Theoretical analysis of core size effect in metalloporphyrins

Density functional theory has been applied to a series of unsubstituted planar metalloporphyrins (MPs) to elucidate how geometry and frequencies correlate with the metal-nitrogen distance, referred to as the core size. Different transition metals can invoke expansion or contraction of the porphyrin core due to electronic effects resulting from the amount of d-electron pairing as well as occupancy of the d(x(2)(-y(2))) orbital. A full vibrational analysis consisting of all in-plane and out-of-plane frequencies was carried out, and the resulting modes were plotted against core size for a linear analysis and grouped within symmetry blocks. The modes were separated according to planarity, and all modes with a large slope and best fit greater than 0.8 were considered sensitive to metal-nitrogen distances. All planar skeletal modes above 1450 cm(-1), including the pyrolle ring deformations, are found to be core-size sensitive. The most significant out-of-plane modes sensitive to core size are gamma(8) and gamma(9), which are infrared active and grouped within the A(2u) symmetry block. The present work also opens possible quantitative applications for the correlation of spectroscopic properties of MPs and heme proteins with actual structural parameters.     

SLIM: A Short‐Linked,Highly Redox‐Stable Trityl Label for High‐Sensitivity In‐Cell EPR Distance Measurements

The understanding of biomolecular function is coupled to knowledge about the structure and dynamics of these biomolecules, preferably acquired under native conditions. In this regard, pulsed dipolar EPR spectroscopy (PDS) in conjunction with site‐directed spin labeling (SDSL) is an important method in the toolbox of biophysical chemistry. However, the currently available spin labels have diverse deficiencies for in‐cell applications, for example, low radical stability or long bioconjugation linkers. In this work, a synthesis strategy is introduced for the derivatization of trityl radicals with a maleimide‐functionalized methylene group. The resulting trityl spin label, called SLIM, yields narrow distance distributions, enables highly sensitive distance measurements down to concentrations of 90 nm , and shows high stability against reduction. Using this label, the guanine‐nucleotide dissociation inhibitor (GDI) domain of Yersinia outer protein O (YopO) is shown to change its conformation within eukaryotic cells.     

The origin of open circuit voltage of porphyrin-sensitised TiO(2) solar cells

Electron lifetime and diffusion coefficient measurements in highly efficient porphyrin-sensitised TiO(2) solar cells showed reduced electron lifetime, and consequently, lower photo-induced electron density under illumination compared to commonly used ruthenium dye (N719)-sensitised solar cells, which is proposed to be the origin of the generally lower open circuit voltage.     

Atomic Hydrogen Induced Chemical Vapor Deposition of Silicon Oxycarbide Thin Films Derived from Diethoxymethylsilane Precursor

Amorphous silicon oxycarbide (a-SiOC:H) films produced by remote plasma RPCVD from diethoxymethylsilane (DEMS) were characterized in terms of their basic properties related to the coatings deposited using conventional plasma enhanced PECVD method. The effect of substrate temperature (T_S) on the growth rate, chemical composition, structure, and properties of resulting a-SiOC:H films is reported. Film growth is an adsorption-controlled process, wherein two mechanisms can be distinguished with a transition at about T_S=70°C. Depending on the temperature, films of different nature can be obtained, from polymer-like to highly crosslinked material with C-Si-O network. The chemical structure of a-SiOC:H films was characterized by FTIR, ¹³C and ²⁹Si solid-state NMR, and X-ray photoelectron spectroscopes. The a-SiOC:H films were also characterized in terms of their density, refractive index, surface morphology, conformality of coverage, hardness, adhesion to a substrate, and friction coefficient. The films were found to be morphologically homogeneous materials exhibiting good conformality of coverage and small surface roughness. Their refractive index exhibits anomalous effect revealing a minimum value at T_S=125°C. Due to their exceptional physical properties a-SiOC:H films produced by RPCVD from DEMS precursor seems to be useful as potential dielectric materials or coatings for various encapsulation applications.     

Effective Control of the Electron-donating Ability of Phosphines by using Phosphazenyl and Phosphoniumylidyl Substituents

Phosphoniumylidyl and phosphazenyl groups are effective substituents to increase the electron-donating ability of tertiary phosphines. However, the influence of structural variations among those substituents on the electronic properties of the phosphines is little explored. Herein, we show that protonation of the ylidic carbon atom of phosphoniumylidyl phosphines increases the Tolman electronic parameter (TEP) by ΔTEP = 16.0–18.8 cm^–1. Furthermore, phosphazenyl phosphines were synthesized with isopropyl groups (NP{iPr}₃) and tetramethylguanidino groups (NP{tmg}₃) at the phosphonium center. Determination of their TEP values reveals a remarkable low substituent parameter of χ = –18.5 cm^–1 for the NP(tmg)₃ group. In addition, we prepared the corresponding gold(I) complexes and determined their solid-state structures using single-crystal X-ray diffraction studies to analyze the steric profile of the new phosphine ligands.     

Late-Stage Functionalization by Chan–Lam Amination: Rapid Access to Potent and Selective Integrin Inhibitors

A late-stage functionalization of the aromatic ring in amino acid derivatives is described. The key step is a copper-catalysed diversification of a boronate ester by amination (Chan–Lam reaction) that can be carried out on a complex β-aryl-β-amino acid scaffold. This not only considerably extends the substrate scope of amination partners, but also delivers an array of potent and selective integrin inhibitors as potential treatment agents of idiopathic pulmonary fibrosis (IPF). This versatile chemical strategy, which is amenable to high-throughput-array protocols, allows the installation of pharmaceutically valuable heteroaromatic fragments at a late stage by direct coupling to NH heterocycles, leading to compounds with drug-like attributes. It thus constitutes a useful addition to the medicinal chemist's repertoire.     

Non-linear effects in acyclic amino acid-catalyzed direct asymmetric aldol reactions

Non-linear effects were observed in acyclic amino acid-catalyzed direct asymmetric intermolecular aldol reactions. The non-linear effects are due to the equilibrium solid-liquid phase behavior of amino acids. The results suggest that the phase behavior of amino acids linked to asymmetric catalysis may have implications to the evolution of homochirality.     

Analysis of uncertainties in polymer viscoelastic properties obtained from equilibrium computer simulations

We critically evaluate the uncertainties in the stress autocorrelation function obtained from equilibrium molecular dynamics simulation of model polymer melts. This quantity is central to evaluating transport properties, e.g., the complex modulus and the viscosity. In contrast to the intuitive expectation that simulations have to be run five to six orders of magnitude longer than the chain relaxation time to reduce uncertainties to acceptable levels, our analysis shows that the majority of the uncertainty is associated with rapidly oscillating bonded interactions. These fluctuations occur on time scales which are approximately 10(4) times shorter than the relaxation time of a chain of length 80. Consequently, the effects of these oscillations on the stress autocorrelation function can be dramatically reduced by (i) conducting long simulations (typically 10(6) times longer than the bond relaxation times or only 10(2) chain relaxation times) and (ii) by performing running averages with time windows whose time scales are much longer than these oscillations. Conducting such long simulations also allows for the accurate determination of the melt viscosity and the low-frequency complex modulus, but performing running averages do not impact these quantities since they are time integrals of the stress autocorrelation function.     

DFT analysis of co-alkyl and co-adenosyl vibrational modes in B12-cofactors

Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.     

Resonance Raman studies of beta-substituted porphyrin systems with unusual electronic absorption properties.

Zn(II) and Cu(II) porphyrins with beta-conjugated barbiturate functional groups have low-energy electronic transitions which are unusual in that there are two strong bands in the Soret region. Resonance excitation of the two bands shows that each has features characteristic of both the porphyrin and barbiturate groups, with some perturbation to these features caused by the interaction of the two chromophores. The resonance Raman (RR) spectrum (lambda(exc)=413.1 nm) of the 412 nm band shows two bands at 1722 and 1743 cm(-1) attributable to C==O stretches in the substituent. Changes in frequency of porphyrin core modes due to the differing metal centres are reproduced by density functional theory calculations. The Q band RR spectra show modes with anomalous polarization which may be attributed to A(2g) modes, however no overtone or combination bands are observed.