Mikael P. Johansson

Torsional Barriers and Equilibrium Angle of Biphenyl: Reconciling Theory with Experiment.

The barriers of internal rotation of the two phenyl groups in biphenyl are investigated using a combination of coupled cluster and density functional theory. The experimental barriers are for the first time accurately reproduced; our best estimates of the barriers are 8.0 and 8.3 kJ/mol around the planar and perpendicular conformations, respectively. The use of flexible basis sets of at least augmented quadruple-ζ quality is shown to be a crucial prerequisite. Further, to finally reconcile theory with experiment, extrapolations of both the basis set toward the basis set limit and electron correlation toward the full configuration-interaction limit are necessary. The minimum of the torsional angle is significantly increased by free energy corrections, which are needed to reach an agreement with experiment. The density functional B3LYP approach is found to perform well compared with the highest level ab initio results.

Properties of WAu12

The icosahedral cluster-compound WAu12 was recently predicted by Pyykko and Runeberg and experimentally prepared in the gas phase by the group of Lai-Sheng Wang. The photoelectron spectra and electron affinity were reported; the other physical properties remain unknown. Anticipating further experimental studies on it, we report here predicted vibrational spectra, NMR chemical shifts, spin–spin coupling constants and quadrupole coupling constants as well as optical spectra at the level of single and double excitations. The population analysis is non-trivial. By direct numerical integration, a charge of roughly +1 is obtained for the central tungsten atom. The charge distribution is strongly delocalised but bonding regions are clearly seen. A considerable electric field gradient exists at the gold nuclei. Although the radial bonds are strong, the system is quite elastic. The DFT activation energy for rotating one hemisphere against the other one, at a D5h transition state, is only about 20 kJ mol−1. The corresponding hu vibrational frequency is predicted to be slightly below 30 cm−1.

Manipulating the torsion of molecules by strong laser pulses.

We demonstrate that strong laser pulses can induce torsional motion in a molecule consisting of a pair of phenyl rings. A nanosecond laser pulse spatially aligns the carbon-carbon bond axis, connecting the two phenyl rings, allowing a perpendicularly polarized, intense femtosecond pulse to initiate torsional motion accompanied by an overall rotation about the fixed axis. We monitor the induced motion by femtosecond time-resolved Coulomb explosion imaging. Our theoretical analysis accounts for and generalizes the experimental findings.

Charge parameterization of the metal centers in cytochrome c oxidase

Reliable atomic point charges are of key importance for a correct description of the electrostatic interactions when performing classical, force field based simulations. Here, we present a systematic procedure for point charge derivation, based on quantum mechanical methodology suited for the systems at hand. A notable difference to previous procedures is to include an outer region around the actual system of interest. At the cost of increasing the system sizes, here up to 265 atoms, including the surroundings achieves near‐neutrality for the systems as well as structural stability, important factors for reliable charge distributions. In addition, the common problem of converting between CH bonds and CC bonds at the border vanishes. We apply the procedure to the four redox‐active metal centers of cytochrome c oxidase: CuA, haem a, haem a3, and CuB. Several relevant charge and ligand states are considered. Charges for two different force fields, CHARMM and AMBER, are presented.

Coupled-cluster and density functional theory studies of the electronic excitation spectra of trans-1,3-butadiene and trans-2-propeniminium

The electronic excitation spectra of trans-1,3-butadiene (CH(2)=CH-CH=CH(2)) and trans-2-propeniminium (CH(2)=CH-CH=NH(2)(+)) have been studied at several coupled-cluster and time-dependent density functional theory levels using the linear response approach. Systematic studies employing large correlation-consistent basis sets show that approximate singles and doubles coupled-cluster calculations yield excitation energies in good agreement with experiment for all states except for the two lowest excited A(g) states of trans-1,3-butadiene which have significant multiconfigurational character. Time-dependent density functional theory calculations employing the generalized gradient approximation and hybrid functionals yield too low excitation energies in the basis set limit. In trans-1,3-butadiene, increasing the basis set size by augmenting multiple diffuse functions is observed to reduce the high-lying excitation energies with most density functionals. The decrease in the energies is connected to the incorrect asymptotic behavior of the exchange-correlation potential. The results also demonstrate that standard density functionals are not capable of providing excitation energies of sufficient accuracy for experimental assignments.

Nanosecond electron tunneling between the hemes in cytochrome bo3

Biological electron transfer (eT) between redox-active cofactors is thought to occur by quantum-mechanical tunneling. However, in many cases the observed rate is limited by other reactions coupled to eT, such as proton transfer, conformational changes, or catalytic chemistry at an active site. A prominent example of this phenomenon is the eT between the heme groups of mitochondrial cytochrome c oxidase, which has been reported to take place in several different time domains. The question of whether pure eT tunneling in the nanosecond regime between the heme groups can be observed has been the subject of some experimental controversy. Here, we report direct observations of eT between the heme groups of the quinol oxidase cytochrome bo3 from Escherichia coli, where the reaction is initiated by photolysis of carbon monoxide from heme o3. eT from CO-dissociated ferrous heme o3 to the low-spin ferric heme b takes place at a rate of (1.2 ns)−1 at 20°C as determined by optical spectroscopy. These results establish heme–heme electron tunneling in the bo3 enzyme, a bacterial relative to the mitochondrial cytochrome c oxidase. The properties of eT between the closely lying heme groups in the heme–copper oxidases are discussed in terms of the reorganization energy for the process, and two methods for assessing the rate of electron tunneling are presented.

Change in electron and spin density upon electron transfer to haem

Haems are the cofactors of cytochromes and important catalysts of biological electron transfer. They are composed of a planar porphyrin structure with iron coordinated at the centre. It is known from spectroscopy that ferric low-spin haem has one unpaired electron at the iron, and that this spin is paired as the haem receives an electron upon reduction (I. Bertini, C. Luchinat, NMR of Paramagnetic Molecules in Biological Systems, Benjamin/Cummins Publ. Co., Menlo Park, CA, 1986, pp. 165-170; H.M. Goff, in: A.B.P. Lever, H.B. Gray (Eds.), Iron Porphyrins, Part I, Addison-Wesley Publ. Co., Reading, MA, 1983, pp. 237-281; G. Palmer, in: A.B.P. Lever, H.B. Gray (Eds.), Iron Porphyrins, Part II, Addison-Wesley Publ. Co., Reading, MA, 1983, pp. 43-88). Here we show by quantum chemical calculations on a haem a model that upon reduction the spin pairing at the iron is accompanied by effective delocalisation of electrons from the iron towards the periphery of the porphyrin ring, including its substituents. The change of charge of the iron atom is only approx. 0.1 electrons, despite the unit difference in formal oxidation state. Extensive charge delocalisation on reduction is important in order for the haem to be accommodated in the low dielectric of a protein, and may have impact on the distance dependence of the rates of electron transfer. The lost individuality of the electron added to the haem on reduction is another example of the importance of quantum mechanical effects in biological systems.

Fixing the chirality and trapping the transition state of helicene with atomic metal glue.

By combining the intriguing geometrical properties of two classes of well-established molecules, the metallocenes and the helicenes, we propose a hybrid class of structures-the metallohelicenes. In these, the outer most aryl groups of a specific helicene are glued together by a complexing metal atom. This effectively fixes the chirality of the parent helicene, which otherwise easily undergoes thermal racemization. The fixed chirality suggests several interesting applications, ranging from building blocks of stable molecules with high circular dichroism and optical activity to chiral ligands and catalysts. Alternatively, the metal glue can trap the non-chiral transition state structure of helicene. High-level quantum chemical calculations show the readiness of formation and stability of the proposed complexes.

Spin and charge distribution in iron porphyrin models: A coupled cluster and density-functional study

We recently performed detailed analyses of the electronic structure of low-spin iron porphyrins using density-functional theory (DFT). Both the spin-density distributions of the oxidized, ferric forms, as well as the changes in total charge density upon reduction to the ferrous forms have been explored. Here, we compare the DFT results with wave-function theory, more specifically, with the approximate singles and doubles coupled-cluster method (CC2). Different spin states are considered by studying representative models of low spin, intermediate spin, and high spin species. The CC2 calculations corroborate the DFT results; the spin density exhibits the same amount of molecular spin polarization, and the charge delocalization is of comparable magnitude. Slight differences in the descriptions are noted and discussed.

Interheme electron tunneling in cytochrome c oxidase

Cytochrome c oxidase (CcO) is the terminal enzyme of the respiratory chain that catalyzes respiratory reduction of dioxygen (O2) to water in all eukaryotes and many aerobic bacteria. CcO, and its homologs among the heme-copper oxidases, has an active site composed of an oxygen-binding heme and a copper center in the vicinity, plus another heme group that donates electrons to this site. In most oxidoreduction enzymes, electron transfer (eT) takes place by quantum-mechanical electron tunneling. Here we show by independent molecular dynamics and quantum-chemical methods that the heme-heme eT in CcO differs from the majority of cases in having an exceptionally low reorganization energy. We show that the rate of interheme eT in CcO may nevertheless be predicted by the Moser-Dutton equation if reinterpreted as the average of the eT rates between all individual atoms of the donor and acceptor weighed by the respective packing densities between them. We argue that this modification may be necessary at short donor/acceptor distances comparable to the donor/acceptor radii.