Jan P. Götze

Computing UV/vis spectra from the adiabatic and vertical Franck-Condon schemes with the use of Cartesian and internal coordinates

We address the effects of using Cartesian or internal coordinates in the adiabatic Franck-Condon (AFC) and vertical Franck-Condon (VFC) approaches to electronic spectra. The adopted VFC approach is a simplified variant of the original approach [A. Hazra, H. H. Chang, and M. Nooijen, J. Chem. Phys. 151, 2125 (2004)], as we omit any contribution from normal modes with imaginary frequency. For our test molecules ranging from ethylene to flavin compounds, VFC offers several advantages over AFC, especially by preserving the properties of the FC region and by avoiding complications arising from the crossing of excited-state potential surfaces or from the failure of the harmonic approximation. The spectral quality for our target molecules is insensitive to the chosen approach. We also explore the effects of Duschinsky rotation and relate the need for internal coordinates to the absence of symmetry elements. When using Duschinsky rotation and treating larger systems without planar symmetry, internal coordinates are found to outperform Cartesian coordinates in the AFC spectral calculations.

Serine in BLUF domains displays spectral importance in computational models

The BLUF (blue-light sensing using flavine) domain of the AppA photoreceptor protein from Rhodobacter sphaeroides was modelled by using quantum chemical chromophore plus amino acid models at the (TD-)B3LYP/6-31G * level of theory. The models were based on NMR structures, and further refined by CHARMM force field molecular dynamics simulations. The goal is to explain the total redshift by about 10nm in the UV/Vis spectra of BLUF domains after illumination, and to relate it to structural changes. For this purpose UV/Vis spectra of the available NMR structures were calculated and related to geometrical features. In particular, the hydrogen network embedding the central chromophore is discussed. Specifically, the position of a conserved glutamine, Q63, is found to be important in agreement with findings from previous works. Additionally, however, we find a systematic dependence also on the geometry of a conserved serine, S41. Based on a series of calculations with known structures and with artificial structural models, we argue that indeed the light-induced switching of both Q63 and S41 is necessary to explain the full approximately 10nm redshift in the light (signalling) state of serine containing BLUF domains. Following or accompanying the double switching, two structurally highly important residues W104 and M106 exchange places, but do not affect the overall UV/Vis properties of the chromophore.

Assessment of Franck–Condon Methods for Computing Vibrationally Broadened UV–vis Absorption Spectra of Flavin Derivatives: Riboflavin, Roseoflavin, and 5-Thioflavin

We address the performance of the vertical and adiabatic Franck-Condon (VFC/AFC) approaches combined with time-independent or time-dependent (TI/TD) formalisms in simulating the one-photon absorption spectra of three flavin compounds with distinct structural features. Calculations were done in the gas phase and in two solvents (water, benzene) for which experimental reference measurements are available. We utilized the independent mode displaced harmonic oscillator model without or with frequency alteration (IMDHO/IMDHO-FA) and also accounted for Duschinsky mixing effects. In the initial validation on the first excited singlet state of riboflavin, the range-separated functionals, CAM-B3LYP and ωB97xD, showed the best performance, but B3LYP also gave a good compromise between peak positions and spectral topology. Large basis sets were not mandatory to obtain high-quality spectra for the selected systems. The presence of a symmetry plane facilitated the computation of vibrationally broadened spectra, since different FC variants yield similar results and the harmonic approximation holds rather well. Compared with the AFC approach, the VFC approach performed equally well or even better for all three flavins while offering several advantages, such as avoiding error-prone geometry optimization procedures on excited-state surfaces. We also explored the advantages of curvilinear displacements and of a Duschinsky treatment for the AFC spectra in cases when a rotatable group is present on the chromophore. Taken together, our findings indicate that the combination of the VFC approach with the TD formalism and the IMDHO-FA model offers the best overall performance.

Carotenoids as a shortcut for chlorophyll Soret-to-Q band energy flow.

It is proposed that xanthophylls, and carotenoids in general, may assist in energy transfer from the chlorophyll Soret band to the Q band. Ground-state (1Ag ) and excited-state (1Bu ) optimizations of violaxanthin (Vx) and zeaxanthin (Zx) are performed in an environment mimicking the light-harvesting complex II (LHCII), including the closest chlorophyll b molecule (Chl). Time-dependent density functional theory (TD-DFT, CAM-B3LYP functional) is used in combination with a semi-empirical description to obtain the excited-state geometries, supported by additional DFT/multireference configuration interaction calculations, with and without point charges representing LHCII. In the ground state, Vx and Zx show similar properties. At the 1Bu minimum, the energy of the Zx 1Bu state is below the Chl Q band, in contrast to Vx. Both Vx and Zx may act as acceptors of Soret-state energy; transfer to the Q band seems to be favored for Vx. These findings suggest that carotenoids may generally mediate Soret-to-Q energy flow in LHCII.

The central role of Gln63 for the hydrogen bonding network and UV-visible spectrum of the AppA BLUF domain.

In blue-light sensing using flavin (BLUF) domains, the side-chain orientation of key residues close to the flavin chromophore is still under debate. We report quantum refinements of the wild-type AppA BLUF protein from Rhodobacter sphaeroides starting from two published X-ray structures (1YRX and 2IYG) with different arrangements of the residues around the chromophore. Quantum refinement uses the same experimental X-ray raw data as conventional refinement, but includes data from quantum mechanics/molecular mechanics (QM/MM) calculations as restraints, which is expected to be more reliable than the normally employed MM data. In addition to quantum refinement, pure QM/MM geometry optimizations are performed for the 1YRX and 2IYG structures and for five models derived therefrom. Vertical excitation energies are computed at the QM(DFT/MRCI)/MM level to assess the resulting structures. The experimental absorption maximum of the dark state of wild-type AppA is well reproduced for structures that contain the Gln63 residue in 1YRX-type orientation. The computed excitation energies are red-shifted for structures with a flipped Gln63 residue in 2IYG-type orientation. The calculated 1YRX- and 2IYG-type hydrogen-bonding networks are discussed in detail, particularly with regard to the orientation of the chromophore and the Gln63, Trp104, and Met106 residues.

Modeling of a violaxanthin-chlorophyll b chromophore pair in its LHCII environment using CAM-B3LYP

Collecting energy for photosystem II is facilitated by several pigments, xanthophylls and chlorophylls, embedded in the light harvesting complex II (LHCII). One xanthophyll, violaxanthin (Vio), is loosely bound at a site close to a chlorophyll b (Chl). No final answer has yet been found for the role of this specific xanthophyll. We study the electronic structure of Vio in the presence of Chl and under the influence of the LHCII environment, represented by a point charge field (PCF). We compare the capability of the long range corrected density functional theory (DFT) functional CAM-B3LYP to B3LYP for the modeling of the UV/vis spectrum of the Vio+Chl pair. CAM-B3LYP was reported to allow for a very realistic reproduction of bond length alternation of linear polyenes, which has considerable impact on the carotenoid structure and spectrum. To account for the influence of the LHCII environment, the chromophore geometries are optimized using an ONIOM(DFT/6-31G(d):PM6) scheme. Our calculations show that the energies of the locally excited states are almost unaffected by the presence of the partner chromophore or the PCF. There are, however, indications for excitonic coupling of the Chl Soret band and Vio. We propose that Vio may accept energy from blue-light excited Chl.

Dynamics of Azobenzene Dimer Photoisomerization: Electronic and Steric Effects

While azobenzenes readily photoswitch in solution, their photoisomerization in densely packed self-assembled monolayers (SAMs) can be suppressed. Reasons for this can be steric hindrance and/or electronic quenching, e.g., by exciton coupling. We address these possibilities by means of nonadiabatic molecular dynamics with trajectory surface hopping calculations, investigating the trans → cis isomerization of azobenzene after excitation into the ππ* absorption band. We consider a free monomer, an isolated dimer and a dimer embedded in a SAM-like environment of additional azobenzene molecules, imitating in this way the gradual transition from an unconstrained over an electronically coupled to an electronically coupled and sterically hindered, molecular switch. Our simulations reveal that in comparison to the single molecule the quantum yield of the trans → cis photoisomerization is similar for the isolated dimer, but greatly reduced in the sterically constrained situation. Other implications of dimerization and steric constraints are also discussed.

Slow deactivation of ribulose 1,5-bisphosphate carboxylase/oxygenase elucidated by mathematical models

Ribulose 1,5‐bisphosphate carboxylase/oxygenase (RuBisCO) is the key enzyme of the Calvin cycle, catalyzing the fixation of inorganic carbon dioxide to organic sugars. Unlike most enzymes, RuBisCO is extremely slow, substrate unspecific, and catalyzes undesired side‐reactions, which are considered to be responsible for the slow deactivation observed in vitro, a phenomenon known as fallover. Despite the fact that amino acid sequences and the 3D structures of RuBisCO from a variety of species are known, the precise molecular mechanisms for the various side reactions are still unclear. In the present study, we investigate the kinetic properties of RuBisCO using mathematical models. Initially, we formulate a minimal model that quantitatively reflects the kinetic behavior of RuBisCOs from different organisms. By relating rate parameters for single molecular steps to experimentally determined Km and Vmax values, we can examine mechanistic differences among species. The minimal model further demonstrates that two inhibitor producing side reactions are sufficient to describe experimentally determined fallover kinetics. To explain the observed kinetics of the limited capacity of RuBisCO to accept xylulose 1,5‐bisphosphate as substrate, the inclusion of other side reactions is necessary. Our model results suggest a yet undescribed alternative enolization mechanism that is supported by the molecular structure. Taken together, the presented models serve as a theoretical framework to explain a wide range of observed kinetic properties of RuBisCOs derived from a variety of species. Thus, we can support hypotheses about molecular mechanisms and can systematically compare enzymes from different origins.

BLUF hydrogen network dynamics and UV/Vis spectra: a combined molecular dynamics and quantum chemical study.

Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (“Win”/“Wout”), structure determination (X‐ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time‐dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red‐shifted and thermally broadened for all calculated π → π* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach.

A proposal for a dipole-generated BLUF domain mechanism

The resting and signaling structures of the blue-light sensing using flavin (BLUF) photoreceptor domains are still controversially debated due to differences in the molecular models obtained by crystal and NMR structures. Photocycles for the given preferred structural framework have been established, but a unifying picture combining experiment and theory remains elusive. We summarize present work on the AppA BLUF domain from both experiment and theory. We focus on IR and UV/vis spectra, and to what extent theory was able to reproduce experimental data and predict the structural changes upon formation of the signaling state. We find that the experimental observables can be theoretically reproduced employing any structural model, as long as the orientation of the signaling essential Gln63 and its tautomer state are a choice of the modeler. We also observe that few approaches are comparative, e.g., by considering all structures in the same context. Based on recent experimental findings and a few basic calculations, we suggest the possibility for a BLUF activation mechanism that only relies on electron transfer and its effect on the local electrostatics, not requiring an associated proton transfer. In this regard, we investigate the impact of dispersion correction on the interaction energies arising from weakly bound amino acids.