Prediction of vibrational spectra by the CNDO/2 force method

Panchenko, Yu. N.; Pulay, P.; Török, Ferenc

doi:10.1016/0022-2860(76)82012-1

Cited by 94 publications

(17 citation statements)

References 27 publications

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“…Vibrational studies on s-trans and s-cis butadiene and acrolein have shown that s-trans --s-cis isomerization has a dramatic effect on the frequency of the C-C stretch. In s-cis butadiene (17)(18)(19), the central C-C stretch is calculated from 134 to 300 cm-' below the frequency in the s-trans isomer. In s-cis acrolein, the single-bond stretch is observed 240 cm-' below the s-trans frequency, in agreement with CNDO calculations (19).…”

Section: Resultsmentioning

confidence: 99%

“…In s-cis butadiene (17)(18)(19), the central C-C stretch is calculated from 134 to 300 cm-' below the frequency in the s-trans isomer. In s-cis acrolein, the single-bond stretch is observed 240 cm-' below the s-trans frequency, in agreement with CNDO calculations (19). To estimate the magnitude of the frequency shift upon isomerization about the C14-C15 bond in retinal pigments, we calculated the vibrational frequencies and shifts for a series of PSBs.…”

Section: Resultsmentioning

confidence: 99%

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Are C14-C15 single bond isomerizations of the retinal chromophore involved in the proton-pumping mechanism of bacteriorhodopsin?

Smith¹,

Hornung²,

Steen³

et al. 1986

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

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Resonance Raman spectroscopy is used to examine the possibility that C14-C15 single bond isomerizations of the retinal prosthetic group are involved in the photochemical reactions of bacteriorhodopsin. Normal mode calculations show that the vibration that contains predominantly C14`C15 stretch character is -70 cm-' lower in frequency in the 14-s-cis conformer than in the s-trans case. This geometric effect is insensitive to out-of-plane twists and should be observed in the sterically hindered 13-cis, 14-s-cis retinal protonated Schiff base, which has been proposed as the chromophore in the K and L intermediates of bacterio- has a localized C14-C15 stretch at 1172 cm-', consistent with a 14-s-trans chromophore. These results argue that the primary step in bacteriorhodopsin is a C13=C14 trans -* cis photoisomerization that does not involve C14-C15 s-cis structures.There is a great deal of interest in the mechanism by which changes in retinal chromophore structure in bacteriorhodopsin (BR) of this model is that thermal 14-s-cis --14-s-trans isomerization could occur after deprotonation of the Schiff base and function as a "proton switch." An analogous model has been presented recently by Liu and coworkers (6). These suggestions have remained untested due to the lack of a method for determining C-C single bond conformation in retinal pigments.Resonance Raman spectroscopy can be used to probe the in situ structure of the retinal chromophore in BR (7,8 In this paper we show that an s-trans --s-cis isomerization produces a characteristic "100 cm-' lowering of the C-C stretching frequency of the isomerized bond. To establish the conformation of the C,4-C15 bond in BR, the contribution of C14-C15 stretching character to the fingerprint normal modes must first be determined by selective 13C-or 2H-labeling. Comparison of the C14-C15 frequency in the pigment with that of the s-trans retinal PSB model compounds can then be used to determine the C14-C15 conformation in BR568, K625, and L550. EXPERIMENTALThe synthesis of the 10-13C, 11-13C, 14-13C, and 15-13C retinal isotopic derivatives has been described by Lugtenburg (10). Incorporation of deuterium at C15 was accomplished by reducing the retinoic ester or acid with lithium aluminum deuteride prior to oxidation. The isotopic purity was -98% Abbreviations: BR, bacteriorhodopsin; PSB, protonated Schiffbase.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Are C14-C15 single bond isomerizations of the retinal chromophore involved in the proton-pumping mechanism of bacteriorhodopsin?

Smith¹,

Hornung²,

Steen³

et al. 1986

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

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“…Therefore, we have adopted this mixed approach (experimental vibrational frequencies from ref. [40] and normal-mode Cartesian displacements from the theoretical force fields).…”

Section: Vibrational Averagingmentioning

confidence: 99%

“…[40] are also used, instead of the theoretical values. The calculations are carried out by excluding/including the torsional frequency, and the results are reported in Table 6 (columns III and IV, respectively).…”

Section: Optimization Of the "Ene" Fragmentmentioning

confidence: 99%

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Intrinsic Information Content of NMR Dipolar Couplings: A Conformational Investigation of 1,3‐Butadiene in a Nematic Phase

Celebre

Concistrè

et al. 2006

ChemPhysChem

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The conformational equilibrium of 1,3-butadiene in a condensed fluid phase is investigated by liquid-crystal NMR spectroscopy. The full set of D(HH) and D(CH) dipolar couplings is determined from the analysis of the (1)H spectra of the three 1,3-butadiene most-abundant isotopomers (i.e. the all (12)C and the two single-labeled (13)C isotopomers) for a total of 21 independent dipolar couplings. A very good starting set of spectral parameters for the analysis of the (1)H spectrum is determined in a semiautomated way by the analysis of the (N-1) (specifically, N=6, the number of 1/2 spin nuclei in the spin system) quantum refocused (5QR), and not (5Q), spectra. As an alternative approach, a Monte Carlo (MC) numerical simulation, capable of predicting the solute ordering, is tested to simulate the 5QR spectrum. The set of D(ij) couplings is very good, proving that the MC method can represent a novel, valid alternative to the existing spectral simplification procedures. The experimentally determined dipolar-coupling data set is fully compatible with the 1,3-butadiene conformational distribution reported in the literature for isolated molecules, indicating the presence of about 99 % of s-trans conformer. With regards to the remaining 1 %, in spite of the direct and very strong dependence of the observables on the molecular structure, it was not possible to discriminate between the planar s-cis and s-gauche forms, both of which produce a very good fit of the dipolar couplings. Vibrational corrections, up to the anharmonic term, were applied; the calculated geometrical parameters are in good- although not exact-agreement with those reported in the literature from experimental and theoretical investigations. This result can be considered as supporting the methodology used for obtaining the structure and conformational distribution of a flexible molecule in a liquid phase.

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Evidence for light-induced 13-cis , 14-s-cis isomerization in bacteriorhodopsin obtained by FTIR difference spectroscopy using isotopically labelled retinals

1986

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We have obtained by Fourier transformed infra‐red (FTIR)‐spectroscopy BR‐K, BR‐L and BR‐M difference spectra of bacteriorhodopsin regenerated with isotopically labelled retinals. Thereby, we are able to assign reliably the C14–C15 and C=N stretching vibrations of the various intermediates. The lower C14–C15 stretching vibration frequency in L as compared with 13‐cis protonated Schiff base model compounds indicates a 13‐cis, 14‐s‐cis configuration of the retinal in this species. The unusually low C=N stretching vibration in K at 1615 cm−1 indicates less stabilization of the positive charge at the Schiff base by the protein environment. Based on these results, a mechanism is suggested by which the stored light energy is transformed into proton transfers.

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Prediction of vibrational spectra by the CNDO/2 force method

Cited by 94 publications

References 27 publications

Are C14-C15 single bond isomerizations of the retinal chromophore involved in the proton-pumping mechanism of bacteriorhodopsin?

Are C14-C15 single bond isomerizations of the retinal chromophore involved in the proton-pumping mechanism of bacteriorhodopsin?

Intrinsic Information Content of NMR Dipolar Couplings: A Conformational Investigation of 1,3‐Butadiene in a Nematic Phase

Evidence for light-induced 13-cis , 14-s-cis isomerization in bacteriorhodopsin obtained by FTIR difference spectroscopy using isotopically labelled retinals

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