Theoretical study of the electronic properties of biological purines and pyrimidines. II. The effect of configuration mixing

Berthod, Hélène; Giessner‐Prettre, Claude; Pullman, Alberte

doi:10.1002/qua.560010202

Cited by 78 publications

(34 citation statements)

References 15 publications

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“…Since the interpretation of the calculated circular dichroism spectra has been shown to be dependent upon the relative transition moment directions of the component bases" and because the above calculations involved transition moment directions that were calculated from the electronic charge distributions for the bases that resulted from the self-consistent field configuration interaction coefficients of Berthold et al, 23 we found it necessary to determine whether our results were the same when transition moment directions for the bases consistent with those measured experimentally were used.…”

Section: Section 11: Resultsmentioning

confidence: 99%

Origins of the differences between the circular dichroism of DNA and RNA: Theoretical calculations

Moore

Wagner

1973

Biopolymers

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SynopsisTheoretical calculations of the circular dichroism of double-helical DNA and RNA by the method of Johnson and Tinoco were performed in order to investigate the origins of the optical activity spectral differences between these polynucleotides. Calculations were performed using transition moment directions arising from molecular orbital calculations as well as transition moment directions in agreement with experimental directions. The results of these calculations indicate that the conservative circular dichroism spectrum of B-form DNA and the nonconservative spectrum of RNA (and A-form DNA) arise as a consequence of the distance between the paired bases and the helix axis. The negative nonconservative spectrum of C-form DNA was calculated and shown also to result from the distance of the paired bases from the helix axis. Several other conspicuous geometric parameters of DNA and RNA were investigated and were found to be less significant in their effects upon the spectral differences. Theoretical calculations on a four-stranded DNA model which has paired bases similarly related to the helix axis as RNA and A-form DNA was found to yield a low intensity, nonconservative circular dichroism spectrum.

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Section: Section 11: Resultsmentioning

confidence: 99%

Origins of the differences between the circular dichroism of DNA and RNA: Theoretical calculations

Moore

Wagner

1973

Biopolymers

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“…Stewart and Davidson showed that the polarization direction of the main band in 9-methyladenine is along the y axis [43]. The calculated polarizations for adenine and other natural bases have been reported [42,44,451. However, it has not been established unequivocally whether the main absorption (26 1 mp) is y-axis [43] or x-axis polarized [34].…”

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confidence: 94%

Electronic structures and spectra of halogenated purines and pyrimidines II.π‐Electronic structure of 2‐chloropurine and its related derivatives

Song

1968

Int J of Quantum Chemistry

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AbstractsElectronic structures and spectra of "non-alternant" heterocyclic 2-chloropurine and its analogs have been computed with different MO techniques, namely, HMO, O-SCF-HMO (o = 1.4 and 0.5), and PPP semiempirical SCF-ASMO-CI. Triplet-state energies have been calculated by the last method. In general, it is found that at least semiquantitatively consistent results on the ground-state properties of the molecules are obtained from the different MO methods. As expected, excited states of the molecules are not satisfactorily treated by the HMO and o techniques. However, an excellent agreement between the observed and calculated n** transition energies has been obtained with the PPP method. In view of the semiquantitative consistency of the ground-state properties, the use of simple methods such as HMO and W ( = O.~)-SCF techniques is justifiable for limited application to molecular biology.Results on the molecular geometry, dipole moments, ionization potentials, xanthine oxidase reactivity and spectra have been discussed with regard to the halogen substitutions in the purine base. The significance of these results with reference to the biological uses of substituted purines is briefly described. Les tnergies des ttats triplets ont t t t calcultes au moyen de la derniere mtthode. On trouve en gtntral, au moins du point de vue "stmi-quantitatif", des rtsultats consistants pour les proprittts de l'ttat fondamental, en comparant les mtthodes difftrentes. Les ttats excitts des moltcules ne sont pas traitts d'une manitre satisfaisante par les mtthodes HMO et W-SCF, ce qui ttait prtvu. Cependant la mtthode PPP donne un accord excellent entre les tnergies de transition M* observtes et calcultes. I1 nous semble que la consistance "stmi-quantitative" des proprittts de l'ttat fondamental justifie l'application limitte en biologie moltculaire des mtthodes simples comme HMO et w ( = O.~)-SCF.Les rtsultats sur la gtomttrie moltculaire, les moments dipolaires, les potentiels d'ionization, la reactivitt de la xanthine oxidase et les spectres ont t t t discutts en tenant comte des substitutions halogtnoides dans la base purique. L'importance de ces rtsultats-ci pour l'emploi biologique des purines substitutes a t t t discutte brievement.

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“…Polarized reflectance studies on single crystals of cytosine monohydrate and l-methylcytosine shoved the lowest energy ?r --t ?r* transition (265 nm) oriented at 12" f 3 and the next ?r + ?r* transition (230 nm) oriented a t for the next transition of cytosine all lie between 156" to -181", which agrees with the most probable experimental valw of about 0" (or ISO" considering the uncertainty of the absolute value of the dipole direction) cstablished from the polarized absorbance and reflectancc spectra. Thc stretched film spectra of cytosine taken by 1;ucaloro and l;orster*' using cytosine that had bcen dissolved in a polyvinyl alcohol sheet, which was thcn strctchcd so as to orient the cytosine, partially revealcd that the two transitions of cytosine u-crc nearly parallel to each othcr, implying that thc wavc functions of Hug and Tinoco'j give a better calculated orientation for the long-wavelength transition in cytosinc than those of Bcrthod et al 5 In any event thc transition directions used for cytosine in thcsc calculations werc those calculatcd using the same 11 avc' functions employed to calculate the coupling energy. It is intcrcsting to note that the final results obtained from Hug and Tinoco's 11 ave functions and transition directions, which are in good agreement with experiment for both transitions in cytosine, are no better and somctimcs worse than the results obtained from the wave functions of Berthod ct al.,5 which predict tn-o transitions nearly perpendicular to each other.…”

Section: Cytosinementioning

confidence: 95%

Calculation of the circular dichroism of double‐helical nucleic acids. III. Dependence of the results on the choice of wave functions for purines and pyrimidines

Studdert

Davis

1974

Biopolymers

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SynopsisThe circular dichroism of double-helical nucleic acids was calculated using three different sets of wave functions for the purine and pyrimidine chroniophores. Different wave functions give qualitatively the same types of spectra. Qnantitatively, the differences are very substantial. However, the dependence of calculated circular dichroism spectra on nucleic acid geometry and base composition is very similar for the three different sets of wave functions. Each set of wave functions could be used to reproduce some, but not all experimentally observed spectra. The geometries required to reproduce experimentally observed spectra consistently require double-helical geometries similar to the B or C forms of DNA. INTRODUCTIONCalculation of the optical activity of a molecule as complicated as a iiucleic acid entails a large number of simplifying assumptions. One must take approximate wave functions, use them in approximate theories, and apply them to assumed geometries. In the two preceding papers1t2 we have discussed the dependence of the calculated circular dichroism (CD) spectra on geometry and to a limited extent, the dependence of the calculated spectra on the approximations used to makc the calculations viable. I n this paper we explore some of the problrms relating to the choice of wave functions for the purine and pyrimidine chromophores.It is not obvious how one should trst the dependence of calculated results on the choice of wave functions. There are many different approaches to calculating wave functions so that it is not possible to present simply the dependence of the calculated CD on a small number of parametem, as it was in describing the geometric dependence.' We will present results using three different sets of wave functions. Teng et aL3 have shown that for nucleosides and nucleotides the choice of wave function can have a substantial effect on the calculated results. Wc are not familiar with studies on larger systems relating to nucleic acids. 1406STUDDERT AND DAVIS The calculations reported hcrc incorporate effects of n -. t n* transitions as u-cll as n + n* transitions. They \\ ere carried out as described in the previous two with the only changes bcing in the wavc functions used. Calculations of P --f n* terms were made using SC1; and SCF-Cf 1\10 wave functions of Bcrthod ct al.435 and SCE'-CI A 1 0 wave function,.; of Hug and Tinoco.6 The major differcncc bctwen the t v o sets of SCF-CI A 1 0 wave functions was that Hug and Tinoco included all valence electrons. Transition monopoles for n -n* transitions were multiplicd by a scaling factor so that the calculated and measured magnitudes of the transition dipoles werc matched.As beforel1e2 B~s h ' s~,~ extended Huckcl wavc functions werc used for calculating all terms involving ?t --f n* transitions. Consequcntly, diff crences between spectra calculated using different wave functions reflect only changes involving the n -n* terms as developed by Johnson and T i n o c~.~ All spectra prcsentcd in this paper are calculated including effects ...

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Theoretical study of the electronic properties of biological purines and pyrimidines. II. The effect of configuration mixing

Cited by 78 publications

References 15 publications

Origins of the differences between the circular dichroism of DNA and RNA: Theoretical calculations

Origins of the differences between the circular dichroism of DNA and RNA: Theoretical calculations

Electronic structures and spectra of halogenated purines and pyrimidines II.π‐Electronic structure of 2‐chloropurine and its related derivatives

Calculation of the circular dichroism of double‐helical nucleic acids. III. Dependence of the results on the choice of wave functions for purines and pyrimidines

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