Large-scale nonlocality in “doubly special relativity” with an energy-dependent speed of light

There are two major alternatives for violating the (usual) Lorentz invariance at large (Planckian) energies or momenta—either not all inertial frames (in the Planck regime) are equivalent (e.g., there is an effectively preferred frame) or the transformations from one frame to another are (nonlinearly) deformed (“doubly special relativity”). We demonstrate that the natural (and reasonable) assumption of an energy-dependent speed of light in the latter method goes along with violations of locality/separability (and even translational invariance) on macroscopic scales.     

Application of the pKa rule to synthesize salts of bezafibrate

ABSTRACT

Co-crystallization frequently employs forces such as hydrogen bonds, halogen bonds, and π-π stacking to assemble molecules in a multi-component crystal. In an effort to increase the strength of the intermolecular interaction between the anti-cholesterol drug bezafibrate (BEZA), a wastewater contaminant, and hydrogen-bond-acceptor molecules, we modified the pK_a values of the acceptors. Here, we describe the first series of salts incorporating BEZA and achieve a variety of supramolecular architectures including discrete assemblies, 1D chains, tapes, and 2D sheets. We discuss exceptions to the pK_a rule, and demonstrate that the presence of hydrogen-bond-donor atoms on the acceptor molecule supports salt formation.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Quantitation of the global secondary structure of globular proteins by FTIR spectroscopy: Comparison with X-ray crystallographic structure

Fourier transform infrared spectroscopy (FTIR) is potentially a powerful tool for determining the global secondary structure of proteins in solution, providing the spectra are analyzed using a statistically and theoretically justified methodology. We have performed FTIR experiments on 14 globular proteins and two synthetic polypeptides whose X-ray crystal structures are known to exhibit varying types and amounts of secondary structures. Calculation of the component structural elements of the vibrational bands was accomplished using nonlinear regression analysis, by fitting both the amide I and amide II bands of the Fourier self-deconvoluted spectra, the second-derivative spectra, and the original spectra. The methodology was theoretically justified by comparing (via nonlinear regression analysis) the global secondary structure determined after deconvolving into component bands the vibrational amide I envelopes with the calculated structure determined by first principles from Ramachandran analysis of the X-ray crystallographic structure of 14 proteins from the Brookhaven protein data bank. Justification of the nonlinear regression analysis model with respect to experimental and instrumental considerations was achieved by the decomposition of all the bands of benzene and an aqueous solution of ammonium acetate into component bands while floating the Gaussian/Lorentzian character of the line shapes. The results for benzene yield all pure Lorentzian line shapes with no Gaussian character while the ammonium acetate spectra yielded all Gaussian line shapes with no Lorentzian character. In addition, all-protein spectra yielded pure Gaussian line shapes with no Lorentzian character. Finally, the model was statistically justified by recognizing random deviation patterns in the regression analysis from all fits and by the extra sum of squares F-test which uses the degrees of freedom and the root mean square values as a tool to determine the optimum number of component bands required for the nonlinear regression analysis. Results from this study demonstrate that the globular secondary structure calculated from the amide I envelope for these 14 proteins from FTIR is in excellent agreement with the values calculated from the X-ray crystallographic data using three-dimensional Ramachandran analysis, providing that the proper contribution from GLN and ASN side chains to the 1667 and 1650 cm(-1) component bands has been taken into account. The standard deviation of the regression analysis for the per cent helix, extended, turn and irregular conformations was found to be 3.49%, 2.07%, 3.59% and 3.20%, respectively.     

Lewis acid-base adducts of zwitterionic alkali metal methanides and silanides with BH3

The synthesis, structures and spectroscopic properties of M(MeOCH₂CH₂OMe₂Si)₃CBH₃ (M-1-BH₃) and M(MeOCH₂CH₂OMe₂Si)₃SiBH₃ (M-2-BH₃) (M?=?Li, Na, K) derived from reactions of BH₃ with the alkali metal zwitterions [M(MeOCH₂CH₂OMe₂Si)₃C] (M-1) and [M(MeOCH₂CH₂OMe₂Si)₃Si] (M-2) (M?=?Li, Na, K), resp., are reported. X-ray analysis and DFT calculations reveal discrete zwitterionic structures with the octahedral alkali metal cations rigidly locked and charge separated from the BH₃ units via pendant donors groups. Solution experiments with the hydride acceptors B(C₆F₅)₃ and [Ph₃C]₂[B₁₂C₁₂] indicate that Na-1-BH₃ can donate hydrides to form cations of formula [Na(MeOCH₂CH₂OMe₂Si)₃CBH₂]⁺.     

Properties of a new ferroelectric crystal family: MCd(NO2)3 [M=NH4, K,Rb, Cs,Tl]

Single crystals of MCd(NO₂)₃, with M=NH₄, K, Rb, Cs, and Tl, respectively, were grown and investigated by means of optical and dielectric methods. The crystals show rhombohedral symmetry (possible space group R 3) and multi-domain patterns at ambient temperature. The compounds exhibit phase transitions above room-temperature of first (M=K) and second order (M=Rb, Cs, Tl), respectively, into cubic high-temperature phases. Observed dielectric anomalies and hysteresis loops point to ferroelectric properties and suggest a relaxational order-disorder mechanism of the nitrite ions to be responsible for the transitions. The MCd-(NO₂)₃-compounds are seen to represent a new family of ferroelectrics with a cubic prototypic phase closely related to the structural type of the perovskites. The transions are classified by symmetry considerations, and a possible structure of the cubic high-temperature phase with space group Pm3 is proposed.