Kinetics of the Antibody Recognition Site in the Third IgG‐Binding Domain of Protein G

Protein dynamics occurring on a wide range of timescales play a crucial role in governing protein function. Particularly, motions between the globular rotational correlation time ( ) and 40 μs (supra‐ window), strongly influence molecular recognition. This supra‐ window was previously hidden, owing to a lack of experimental methods. Recently, we have developed a high‐power relaxation dispersion (RD) experiment for measuring kinetics as fast as 4 μs. For the first time, this method, performed under super‐cooled conditions, enabled us to detect a global motion in the first β‐turn of the third IgG‐binding domain of protein G (GB3), which was extrapolated to 371±115 ns at 310 K. Furthermore, the same residues show the plasticity in the model‐free residual dipolar coupling (RDC) order parameters and in an ensemble encoding the supra‐ dynamics. This β‐turn is involved in antibody binding, exhibiting the potential link of the observed supra‐ motion with molecular recognition.     

Deriving Structural Information from Experimentally Measured Data on Biomolecules

During the past half century, the number and accuracy of experimental techniques that can deliver values of observables for biomolecular systems have been steadily increasing. The conversion of a measured value Q^exp of an observable quantity Q into structural information is, however, a task beset with theoretical and practical problems: 1) insufficient or inaccurate values of Q^exp, 2) inaccuracies in the function used to relate the quantity Q to structure , 3) how to account for the averaging inherent in the measurement of Q^exp, 4) how to handle the possible multiple‐valuedness of the inverse of the function , to mention a few. These apply to a variety of observable quantities Q and measurement techniques such as X‐ray and neutron diffraction, small‐angle and wide‐angle X‐ray scattering, free‐electron laser imaging, cryo‐electron microscopy, nuclear magnetic resonance, electron paramagnetic resonance, infrared and Raman spectroscopy, circular dichroism, Förster resonance energy transfer, atomic force microscopy and ion‐mobility mass spectrometry. The process of deriving structural information from measured data is reviewed with an eye to non‐experts and newcomers in the field using examples from the literature of the effect of the various choices and approximations involved in the process. A list of choices to be avoided is provided.     

LaSr3NiRuO4H4: A 4d Transition‐Metal Oxide–Hydride Containing Metal Hydride Sheets

The synthesis of the first 4d transition metal oxide–hydride, LaSr₃NiRuO₄H₄, is prepared via topochemical anion exchange. Neutron diffraction data show that the hydride ions occupy the equatorial anion sites in the host lattice and as a result the Ru and Ni cations are located in a plane containing only hydride ligands, a unique structural feature with obvious parallels to the CuO₂ sheets present in the superconducting cuprates. DFT calculations confirm the presence of S= Ni⁺ and S=0, Ru²⁺ centers, but neutron diffraction and μSR data show no evidence for long‐range magnetic order between the Ni centers down to 1.8 K. The observed weak inter‐cation magnetic coupling can be attributed to poor overlap between Ni 3d and H 1s in the super‐exchange pathways.     

Head–Tail Asymmetry as the Determining Factor in the Formation of Polymer Cubosomes or Hexasomes in a Rod–Coil Amphiphilic Block Copolymer

The self‐assembly of a rod–coil amphiphilic block copolymer (ABCP) led to Im m and Pn m polymer cubosomes and p6mm polymer hexasomes. This is the first time that these structures are observed in a rod–coil system. By varying the hydrophobic chain length, the initial concentration of the polymer solution, or the solubility parameter of the mixed solvent, head–tail asymmetry is adjusted to control the formation of polymer cubosomes or hexasomes. The formation mechanism of the polymer cubosomes was also studied. This research opens up a new way for further study of the bicontinuous and inverse phases in different ABCP systems.     

Water Formation under Silica Thin Films: Real‐Time Observation of a Chemical Reaction in a Physically Confined Space

Using low‐energy electron microscopy and local photoelectron spectroscopy, water formation from adsorbed O and H₂ on a Ru(0001) surface covered with a vitreous SiO₂ bilayer (BL) was investigated and compared to the same reaction on bare Ru(0001). In both cases the reaction is characterized by moving reaction fronts. The reason for this might be related to the requirement of site release by O adatoms for further H₂‐dissociative adsorption. Apparent activation energies ( ) are found for the front motion of 0.59 eV without cover and 0.27 eV under cover. We suggest that the smaller activation energy but higher reaction temperature for the reaction on the SiO₂ BL covered Ru(0001) surface is due to a change of the rate‐determining step. Other possible effects of the cover are discussed. Our results give the first values for in confined space.     

Rapid Room‐Temperature,Chemoselective C −C Coupling of Poly(pseudo)halogenated Arenes Enabled by Palladium(I) Catalysis in Air

While chemoselectivities in Pd⁰‐catalyzed coupling reactions are frequently non‐intuitive and a result of a complex interplay of ligand/catalyst, substrate, and reaction conditions, we herein report a general method based on Pd^I that allows for an a priori predictable chemoselective C −C coupling at C−Br in preference to C−OTf and C−Cl bonds, regardless of the electronic or steric bias of the substrate. The C−C bond formations are extremely rapid (<5 min at RT) and are catalyzed by an air‐ and moisture‐stable Pd^I dimer under open‐flask conditions.     

Ligand‐Enabled Enantioselective C –H Activation of Tetrahydroquinolines and Saturated Aza‐Heterocycles by RhI

The first rhodium(I)‐catalyzed enantioselective intermolecular C –H activation of various saturated aza‐heterocycles including tetrahydroquinolines, piperidines, piperazines, azetidines, pyrrolidines, and azepanes is presented. The combination of a rhodium(I) precatalyst and a chiral monodentate phosphonite ligand is shown to be a powerful catalytic system to access a variety of important enantio‐enriched heterocycles from simple starting materials. Notably, the C –H activation of tetrahydroquinolines is especially challenging due to the adjacent C −H bond. This redox‐neutral methodology provides a new synthetic route to α‐N‐arylated heterocycles with high chemoselectivity and enantioselectivity up to 97 % ee.     

Ruthenium(II) complexes bearing pyridine‐based tridentate and bidentate ligands: catalytic activity for transfer hydrogenation of aryl ketones

Ru(II) complexes of the general formula [RuCl₂(′′)(L)] (1: ′N = N_b, L = MeOH; 2: ′N = N_b, L = CH₃CN; 3: ′N = N_d, L = CH₃CN; 4: ′N = N_p, L = CH₃CN), [Ru(p‐cymene)(_a–b)Cl]Cl (5a: N N_a = 2,2′‐bipyridine; 5b: N N_b = 4,4′‐dimethyl–2,2′‐bipyridine), [Ru(′′)(_a–b)Cl]Cl (6a: ′N = N_b, _a = 2,2′‐bipyridine; 6b: ′N = N_b, _b = 4,4′‐dimethyl‐2,2′‐bipyridine; 7a: ′N = N_d, _a = 2,2′‐bipyridine; 7b: ′N = N_d, _b = 4,4′‐dimethyl‐2,2′‐bipyridine; 8a: ′N = N_p, _a = 2,2′‐bipyridine; 8b: ′N = N_p, _b = 4,4′‐dimethyl‐2,2′‐bipyridine) and [Ru(′′)(_a)Cl]BF₄ (9a: ′N = N_b; _a = 2,2′‐bipyridine) were synthesized from the corresponding [RuCl₂(p‐cymene)]₂ dimer, ′′ and _a–b ligands. The compounds were characterized by elemental analysis, IR and NMR. Complex 9a was studied by X‐ray diffraction, confirming its cationic‐mononuclear [RuCl(_bb)(_a)]⁺ nature. The synthesized Ru(II) complexes (1–8) were employed as catalysts for the transfer hydrogenation of ketones to secondary alcohols in the presence of KOH using 2‐propanol as a hydrogen source at 82°C. The rates of the transfer hydrogenation reactions strongly depended on the type of and ancillary ligands. Copyright © 2012 John Wiley & Sons, Ltd.     

Catalytic and Atom‐Economic C −C Bond Formation: Alkyl Tantalum Ureates for Hydroaminoalkylation

Atom‐economic and regioselective C ?C bond formation has been achieved by rapid C?H alkylation of unprotected secondary arylamines with unactivated alkenes. The combination of Ta(CH₂SiMe₃)₃Cl₂, and a ureate N,O‐chelating‐ligand salt gives catalytic systems prepared in situ that can realize high yields of β‐alkylated aniline derivatives from either terminal or internal alkene substrates. These new catalyst systems realize C?H alkylation in as little as one hour and for the first time a 1:1 stoichiometry of alkene and amine substrates results in high yielding syntheses of isolated amine products by simple filtration and concentration.     

Geometry of the canonical Van Vleck transformation

Bloch's transformation from the zeroth‐order space for a perturbation problem to the corresponding space of exact eigenvectors, was found as a geometrically defined alternative to the algebraically constructed Van Vleck transformation. Klein's theorem of uniqueness transferred some of this geometrical interpretation to its canonical form . Quite recently Kvaal has taken a large step further by writing as a product of commuting planar rotations, obtained by describing and in terms of certain principal vectors and canonical angles. Kvaal's approach is now developed further, using a new commutation relation which simplifies algebraic manipulations substantially. It allows for a simple definition of an operator for the angle between and which has Kvaal's vectors and angles as eigenvectors and eigenvalues. Klein's theorem is refined in various ways. The impact of the approach on a number of previous results is considered. © 2015 Wiley Periodicals, Inc.     

Theoretical prediction of the optical rotation of chiral molecules in ordered media: A computational study of (Ra)‐1,3‐dimethylallene, (2R)‐2‐methyloxirane,and (2R)‐N‐methyloxaziridine

A theoretical procedure has been developed and implemented to calculate the optical rotation of chiral molecules in ordered phase via origin‐independent diagonal components , of the optical activity tensor and origin‐independent components , for , of the mixed electric dipole‐electric quadrupole polarizability. Origin independence was achieved by referring these tensors to the principal axis system of the electric dipole dynamic polarizability at the same laser frequency ω. The approach has been applied, allowing for alternative quantum mechanical methods based on different gauges, to estimate near Hartree–Fock values for three chiral molecules, (2R)‐N‐methyloxaziridine C₂NOH₅, (2R)‐2‐methyloxirane (also referred to as propylene oxide) C₃OH₆, and ( )‐1,3‐dimethylallene C₅H₈, at two frequencies. The theoretical predictions can be useful for an attempt at measuring correspondent experimental values in crystal phase. © 2015 Wiley Periodicals, Inc.     

Formation of a Double Diamond Cubic Phase by Thermotropic Liquid Crystalline Self‐Assembly of Bundled Bolaamphiphiles

A quaternary amphiphile with swallow‐tail side groups displays a new bicontinuous thermotropic cubic phase with symmetry Pn m and formed by two interpenetrating networks where cylindrical segments are linked by H bonds at tetrahedral junctions. Each network segment contains two bundles, each containing 12 rod‐like mesogens, lying along the segment axis. This assembly leads to the first thermotropic structure of the “double diamond” type. A quantitative geometric model is proposed to explain the occurrence of this rare phase.     

Electronic Spectroscopy of Methylcyanodiacetylene (CH3C5N)

The results of a study devoted to the electronic spectroscopy of gaseous, solid, and cryogenic matrix‐isolated methylcyanodiacetylene (CH₃C₅N) are reported. UV absorption and optical phosphorescence spectra of the compound are described here for the first time, and the corresponding vibronic assignments are proposed. UV absorption, studied directly or through the excitation of phosphorescence, revealed the ¹E‐‐ ¹A₁ system, very weak ¹A₂– ¹A₁ bands, and a strong, broad absorption feature, tentatively identified as ¹E– ¹A₁. Spectral measurements were assisted by quantum chemical calculations at the DFT and ab initio (coupled cluster) levels of theory.     

Additivity in kramers pairs symmetry: Multiplets with up to four unpaired electrons

Many fermions Kramers pairs formalism is considered from the prospective of the sum of individual single fermion time‐reversal operators. The obtained many fermions “pseudo Kramers pairs operator” ( ), as well as its square ( ), have formally the same structure as the many fermion spin operators and . Nevertheless, the shape of eigenfunctions with respect to and is different. Herein all Kramers adapted eigenfunctions of for cases of up to four unpaired fermions are compiled, and their properties with respect to further advocated. It will be shown that degeneracy of the multiplets recovers the proper behavior with respect to Pascal's triangle. A projection operator for obtaining the “high spin” Kramers adapted eigenfunctions is suggested. Noncommutation of with spin and angular momentum operators and degeneracy is discussed at last. © 2016 Wiley Periodicals, Inc.     

Experimental and Kinetic Modeling Study of Methanol Ignition and Oxidation at High Pressure

A detailed chemical kinetic model for oxidation of CH₃OH at high pressure and intermediate temperatures has been developed and validated experimentally. Ab initio calculations and Rice–Ramsperger–Kassel–Marcus/transition state theory (RRKM/TST) analysis were used to obtain rate coefficients for , , , and . The experiments, involving CH₃OH/O₂ mixtures diluted in N₂, were carried out in a high‐pressure flow reactor at 600–900 K and 20–100 bar, varying the reaction stoichiometry from very lean to fuel‐rich conditions. Under the conditions studied, the onset temperature for methanol oxidation was not dependent on the stoichiometry, whereas increasing pressure shifted the ignition temperature toward lower values. Model predictions of the present experimental results, as well as rapid compression machine data from the literature, were generally satisfactory. The governing reaction pathways have been outlined based on calculations with the kinetic model. Unlike what has been observed for unsaturated hydrocarbons, the oxidation pathways for CH₃OH under the investigated conditions were very similar to those prevailing at higher temperatures and lower pressures. At the high pressures, the modeling predictions for onset of reaction were particularly sensitive to the reaction.     

Ritz variational calculation for the singly excited states of compressed two‐electron atoms

A detailed analysis on the effect of spherical impenetrable confinement on the structural properties of two‐electron ions in states has been performed. The energy values of 1sns [ ] ( ) states of helium‐like ions ( ) are estimated within the framework of Ritz variational method using explicitly correlated Hylleraas‐type basis sets. The correlated wave functions used here are consistent with the finite boundary conditions due to spherical confinement. A comparative study between the singlet and triplet states originating from a particular electronic configuration shows incidental degeneracy and the subsequent level‐crossing phenomena. The thermodynamic pressure felt by the ion inside the sphere pushes the energy levels toward continuum. Critical pressures for the transition to strong confinement regime (where the singly excited two‐electron energy levels cross the corresponding one‐electron threshold) as well as for the complete destabilization are also estimated.     

Linear Chains of Magnetic Ions Stacked with Variable Distance: Ferromagnetic Ordering with a Curie Temperature above 20 K

We have studied the magnetic properties of the SURMOF‐2 series of metal–organic frameworks (MOFs). Contrary to bulk MOF‐2 crystals, where Cu²⁺ ions form paddlewheels and are antiferromagnetically coupled, in this case the Cu²⁺ ions are connected via carboxylate groups in a zipper‐like fashion. This unusual coupling of the spin ions within the resulting one‐dimensional chains is found to stabilize a low‐temperature, ferromagnetic (FM) phase. In contrast to other ordered 1D systems, no strong magnetic fields are needed to induce the ferromagnetism. The magnetic coupling constants describing the interaction between the individual metal ions have been determined in SQUID experiments. They are fully consistent with the results of ab initio DFT electronic structure calculations. The theoretical results allow the unusual magnetic behavior of this exotic, yet easy‐to‐fabricate, material to be described in a detailed fashion.     

Fast search algorithms for computational protein design

One of the main challenges in computational protein design (CPD) is the huge size of the protein sequence and conformational space that has to be computationally explored. Recently, we showed that state‐of‐the‐art combinatorial optimization technologies based on Cost Function Network (CFN) processing allow speeding up provable rigid backbone protein design methods by several orders of magnitudes. Building up on this, we improved and injected CFN technology into the well‐established CPD package Osprey to allow all Osprey CPD algorithms to benefit from associated speedups. Because Osprey fundamentally relies on the ability of to produce conformations in increasing order of energy, we defined new strategies combining CFN lower bounds, with new side‐chain positioning‐based branching scheme. Beyond the speedups obtained in the new ‐CFN combination, this novel branching scheme enables a much faster enumeration of suboptimal sequences, far beyond what is reachable without it. Together with the immediate and important speedups provided by CFN technology, these developments directly benefit to all the algorithms that previously relied on the DEE/ combination inside Osprey* and make it possible to solve larger CPD problems with provable algorithms. © 2016 Wiley Periodicals, Inc.     

The “bound wavefunction” on the repulsive excited ( ) state of the HD+ molecule

The time‐independent Schrödinger equation for the HD+ molecule is solved beyond the Born–Oppenheimer (B‐O) approximation. In the adiabatic representation, the wavefunction of the ground vibrational eigenstate is found to contain two parts: One is on the ground ( ) state which is dominant, and the other is on the repulsive excited ( ) state in the range from R = 0.0 to R = 5.0 Bohr. This is because the nonadiabatic coupling between the ground ( ) and excited ( ) states is strong in that region. The influences of the nonadiabatic coupling on the vibrational eigenfunctions are discussed in detail.     

Rate Constants for the Gas‐Phase Reactions of Ozone and Nitrate Radicals with the Sesquiterpenes: Valencene and Farnesol

Sesquiterpenes are constituents of a variety of essential oils that are used in flavorings, perfumes, personal care, and cleaning products. Two sesquiterpenes that are commonly used as indoor fragrances are valencene and farnesol. Knowing the reaction rate constants of these chemicals with ozone (O₃) and nitrate radical () is an important factor in determining their fate indoors. In this study, the bimolecular rate constants of , , , and were measured using the relative rate technique at 297 ± 3 K and 1 atm total pressure. Using the rate constants reported here and measured/modeled indoor concentrations of O₃ and (20 ppb and 1 ppt, respectively), pseudo–first‐order‐rate lifetimes , , , and were determined.