Heats of formation of Co(CO)(2)NOPR(3), R = CH(3) and C(2)H(5), and its ionic fragments

A joint threshold photoelectron photoion coincidence spectrometry (TPEPICO) and collision-induced dissociation (CID) study on the thermochemistry of Co(CO)(2)NOPR(3), R = CH(3) (Me) and C(2)H(5) (Et), complexes is presented. Adiabatic ionization energies of 7.36 +/- 0.04 and 7.24 +/- 0.04 eV, respectively, were extracted from scans of the total ion and threshold electron signals. In the TPEPICO study, the following 0 K onsets were determined for the various fragment ions: CoCONOPMe(3)(+), 8.30 +/- 0.05 eV; CoNOPMe(3)(+), 9.11 +/- 0.05 eV; CoPMe(3)(+) 10.80 +/- 0.05 eV; CoCONOPEt(3)(+), 8.14 +/- 0.05 eV; CoNOPEt(3)(+), 8.92 +/- 0.05 eV; and CoPEt(3)(+), 10.66 +/- 0.05 eV. These onsets were combined with the Co(+)-PR(3) (R = CH(3) and C(2)H(5)) bond dissociation energies of 2.88 +/- 0.11 and 3.51 +/- 0.17 eV, obtained from the TCID experiments, to derive the heats of formation of the neutral and ionic species. Thus, the Co(CO)(2)NOPR(3) (R = CH(3) and C(2)H(5)) 0 K heats of formation were found to be -350 +/- 13 and -376 +/- 18 kJ x mol(-)(1), respectively. These heats of formation were combined with the published heat of formation of Co(CO)(3)NO to determine the substitution enthalpies of the carbonyl to phosphine substitution reactions. Room-temperature values of the heats of formation are also given using the calculated harmonic vibrational frequencies. Analysis of the TCID experimental results provides indirectly the adiabatic ionization energies of the free phosphine ligands, P(CH(3))(3) and P(C(2)H(5))(3), of 7.83 +/- 0.03 and 7.50 +/- 0.03 eV, respectively.     

Film structures of poly(amido amine) dendrimers with an azacrown core and long alkyl chain spacers on water or Ag nanoparticle suspension

Newly designed poly(amido amine) dendrimers, which have an azacrown core, hexyl spacers, and methyl ester terminals (aza-C6-PAMAM dendrimer), were spread at the air-water and air-silver nanoparticle suspension interfaces, and their film structures were examined by surface pressure-area (pi-A) and surface potential-area (DeltaV-A) isotherms and epifluorescence microscopy. It was revealed that generation (G) 1.5 aza-C6-PAMAM dendrimer on a water subphase formed homogeneous film with face-on configuration, and this configuration was maintained during compression. On the other hand, a G2.5 dendrimer film on the air-water interface took initially homogeneous and face-on configuration that was followed by the conformational change during compression. Using a silver nanoparticle suspension as subphase, G1.5 film was significantly reinforced, and the partial collapse (cracks) in the film appeared as network texture. For a G2.5 dendrimer film, the pi-A and DeltaV-A isotherm properties were similar to that on the water subphase except for the collapsed film; small spots instead of cracks were formed under the film after collapse. These effects of the silver nanoparticle may be due to the formation of a dendrimer/silver nanoparticle composite. The formation process of the nanocomposite film was verified by UV-vis spectroscopy. For the G1.5 dendrimer, silver clusters and nanoparticles adsorbed to the dendrimer film after spreading and formed a small amount of aggregates. During compression, the aggregation proceeded even at low surface pressure. For the G2.5 dendrimer, a dendrimer/nanoparticle composite was also formed after spreading. However, with the initial compression, the absorption bands of clusters, nanoparticles, and aggregate increased together. Upon further compression, while the bands of cluster and nanoparticles decreased, the bands of aggregate still increased. These results suggest that the G2.5 dendrimer covered the cluster and nanoparticles more efficiently than the G1.5 dendrimer did because of the larger molecular size.     

Use of molecular dynamics in the design and structure determination of a photoinducible beta-hairpin

The study presented here consists of three parts. In the first, the ability of a set of differently substituted diazobenzene-based linkers to act as photoswitchable beta-turn building blocks was assessed. A 12-residue peptide known to form beta-hairpins was taken as the basis for the modeling process. The central (beta-turn) residue pair was successively replaced by six symmetrically ((o,o), (m,m), or (p,p)) substituted (aminomethyl/carboxymethyl or aminoethyl/carboxyethyl) diazobenzene derivatives leading to a set of peptides with a photoswitchable backbone conformation. The folding behavior of each peptide was then investigated by performing molecular dynamics simulations in water (4 ns) and in methanol (10 ns) at room temperature. The simulations suggest that (o,o)- and (m,m)-substituted linkers with a single methylene spacer are significantly better suited to act as photoswitchable beta-turn building blocks than the other linkers examined in this study. The peptide containing the (m,m)-substituted linker was synthesized and characterized by NMR in its cis configuration. In the second part of this study, the structure of this peptide was refined using explicit-solvent simulations and NOE distance restraints, employing a variety of refinement protocols (instantaneous and time-averaged restraining as well as unrestrained simulations). We show that for this type of systems, even short simulations provide a significant improvement in our understanding of their structure if physically meaningful force fields are employed. In the third part, unrestrained explicit-solvent simulations starting from either the NMR model structure (75 ns) or a fully extended structure (25 ns) are shown to converge to a stable beta-hairpin. The resulting ensemble is in good agreement with experimental data, indicating successful structure prediction of the investigated hairpin by classical explicit-solvent molecular dynamics simulations.     

Surface chemistry studies of (CdSe)ZnS quantum dots at the air-water interface

Trioctylphosphine oxide- (TOPO-) capped (CdSe)ZnS quantum dots (QDs) were prepared through a stepwise synthesis. The surface chemistry behavior of the QDs at the air-water interface was carefully examined by various physical measurements. The surface pressure-area isotherm of the Langmuir film of the QDs gave an average diameter of 4.4 nm, which matched very well with the value determined by transmission electron microscopy (TEM) measurements if the thickness of the TOPO cap was counted. The stability of the Langmuir film of the QDs was tested by two different methods, compression/decompression cycling and kinetic measurements, both of which indicated that TOPO-capped (CdSe)ZnS QDs can form stable Langmuir films at the air-water interface. Epifluorescence microscopy revealed the two-dimensional aggregation of the QDs in Langmuir films during the early stage of the compression process. However, at high surface pressures, the Langmuir film of QDs was more homogeneous and was capable of being deposited on a hydrophobic quartz slide by the Langmuir-Blodgett (LB) film technique. Photoluminescence (PL) spectroscopy was utilized to characterize the LB films. The PL intensity of the LB film of QDs at the first emission maximum was found to increase linearly with increasing number of layers deposited onto the hydrophobic quartz slide, which implied a homogeneous deposition of the Langmuir film of QDs at surface pressures greater than 20 mN.m(-1).     

On the parallel mechanism of the dissociation of energy-selected P(CH3)3+ ions

Energy selected trimethyl phosphine ions were prepared by threshold photoelectron photoion coincidence (TPEPICO) spectroscopy. This ion dissociates via H, CH(3), and CH(4) loss, the latter two involving hydrogen transfer steps. The ion time-of-flight distribution and the breakdown diagram are analyzed in terms of the statistical RRKM theory, which includes tunneling. Ab initio and DFT calculations provide the vibrational frequencies required for the RRKM modeling. CH(3) loss could produce both the P(CH(3))(2)(+) by a simple bond dissociation step, and the more stable HP(CH(2))CH(3)(+) ion by a hydrogen transfer step. Quantum chemical calculations are extensively used to uncover the reaction scheme, and they strongly suggest that the latter product is exclusively formed via an isomerization step in the energy range of the experiment. The data analysis, which includes modeling with the trimethyl phosphine thermal energy distribution, provides accurate onset energies for both H (E(0K) = 1024.1 +/- 3.5 kJ/mol) and CH(3) (E(0K) = 1024.8 +/- 3.5 kJ/mol) loss reactions. From this analysis, we conclude that the Delta(f)H(298K) degrees [HP(CH(2))(CH(3))(+)] = 783 +/- 8 kJ/mol and Delta(f)H(298K) degrees [P(CH(2))(CH(3))(2)(+)] = 711 +/- 8 kJ/mol.     

How well does molecular simulation reproduce environment-specific conformations of the intrinsically disordered peptides PLP,TP2 and ONEG?

Understanding the conformational ensembles of intrinsically disordered proteins and peptides (IDPs) in their various biological environments is essential for understanding their mechanisms and functional roles in the proteome, leading to a greater knowledge of, and potential treatments for, a broad range of diseases. To determine whether molecular simulation is able to generate accurate conformational ensembles of IDPs, we explore the structural landscape of the PLP peptide (an intrinsically disordered region of the proteolipid membrane protein) in aqueous and membrane-mimicking solvents, using replica exchange with solute scaling (REST2), and examine the ability of four force fields (ff14SB, ff14IDPSFF, CHARMM36 and CHARMM36m) to reproduce literature circular dichroism (CD) data. Results from variable temperature (VT) ¹H and Rotating frame Overhauser Effect SpectroscopY (ROESY) nuclear magnetic resonance (NMR) experiments are also presented and are consistent with the structural observations obtained from the simulations and CD. We also apply the optimum simulation protocol to TP2 and ONEG (a cell-penetrating peptide (CPP) and a negative control peptide, respectively) to gain insight into the structural differences that may account for the observed difference in their membrane-penetrating abilities. Of the tested force fields, we find that CHARMM36 and CHARMM36m are best suited to the study of IDPs, and accurately predict a disordered to helical conformational transition of the PLP peptide accompanying the change from aqueous to membrane-mimicking solvents. We also identify an α-helical structure of TP2 in the membrane-mimicking solvents and provide a discussion of the mechanistic implications of this observation with reference to the previous literature on the peptide. From these results, we recommend the use of CHARMM36m with the REST2 protocol for the study of environment-specific IDP conformations. We believe that the simulation protocol will allow the study of a broad range of IDPs that undergo conformational transitions in different biological environments.

A protocol for simulating intrinsically disordered peptides in aqueous and hydrophobic solvents is proposed. Results from four force fields are compared with experiment. CHARMM36m performs the best for the simulated IDPs in all environments.     

Sequential ortho effects: characterization of novel [M - 35]+ fragment ions in the mass spectra of 2-alkyl-4, 6-dinitrophenols

High-resolution mass spectrometry (HRMS), hybrid tandem mass spectrometry (MS/MS) (EBqQ), and photoelectron-photoion coincidence (PEPICO) experiments were conducted to examine a possible ortho-ortho effect resulting in a novel [M - 35]⁺ fragment ion in 2-alkyl-4, 6-dinitrophenols. For compounds having ethyl or larger alkyl substituents, [M35]⁺ was observed only when [M - 18]⁺ ions were present, with the ortho nitro group being involved in the reaction to [M- 35]⁺. For [M - 18]⁺ and [M - 35]⁺, HRMS results were consistent with losses of H₂O and H₂O + OH, respectively, whereas MS/MS results indicated a sequential reaction due to metastable dissociations. The appearance energy determined by PEPICO for [M - 35]⁺ was found to be greater than the appearance energy for [M - 18]⁺, thus supporting a sequential reaction. 69–75).     

ABSORPTION SPECTRAL SHIFTS OF CAROTENOIDS RELATED TO MEDIUM POLARIZABILITY

Abstract–Solvent induced absorption spectral shifts of the electronic transition from ground 1 A_g state to the excited 1B_u state in carotenoids have been studied. It is shown that the shift depends only on dispersion interactions in non-polar solvents. In polar media there is just a small extra contribution to the red-shift, due to other forms of interactions. The spectral shifts are well described by the theory, which expresses the shift relative to the gas phase value, as a function of solvent polarizability. The main conclusion is that the dominating mechanism behind the large red-shifted absorbance of carotenoids in the proteinacous environment, in vivo, is the mutual polarizability interactions between the carotenoids and the surrounding medium. The solution-phase values of the dipole moments of the lA_g to 1B_u transitions and the differences of isotropic polarizability between 1B_u and lA_g states of carotenoids in non-polar solvents are calculated and found to be around 13 D and 360 ų respectively. From the great overlap of absorption spectra between carotenoids in quinoline and carotenoids in vivo in purple bacterial antenna complexes, it can be expected that the carotenoids are surrounded by several aromatic amino acids in vivo. Comparisons have been done between the exicted states in carotenoids and in linear conjugated polyenes.