Some basics for operating and analyzing data using the thickness shear mode resonator

The promises of obtaining meaningful measurements on physical systems loading the quartz crystal microbalance are extremely bright. The two aspects of this process, namely the gathering of faithful data and reductions of these data by way of modelling, need careful consideration to avoid some very common missteps which could frustrate this effort. The experimental techniques are emphasized here but a brief introduction to the basic methodologies of modelling is also given.     

Electrically induced deformation of giant liposomes monitored by thickness shear mode resonators

Thickness shear mode resonators are capable of registering small changes in the thickness and viscoelastic properties of ultrathin films attached to their surface. It was found that it is possible to monitor the deformation of surface-bound giant liposomes by applying an electric field with small amplitudes. Changes in the apparent height of attached vesicles in the nanometer range were easily detected as a function of lipid composition. Increasing the bending modulus by adding cholesterol results in a significantly reduced deformation from 16.8 nm (5% cholesterol) down to 3.2 nm (20% cholesterol), rendering this new method a robust and sensitive tool to detect the bending elasticity of liposomes on small length scales. Deformation could be further suppressed by adding anchor groups (biotinylated lipids), resulting in a strongly flattened liposome on an avidin-coated resonator.     

Bond rupture force measurement by means of a quartz resonator

Methods to measure the bond rupture force are considered. It is proposed to use a quartz resonator as an active element rather than simply a sensor. When the surface oscillation amplitude of an AT quartz resonator increases smoothly (rupture event scanning), a particle attached to the quartz surface is removed by inertial forces, and from their values it is easy to obtain the bond dissociation value. This procedure provides reliable measurements of the rupture force of about 10 pN. As the atomic force microscopy method, the rupture event scanning does not apply electromagnetic radiation, but has simpler instrumental set-up. The scanning requires minimum sample preparation, can be performed in various media (vacuum, air, liquid), and takes only a few minutes.     

A simple method of determining copolymerization reactivity ratios by means of a computer

A Fortran IV program for determining copolymerization reactivity ratios is proposed. The program is based on the curve-fitting method and has the advantage of delivering values free of personal judgement. To check its validity the system benzylacrylate (BeA)/methylmethacrylate (MMA) was investigated. The reactivity ratios obtained from the Fineman-Ross plots (r₁ = 0 · 34 ± 10 per cent and r₂ = 1 · 7 ± 10 per cent) are in good agreement with values obtained by using the proposed method (r₁ = 0 · 36 and r₂ = 1 · 78).     

A thin liquid film thickness shear mode bulk acoustic wave sensor for determination of Proteus mirabilis

A thickness shear mode bulk acoustic wave sensor coated with a thin liquid culture medium film was developed and applied to determine the concentration of Proteus mirabilis (P. mirabilis). Experiments demonstrated that there was a good linear relationship between the turning point time and the logarithm of the P. mirabilis concentration in the range 2.0 x 10(2)-2.0 x 10(6) cells ml(-1). The detection was fast and accurate because of the sharp turning point of the response due to the thin culture film on the sensor surface. Other problems concerning the experiments are discussed in detail.     

Construction of spatial molecular models by means of a computer

Journal of Structural Chemistry -     

Effects of surface heterogeneity of carbon nanotubes in adsorption of colloid nanoparticles studied by means of computer simulations

This work deals with a construction of an implicit solvent model which can be used in molecular dynamics simulations of systems comprising colloid nanoparticles and carbon nanotubes. Such systems, due to finite sizes of both components, cannot be accurately approximated by a smaller slab geometry and thus represent a particularly difficult case in terms of computer simulations. Adsorption of large colloid nanoparticles on the surfaces of carbon nanotubes were studied and we determined the adsorption energy profiles of the nanoparticles on the carbon nanotubes surfaces. We also determined the adsorption isotherms which help to understand a preferred location of the nanoparticles on the nanotubes surfaces.     

Structures of neat and hydrated 1-octanol from computer simulations

Molecular dynamics computer simulations of 1-octanol and its mixtures with water have been performed. The liquid is composed of regions enriched in either hydrocarbons or hydroxyl groups. In neat octanol, the hydroxyl groups form clusters of long, thin chains. Upon the addition of water, the clusters become longer and more spherical, forming a structure that can be described as consisting of "overlapping elongated inverse micelles". The structures of the mixtures obtained at different hydration levels are consistent with those of experimental diffraction studies of water/octanol mixtures and previous computer simulations of neat and water-saturated octanol. The saturation point of the model has been calculated using the cavity-bias particle insertion method. The solubility of water in octanol is slightly too low compared to experimental results, and suggestions for possible improvements to the force field are made.     

An unexpected bonding interaction between dxy and a1u orbitals mediated by porphyrin deformation

Through density functional calculation and NMR spectroscopy, an unusual intermediate-spin electronic structure (d(xz)d(yz))3(d(xy))1(d(z)2)1 has been assigned to the six-coordinate saddled [Fe(OETPP)(THF)2]+ complex instead of the corresponding ruffled [Fe(TiPrP)(THF)2]+ complex.     

Study of the interaction of GFG tripeptide with cesium perfluorooctanoate micelles by means of NMR spectroscopy and MD simulations

The interaction of glycyl-phenylalanyl-glycine (GFG) with bilayers formed by cesium perfluorooctanoate (CsPFO) in water was investigated in the isotropic phase by means of 1H NMR and molecular dynamics (MD) simulations. Details on the preferential location of the different residues of GFG were obtained from selective variations of chemical shift with peptide concentration and of line width in the presence of the paramagnetic ion Mn2+. The analysis of 1H NMR spectra recorded at different concentrations and temperatures allowed the association constant and the enthalpy change upon binding to be evaluated. MD simulations highlighted the hydrogen bonds formed between the different GFG functional groups and the micelle. Both NMR and MD gave indications of high affinity of GFG with the micelle, with the N-terminal residue anchoring on the surface via hydrogen bonds with the micelle COO(-) groups.     

A GRID-derived water network stabilizes molecular dynamics computer simulations of a protease

Structural water molecules are crucial for the stability and function of proteins. Recently, we presented a molecular dynamics (MD) study on blood coagulation factor Xa (fXa) to investigate the effect of water molecules on the flexibility of the protein structure. We showed that neglecting important water positions at the outset of the simulation leads to severe structural distortions during the MD simulations: A stable trajectory was obtained with a water set that was derived from all 73 X-ray structures of the protein. However, for many proteins of interest, only limited structural data is available, which precludes the merging of information from many X-ray structures. Here, we show that an in silico assembled water network, derived from molecular interaction fields generated with the GRID program, is a viable alternative to X-ray data. MD simulations with the GRID water set show a significantly improved stability over alternative setups without water or the X-ray resolved water molecules in the starting structure. The performance is comparable to a water setup derived from a recently presented clustering approach.     

Specific search for heterocycles for cyanine dyes by means of a computer

A method for the selection by means of a computer of terminal heterocyclic groups for cyanine dyes that absorb over a predesignated spectral range is described. New monoazaheterocycles, the introduction of which into the compositions of cyanine dyes as terminal groups should ensure absorption in the near-IR region of the spectrum, are presented as examples.Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 2, pp. 217–222, February, 1984.     

Thermal study of fast reactions by means of apparatus connected directly to a computer

An automated system of thermal analysis is described for the study of fast exothermic reactions (intensive burning, self-inflammation, transition from the non-equilibrium state to the equilibrium state, etc.). The system includes a complex of technical means for connecting the measuring instrument with the computer (hardware), and a special mathematical supply (software).The use of this system provides data required for thermal and chemical calculations in the high-temperature range.Two examples of DTA data-processing are presented.

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Zusammenfassung Ein automatisches Thermoanalyse-System zum Studium schneller exothermer Reaktionen (intensives Brennen, Selbstzündung, Übergang vom Nicht-Gleichgewichtszustand in den Gleichgewichtszustand usw.) wird beschrieben. Das System enthält eine Reihe technischer Vorrichtungen zur Verbindung des Meßgerätes mit dem Komputer und dem speziellen mathematischen Apparat.Die Anwendung dieses Systems ermöglicht die Ermittelung von Daten, welche zu thermischen und chemischen Berechnungen im Hochtemperatur-Bereich nötig sind.Zwei Beispiele der DTA-Datenverarbeitung werden gegeben.

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Résumé On décrit un système automatique d'analyse thermique pour l'étude de réactions exothermiques rapides (combustion intense, autoinflammation, transition de l'état de nonéquilibre à celui d'équilibre, etc....). Le système comprend un ensemble de moyens techniques pour coupler l'instrument de mesure à l'ordinateur et à l'appareillage mathématique spécial.L'utilisation de ce système permet d'obtenir les données nécessaires aux calculs des effets thermiques et chimiques dans le domaine des températures élevées.On présente deux exemples du traitement des données de l'ATD.

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Self-organization and pattern formation of janus particles in two dimensions by computer simulations

The phase behavior and associated pattern formation of two-dimensional systems of hard disks decorated with amphiphilic coronae (Janus disks) are studied by means of Monte Carlo computer simulations. A primitive interaction potential that captures the essential interparticle interactions is introduced. Despite its simplicity, the system exhibits a very rich phase polymorphism. Apart from the isotropic phase and depending upon the coronal thickness, the simulated systems self-organize in a number of two-dimensional mesophases of various symmetries exhibiting a variety of novel patterns. The results of these simulations suggest that 2D Janus particles are promising candidates for bottom-up design of precise two-dimensional templates.     

Excitation of the shear horizontal mode in a monolayer by inelastic helium atom scattering

Inelastic scattering of a low-energy atomic helium beam (HAS) by a physisorbed monolayer is treated in the one-phonon approximation using a time-dependent wave packet formulation. The calculations show that modes with shear horizontal polarization can be excited near high symmetry azimuths of the monolayer, in agreement with recent experiments. The parameters of the calculations are chosen to match the conditions of HAS experiments for triangular incommensurate monolayer solids of xenon, krypton, and argon adsorbed on the (111) face of platinum, and the results show many of the systematic experimental trends for relative excitation probability of the shear horizontal and longitudinal acoustic phonon branches. The inelastic scattering at beam energies near 8 meV is exceedingly sensitive to small misalignment between the scattering plane and the high symmetry directions of the monolayer solid. The diffraction and inelastic processes arise from a strong coupling of the incident atom to the target and the calculated results show large departures from expectations based on analogies to inelastic thermal neutron scattering.     

A combination of solid-state NMR and MD simulations reveals the binding mode of a rhomboid protease inhibitor

Intramembrane proteolysis plays a fundamental role in many biological and pathological processes. Intramembrane proteases thus represent promising pharmacological targets, but few selective inhibitors have been identified. This is in contrast to their soluble counterparts, which are inhibited by many common drugs, and is in part explained by the inherent difficulty to characterize the binding of drug-like molecules to membrane proteins at atomic resolution. Here, we investigated the binding of two different inhibitors to the bacterial rhomboid protease GlpG, an intramembrane protease characterized by a Ser–His catalytic dyad, using solid-state NMR spectroscopy. H/D exchange of deuterated GlpG can reveal the binding position while chemical shift perturbations additionally indicate the allosteric effects of ligand binding. Finally, we determined the exact binding mode of a rhomboid protease-inhibitor using a combination of solid-state NMR and molecular dynamics simulations. We believe this approach can be widely adopted to study the structure and binding of other poorly characterized membrane protein–ligand complexes in a native-like environment and under physiological conditions.

Proton-detected solid-state NMR in combination with molecular docking and molecular dynamics (MD) simulations allow the study of rhomboid protease inhibition under native-like conditions.     

Development of a thickness shear mode acoustic sensor based on an electrosynthesized molecularly imprinted polymer using an underivatized amino acid as the template

The preparation and characterization of electrosynthesized poly(o-phenylenediamine) (iPoPD) as a molecular imprinting material were studied by an in situ quartz crystal impedance method. The changes of delta f0, delta R1, delta L1 and delta C0 suggest that the polymer film was compact and rigid. The thickness shear mode (TSM) acoustic sensor modified with this material exhibits molecular recognition ability to the template molecule of DL-phenylalanine. In the range 2-20 mM, a linear relationship between the frequency shift delta f0 and logC was found from the calibration graph. Scatchard analysis of the relevant calibration graph offers information on the equilibrium of the binding interaction and the recognition sites. Using this electropolymerization technology, the preparation of the sensor was very simple and the reproducibility of preparation was very good. In particular, it offers possibilities for sensor miniaturization.