Harmonic analysis of large systems. II. Comparison of different protein models

A series of normal mode analyses of bovine pancreatic trypsin inhibitor (BPTI) has been performed. The results of modifying the long-range truncation of electrostatics, reducing the conformational space of the system (reduced basis normal mode analysis), and using different parameter sets and models for the potential function are reported. Both explicit (904 atoms) and polar hydrogen (580 atoms) representations of BPTI were examined and produced nearly identical normal mode vectors but slightly modified vibrational frequencies. The truncation methods—no cutoff, shift, and switch—were examined, and the use of a short switching function was found to alter harmonic motion greatly. A table relating the different cutoff methods to several previously published frequencies for BPTI indicates that the diversity of published lowest frequencies is due to the use of different electrostatic models rather than to inherent differences in the models or energy parameters. Examining reduced basis results demonstrates that a dihedral basis yields similar normal mode vectors, though the vibrational frequencies are shifted to higher values. The analysis of BPTI harmonic dynamics using a spherical harmonic reduced basis set yields significantly altered dynamics, indicating that BPTI is not well represented as a homogeneous object at low temperatures. © 1995 John Wiley & Sons, Inc.

1 This article is a U.S. Government work and, as such, is in the public domain in the United States of America.

     

Cyto-mechanoresponsive polyelectrolyte multilayer films

Cell adhesion processes take place through mechanotransduction mechanisms where stretching of proteins results in biological responses. In this work, we present the first cyto-mechanoresponsive surface that mimics such behavior by becoming cell-adhesive through exhibition of arginine-glycine-aspartic acid (RGD) adhesion peptides under stretching. This mechanoresponsive surface is based on polyelectrolyte multilayer films built on a silicone sheet and where RGD-grafted polyelectrolytes are embedded under antifouling phosphorylcholine-grafted polyelectrolytes. The stretching of this film induces an increase in fibroblast cell viability and adhesion.     

In situ synthesis of Cu-BTC (HKUST-1) in macro-/mesoporous silica monoliths for continuous flow catalysis

The metal-organic framework Cu-BTC has been successfully synthesized as nanoparticles inside the mesopores of silica monoliths featuring a homogeneous macropore network enabling the use of Cu-BTC for continuous flow applications in liquid phase with low pressure drop. High productivity was reached with this catalyst for the Friedl?nder reaction.     

Fluorescence imaging of potassium ions in living cells using a fluorescent probe based on a thrombin binding aptamer-peptide conjugate

When a biotinylated FRET probe based on a peptide-thrombin binding aptamer conjugate was introduced together with streptavidin and biotinylated nuclear export signal peptide into HeLa cells, the resulting ternary complex enabled visualization of K(+) concentration changes in the cell.     

Acid–Base‐Controlled Stereoselective Metalation of Overhanging Carboxylic Acid Porphyrins: Consequences for the Formation of Heterobimetallic Complexes

Overhanging carboxylic acid porphyrins have revealed promising ditopic ligands offering a new entry in the field of supramolecular coordination chemistry of porphyrinoids. Notably, the adjunction of a so‐called hanging‐atop (HAT) Pb^II cation to regular Pb^II porphyrin complexes allowed a stereoselective incorporation of the N‐core bound cation, and an allosterically controlled Newton’s cradle‐like motion of the two Pb^II ions also emerged from such bimetallic complexes. In this contribution, we have extended this work to other ligands and metal ions, aiming at understanding the parameters that control the HAT Pb^II coordination. The nature of the N‐core bound metal ion (Zn^II, Cd^II), the influence of the deprotonation state of the overhanging COOH group and the presence of a neutral ligand on the opposite side (exogenous or intramolecular), have been examined through ¹H NMR spectroscopic experiments with the help of radiocrystallographic structures and DFT calculations. Single and bis‐strap ligands have been considered. They all incorporate a COOH group hung over the N‐core on one side. For the bis‐strap ligands, either an ester or an amide group has been introduced on the other side. In the presence of a base, the mononuclear Zn^II or Cd^II complexes incorporate the carbonyl of the overhanging carboxylate as apical ligand, decreasing its availability for the binding of a HAT Pb^II. An allosteric effector (e.g., 4‐dimethylaminopyridine (DMAP), in the case of a single‐strap ligand) or an intramolecular ligand (e.g., an amide group), strong enough to compete with the carbonyl of the hung COO^?, is required to switch the N‐core bound cation to the opposite side with concomitant release of the COO^?, thereby allowing HAT Pb^II complexation. In the absence of a base, Zn^II or Cd^II binds preferentially the carbonyl of the intramolecular ester or amide groups in apical position rather than that of the COOH. This better preorganization, with the overhanging COOH fully available, is responsible for a stronger binding of the HAT Pb^II. Thus, either allosteric or acid–base control is achieved through stereoselective metalation of Zn^II or Cd^II. In the latter case, according to the deprotonation state of the COOH group, the best electron‐donating ligand is located on one or the other side of the porphyrin (COO^?>CONHR>COOR>COOH): the lower affinity of COOH for Zn^II and Cd^II, the higher for a HAT Pb^II. These insights provide new opportunities for the elaboration of innovative bimetallic molecular switches.     

Performance of density functional theory in computing nonresonant vibrational (hyper)polarizabilities

A set of exchange‐correlation functionals, including BLYP, PBE0, B3LYP, BHandHLYP, CAM‐B3LYP, LC‐BLYP, and HSE, has been used to determine static and dynamic nonresonant (nuclear relaxation) vibrational (hyper)polarizabilities for a series of all‐trans polymethineimine (PMI) oligomers containing up to eight monomer units. These functionals are assessed against reference values obtained using the Møller–Plesset second‐order perturbation theory (MP2) and CCSD methods. For the smallest oligomer, CCSD(T) calculations confirm the choice of MP2 and CCSD as appropriate for assessing the density functionals. By and large, CAM‐B3LYP is the most successful, because it is best for the nuclear relaxation contribution to the static linear polarizability, intensity‐dependent refractive index second hyperpolarizability, static second hyperpolarizability, and is close to the best for the electro‐optical Pockels effect first hyperpolarizability. However, none of the functionals perform satisfactorily for all the vibrational (hyper)polarizabilities studied. In fact, in the case of electric field‐induced second harmonic generation all of them, as well as the Hartree–Fock approximation, yield the wrong sign. We have also found that the Pople 6–31+G(d) basis set is unreliable for computing nuclear relaxation (hyper)polarizabilities of PMI oligomers due to the spurious prediction of a nonplanar equilibrium geometry. © 2013 Wiley Periodicals, Inc.     

Introduction of a Carboxymethylamino(or oxy Or thio) Group in the 3 Position of 2-Aryl(or Arylmethyl)isoindol-1-ones from α Hydroxylactams

The preparation of 3-carboxymethylamino (or oxy or thio)-2-aryl (or arylmethyl)-isoindol-1-ones are described from hydroxylactams according to three different pathways.     

The double‐stranded ladder‐like structure of poly[[bis(μ2‐acetato‐κ2O:O′)bis(acetato‐κO)bis(μ‐4,4′‐bipyridine‐κ2N:N′)dicopper(II)] 4‐nitrophenol disolvate tetrahydrate]

The reaction of 4,4′‐bipyridine with copper acetate in the presence of 4‐nitrophenol led to the formation of the title compound, {[Cu(CH₃COO)₂(C₁₀H₈N₂)]·C₆H₅NO₃·2H₂O}_n. The complex forms a double‐stranded ladder‐like coordination polymer extending along the b axis. The double‐stranded polymers are separated by 4‐nitrophenol and water solvent molecules. The two Cu^II centres of the centrosymmetric Cu₂O₂ ladder rungs have square‐pyramidal coordination environments, which are formed by two acetate O atoms and two 4,4′‐bipyridine N atoms in the basal plane and another acetate O atom at the apex. The ladder‐like double strands are separated from each other by one unit‐cell length along the c axis, and are connected by the water and 4‐nitrophenol molecules through a series of O—H...O and C—H...O hydrogen‐bonding interactions and two unique intermolecular π–π interactions.