Molecular Gating of an Engineered Enzyme Captured in Real Time.

Enzyme engineering tends to focus on the design of active sites for the chemical steps, while the physical steps of the catalytic cycle are often overlooked. Tight binding of a substrate in an active site is beneficial for the chemical steps, whereas good accessibility benefits substrate binding and product release. Many enzymes control the accessibility of their active sites by molecular gates.

Rydberg Molecules for Ion-Atom Scattering in the Ultracold Regime.

We propose a novel experimental method to extend the investigation of ion-atom collisions from the so far studied cold, essentially classical regime to the ultracold, quantum regime. The key aspect of this method is the use of Rydberg molecules to initialize the ultracold ion-atom scattering event. We exemplify the proposed method with the lithium ion-atom system, for which we present simulations of how the initial Rydberg molecule wave function, freed by photoionization, evolves in the presence of the ion-atom scattering potential.

Microporous Lead-Organic Framework for Selective CO Adsorption and Heterogeneous Catalysis.

A novel microporous metal-organic framework, {[Pb(μ-MTB)(HO)]·5DMF·HO} (1; MTB = methanetetrabenzoate and DMF = N,N'-dimethylformamide), was successfully synthesized by a solvothermal reaction and structurally characterized by single-crystal X-ray diffraction. The framework exhibits a unique tetranuclear [Pb(μ-COO)(μ-COO)(COO)(HO)] secondary building unit (SBU). The combination of the SBU with the tetrahedral symmetry of MTB results in a three-dimensional network structure, with one-dimensional jarlike cavities having sizes of about 14.

Effect of Ethanethiolate Spacer on Morphology and Optical Responses of Ag Nanoparticle Array-Single Layer Graphene Hybrid Systems.

Single layer graphene (SLG) and two-dimensional (2-D) plasmonic Ag nanoparticle arrays assembled by chemisorption of ethanethiol (ET) molecules (AgNPs-ET) were employed as components of two types of hybrid systems designed for surface-enhanced Raman scattering (SERS) spectral probing of SLG localized in the vicinity of plasmonic NPs. Both hybrids were characterized by optical microscopy, transmission electron microscopy (TEM), surface plasmon extinction (SPE), and SERS microRaman spectral measurements at four excitation wavelengths spanning the 445-780 nm range. SERS spectral probing of the glass/SLG/AgNPs-ET hybrid prepared by overdeposition of SLG on glass by the array of ET-modified Ag NPs has shown that the chemisorbed ET acts as an efficient molecular spacer between SLG and Ag NPs surface which, in turn, enabled to obtain SERS spectra of SLG unperturbed by doping or strain.

Interaction of Newly Platinum(II) with Tris(2-carboxyethyl)phosphine Complex with DNA and Model Lipid Membrane.

Structural properties of plasmid DNA and model lipid membrane treated with newly synthesized platinum(II) complex cis-[PtCl{P(CHCHCOOH)}] (cis-DTCEP for short) were studied and compared with effects of anticancer drug cisplatin, cis-[Pt(NH)Cl] (cis-DDP for short). Time Correlated Single Photon Counting Fluorescence Correlation Spectroscopy (TCSPC-FCS) was employed to study interactions between those platinum complexes and DNA. The TCSPC-FCS results suggest that bonding of cis-DTCEP derivative to DNA leads to plasmid strain realignment towards much more compact structure than in the case of cis-DDP.

A simple photoacoustic detector for highly corrosive gases.

In this work, we present a new design of a cantilever-type photoacoustic (PA) detector with high chemical resistance to be used for a broad range of gaseous samples including highly corrosive gasses. A thin mica cantilever used to sense the PA pressure is the only part that comes into direct contact with the sample gas as its deflection is sensed by a probe laser from outside of the gas cell. The design of the detector is simple, compact, and affordable.

A Pilot Study of Ion - Molecule Reactions at Temperatures Relevant to the Atmosphere of Titan.

Reliable theoretical models of the chemical kinetics of the ionosphere of Saturn's moon, Titan, is highly dependent on the precision of the rates of the reactions of ambient ions with hydrocarbon molecules at relevant temperatures. A Variable Temperature Selected Ions Flow Tube technique, which has been developed primarily to study these reactions at temperatures within the range of 200-330 K, is briefly described. The flow tube temperature regulation system and the thermalisation of ions are also discussed.

Nanocarbon Allotropes-Graphene and Nanocrystalline Diamond-Promote Cell Proliferation.

Two profoundly different carbon allotropes - nanocrystalline diamond and graphene - are of considerable interest from the viewpoint of a wide range of biomedical applications including implant coating, drug and gene delivery, cancer therapy, and biosensing. Osteoblast adhesion and proliferation on nanocrystalline diamond and graphene are compared under various conditions such as differences in wettability, topography, and the presence or absence of protein interlayers between cells and the substrate. The materials are characterized in detail by means of scanning electron microscopy, atomic force microscopy, photoelectron spectroscopy, Raman spectroscopy, and contact angle measurements.

Covalent Reactions on Chemical Vapor Deposition Grown Graphene Studied by Surface-Enhanced Raman Spectroscopy.

Graphene is a material of unmatched properties and eminent potential in disciplines ranging from physics, to chemistry, to biology. Its advancement to applications with a specific function requires rational design and fine tuning of its properties, and covalent introduction of various substituents answers this requirement. We challenged the obstacle of non-trivial and harsh procedures for covalent functionalization of pristine graphene and developed a protocol for mild nucleophilic introduction of organic groups in the gas phase.

A novel zinc(ii) metal-organic framework with a diamond-like structure: synthesis, study of thermal robustness and gas adsorption properties.

A solvothermal reaction of Zn(ii) salt with methanetetrabenzoic acid (H4MTB) and 1,4,8,11-tetraazacyclotetradecane (cyclam, CYC) created a new microporous metal-organic framework {[Zn2(μ4-MTB)(κ(4)-CYC)2]·2DMF·7H2O}n (DMF = N,N'-dimethylformamide). Single crystal X-ray diffraction showed that the complex exhibits a four-fold interpenetrated diamond-like structure topology with 1D jar-like channels with sizes about 14.1 × 14.

New cytotoxic butyltin complexes with 2-sulfobenzoic acid: Molecular interaction with lipid bilayers and DNA as well as in vitro anticancer activity.

New butyltin complexes with 2-sulfobenzoic acid: [Sn(C4H9)2{O3SC6H4COO-2}(H2O)]·(C2H5OH) (DBTsbz), [Sn(C4H9)3{O3SC6H4COOH-2}] (TBTsbz) and [Sn2(C4H9)6{μ-O3SC6H4COO-2}] (DTBTsbz) are very effective cytotoxic agents against tumor cells. The molecular interaction of these complexes with lipid membranes and DNA has been investigated. The IR spectra and changes of (1)H, (13)C chemical shifts suggest that SO3 and COO groups of 2-sulfobenzoato ligand interact with O atom of glycerin fragment of DPPC.

Multipurpose Nature of Rapid Covalent Functionalization on Carbon Nanotubes.

In the vast field of functionalization routes to carbon nanoforms, the fulfillment of such critical requirements as quick and nonharsh methods, good dispersibility, introduction of reactive groups, short reaction time, and low cost can be quite challenging. Traditional thermally induced diazonium chemistry on single-walled carbon nanotubes (SWCNTs) is revisited by using commercial anilines and providing useful insight into the versatility of this approach. Functionalized SWCNTs with multiple controllable features, such as degree (and ratio) of coverage, orthogonalization, doping, and high water dispersibility, are obtained by introducing benzenesulfonic acid and benzylamine moieties.

OH-stretch overtone of methanol: empirical assignment using a two temperature technique in a supersonic jet.

This paper describes a novel approach for empirical lower state assignments in complex high resolution ro-vibrational overtone spectra of molecules with low rotational constants and complex intramolecular dynamics. Methanol, CH3OH, was chosen as a representative of such molecules - it is an asymmetric top with two non-hydrogen nuclei and hindered internal rotation leading to dense and disordered rotational structure of vibrational overtone bands. We report the first rotationally resolved methanol spectra of the OH-stretch overtone 2ν1 band using sub-Doppler diode laser spectroscopy in a supersonic jet, and describe how the combination of two temperature analysis (TTA) and analysis by ground state combination differences (GSCDs) is used to reliably identify spectral lines that originate from lowest rotational states.

Site-specific analysis of protein hydration based on unnatural amino acid fluorescence.

Hydration of proteins profoundly affects their functions. We describe a simple and general method for site-specific analysis of protein hydration based on the in vivo incorporation of fluorescent unnatural amino acids and their analysis by steady-state fluorescence spectroscopy. Using this method, we investigate the hydration of functionally important regions of dehalogenases.

Reactions of State-Selected Atomic Oxygen Ions O(+)((4)S, (2)D, (2)P) with Methane.

An experimental study has been carried out on the reactions of state selected O(+)((4)S, (2)D, (2)P) ions with methane with the aims of characterizing the effects of both the parent ion internal energy and collision energy on the reaction dynamics and determining the fate of oxygen species in complex media, in particular the Titan ionosphere. Absolute cross sections and product velocity distributions have been determined for the reactions of (16)O(+) or (18)O(+) ions with CH4 or CD4 from thermal to 5 eV collision energies by using the guided ion beam (GIB) technique. Dissociative photoionization of O2 with vacuum ultraviolet (VUV) synchrotron radiation delivered by the DESIRS beamline at the SOLEIL storage ring and the threshold photoion photoelectron coincidence (TPEPICO) technique are used for the preparation of purely state-selected O(+)((4)S, (2)D, (2)P) ions.

The unimolecular chemistry of protonated and deprotonated 2,2-dinitroethene-1,1-diamine (FOX-7) studied by tandem mass spectrometry and computational chemistry.

2,2-Dinitroethene-1,1-diamine (FOX-7) was studied by means of electrospray ionization (ESI) and chemical ionization (CI) mass spectrometry in both positive and negative ion mode. Detailed mechanisms of unimolecular fragmentations of protonated and deprotonated FOX-7 were investigated using high- and low- energy collision-induced dissociation (CID) mass spectrometry, neutral fragment reionization mass spectrometry and quantum chemistry calculations. In deprotonated FOX-7, elimination of the carbodiimide molecule was identified as the energetically most favored fragmentation channel, closely resembling the base hydrolysis of FOX-7.

High-resolution adsorption analysis of pillared zeolites IPC-3PI and MCM-36.

The porous structure of pillared zeolites IPC-3PI and MCM-36 and their precursors IPC-3P and MCM-22P, respectively, has been investigated by means of a high-resolution adsorption analysis. The analysis was based on argon adsorption isotherms measured at 87 K from the relative pressure of 10(-6). The isotherms were processed by means of the t-plot method, which made it possible to distinguish adsorption in micropores from adsorption in mesopores.

Dynamics and hydration explain failed functional transformation in dehalogenase design.

We emphasize the importance of dynamics and hydration for enzymatic catalysis and protein design by transplanting the active site from a haloalkane dehalogenase with high enantioselectivity to nonselective dehalogenase. Protein crystallography confirms that the active site geometry of the redesigned dehalogenase matches that of the target, but its enantioselectivity remains low. Time-dependent fluorescence shifts and computer simulations revealed that dynamics and hydration at the tunnel mouth differ substantially between the redesigned and target dehalogenase.

Are time-dependent fluorescence shifts at the tunnel mouth of haloalkane dehalogenase enzymes dependent on the choice of the chromophore?

Time-dependent fluorescence shifts (TDFS) of chromophores selectively attached to proteins may give information on the dynamics of the probed protein moieties and their degree of hydration. Previously, we demonstrated that a coumarin dye selectively labeling the tunnel mouth of different haloalkane dehalogenases (HLDs) can distinguish between different widths of tunnel mouth openings. In order to generalize those findings analogous experiments were performed using a different chromophore probing the same region of these enzymes.

The effect of detergents on trimeric G-protein activity in isolated plasma membranes from rat brain cortex: correlation with studies of DPH and Laurdan fluorescence.

The effect of non-ionic detergents on baclofen (GABAB-R agonist)-stimulated G-protein activity was measured as a [(35)S]GTPgammaS binding assay in the plasma membranes (PM) isolated from the brain tissue. The effect was clearly biphasic--a decrease in the activity was followed by an activation maximum and finally, at high concentrations, drastic inhibition of the G-protein activity was noticed. Contrarily, specific radioligand binding to GABAB-receptor was inhibited in the whole range of detergent concentrations step by step, i.

Properties of mixed cationic membranes studied by fluorescence solvent relaxation.

The need for detailed biophysical description of cationic lipid membranes, which are commonly used as gene transfection vectors, led us to study the properties of mixed cationic/zwitterionic lipid bilayers. Fluorescence solvent relaxation measurements of 6-dodecanoyl-2-dimethylaminonaphthalene (Laurdan) incorporated in a membrane consisting of cationic dimyristoyltrimethylammoniumpropane (DMTAP) and zwitterionic dimyristoylphosphatidylcholine (DMPC) were performed. The obtained results are compared with a recently measured system consisting of dioleoyltrimethylammoniumpropane (DOTAP) and dioleoylphosphatidylcholine (DOPC) (Jurkiewicz et al.