Schmitz M., Tavan P., and Nonella M.
Vibrational analysis of carbonyl modes in different stages of light-induced cyclopyrimidine dimer repair reactions.
Chem. Phys. Lett. 349, 2001, 342-348.
The formation of cyclopyrimidine dimers is a DNA defect, which is repaired by the enzyme DNA photolyase in a light-induced reaction. Radical anions of the dimers have been suggested to occur as short-lived intermediates during repair. For their identification time-resolved FTIR spectroscopy will be a method of choice. To support and guide such spectroscopic studies we have calculated the vibrational spectra of various pyrimidine compounds using density functional methods. Our results suggest that the carbonyl vibrations of these molecules can serve as marker modes to identify and distinguish intermediates of the repair reaction.
Electrostatic protein-chromophore interactions promote the all-trans 13-cis isomerization of the protonated retinal Schiff base in Bacteriorhodopsin: An ab initio CASSCF/MRCI study.
J. Phys. Chem. 104B, 2000, 11379-11388.
Ab initio calculations of the potential energy surfaces of the states S, S, and S of protonated Schiff base model molecules containing three, four, and five conjugated double bonds have been carried out at the HF/MRCI and CASSCF/MRCI level of theory. Our calculations demonstrate that predictions of crossings of electronic states depend on the method of calculation and are different at the CASSCF and CASSCF/MRCI levels. Moreover, when a counterion is added in the vicinity of a protonated Schiff base, HF/MRCI and CASSCF/MRCI calculations predict different regions for S/S crossing. The length of the conjugated system seems not to affect such qualitative results considerably. Our calculations suggest that (i) the second excited state is of no importance for the primary step of the photocycle of Bacteriorhodopsin, that (ii) an efficient decay into the electronic ground state during an all-trans 13-cis isomerization is only possible due to the interaction of the protonated Schiff base with a counterion, that (iii) this isomerization reaction can occur spontaneously only after a preceding relaxation of bond lengths in the excited state, and that (iv) an all-trans 13,14-dicis double isomerization is most likely inefficient due to a non-vanishing barrier in the excited state.
Nonella, M. and Suter, H.U.
Formation of phenolate anion-counter ion complexes can explain the vibrational properties of the phenolate anion in solution
J. Phys. Chem. 103A, 1999, 7867-7871.
Structures of enolate-counter ion complexes and structures and vibrational spectra of phenolate anion-counter ion complexes have been calculated by means of MP2 and density functional methods. Compared to corresponding monomeric complexes, higher complexes reveal longer C-O bond lengths which causes a downshift of the C-O stretching mode. In the case of phenolate we find C-O stretching frequencies and isotope shifts upon O and d labeling which are in good agreement with recent IR data of phenolate generated in solution. The C-O stretching frequency, for example, is predicted to be around 1270 cm compared to an experimental value of 1273 cm and the O shift of this mode is calculated to be 18 cm compared to an experimental shift of 17 cm. For a free phenolate anion, our calculations predict a C-O stretching frequency of 1350 cm. The vibrational spectrum of phenolate anions in solution can thus be explained in terms of higher phenolate anion-counter ion complexes in agreement with recent NMR experiments of Jackman and Smith (J. Am. Chem. Soc. 1988, 110, 3829).
A Generalized Resonance Model for Substituted 1,4-Benzoquinones
J. Phys. Chem. 103A, 1999, 7069-7075.
Resonance effects are known to affect vibrational spectra and electrochemical properties of substituted quinones. On the basis of the results of density functional calculations on several singly substituted 1,4-benzoquinones we propose an extended resonance model which can account for the most prominent substituent effects onto the force constants of carbon-carbon and carbon-oxygen bonds. The calculations show that the two proposed resonance mechanisms are closely coupled. This interplay of the two effects renders a quantitative prediction of force constants of substituted 1,4-benzoquinone difficult. We nevertheless can give some simple rules which in many cases can give a good estimate for expected force constant changes upon substitution of 1,4-benzoquinone.
Nonella, M., Boullais, C., Mioskowski, C.,
Nabedryk, E., and Breton,J.
Vibrational spectrum and torsional potential of 2-methoxy-3-methyl-1,4-benzoquinone
J. Phys. Chem. 103B, 1999, 6363-6370.
Stable conformations and vibrational spectra of 2-methoxy-3-methyl-1,4-benzoquinone were calculated using density functional methods. Two stable conformers have been found which differ in their vibrational spectrum. Although the calculated infrared spectra of the two conformers differ with respect to several modes, a definite assignment of the experimentally available bands to one of the two conformers is difficult. Protein - chromophore interactions have been studied by modeling quinone - HO, quinone - Li, and quinone - NH complexes. A complexation with water already considerably affects the relative energies of the two conformers and the torsional barrier for the rotation of the methyl part of the methoxy group. In fully optimized quinone - water complexes, vibrational modes in the C=O and C=C stretching mode region are affected through the complexation. Complexation with a positively charged counter ion dramatically changes the energetics of the system and changes the former minimum energy conformation into a saddle point. Vibrational frequencies are more strongly affected than upon complexation with a water molecule.
Suter, H.U. and Nonella, M.
A Quantum Chemical Investigation of the C-O Bond Length and Stretching Mode of the Phenolate Anion
J. Phys. Chem. 102A, 1998, 10128-10133.
Structure and vibrational spectrum of the phenolate anion have been calculated with various quantum chemical methods. Correlated methods predict a C-O bond length between 1.28 and 1.29 Å which is significantly shorter than an earlier suggested value of 1.40 Å. This indicates a partial double bond character for the C-O bond in the phenolate anion which is explained in terms of resonance structures. IR frequencies determined with pure density functional methods agree well with FTIR data in the case of the modes n4 and n5 while the frequency of the C-O mode is significantly overestimated in all calculations. The calculations of the isolated phenolate anion do thus poorly agree with experimental data. We demonstrate, that upon complexation of the phenolate anion with a positively charged counter ion the C-O bond is elongated and becomes considerable single bond character. The intermolecular interaction also causes a down shift of 30 cm-1 of the C-O stretching mode and thus reveals a better agreement with experimental data.
A quantum chemical investigation of structures, vibrational spectra and electron affinities of the radicals of quinone model compounds
Photosynthesis Research 55, 1998, 253-259.
In the present study, the first quantum chemical calculations of structures and vibrational spectra of radicals of 1,4-naphthoquinone and 2-methoxy-1,4-benzoquinone that account for electron correlation are presented. In the case of 1,4-naphthoquinone a good agreement between calculated vibrational frequencies and 18O-shifts of t he 1,4-naphthoquinone radical (protonated radical anion) with experimental data of a species detected after irradiation of vitamin K1 in solution is found. Our calculations, thus, support the previous assignment. In the case of 2-methoxy-1,4-benzoquinone we have localized the stable conformations with respect to the orientation of the methoxy group and we have determined the harmonic force fields for these structures. Our calculations suggest that, while the frequencies of the two conformers are similar, the 18O-shift of th e most intensive absorptions in the spectral region between 1400 and 1700 cm-1 of the two conformers differ significantly and might serve as a tool to distinguish between the two conformers. The applied DFT method is shown to predict electron affinities which are systematically underestimated by 10%.
Boullais, C., Nabedryk, E., Burie, J.-R., Nonella, M., Mioskowski, C., and Breton, J.
Site-specific isotope labeling demonstrates a large mesomeric resonance effect of the methoxy groups on the carbonyl frequency of ubiquinones
Photosynthesis Research 55, 1998, 247-252.
The splitting of the carbonyl infrared bands of 2-methoxy-1,4-benzoquinone in solution can be related to a mesomeric resonance phenomenon leading to a conformation of the O-CH3 bond coplanar to the quinone ring. The delocalization of the electron density induces a frequency downshift of the C4=O carbonyl compared to 1,4-benzoquinone. This in turns decouples the two carbonyls leading to an upshift of the C1=O vibration. Using selective 13C-labeling of Q0 (2,3-dimethoxy-5-methyl-1,4-benzoquinone), we show that the effect of mesomeric resonance is an essential determinant of the carbonyl frequencies of ubiquinone in solution.
A Density Functional Investigation of Model Molecules for Ubisemiquinone Radical Anions
J. Phys. Chem. 102B, 1998, 4217-4225.
We have applied density functional methods for the determination of structures, vibrational spectra, electron affinities, and isotropic hyperfine coupling constants of the radical anions of 2,3-dimethoxy-1,4-benzoquinone and 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone. Our calculations predict three stable conformers with respect to the orientation of the two methoxy groups for both molecules. Different orientations of the methoxy groups are shown to affect force constants and vibrational spectra less dramatically than in the corresponding neutral quinone. The different mode decompositions predicted in symmetrical and non-symmetrical conformers, respectively, suggest that site specific labeling of one carbonyl group might allow to distinguish among these conformers. The presented calculations allow us to provide a mode assignment for the C=C and C=O modes which, in most cases, agrees well with previous assignments based solely on experimental data. Electron affinities are shown to vary by up to 40 kJ/mol for different orientation of the methoxy groups. Our calculations demonstrate that the two additional methyl groups at positions 5 and 6 have to be considered if the molecule is supposed to serve as a model compound for quinones participating in bacterial photosynthesis.
A reinvestigation of the n2 and n3 modes of 1,4-benzoquinone on the basis of a quantum mechanical harmonic force field
Chem. Phys. Lett. 280, 1997, 91-94.
The assignment of the modes n2 and n3 of 1,4-benzoquinone has been the topic of many studies. In a recent investigation Zhao, Imahori, Zhan, Mizutani, Sakata and Kitagawa reported an assignment which differs from the previous assignment of Becker. With small variations of selected force constants of a quantum chemically derived force field, we can achieve a good agreement with Becker's data for the n2 and n3 modes of unlabeled 1,4-benzoquinone and its isotopomers 18O2 and d4. In contrast, no satisfactory agreement can be found with frequencies reported by Zhao et al. A systematic investigation of 18O2 and d4 shifts suggest that isotopic shifts of n3 assigned by Zhao et al. are most likely incompatible with the theoretical force field.
Burie, J.-R., Boullais, C., Nonella, M., Mioskowski, C., Nabedryk, E. and Breton, J.
Importance of the Conformation of Methoxy Groups on the Vibrational and Electrochemical Properties of Ubiquinones
J. Phys. Chem. 101B, 1997, 6607-6617.
On the basis of semiempirical calculations, the present study proposes a comprehensive interpretation of the crystallographic, vibrational, and electrochemical data on methoxy- substituted quinones, and in particular for ubiquinones, in terms of the orientation of the methoxy groups relative to the quinone ring plane. "Hindered" and "free" methoxy groups are considered depending on the presence or absence on the quinone ring of a bulky group in ortho position of the considered methoxy group, respectively. The free methoxy groups have their O-CH3 bond in the quinone ring plane while the hindered methoxy groups cannot adopt this conformation and have their methyl group tilted out of the quinone ring plane. The electron donation of the methoxy is dependent on the orientation of the O-CH3 bond and is maximum for a free methoxy group. This effect is revealed by the analysis of both electrochemical and IR data. An assignment of the n(C=O) modes of the quinones bearing such groups is proposod. From electrochemical data in literature, a new coefficient spara, used in the Hammett equation, is determined for a hindered methoxy group s =- 0.07 compared to -0.27 for a free methoxy group). In the specific and biologically important case of the bulky group being another methoxy group, such as in ubiquinones (2,3-dimethoxy-substituted 1,4-benzoquinones), two types of conformation have to be considered. In the first type (conformer A), one methoxy adopts the conformation of a free methoxy group and the second that of a hindered methoxy group. In the second type (conformer B), both methoxy groups adopt the conformation of a hindered methoxy group. Both conformers appear equiprobable within the precision of our semiempirical calculations and a low rotational barrier, compared to kBT at room temperature, is found between them. Only conformers A are encountered in crystals. Using specific 13C labeling, IR data show that conformers A are mostly encountered at room temperature in solution while a mixture of both conformers is present at low temperature. On the other hand, electrochemical data on these quinones are best interpreted as the reduction of conformers B. This is explained by the higher electron affinity of conformers B compared to conformers A and by the low rotational barrier between the two conformers. Taking into account IR data of ubiquinone in the bacterial photosynthetic reaction center of Rhodobacter sphaeroides, the 70 mV difference found in the redox potential of ubiquinone in the two quinone binding sites can be explained by a difference of orientation of the methoxy groups imposed by the protein. By selecting a different orientation of the methoxy groups in the two sites, the protein would thus tune the redox potential of the quinone present in each site.
Suter, H.U. and Nonella, M.
Quantum Chemical Investigation of Structures, Rotational Barriers, and Vibrational Spectra of the Rotamers of Ethyl Nitrite (CH3CH2ONO)
J. Phys. Chem. 101A, 1997, 5580-5586.
Ab initio and DFT methods were used to investigate the conformers of Ethylnitrite. The potential energy surface for rotations around the C-O and the O-N bonds was calculated. From the four geometrically possible conformers only three were found to be stable in the calculations using correlated methods. This is consistent with the microwave study Turner (J.Chem.Soc.Faraday Trans. 2, (1979), 317) and with a presented matrix IR spectrum which clearly shows three N=O stretching modes. A simulated ir spectra using the results of the DFT calculations was in good agreement with this matrix spectrum and allowed a tentative assignment of groups of frequencies.
Effect of Charge Distribution on the Electrostatic Chromophore-Protein Interactions in Bacteriorhodopsin
J. Comp. Chem. 18, 1997, 677-693.
Charge distributions for a protonated and unprotonated Schiff base model compound have been determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between model molecule and protein have been calculated. Such interaction energies and, thus, also calculated pK1/2 values of the model molecule, are shown to considerably depend on the chosen charge distribution. A fairly good agreement with a calculated reference pK1/2 of this model molecule has also been found in the case of some non-potential derived charge distributions and has been shown to be caused by cancellation of errors in contributing terms. Electrostatic potential derived partial charges determined at different ab initio levels are shown to reveal interaction energies between the model molecule and proximate groups like ARG-82, ASP-85, and ASP-212, which vary by not more than 5% among the different charge distributions. Larger deviations are found in the case of Mulliken charge distributions. Based on the results of the present study we propose a new set of partial charges for the protonated and unprotonated retinal Schiff base to be used in molecular dynamics simulations and electrostatics calculations.
Structures and Vibrational Spectra of p-Benzoquinone in Different Oxidation and Protonation States: A Density Functional Study
J. Phys. Chem. 101, 1997, 1235-1246.
The structures and harmonic force fields of p-benzoquinone in various oxidation and protonation states have been calculated by means of density functional methods. In general, good agreement between experimental and theoretical vibrational frequencies in the 1400 - 1700 cm-1 frequency region has been found. Occasionally, the applied BP86 density functional method combined with the 6-31G** basis set results in poor agreement with experimental data. The inaccurate prediction of a ring-bending mode and of CH out-of-plane vibrations in benzene, p-benzoquinone, and p-hydroquinone can most likely be identified as a systematic error of the applied method. Such modes which are poorley described with this quantum chemical method can occasionally be better reproduced when a smaller basis set of 3-21G quality or a hybrid Hartree-Fock/density functional method is applied.
Density Functional Investigation of Structures and Harmonic Force Fields of Methyl-Substituted p-Benzoquinones
J. Phys. Chem. 100, 1996, 20148-20155.
Structures and harmonic force fields of the methyl substituted p-benzoquinones 2-methyl-1,4-benzoquinone, 2,3-dimethyl-1,4-benzoquinone, 2,6-dimethyl-1,4-benzoquinone, and 2,3,5,6-tetramethyl-1,4-benzoquinone (duroquinone DQ) have been calculated by using density functional methods. The calculations can successfully predict experimentally detected frequencies in the 1500 to 1700 cm-1} region of the spectrum in all four molecules. Occasionally, the mode assignment predicted by the calculation differs from previously postulated assignments. In particular in the case of DQ the calculations can successfully predict (i) the downshift of the most intensive carbonyl mode from 1666 cm-1 in p-benzoquinone to around 1640 cm-1 in DQ due to a reduction of the force constant of the carbonyl bond and (ii) the appearence of two isotopic shifts of similar size upon 18O labeling of both carbonyl groups as it has been found experimentally in vitro and in photosynthetic reaction centers.
Dobado, J.A. and Nonella, M.
MRCI Calculations of the Ground and Excited State Potential Energy Surfaces of the 2,4-Pentadien-1-iminium Cation.
J. Phys. Chem. 100, 1996, 18282-18288.
Quantum chemical calculations of the electronic ground and first excited singlet states S0 and S1 of the protonated Schiff base 2,4-pentadien-1-iminium cation (CH2=CH-CH=CH-CH=NH2)+ are presented. In order to compare different multi reference CI approaches which differ in their choice of reference configurations and basis sets, potential energy surfaces with respect to two dihedral angles have been calculated for the states S0 and S1. The study reveals that the characteristic features of the two potential energy surfaces, i.e. the appearence of two minima and four maxima in the case of the S0 surface, and of three maxima and two minima in the case of the S1 surface are correctly predicted at all applied levels of theory. The energies of torsional barriers and of higher energy maxima, however, depend considerably on the applied quantum chemical procedure. Ground state calculations are also compared to the results of Møller-Plesset perturbation theory calculations up to the MP4 level.
Cobo, J., Melguizo, M., Nogueras, M.,
Sanchez, A., Dobado, J.A. and Nonella, M.
Theoretical Investigation on the Reactivity of 6-amino-3-methylpyrimidin- 4(3H)-ones Towards DMAD, Tandem Diels-Alder Retro Diels-Alder (DA/RDA) Reaction.
Tetrahedron 52, 1996, 13721-13732.
The reactivity of 6-aminopyrimidin-4(3H)-ones towards DMAD is successfully explained by theoretical investigation (PM3 semiempirical methods). All the PM3 results ( activation energies (AE) for the transition states and the heat of formation (DH) for the products) support our previous experimental work [J. Cobo et all. Synlett. 1993, 4, 297-299; Tetrahedron 1994, 50, 10345-10354]. In those reactions two main products were obtained: the pyridine derivatives 5 as major ones, which are formed by a tandem DA/RDA reaction with extrusion of the methylisocyanate fragment; and 5-ethenylpyrimidin-4(3H)-ones 10 as minor ones, which arised from a Michael addition, being in competition with the above normal DA.
Nonella, M. and Brändli, C.
Density Functional Investigation of Methoxy-Substituted p-Benzoquinones: Conformational Analysis and Harmonic Force Fields of 2-Methoxy- and 2,3- Dimethoxy-1,4-benzoquinone.
J. Phys. Chem. 100, 1996, 14549-14559.
Structure and harmonic force fields of methoxy substituted p-benzoquinones have been calculated applying density functional methods. Structural parameters, harmonic force constants, and vibrational frequencies have shown to depend on the orientation of the methoxy substituents. Stable conformations of the methoxy groups, as predicted by semiempirical or ab initio Hartree-Fock methods differ qualitatively from those predicted by methods which are considering correlation effects. The agreement of the calculated C=C and C=O modes with experimental data is generally very satisfactory. Due to additional substituents such as methyl or allyl groups the energetic sequence of C=C and C=O modes is not found to be altered. Calculated frequencies are only slightly affected due to such substituents whereas intensities, mode decompositions, and isotopic shifts are considerably influenced.
Structures and harmonic force fields of 1,4-naphthoquinone and naphthalene: a density functional study.
J. Molec. Struct. (THEOCHEM) 362, 7-21, (1996)
Structures and harmonic force fields of 1,4-naphthoquinone and naphthalene have been calculated using density functional methods. In contrast to X-ray investigations and in agreement with semi empirical and ab initio Hartree-Fock calculations, our study reveals that 1,4-naphthoquinone can be considered in good approximation as a system of weakly interacting p-benzoquinone and benzene molecules where only the bond connecting the two moieties is considerably perturbed. This bond is increased by about 0.015 Å compared to the bond length of benzene. Vibrational frequencies calculated with the quantum chemically derived unscaled harmonic force field are generally in good agreement with experimental data. In contradiction to previous semi empirical and ab initio Hartree-Fock calculations, a similar but smaller enlargement of the connecting bond is also found in naphthalene. Previous calculations of vibrational frequencies based on theoretical, scaled Hartree-Fock force fields have shown that the length of this connecting bond is one of the crucial parameters which determines the agreement theoretical frequencies with experimental data.
Nonella, M. and Tavan, P.
An unscaled quantum mechanical harmonic force field for
Chem. Phys. 199, 19-32, (1995)
Structure and harmonic vibrational frequencies of p-benzoquinone have been calculated using quantum chemical ab initio and density functional methods. Our calculations show that a satisfactory description of fundamentals and normal mode compositions is achieved upon consideration of correlation effects by means of Møller-Plesset perturbation expansion (MP2) or by density functional theory (DFT). Furthermore, for correct prediction of C=O bondlength and force constant, basis sets augmented by polarization functions are required. Applying such basis sets, MP2 and DFT calculations both give results which are generally in reasonable agreement with experimental data. The quantitatively better agreement, however, is achieved with the computationally less demanding DFT method. This method particularly allows very precise prediction of the experimentally important absorptions in the frequency region between 1500 cm-1 and 1800 cm-1 and of the isotopic shifts of these vibrations due to 13C or 18O substitution.
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