Unimolecular net heterolysis of symmetric and homopolar σ-bonds.

The unimolecular heterolysis of covalent σ-bonds is integral to many chemical transformations, including S1-, E1- and 1,2-migration reactions. To a first approximation, the unequal redistribution of electron density during bond heterolysis is governed by the difference in polarity of the two departing bonding partners. This means that if a σ-bond consists of two identical groups (that is, symmetric σ-bonds), its unimolecular fission from the S, S, or T states only occurs homolytically after thermal or photochemical activation.

Multiple Triplet Metal-Centered Jahn-Teller Isomers Determine Temperature-Dependent Luminescence Lifetimes in [Ru(bpy) ].

Understanding the factors that determine the luminescence lifetime of transition metal compounds is key for applications in photocatalysis and photodynamic therapy. Here we show that for (bpy = 2,2'-bipyridine), the generally accepted idea that emission lifetimes can be controlled optimizing the energy barrier from the emissive triplet metal-to-ligand charge-transfer ( MLCT) state to the thermally-activated triplet metal-centered ( MC) state or the energy gap between both states is a misconception. Further, we demonstrate that considering a single relaxation pathway determined from the minimum that is lowest in energy leads to wrong temperature-dependent emission lifetimes predictions.

Alignment and photooxidation dynamics of a perylene diimide chromophore in lipid bilayers.

We present a method of enabling photochemical reactions in water by using biomimetic, water-soluble liposomes and a specifically functionalized perylene diimide chromophore. Linking two flexible saturated C4-alkyl chains with terminal positively charged trimethylammonium groups to the rigid perylene diimide core yielded 1 allowing for its co-assembly at the lipid bilayer interface of DOPG liposomes (DOPG = 1,2-dioleoyl--3-phospho-(1'--glycerol)) with a preferred orientation and in close proximity to the water interface. According to molecular dynamics simulations the chromophore aligns preferably parallel to the membrane surface which is supported by confocal microscopy.

Computation of Förster Resonance Energy Transfer in Lipid Bilayer Membranes.

Calculations of Förster Resonance Energy Transfer (FRET) often neglect the influence of different chromophore orientations or changes in the spectral overlap. In this work, we present two computational approaches to estimate the energy transfer rate between chromophores embedded in lipid bilayer membranes. In the first approach, we assess the transition dipole moments and the spectral overlap by means of quantum chemical calculations in implicit solvation, and we investigate the alignment and distance between the chromophores in classical molecular dynamics simulations.

Activation by oxidation and ligand exchange in a molecular manganese vanadium oxide water oxidation catalyst.

Despite their technological importance for water splitting, the reaction mechanisms of most water oxidation catalysts (WOCs) are poorly understood. This paper combines theoretical and experimental methods to reveal mechanistic insights into the reactivity of the highly active molecular manganese vanadium oxide WOC [MnVO(OAc)] in aqueous acetonitrile solutions. Using density functional theory together with electrochemistry and IR-spectroscopy, we propose a sequential three-step activation mechanism including a one-electron oxidation of the catalyst from [Mn Mn ] to [MnMn ], acetate-to-water ligand exchange, and a second one-electron oxidation from [MnMn ] to [Mn ].

Strong Ligand Stabilization Based on π-Extension in a Series of Ruthenium Terpyridine Water Oxidation Catalysts.

The substitution behavior of the monodentate Cl ligand of a series of ruthenium(II) terpyridine complexes (terpyridine (tpy)=2,2':6',2''-terpyridine) has been investigated. H NMR kinetic experiments of the dissociation of the chloro ligand in D O for the complexes [Ru(tpy)(bpy)Cl]Cl (1, bpy=2,2'-bipyridine) and [Ru(tpy)(dppz)Cl]Cl (2, dppz=dipyrido[3,2-a:2',3'-c]phenazine) as well as the binuclear complex [Ru(bpy) (tpphz)Ru(tpy)Cl]Cl (3 b, tpphz=tetrapyrido[3,2-a:2',3'-c:3'',2''-h:2''',3'''-j]phenazine) were conducted, showing increased stability of the chloride ligand for compounds 2 and 3 due to the extended π-system. Compounds 1-5 (4=[Ru(tbbpy) (tpphz)Ru(tpy)Cl](PF ) , 5=[Ru(bpy) (tpphz)Ru(tpy)(C H OS)/(H O)](PF ) , tbbpy=4,4'-di-tert-butyl-2,2'-bipyridine) are tested for their ability to run water oxidation catalysis (WOC) using cerium(IV) as sacrificial oxidant.

BitQT: a graph-based approach to the quality threshold clustering of molecular dynamics.

Motivation: Classical Molecular Dynamics (MD) is a standard computational approach to model time-dependent processes at the atomic level. The inherent sparsity of increasingly huge generated trajectories demands clustering algorithms to reduce other post-simulation analysis complexity. The Quality Threshold (QT) variant is an appealing one from the vast number of available clustering methods.

Diastereoselective Synthesis of Steroid-[60]Fullerene Hybrids and Theoretical Underpinning.

The reaction of C with pregnen-20-carboxaldehyde, a biologically active synthetic steroid, by using a 1,3-dipolar cycloaddition reaction (Prato's protocol) results in the formation of pyrrolidine rings bearing a new stereogenic center on the C2 of the five-membered ring. The formation of the fullerene-steroid hybrids proceeds with preference for the face of the 1,3-dipole, with formation of a diastereomeric mixture in 73:15 ratio. The investigation of the chiroptical properties of these conjugates allowed determining the absolute configuration of the new fulleropyrrolidines.

BitClust: Fast Geometrical Clustering of Long Molecular Dynamics Simulations.

The growing computational capacity allows the investigation of large biomolecular systems by increasingly extensive molecular dynamics simulations. The resulting huge trajectories demand efficient partition methods to discern relevant structural dissimilarity. Clustering algorithms are available to address this task, but their implementations still need to be improved to gain in computational speed and to reduce the consumption of random access memory.

Quality Threshold Clustering of Molecular Dynamics: A Word of Caution.

Clustering Molecular Dynamics trajectories is a common analysis that allows grouping together similar conformations. Several algorithms have been designed and optimized to perform this routine task, and among them, Quality Threshold stands as a very attractive option. This algorithm guarantees that in retrieved clusters no pair of frames will have a similarity value greater than a specified threshold, and hence, a set of strongly correlated frames are obtained for each cluster.

Conceptual DFT analysis of the regioselectivity of 1,3-dipolar cycloadditions: nitrones as a case of study.

The regioselectivity of the 1,3-dipolar cycloaddition of a model nitrone with a set of dipolarophiles, presenting diverse electronic effects, is analyzed using conceptual density functional theory (DFT) methods. We deviate from standard approaches based on frontier molecular orbitals and formulations of the local hard/soft acid/base principle and use instead the dual descriptor. A detailed analysis is carried out to determine the influence of the way to calculate the dual descriptor, the computational procedure, basis set and choice of method to condensate the values of this descriptor.