Estimating the temperature dependence of peptide folding entropies and free enthalpies from total energies in molecular dynamics simulations

The temperature dependence of thermodynamic quantities, such as heat capacity, entropy and free enthalpy, may be obtained by using well-known equations that relate these quantities to the enthalpy of the molecular system of interest at a range of temperatures. In turn, the enthalpy of a molecular system can be estimated from molecular dynamics simulations of an appropriate model. To demonstrate this, we have investigated the temperature dependence of the enthalpy, heat capacity, entropy and free enthalpy of a system that consists of a beta-heptapeptide in methanol and have used the statistical mechanics relationships to describe the thermodynamics of the folding/unfolding equilibrium of the peptide. The results illustrate the power of current molecular simulation force fields and techniques in establishing the link between thermodynamic quantities and conformational distributions.     

Operation of the proton wire in green fluorescent protein. A quantum dynamics simulation

A nuclear quantum dynamical simulation of the proton shuttle operating in the green fluorescent protein has been carried out on a high-quality, high-dimensionality potential energy surface describing the photoactive pipi* excited state, and including motion of both the three protons and of the donor and acceptor atoms of the hydrogen bonds in a closed proton wire. The results of the simulations show that proton transfer along the wire is essentially concerted, synchronous, and very fast, with a substantial amount of the green fluorescent species forming within several tens of femtoseconds. In this regard, analysis of the population of the fluorescent species indicates that at least two dynamical regimes are present for its formation. Within the first hundreds of femtoseconds, dynamics is very fast and impulsive. Later on, a slower pace of formation appears. It is discussed that the two largest decay times for the protonated chromophore reported experimentally (Chattoraj, M.; King, B. A.; Bublitz, G. U.; Boxer, S. G. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 8362-8367) might correspond to some irreversible process occurring after formation of the fluorescent species, rather than to cleavage of the chromophore's phenolic O-H bond.     

A Markov dilation for self-adjoint Schur multipliers

We give a formula for Markov dilation in the sense of Anantha- raman-Delaroche for real positive Schur multipliers on .

     

Charge-transfer pipi* excited state in the 7-azaindole dimer. A hybrid configuration interactions singles/time-dependent density functional theory description

The hybrid configuration interaction singles/time dependent density functional theory approach of Dreuw and Head-Gordon [Dreuw, A.; Head-Gordon, M. J. Am. Chem. Soc. 2004, 126, 4007] has been applied to study the potential energy landscape and accessibility of the charge-transfer pipi* excited state in the dimer of 7-azaindole, which has been traditionally considered a model for DNA base pairing. It is found that the charge-transfer pipi* excited state preferentially stabilizes the product of a single proton transfer. In this situation, the crossing between this state and the photoactive electronic state of the dimer is accessible. It is found that the charge-transfer pipi* excited state has a very steep potential energy profile with respect to any single proton-transfer coordinate and, in contrast, an extremely flat potential energy profile with respect to the stretch of the single proton-transfer complex. This is predicted to bring about a pair of rare fragments of the 7-azaindole dimer, physically separated and hence having very long lifetimes. This could have implications in the DNA base pairs of which the system is an analogue, in the form of replication errors.     

4,6-bis(supermesitylphosphanylidenemethyl)dibenzofuran. Synthesis, X-ray structure and reactivity towards group 11 metals

New kinetically stabilized mono- and bis-phosphaalkene ligands (2 and 3, respectively) were synthesized via the phospha-Wittig approach. Ligand 3 was characterized by X-ray diffraction. The coordinating behaviour of the bidentate ligand was investigated towards group 11 metal centers in order to test its capacity to bind two coordination sites located in a trans-fashion. The [Au(3)][BF4], [Ag(3)(H2O)][BF4] and [Cu(3)(CH3CN)][BF4] complexes 4 , 5 and 6, respectively, were characterized by X-ray diffraction. The peculiar geometries of 4 and 6 were rationalized by means of DFT calculations.     

Direct orthoruthenation of planar prochiral pyridine derivatives by C-H bond activation with [Ru(CO)2Cl2]n and its unexpected stereoselectivity

The treatment of planar prochiral pyridine derivatives with d6 [Ru(CO)2Cl2]n stereoselectively and efficiently produces new dimeric ortho-ruthenated complexes.     

Leachability and analytical speciation of antimony in coal fly ash

A new procedure was described with multiwalled carbon nanotubes as solid phase extraction packing material for the trace analysis of nicosulfuron, thifensulfuron and metsulfuron-methyl in water samples. The possible parameters influencing the enrichment were optimized and the optimal conditions were as followed: eluent, sample pH, flow rate and sample volume were acetonitrile containing 1% acetic acid, pH 3, 8 mL min⁻¹ and 500 mL, respectively. Under the optimal chromatographic separation and SPE conditions, the linear range, detection limit (S/N = 3) and precision (R.S.D., n = 6) were 0.04-40 ng mL⁻¹, 6.8 ng L⁻¹ and 2.5% for nicosulfuron, 0.04-40 ng mL⁻¹, 11.2 ng L⁻¹ and 5.4% for thifensulfuron, 0.02-20 ng mL⁻¹, 5.9 ng L⁻¹, 2.1% for metsulfuron-methyl, respectively. The established method was well employed to determine nicosulfuron, thifensulfuron and metsulfuron-methyl in tap water, seawater, reservoir water and well water samples, and satisfactory results were obtained, the spiked recoveries in the range of 87.2-100.7%, 96.5-105.6% and 83.7-111.1% for them each, respectively.     

Establishment of multivariate specifications for food commodities with discriminant partial least squares

A novel method for establishing multivariate specifications of food commodities is proposed. The specifications are established for discriminant partial least squares (DPLS) by setting limits on the predictions of the DPLS model together with Hotelling T² and square error of prediction (SPE). These limits can be tuned depending on whether type I error (i.e. a correct sample is declared out-of-specification) or type II error (i.e. an out-of-specification sample is declared within specifications) need to be minimized. The methodology is illustrated with a set of NIR spectra of Italian olive oils, corresponding to five regions and the class Liguria is the class of interest. The results demonstrate the possibility of establishing multivariate specification for olive oils from the Liguria region on the basis of spectral data obtaining type I and type II errors lower than 5%.     

Glyphosate–Exonuclease Interactions: Reduced Enzymatic Activity as a Route to Glyphosate Biosensing

N-phosphonomethyle-glycine (glyphosate) is the most widely used pesticide worldwide due to its effectiveness in killing weeds at a moderate cost, bringing significant economic benefits. However, owing to its massive use, glyphosate and its residues contaminate surface waters. On site, fast monitoring of contamination is therefore urgently needed to alert local authorities and raise population awareness. Here the hindrance of the activity of two enzymes, the exonuclease I (Exo I) and the T5 exonuclease (T5 Exo) by glyphosate, is reported. These two enzymes digest oligonucleotides into shorter sequences, down to single nucleotides. The presence of glyphosate in the reaction medium hampers the activity of both enzymes, slowing down enzymatic digestion. It is shown by fluorescence spectroscopy that the inhibition of ExoI enzymatic activity is specific to glyphosate, paving the way for the development of a biosensor to detect this pollutant in drinking water at suitable detection limits, i.e., 0.6 nm .