Enantioselective palladium-catalyzed hydrosilylation of styrene: Detailed reaction mechanism from first-principles and hybrid QM/MM molecular dynamics simulations

The mechanism of the enantioselective hydrosilylation of styrene catalyzed by Pd-0 species generated in situ from dichloro {1-{(R)-1-[(S)-2(diphenylphosphino-kappaP)ferrocenyl]ethyl}-3-trimethylphenyl-5-1H-pyrazole-kappaN}palladium, 1, has been investigated in detail through ab initio molecular dynamics and hybrid ab initio molecular dynamics/molecular mechanics (QM/MM) calculations. Different QM/MM models have been adopted in order to probe the specific steric and electronic contributions of different substituents. The catalytic cycle is initiated by the formation of a weakly bound pi-complex (DeltaE approximate to -5.4 kcal/mol) under simultaneous detachment of the pyrazole ligand. In agreement with a Chalk-Harrod mechanism, this is followed by the migratory insertion of the hydride, which leads to a eta(3)-coordination mode of the benzylic fragment. The significant stabilization of the allylic intermediate (DeltaE approximate to -11 kcal/mol) is responsible for the high regioselectivity of the reaction (as well as for its enantioselectivity). The rate-determining step with an activation barrier of 16 kcal/mol is the migration of the silyl ligand to the a-carbon of the substrate with concomitant closure of the ligand chelate ring. This step leads to the formation of an intermediate in which the phenyl moiety of the product remains coordinated in an eta(2)-mode to the palladium. The addition of trichlorosilane leads to product formation and hence to the regeneration of the catalyst. A unimolecular reaction pathway on the other hand, in which the transfer of the silyl ligand to the benzylic fragment is concerted with the addition of a molecule of HSiCl3 to the catalyst, is disfavored by an activation barrier of similar to30 kcal/mol

Unusual Ar-H/Rh-H J(HH) NMR coupling in complexes of rhodium(III): experimental evidence and theoretical support for an eta1-arene structure

The synthesis and structural properties of three new hydridorhodium(III) complexes are reported. Hydrogenolysis of the cyclometalated rhodium dichloride complexes [RhCl2{(S,S)-benbox(Me-2)}] (2a-c) leads to formation of the new complexes [RhCl2(H){(S,S)-ip-benbox(Me-2)H}] (3a-c) in 45% to 85% yield. Compounds 3a-c were found to have unusual features by NMR spectroscopy: in particular, downfield shifted aryl proton resonances (8.88-9.03 ppm) that were coupled to the rhodium hydride resonances. Using X-ray crystallographic studies, a variety of solid- and solution-state characterization techniques, and DFT calculations, these features were attributed to the presence of weak pi-type eta(1)-arene interactions in 3a-c

Emergence of hidden phases of methylammonium lead iodide (CH3NH3PbI3) upon compression

We perform a thorough structural search with the minima hopping method (MHM) to explore low-energy structures of methylammonium lead iodide. By combining the MHM with a forcefield, we efficiently screen vast portions of the configurational space with large simulation cells containing up to 96 atoms. Our search reveals two structures of methylammonium iodide perovskite (MAPI) that are substantially lower in energy than the well-studied experimentally observed low-temperature Pnma orthorhombic phase according to density functional calculations. Both structures have not yet been reported in the literature for MAPI, but our results show that they could emerge as thermodynamically stable phases via compression at low temperatures. In terms of the electronic properties, the two phases exhibit larger band gaps than the standard perovskite-type structures. Hence, the pressure-induced phase selection at technologically achievable pressures (i.e., via thin-film strain) is a viable route towards the synthesis of several MAPI polymorph with variable band gaps

Accuracy of Molecular Simulation-Based Predictions of koff Values: A Metadynamics Study

The koff values of ligands unbinding to proteins are key parameters for drug discovery. Their predictions based on molecular simulation may under- or overestimate experiment in a system- and/or technique-dependent way. Here we use an established method-infrequent metadynamics, based on the AMBER force field-to compute the koff of the ligand iperoxo (in clinical use) targeting the muscarinic receptor M2. The ligand charges are calculated by either (i) the Amber standard procedure or (ii) B3LYP-DFT. The calculations using (i) turn out not to provide a reasonable estimation of the transition-state free energy. Those using (ii) differ from experiment by 2 orders of magnitude. On the basis of B3LYP DFT QM/MM simulations, we suggest that the observed discrepancy in (ii) arises, at least in part, from the lack of electronic polarization and/or charge transfer in biomolecular force fields. These issues might be present in other systems, such as DNA-protein complexes

A Quantum Dynamics Study of the Ultrafast Relaxation in a Prototypical Cu(I)-Phenanthroline

The ultrafast nonadiabatic dynamics of a prototypical Cu(I)phenanthroline complex, [Cu(dmp)(2)](+) (dmp = 2,9-dimethyl-1,10-phenanthroline), initiated after photoexcitation into the optically bright metal-to-ligand charge-transfer (MLCT) state (S-3) is investigated using quantum nuclear dynamics. In agreement with recent experimental conclusions, we find that the system undergoes rapid (similar to 100 fs) internal conversion from S-3 into the S-2 and S-1 states at or near the FranckCondon (FC) geometry. This is preceded by a dynamic component with a time constant of similar to 400 fs, which corresponds to the flattening of the ligands associated with the pseudo JahnTeller distortion. Importantly, our simulations demonstrate that this latter aspect is in competition with subpicosecond intersystem crossing (ISC). The mechanism for ISC is shown to be a dynamic effect, in the sense that it arises from the system traversing the pseudo JahnTeller coordinate where the singlet and triplet states become degenerate, leading to efficient crossing. These first-principles quantum dynamics simulations, in conjunction with recent experiments, allow us to clearly resolve the mechanistic details of the ultrafast dynamics within [Cu(dmp)(2)](+), which have been disputed in the literature

Probing the electronic and geometric structure of ferric and ferrous myoglobins in physiological solutions by Fe K-edge absorption spectroscopy.

We present an iron K-edge X-ray absorption study of carboxymyoglobin (MbCO), nitrosylmyoglobin (MbNO), oxymyoglobin (MbO2), cyanomyoglobin (MbCN), aquomet myoglobin (metMb) and unligated myoglobin (deoxyMb) in physiological media. The analysis of the XANES region is performed using the full-multiple scattering formalism, implemented within the MXAN package. This reveals trends within the heme structure, absent from previous crystallographic and X-ray absorption analysis. In particular, the iron–nitrogen bond lengths in the porphyrin ring converge to a common value of about 2 Å, except for deoxyMb whose bigger value is due to the doming of the heme. The trends of the Fe–Nε (His93) bond length is found to be consistent with the effect of ligand binding to the iron, with the exception of MbNO, which is explained in terms of the repulsive trans effect. We derive a high resolution description of the relative geometry of the ligands with respect to the heme and quantify the magnitude of the heme doming in the deoxyMb form. Finally, time-dependent density functional theory is used to simulate the pre-edge spectra and is found to be in good agreement with the experiment. The XAS spectra typically exhibit one pre-edge feature which arises from transitions into the unoccupied dσ and dπ − πligand* orbitals. 1s → dπ transitions contribute weakly for MbO2, metMb and deoxyMb. However, despite this strong Fe d contribution these transitions are found to be dominated by the dipole (1s → 4p) moment due to the low symmetry of the heme environment

Characterization of Molecular Determinants of the Conformational Stability of Macrophage Migration Inhibitory Factor: Leucine 46 Hydrophobic Pocket

Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer formation, is essential for its keto-enol tautomerase activity and probably mediates several of its interactions and biological activities, including its binding to its receptor CD74 and activation of certain signaling pathways. Therefore, understanding the molecular factors governing the oligomerization of MIF and the role of quaternary structure in modulating its structural stability and multifunctional properties is crucial for understanding the function of MIF in health and disease. Herein, we describe highly conserved intersubunit interactions involving the hydrophobic packing of the side chain of Leu46 onto the β-strand β3 of one monomer within a hydrophobic pocket from the adjacent monomer constituted by residues Arg11, Val14, Phe18, Leu19, Val39, His40, Val41, Val42, and Pro43. To elucidate the structural significance of these intersubunit interactions and their relative contribution to MIF’s trimerization, structural stability and catalytic activity, we generated three point mutations where Leu46 was replaced by glycine (L46G), alanine (L46A) and phenylalanine (L46F), and their structural properties, stability, oligomerization state, and catalytic activity were characterized using a battery of biophysical methods and X-ray crystallography. Our findings provide new insights into the role of the Leu46 hydrophobic pocket in stabilizing the conformational state of MIF in solution. Disrupting the Leu46 hydrophobic interaction perturbs the secondary and tertiary structure of the protein but has no effect on its oligomerization state

Probing wavepacket dynamics using ultrafast x-ray spectroscopy

The advent of x-ray free electron lasers is providing new opportunities for probing the ultrafast excited state dynamics using structurally sensitive techniques. Herein we use excited state wavepacket dynamics of a prototypical Cu(I)-phenanthroline complex, [Cu(dmp)(2)](+) (dmp = 2, 9-dimethyl-1, 10-phenanthroline) to investigate how femtosecond vibrational and electronic relaxation is translated into transient x-ray absorption and emission. Using realistic experimental parameters we also derive the anticipated signal strengths for these transient features. This indicates that although recording a signal capturing the strongest transient (i.e. excited state-ground state) changes will be possible for all cases, only with x-ray absorption near-edge structure and extended x-ray absorption fine structure will it be possible to resolve the fine details associated with the wavepacket dynamics within realistic experimental acquisition times

Vibrational signatures for low-energy intermediate-sized Si clusters

We report low-energy locally stable structures for the clusters Si20 and Si21. The structures were obtained by performing geometry optimizations within the local density approximation. Our calculated binding energies for these clusters are larger than any previously reported for this size regime. To aid in the experimental identification of the structures, we have computed the full vibrational spectra of the clusters, along with the Raman and IR activities of the various modes using a recently developed first-principles technique. These represent, to our knowledge, the first calculations of Raman and IR spectra for Si clusters of this size

Photoemission and photoionization time delays and rates

Ionization and, in particular, ionization through the interaction with light play an important role in fundamental processes in physics, chemistry, and biology. In recent years, we have seen tremendous advances in our ability to measure the dynamics of photo-induced ionization in various systems in the gas, liquid, or solid phase. In this review, we will define the parameters used for quantifying these dynamics. We give a brief overview of some of the most important ionization processes and how to resolve the associated time delays and rates. With regard to time delays, we ask the question: how long does it take to remove an electron from an atom, molecule, or solid? With regard to rates, we ask the question: how many electrons are emitted in a given unit of time? We present state-of-the-art results on ionization and photoemission time delays and rates. Our review starts with the simplest physical systems: the attosecond dynamics of single-photon and tunnel ionization of atoms in the gas phase. We then extend the discussion to molecular gases and ionization of liquid targets. Finally, we present the measurements of ionization delays in femto- and attosecond photoemission from the solid–vacuum interface