The use of the CNDO method in spectroscopy

Ellis, Richard L.; Kuehnlenz, G.; Jaffé, H. H.

doi:10.1007/bf00526540

Cited by 379 publications

(62 citation statements)

References 17 publications

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“…The spectral transition energies were calculated with the CNDO/S method of Del Bene and Jaffe (13)(14)(15), with semiempirical parameters taken from the work of Ellis et al (16), and the repulsion integrals were calculated with the Mataga approximation. Charged amino acids were represented, as in our previous work, as external point charges.…”

Section: Methods Of Calculationmentioning

confidence: 99%

Charged amino acids as spectroscopic determinants for chlorophyll in vivo

Eccles

Honig

1983

Proc. Natl. Acad. Sci. U.S.A.

112

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In this paper we propose that the large spectroscopic red shifts observed for chlorophyll (Chl) and bacteriochlorophyll (BChl) in vivo may be due to charged amino acids in the binding site. Molecular orbital calculations of the transition energies of Chl in the field of external charges are carried out. The calculated wavelength shifts induced by these charges are comparable in magnitude to those observed in vivo. Moreover the size of the shifts increases in the order BChl b > BChl a > Chl a, which is the observed trend. The ability of the calculations to account for both the absolute and relative magnitudes of the wavelength shifts argues for the validity of the model. Further indirect support comes from the recent demonstration that charged amino acids are responsible for the colors of visual pigments and bacteriorhodopsin. In addition to their effects on spectra the presence of external charges induces large changes in the ionization potential of Chl molecules and thus might explain the in vivo alteration of the oxidation potentials in reaction centers.The difference between the properties of chlorophyll (Chl) molecules in solution and identical molecules in vivo has been a subject of great interest, extensive investigation, and much conjecture. It is clear that its local environment endows Chl in vivo with special physical and chemical properties, yet little is known about the nature of the interactions that produce these effects. Because it now appears that most if not all of the Chl in photosynthetic systems is intimately associated with proteins (1), it seems appropriate to consider how specific amino acids might affect the behavior of bound Chl. Properties that are strongly influenced by the protein environment include redox potentials, photochemically induced electron transfer, and absorption maxima. Of these, the latter are easiest to characterize and interpret because spectroscopic transition energies for conjugated systems may be calculated theoretically with considerable accuracy.Chl in vivo and in isolated lipoprotein complexes absorbs light at longer wavelengths than does monomeric Chl in simple organic solvents (2). The magnitude of the shift varies considerably among species and somewhat less for different pigments within a single organism (comparing, for example, reaction center with antenna Chl). In green plants the magnitude of the wavelength shift is between 300 and 800 cm-'. In the case of photosynthetic bacteria the shifts are often much larger, reaching 1,500 cm-' for bacteriochlorophyll (BChl) a-containing species and as much as 2,700 cm-1 for the antenna complex of the BChl b-containing species Rhodopseudomnonas (Rps.) viridis (2).Although the origin of these shifts is a question of some interest in its own right, its more general relevance owes to the possibility that the shift is due to highly specific and functionally important Chl-protein interactions. Thus, identifying the source of the large in vivo red shifts may be an important step in elucidating the mechanism of elec...

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Section: Methods Of Calculationmentioning

confidence: 99%

Charged amino acids as spectroscopic determinants for chlorophyll in vivo

Eccles

Honig

1983

Proc. Natl. Acad. Sci. U.S.A.

112

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“…

4) It is also known that the results of the absorption maxima wavelength calculated by the PPP method for p-electronic systems reflect substantial errors with the use of the NM-g CNDO/S and ZINDO methods.

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confidence: 99%

Improved CNDO/S Calculation of Electronic Spectra of Organic Compounds. I. New CNDO/S Calculation by Using an Improved Method of One-Center Electron Repulsion Integral

Hata

Murakami²,

Shibuya

et al. 2006

CHEMICAL & PHARMACEUTICAL BULLETIN

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The semi-empirical CNDO/S, developed by Jaffé and coworkers, 1,2) and the ZINDO (so-called Zerner INDO/S) 3) methods are useful for the theoretical investigation of the electronic states and spectra of organic compounds. However, the usefulness of these methods for organic chemists is limited at present to the calculations of functional dyes, because the experimental absorption maxima wavelengths beyond approximately 400 nm are observed appreciably longer wavelengths, as compared to those of the ZINDO 3) and the conventional CNDO/S methods (referred to as NM-g CNDO/S) used in our previous paper.4) It is also known that the results of the absorption maxima wavelength calculated by the PPP method for p-electronic systems reflect substantial errors with the use of the NM-g CNDO/S and ZINDO methods. The reason for the large discrepancy between the calculated and observed values suggests that the calculated absorption maxima wavelengths in the organic compounds of larger p-conjugated systems cannot be reproduced within the allowed ranges as the experimental value, because the results of the orbital energies calculated by these theoretical methods result in a large difference between HOMO and LUMO orbital energies.Nishimoto 5) reported that the value of the ionization potential I m decreases, and that of the electron affinity A m increases with an increase in the number of mobile p-electrons in relatively large p-conjugated molecules. Moreover, they reported that this error produced by the conventional PPP method could be greatly improved by the reevaluation of the twocenter electronic repulsion integral (New-g), thus introducing the concept of chemical softness (referred to as New-g PPP).6-12) Furthermore, Nakayama and co-worker 13,14) also reported that the shortcomings of NM-g CNDO/S calculations are appreciably absent among the results of the modified CNDO/S and ZINDO (referred to as New-g CNDO/S and New-g INDO/S) calculations, which introduce a New-g using the concept of chemical softness for a number of polycyclic aromatic hydrocarbons. However, the New-g CNDO/S and New-g INDO/S methods cannot be applied to compounds other than p-conjugated aromatic hydrocarbons, because the New-g values have not yet been determined with respect to the p-conjugated compounds containing various hetero atoms, namely, there is a variable k-function for each bonds C-N, C-O, N-N, etc.In recent years, the time-dependent density functional theory (TD-DFT) has been considerably used for the analysis of the absorption spectra for the hydrocarbons.15,16) However, the absorption maxima wavelengths obtained by this TD-DFT calculations are calculated appreciably longer wavelengths for larger p-conjugated compounds, as compared to the observed maxima wavelengths beyond ca. 400 nm. And this method is too time-consuming to be calculated to the absorption maxima wavelengths for larger p-conjugated compounds.The goal of this investigation was to establish a general modified CNDO/S method of reproducing the observed absorption maxima wavelengths i...

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“…We utilized the semiempirical C N D O /S method [3], which reproduces generally correctly the sequence o f higher occupied and lower virtual Reprint requests to Dr. H. Vogler, Siemens AG, OttoHahn-Ring 6, 8000 München 83. orbitals [4,5] and type and energetical spacing of lower singlet and triplet states [4]. The triplet wavefunctions 3V/ = Z uk) Cik Q ik were obtained by con figuration interaction between all singly excxited triplet configurations Q ik with energies below 10 eV with respect to the ground state and excitations from occupied a orbitals c, = L a sais%s into virtual n orbitals n* = I n , bkt All calculations were carried out using geometries with standard bond lengths [6],…”

Section: Computational Proceduresmentioning

confidence: 99%