Aagaardnixon6307

Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.Single-beam spectrally controlled (SBSC) two-dimensional (2D) Raman spectroscopy is a unique 2D vibrational measurement technique utilizing trains of short pulses that are generated from a single broadband pulse by pulse shaping. This approach overcomes the difficulty of 2D Raman spectroscopy in dealing with small-signal extraction and avoids complicated low-order cascading effects, thus providing a new possibility for measuring the intramolecular and intermolecular modes of molecular liquids using fifth-order 2D Raman spectroscopy. Recently, for quantitatively investigating the mode-mode coupling mechanism, Hurwitz et al. [Opt. Express 28, 3803 (2020)] have developed a new pulse design for this measurement to separate the contributions of the fifth- and third-order polarizations, which are often overlapped in the original single-beam measurements. Here, we describe a method for simulating these original measurements and the new 2D Raman measurements on the basis of a second-order response function approach. We carry out full molecular dynamics simulations for carbon tetrachloride and liquid water using an equilibrium-nonequilibrium hybrid algorithm, with the aim of explaining the key features of the SBSC 2D Raman spectroscopic method from a theoretical point of view. The predicted signal profiles and intensities provide valuable information that can be applied to 2D spectroscopy experiments, allowing them to be carried out more efficiently.Reverse Osmosis (RO) is one of the main membrane technologies currently used for the desalination of seawater and brackish water to produce freshwater. However, the mechanism of transport and separation of ions in RO membranes is not yet fully understood. Besides acid-base reactions (i.e., including the H+-ion), at high concentrations, the salt ions can associate and form ion pairs. In this study, we investigate how to include the formation of these ion pairs in the extended Donnan steric partitioning pore model. We study the desalination of a water source where three ion pairs can be formed (NaCl, MgCl+, and MgCl2) and also include water self-dissociation and the carbonate system. The model assumes infinitely fast reactions, which means that the participating ions are locally at chemical equilibrium with one another. A square stoichiometric reaction matrix composed of active species, moieties, and reactions is formulated. As the final constraint equation, we use the charge balance. The model predicts profiles in concentration, flux, and reaction rates across the membrane for all species and calculates the retention per group of ions. Ion pair formation has an influence on the fluxes of individual ions and therefore influences the retention of ions.A parameter-free bridge functional is presented using a weighted density approximation (WDA). The key point of this scheme is the utilization of Baxter's relation connecting the second-order direct correlation function (DCF) to the higher-order DCF with the density derivative. The free energy density required for the WDA is determined in a self-consistent manner using Baxter's relation and Percus's test particle method. This self-consistent scheme enables us to employ any type of potential model for simple liquids. The new functional is applied to calculate density distribution functions for the inhomogeneous fluids interacting via the hard-sphere, Lennard-Jones, and hard-core Yukawa potentials under an external field from a planar wall and a slit pore.Recently, ground state eigenvectors of the reduced Bardeen-Cooper-Schrieffer (BCS) Hamiltonian, Richardson-Gaudin (RG) states, have been employed as a wavefunction ansatz for strong correlation. This wavefunction physically represents a mean-field of pairs of electrons (geminals) with a constant pairing strength. Selleckchem Sitagliptin To move beyond the mean-field, one must develop the wavefunction on the basis of all the RG states. This requires both practical expressions for transition density matrices and an idea of which states are most important in the expansion. In this contribution, we present expressions for the transition density matrix elements and calculate them numerically for half-filled picket-fence models (reduced BCS models with constant energy spacing). There are no Slater-Condon rules for RG states, though an analog of the aufbau principle proves to be useful in choosing which states are important.