spectra and integrated intensities reveala possibleaggregationof 5’-CMPin2H20 at concentrations higher than 0.3 mol dm-3. This behavior has been observed for the first time, to our knowledge. The absolute intensity of the infrared vS(PO32-) band of 5’-CMP is slightly lower than the absolute intensity of this band for its complementary mononucleotide 5’-GMP, and this can be associated with the reduction
Navarro et al.
9086 The Journal of Physical Chemistry, Vol. 97, No. 36, I993
Raman Ziso spectra of this mode for 5’-GMP give T, values very close to those obtained for 7ir. The theoretical models proposed by Kubo-Rothschild and Oxtoby have been applied to the experimental CF in order to find the modulation times and the corresponding modulation velocities. In general, Oxtoby’s model fits better than KubRothschild’s model the experimental CF. The modulation speed of the vibrational frequency, 1, is of an intermediate regime. Kinetic and not distance effects influence the dynamics of the P032- group, as is suggested by the temperature behavior of the modulation time, and repulsive potentials determine the interactions involved in the vibrational dephasing of the V,(PO~~-) mode.
0.00
ln G ( t )
-
-2.00
I
.
-4.00 4
\
4
-6.00
0.0
1.o
2.0
3.0
5.0
4.0
tlPS Fipw 11. Natural logarithm of the infrared correlation function for the v,(P0s2-) band at (*) 0.009 and (0)0.3225 mol dm-3. Oxtoby’s (solid lines) and Kubo’s (dashed lines) equations were fitted for both conccn-
trations. 2.40
7
1.90
4
0.90
i -j
0.40
0.0
References and Notes (1) Saenger, W. Principles of Nucleic Acid Structure; Springer-Verlag: New York, 1984; pp 81-82. (2) Navarro, R.; Hernanz, A. J . Mol. Srrucr. 1988, 175, 335. (3) Hernanz, A.; Navarro, R. Spectroscopy of Biological MoleculesSrateof the Art; Bertoluzza, A., Fagnano, C., Monti, P., Eds.;Societe Editrice Esculapio: Bologna, 1989; pp 203-204. (4) Hernanz, A.; Navarro, R. Chemistry andPropertiesofBiomolecular Systems; Rizzarelli, E., Theophanides, T., Eds.; Kluwer: Dordrecht, 1991; pp 159-164. (5) Fisk, C. L.; Becker, E. D.; Miles, H. T.; Pinnavaia, T. J. J. Am. Chem. Soc. 1982,104, 3307. (6) Walmsley, J. A.; Barr, R. G.; Bouhoutsos-Brown,E.; Pinnavaia, T. J. J. Phys. Chem. 1984,88, 2599. (7) Carsughi, F.; Ceretti, M.; Mariani, P. Eur. Biophys. J . 1992,21,155. (8) Rothschild, W. G. J . Chem. Phys. 1976.65, 455. (9) Oxtoby, D. W. J . Chem. Phys. 1981, 74, 1503. (10) Dijkman, F. G.;Van der Maas, J. H. Appl. Spectrosc. 1976,30,545. (1 1) Turrell, G.; Leclerc, D.; Aubin, M.; Mushayakarara, E. J. Mol. Liq.
A
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Acknowledgment. This work was supported in part by the Direcci6n General de Investigaci6n CientIfica y T h i c a (Madrid, Spain) under project PS89-0032. The authors express their gratitude for the financial support received from the Institute of Isotopic and Molecular Technology (Cluj-Napoca, Romania) and from the Ministerio de Asuntos Exteriores (Spain) under the terms of the Convenio de Cooperacibn CientfficoT h i c a hispanorumano. It made possible a scientific visit of one of the authors to the Spanish laboratory.
10.0
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t/OC Figure 12. Kubo’s (*) and Oxtoby’s ( 0 ) modulation times, temperature for the mononucleotide at 0.23 mol dm-3.
vs
T ~ ,
inthesizeofthebaseandinitselectronicrsystem.Thetruncated moment analysis reveals quite symmetrical profiles and an increase of the Gaussian contribution to the band shape for the lower concentrations. At these concentrations, the experimental CF approaches well to a Gaussian CF until 1 ps, but it has a Cauchy’s CF decay at longer times. At higher concentrations, an intermediate profile is obtained until 2 ps, and from this time on the Cauchy CF fits better to the experimental CF. Different arguments are in favor of vibrational relaxation as the main contribution to the infrared C F (a) the behavior of the fwhh with concentration and (b) temperature and (c) the fact that the
1983, 27, 37. (12) Wilson, E. B.; Wells, A. J . Chem. Phys. 1946, 14, 578. (13) Jones, R. N.; Seshadri, K. S.;Jonathan, B. W.; Hopkins, J. W. Can. J. Chem. 1963, 41, 750. (14) Rosi, B.; Fontana, M. R. J . Chem. Phys. 1987,87, 6406. (1 5) Bratu, I.; Klostermann, K.;Iliescu, T.; AStilean,S.J . Mol. Liq. 1990, 45, 57. (16) Higuchi, S.;Tanaka, S. Spectrochim. Acta. 1975, 31A, 1003. (17) Rothschild, W. G. Dynamics of Molecular Liquids; John Wiley: New York, 1984; pp 286-287. (1 8) Vincent-Geisse, J. Vibrational Spectroscopy of Molecular Liquids ondsolids; NATO Advanced Study Institutes Series, B, 56; Bratos, S.,Pick, R. M., Eds.; Plenum: New York, 1980; pp 120, 140-141. (19) Stecle, D.;Yarwood, J. Spectroscopy and Relaxation of Molecular Liquids;Stccle, D., Yarwood, J., Eds.; Elsevier: Amsterdam, 1991; pp 38-39. (20) Bulkin, B. J. Chemical, Biological and Industrial Applications of Infrared Spectroscopy; Durig, J. R., Ed.; John Wiley: New York 1985; pp 158-159. (21) Iliescu, T.; Agtilean, S.; Bratu, I. J . Mol. Liq. 1990, 47, 129. (22) Rothschild, W. G.; Cavagnat, R. M. J . Chem. Phys. 1992,97,2900. (23) Abramczyk, H.; Reimschlssel, W. Chem. Phys. 1984,83, 293. (24) Adachi, A.; Kiyoyama, H.; Nakahara, M.; Masuda, Y. H.; Shimizu, A.; Taniguchi, Y . J. Chem. Phys. 1989, 90, 392. (25) Giorgini, M. G.; Mariani, L.; Morresi, A.; Paliani, G.; Cataliotti, R. S. Mol. Phys. 1992, 75, 1089. (26) Ferreira Marques, M. F. R. M.; Amorim da Costa, A. M. J. Chem. SOC.,Faraday Trans. 2 1987,83, 647. (27) Yarwood, J.; Arndt, R.; D6ge, G. Chem. Phys. 1977, 21, 53. (28) Oxtoby, D. W. J. Chem. Phys. 1979, 70, 2605. (29) Lynden-Bell, R. M. Mol. Phys. 1978, 36, 1529.
