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.     

A Unified Treatment of the Relationship Between Ligand Substituents and Spin State in a Family of Iron(II) Complexes

The influence of ligands on the spin state of a metal ion is of central importance for bioinorganic chemistry, and the production of base‐metal catalysts for synthesis applications. Complexes derived from [Fe(bpp)₂]²⁺ (bpp=2,6‐di{pyrazol‐1‐yl}pyridine) can be high‐spin, low‐spin, or spin‐crossover (SCO) active depending on the ligand substituents. Plots of the SCO midpoint temperature (T ) in solution vs. the relevant Hammett parameter show that the low‐spin state of the complex is stabilized by electron‐withdrawing pyridyl (“X”) substituents, but also by electron‐donating pyrazolyl (“Y”) substituents. Moreover, when a subset of complexes with halogeno X or Y substituents is considered, the two sets of compounds instead show identical trends of a small reduction in T for increasing substituent electronegativity. DFT calculations reproduce these disparate trends, which arise from competing influences of pyridyl and pyrazolyl ligand substituents on Fe‐L σ and π bonding.     

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.     

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.     

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.     

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.     

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.     

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.     

Synthesis of gradient copolysiloxanes by simultaneous copolymerization of cyclotrisiloxanes and mechanism for kinetics inverse between anionic and cationic ring‐opening polymerization

Trifluoropropylmethylsiloxane–phenylmethylsiloxane gradient copolysiloxanes were synthesized by anionic and cationic ring‐opening polymerization (ROP) of 1,3,5‐tris(trifluoropropylmethyl)cyclotrisiloxane ( ) and phenylmethylcyclotrisiloxane ( ). The analysis of reactivity ratios revealed that the reactivity of toward anionic ROP was higher than that of ; however, exhibited lower reactivity compared with during the cationic ROP. AB and BAB type gradient copolymers were obtained because of a difference in the reactivity of the monomers. The microstructure of copolymers was characterized by ²⁹Si NMR spectroscopy, gel permeation chromatography, and differential scanning calorimetry. Furthermore, the mechanism for kinetics inverse of copolymerization was proposed based on the results of the optimized molecular configuration. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2016 , 54, 835–843     

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.     

Dealing with the shifted and inverted Tietz–Hua oscillator potential using the J‐matrix method

The tridiagonal J‐matrix approach has been used to calculate the low and moderately high‐lying eigenvalues of the rotating shifted Tietz–Hua (RSTH) oscillator potential. The radial Schrödinger equation is solved efficiently by means of the diagonalization of the full Hamiltonian matrix, with the Laguerre or oscillator basis. Ro–vibrational bound state energies for 11 diatomic systems, namely , , , NO, CO, , , , , , and NO⁺, are calculated with high accuracy. Some of the energy states for molecules are reported here for the first time. The results of the last four molecules have been introduced for the first time using the oscillator basis. Higher accuracy is achieved by calculating the energy corresponding to the poles of the S‐matrix in the complex energy plane using the J‐matrix method. Furthermore, the bound states and the resonance energies for the newly proposed inverted Tietz–Hua IRSTH‐potential are calculated for the H₂‐molecule with scaled depth. A detailed analysis of variation of eigenvalues with n, quantum numbers is made. Results are compared with literature data, wherever possible. © 2015 Wiley Periodicals, Inc.     

Computational study of basis set and electron correlation effects on anapole magnetizabilities of chiral molecules

In the presence of a static, nonhomogeneous magnetic field, represented by the axial vector at the origin of the coordinate system and by the polar vector , assumed to be spatially uniform, the chiral molecules investigated in this paper carry an orbital electronic anapole, described by the polar vector . The electronic interaction energy of these molecules in nonordered media is a cross term, coupling and via , one third of the trace of the anapole magnetizability a_αβ tensor, that is, . Both and W^BC have opposite sign in the two enantiomeric forms, a fact quite remarkable from the conceptual point of view. The magnitude of predicted in the present computational investigation for five chiral molecules is very small and significantly biased by electron correlation contributions, estimated at the density functional level via three different functionals. © 2016 Wiley Periodicals, Inc.     

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.     

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.     

Quantum control of electron‐proton symmetry breaking in dissociative ionization of H2 by intense laser pulses

Forward and backward electron/proton ionization/dissociation spectra from one‐dimensional non‐Born‐Oppenheimer H₂ molecule exposed to ultrashort intense laser pulses ( W/cm², λ = 800 nm) have been computed by numerically solving the time‐dependent Schrödinger equation. The resulting above‐threshold ionization and above‐threshold dissociation spectra exhibit the characteristic forward‐backward asymmetry and sensitivity to the carrier‐envelope phase (CEP), particularly for high energies. A general framework for understanding CEP effects in the asymmetry of dissociative ionization of H₂ has been established. It is found that the symmetry breaking of electron‐proton distribution with π periodic modulation occurs for all CEPs except for ( integer) and the largest asymmetry coming from the CEP of . At least one of the electron and proton distributions is asymmetric when measured simultaneously. Inspection of the nuclear and electron wave packet dynamics provides further information about the relative contribution of the gerade and ungerade states of to the dissociation channel and the time delay of electrons in asymmetric ionization. © 2014 Wiley Periodicals, Inc.     

Reliability of Orientational Order Parameters Determined from Two‐dimensional X‐ray Diffraction Patterns: A Simulation Study

The orientational order parameter is one of the most important quantities to describe the degree of long‐range orientational ordering of liquid crystals. There are several approaches to experimentally measure this order parameter of liquid crystalline phases but every method includes substantial simplifications and assumptions. We present a simulation‐based approach to elucidate the reliability of the method of Davidson, Petermann and Levelut to measure via 2D X‐ray experiments. We have found that this method slightly underestimates by an absolute value of only 0.05 and thus provides reliable measures of by X‐ray diffraction.     

Photodetachment of hydrogen negative ion near inelastic surfaces: Arbitrary laser polarization direction

The photodetachment of hydrogen negative ion near different inelastic surfaces is investigated by the semiclassical closed orbit theory for arbitrary laser polarization direction . A two‐term formula of photodetachment cross section consisting of a smooth background term and an oscillatory term is derived. The oscillatory term contains an extra angular factor that describes the dependence of oscillations in total cross section on the laser polarization direction. It is observed that the amplitude of oscillations in cross section reaches maximum at when laser polarization is parallel to the z‐axis and it approaches zero as the laser polarization direction becomes perpendicular to the z‐axis. It is also observed that as the reflection coefficient , which accounts for the inelastic behavior of the surfaces, increases the amplitude of oscillation also increases. © 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.     

Size of a polymer chain in an environment of quenched chains

We perform high‐coordination three‐dimensional (3D) lattice simulations of a single chain of N monomers embedded in matrices of quenched chains, at different concentrations ρ, using pruned‐enriched Rosenbluth sampling. The partition function is well‐described by the expression, , where is a universal constant, and is the concentration dependent lattice connectivity constant. For sufficiently long chains, , we find that the radius of gyration R varies nonmonotonically with ρ; R decreases gradually from its unperturbed dimensions R₀ until , after which it increases relatively rapidly due to repulsion between monomers. Motivated by the similarity in the shape of the curves, and results on Gaussian chains, we successfully superpose all the simulation data onto a single master curve. Finally, we test the relationship , suggested by a Flory‐type scaling model, where ρ_c is the critical percolation threshold, and is a universal constant. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2015 , 53, 1611–1619     

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.