EPR spectroscopy and molecular dynamics modelling: a combined approach to study liquid crystals

This review outlines the recent theoretical and computational developments for the prediction of motional electron paramagnetic resonance spectra with introduced spin probes from molecular dynamics simulations. The methodology is illustrated with applications to thermotropic and lyotropic liquid crystals at different phases and aggregate states

A combined EPR and MD simulation study of a nitroxyl spin label with restricted internal mobility sensitive to protein dynamics

EPR studies combined with fully atomistic Molecular Dynamics (MD) simulations and an MD-EPR simulation method provide evidence for intrinsic low rotameric mobility of a nitroxyl spin label, Rn, compared to the more widely employed label MTSL (R1). Both experimental and modelling results using two structurally different sites of attachment to Myoglobin show that the EPR spectra of Rn are more sensitive to the local protein environment than that of MTSL. This study reveals the potential of using the Rn spin label as a reporter of protein motions

Enantiopure planar chiral and chiral-at-metal iridacycles derived from bulky cobalt sandwich complexes

Reaction of (η5-(S)-2-(4-methylethyl)oxazolinylcyclopentadienyl)(η4-tetraphenylcyclobutadiene)cobalt with [IrCp*Cl2]2 in acetonitrile with KPF6 and KOt-Bu resulted in S,Sp,SIr and S,Rp,RIr configured acetonitrile and Cp* coordinated cationic iridacycles (d.r. up to 4.8 : 1 – kinetic control), the planar chiral configuration dictating the configuration of the pseudo-tetrahedral iridium-based stereogenic centre. Addition of water to the cycloiridation reaction resulted in an increase in yield (up to 78%) at the cost of diastereoselectivity. Use of the corresponding substrate containing a t-Bu rather than an i-Pr substituted oxazoline gave exclusively the S,Sp,SIr diastereoisomer, and under the same conditions (S)-2-ferrocenyl- 4-(1,1-dimethylethyl)oxazoline cycloiridated to give only the S,Sp,SIr diastereoisomer. Substitution reactions of the title complexes at iridium proceeded with retention of configuration, a computational study revealing the proposed coordinatively unsaturated intermediate of a dissociative mechanism to display a relatively weak Co-Ir interaction, and a pronounced steric effect as the basis of stereocontrol

EPR detection and characterisation of a paramagnetic Mo(III) dihydride intermediate involved in electrocatalytic hydrogen evolution

EPR spectroscopy and theoretical data show that the slow heterogeneous electron-transfer kinetics associated with the reduction of an 18-electron Mo(IV) acetato dihydride are a consequence of an η2−η1 rearrangement of the carboxylate ligand which gives a unique paramagnetic 17-electron Mo(III) dihydride

DEER and RIDME Measurements of the Nitroxide-Spin Labelled Copper-Bound Amine Oxidase Homodimer from Arthrobacter Globiformis

In the study of biological structures, pulse dipolar spectroscopy (PDS) is used to elucidate spin–spin distances at nanometre-scale by measuring dipole–dipole interactions between paramagnetic centres. The PDS methods of Double Electron Electron Resonance (DEER) and Relaxation Induced Dipolar Modulation Enhancement (RIDME) are employed, and their results compared, for the measurement of the dipolar coupling between nitroxide spin labels and copper-II (Cu(II)) paramagnetic centres within the copper amine oxidase from Arthrobacter globiformis (AGAO). The distance distribution results obtained indicate that two distinct distances can be measured, with the longer of these at c.a. 5 nm. Conditions for optimising the RIDME experiment such that it may outperform DEER for these long distances are discussed. Modelling methods are used to show that the distances obtained after data analysis are consistent with the structure of AGAO

Molecular electrometer and binding of cations to phospholipid bilayers

Despite the vast amount of experimental and theoretical studies on the binding affinity of cations -especially the biologically relevant Na+ and Ca2+ - for phospholipid bilayers, there is no consensus in the literature. Here we show that by interpreting changes in the choline headgroup order parameters according to the 'molecular electrometer' concept [Seelig et al., Biochemistry, 1987, 26, 7535], one can directly compare the ion binding affinities between simulations and experiments. Our findings strongly support the view that in contrast to Ca2+ and other multivalent ions, Na+ and other monovalent ions (except Li+) do not specifically bind to phosphatidylcholine lipid bilayers at sub-molar concentrations. However, the Na+ binding affinity was overestimated by several molecular dynamics simulation models, resulting in artificially positively charged bilayers and exaggerated structural effects in the lipid headgroups. While qualitatively correct headgroup order parameter response was observed with Ca2+ binding in all the tested models, no model had sufficient quantitative accuracy to interpret the Ca2+: lipid stoichiometry or the induced atomistic resolution structural changes. All scientific contributions to this open collaboration work were made publicly, using nmrlipids. blogspot.fi as the main communication platform.Peer reviewe

Nitrosylation of Nitric-Oxide-Sensing Regulatory Proteins Containing [4Fe-4S] Clusters Gives Rise to Multiple Iron-Nitrosyl Complexes

The reaction of protein-bound iron–sulfur (Fe-S) clusters with nitric oxide (NO) plays key roles in NO-mediated toxicity and signaling. Elucidation of the mechanism of the reaction of NO with DNA regulatory proteins that contain Fe-S clusters has been hampered by a lack of information about the nature of the iron-nitrosyl products formed. Herein, we report nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations that identify NO reaction products in WhiD and NsrR, regulatory proteins that use a [4Fe-4S] cluster to sense NO. This work reveals that nitrosylation yields multiple products structurally related to Roussin's Red Ester (RRE, [Fe2(NO)4(Cys)2]) and Roussin's Black Salt (RBS, [Fe4(NO)7S3]. In the latter case, the absence of 32S/34S shifts in the Fe−S region of the NRVS spectra suggest that a new species, Roussin's Black Ester (RBE), may be formed, in which one or more of the sulfide ligands is replaced by Cys thiolates

Regioisomeric family of novel fluorescent substrates for SHIP2

ABSTRACT: SHIP2 (SH2-domain containing inositol 5-phosphatase type 2) is a canonical 5-phosphatase which, through its catalytic action on PtdInsP3, regulates the PI3K/Akt pathway and metabolic action of insulin. It is a drug target but there is limited evidence of inhibition of SHIP2 by small molecules in the literature. With the goal to investigate inhibition, we report a homologous family of synthetic, chromophoric benzene phosphate substrates of SHIP2 that display the headgroup regiochemical hallmarks of the physiological inositide substrates that have proved difficult to crystallize with 5-phosphatases. Using time-dependent density functional theory (TD-DFT), we explore the intrinsic fluorescence of these novel substrates and show how fluorescence can be used to assay enzyme activity. The TD-DFT approach promises to inform rational design of enhanced active site probes for the broadest family of inositide-binding / metabolizing proteins, whilst maintaining the regiochemical properties of bona fide inositide substrates

Exploring structural and electronic effects in three isomers of tris{bis(trifluoromethyl)phenyl}borane: Towards the combined electrochemical-frustrated Lewis pair activation of H2

Three structural isomers of tris{bis(trifluoromethyl)phenyl}borane have been studied as the acidic com- ponent of frustrated Lewis pairs. While the 3,5-substituted isomer is already known to heterolytically cleave H2 to generate a bridging-hydride; ortho-substituents in the 2,4- and 2,5-isomers quench such reactivity through electron donation into the vacant boron pz orbital and steric blocking of the boron centre; as shown by electrochemical, structural and computational studies. Electrochemical studies of the corresponding borohydrides identify that the two-electron oxidation of terminal-hydrides occurs at more positive potentials than observed for [HB(C6F5)3]−, while the bridging-hydride oxidizes at a higher poten- tial still, comparable to that of free H2