Density functional theory has been used to calculate harmonic normal mode vibrational frequencies for unlabeled and isotope-labeled ubisemiquinones in both the gas phase and in several solvents. It is shown that four methoxy group conformations are likely to be present in solution at room temperature. Boltzmann weighted infrared and Raman spectra for the four conformers were calculated, and composite spectra that are the sum of the Boltzmann weighted spectra were produced. These composite spectra were compared to experimental FTIR and resonance Raman spectra, and it is shown that the calculated band frequencies, relative band intensities, and
Ubiquinones (
Fourier transform infrared (FTIR) difference spectroscopy (DS) is a sensitive molecular-level probe of pigment-protein interactions, and it is widely used to study both the neutral and reduced states of the quinones occupying the
One basis for developing an understanding of bands in
Few computational studies aimed at modeling the vibrational properties of ubisemiquinones (
In this paper we describe the simulation of FTIR and Raman spectra associated with labeled and unlabeled tail-containing ubisemiquinones in both the gas phase and in solvent.
Molecular geometry optimizations and harmonic vibrational frequency calculations were performed using hybrid density functional theory (DFT) methods, employing the B3LYP functional and the
Calculated normal mode vibrational frequencies presented here were scaled by 0.9808. Such a scale factor is standard for calculations using the specified functional and basis set and was derived by comparing the frequencies of bands in experimental and calculated spectra. Such a scaling of the calculated frequencies is undertaken only to facilitate a comparison between calculated and experimental spectra. We are primarily interested in vibrational frequency changes that occur upon isotope labeling, and these frequency differences are accurately calculated without scaling [
Figure
Structure and atomic numbering scheme for an optimized
Previously we showed that neutral UQ1 can adopt at least eight different methoxy group conformations at room temperature [
A contour plot of energy versus the C2 and C3 dihedral angles is shown in Figure
Calculated optimized energy (in kcal/mol) of
Following single-point energy calculations, the four
Calculated bond lengths, the C6–C10–C11 bond angle, and methoxy group dihedral angles for the various
Calculated bond lengths (in Å) and bond angles (in degrees) for all
|
|
QA | QB | |||||||
---|---|---|---|---|---|---|---|---|---|---|
A | B | E | F | A | B | E | F | |||
C1 |
1.273 | 1.273 | 1.273 | 1.273 | 1.274 | 1.274 | 1.273 | 1.273 | 1.234 | 1.227 |
C4 |
1.272 | 1.272 | 1.271 | 1.271 | 1.247 | 1.274 | 1.274 | 1.274 | 1.232 | 1.221 |
C2 |
1.380 | 1.380 | 1.379 | 1.379 | 1.380 | 1.379 | 1.378 | 1.379 | 1.404 | 1.379 |
C5 |
1.384 | 1.384 | 1.384 | 1.384 | 1.384 | 1.385 | 1.385 | 1.385 | 1.419 | 1.398 |
C6–C10–C11 | 113.4 | 113.5 | 113.5 | 113.5 | 113.3 | 113.2 | 113.3 | 113.2 | 113.0 | 111.0 |
C3–C2–O–CH3 | −121.8 | 120.8 | 116.7 | −117.3 | −118.5 | 116.1 | 111.8 | −113.6 | −57.1 | 79.9 |
C2–C3–O–CH3 | 122.4 | −123.2 | 118.3 | −119.0 | 118.2 | −117.7 | 111.6 | −113.6 | 109.5 | −121.3 |
|
0.537 | 0.646 | 0.106 | 0 | 0.450 | 0.387 | 0.002 | 0 |
The data presented in Table
The hydrocarbon chain (isoprene unit) attached at C6 makes a distinct kink at C10. The C6–C10–C11 angle is close to 113° for all four conformers (Table
Figure
(a) Calculated Boltzmann weighted IR spectra for the four
In the composite spectra an intense band is observed at 1500–1478 cm−1, depending on the solvent. The frequency of this absorption band decreases, and the intensity increases, as the dielectric constant of the solvent increases. The frequency changes as a function of dielectric constant are outlined in the inset in Figure
The calculated composite spectrum for
Calculated vibrational frequencies (in cm−1), intensities (in km/mol), Raman activities (in Å4/amu), and potential energy distributions (%) of normal modes that contain contributions from C
Gas phase
|
IR | Raman | Potential energy distribution |
---|---|---|---|
Unlabeled | |||
| |||
1448 | 94 | 5 | R1(6) − R6(5) + |
1461 | 16 | 10 | R3(9) − R10(5) + |
1495 | 33 | 247 | R9(34) + R3(22) − R10(10) + |
1500 | 287 | 3 | R3(29) − R9(27) + RD(9) + |
1524 | 30 | 21 | R4(33) − R10(16) − R5(6) − R7(6) + |
1608 | 9 | 451 | R4(26) + R10(23) + RD(12) |
| |||
13C | |||
| |||
1419 | 7 | 23 |
|
1430 | 218 | 6 |
|
1443 | 6 | 47 |
|
1458 | 13 | 61 | R3(14) − R4(12) + |
1459 | 195 | 25 | R9(34) + |
1474 | 8 | 130 |
|
1481 | 23 | 23 |
|
1519 | 34 | 18 |
|
1550 | 7 | 384 | R4(23) + R10(22) + RD2(11) |
| |||
18O | |||
| |||
1445 | 160 | 11 |
|
1455 | 11 | 53 | R3(22) + |
1466 | 10 | 33 |
|
1466 | 27 | 17 |
|
1479 | 108 | 115 | R9(37) + |
1482 | 62 | 46 |
|
1486 | 46 | 33 |
|
1488 | 28 | 7 |
|
1522 | 21 | 12 | R4(31) − R10(20) + |
1607 | 10 | 432 | R4(27) + R10(24) + RD2(11) |
CCl4
|
IR | Raman | Potential energy distribution |
---|---|---|---|
Unlabeled | |||
| |||
1450 | 134 | 6 | R3(5) − R1(5) + R6(5) + |
1460 | 17 | 11 | R3(9) + |
1491 | 184 | 328 | R9(56) − R10(8) |
1495 | 238 | 163 | R3(46) + |
1523 | 36 | 27 | R4(32) − R10(17) − R5(6) − R7(6) + |
1607 | 11 | 869 | R4(27) + R10(23) + RD2(12) |
| |||
13C | |||
| |||
1385 | 51 | 33 |
|
1421 | 21 | 42 |
|
1431 | 365 | 7 |
|
1443 | 15 | 91 |
|
1454 | 243 | 48 | R9(32) + |
1458 | 17 | 156 | R3(15) − R4(11) + |
1474 | 7 | 190 |
|
1479 | 27 | 34 |
|
1487 | 39 | 16 |
|
1549 | 9 | 752 | R4(24) + R10(22) + RD2(11) |
| |||
18O | |||
| |||
1446 | 259 | 19 |
|
1455 | 9 | 101 |
|
1465 | 97 | 131 | R9(27) + |
1476 | 112 | 112 |
|
1481 | 55 | 134 |
|
1483 | 52 | 49 |
|
1521 | 26 | 9 | R4(30) − R10(21) + |
1606 | 12 | 828 | R4(28) + R10(24) + RD2(11) |
For
For
In all spectra in Figure
A relatively intense band is found at 1450–1456 cm−1 in all of the spectra in Figure
The calculated spectra of the four
Figure
Calculated Boltzmann weighted composite IR (
As discussed above, for unlabeled
The band at 1449 cm−1 in the IR spectrum for unlabeled
Other than the normal modes just discussed,
In the IR spectrum of unlabeled
In the unlabeled species the relatively pure
The calculated changes in frequency, intensity, and mode composition upon isotope labeling of ubisemiquinone are considerably more complex than those found for the neutral species [
Resonance Raman spectra of unlabeled and 13C-labeled
The ~1608 cm−1 band was assigned to a
Calculated and experimental frequencies of selected normal modes of
Mode | Unlabeled | 13C | 18O | |||||
---|---|---|---|---|---|---|---|---|
Calc | Ramana | FTIRb | Calc | Ramana | FTIRb | Calc | FTIRb | |
C |
1607 | 1605 QA |
— | 1550(57) | 1556(49) QA |
— | 1606(1) | |
C |
1523 | 1523 QA |
— | 1458(65) |
1456(58) |
— | 1521(2) | |
C |
1491 |
1486 QA |
1483 | 1454(37) |
1456(30) |
1442(41) | 1476(15) |
1468(15) |
a
Data from resonance Raman experiments [
In our calculations the
The out-of-phase
Clearly, the calculated out-of-phase
Bands at 1486/1489 cm−1 in resonance Raman spectra of
Electrochemically generated FTIR difference spectra of UQ in various solvents have been obtained [
In experimental FTIR difference spectra for
Experimentally, for
From electrochemically generated FTIR difference spectra of 13C-labeled
Another group, which undertook identical labeling experiments [
Resonance Raman spectra for
Our calculated spectra for
In
DFT-based vibrational frequency calculations (using the BP86 functional) have been undertaken for 2,3-dimethoxy-1,4-benzoquinone and 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone in the gas phase [
One problem with previous DFT calculations (in the gas phase) [
Furthermore, the antisymmetrically coupled
Clearly, previous DFT calculations [
We calculate that four
Calculations show that upon isotope labeling the out-of-phase
Density functional theory
Difference spectra
Fourier transform infrared
Infrared
Integral equation formalism
Purple bacterial reaction centers
Polarizable continuum model
Potential energy distribution
Ubiquinone
Ubisemiquinone.
H. P. Lamichhane acknowledge support from a fellowship from the Molecular Basis of Disease Program at Georgia State University. G. Hastings acknowledges the support from Qatar National Research Fund.