Search results for "Biomolecules"
showing 10 items of 549 documents
Snapshots of a solid-state transformation: coexistence of three phases trapped in one crystal† †Electronic supplementary information (ESI) available:…
2016
Solvent extrusion leads to crystallographic–magnetic transition within a molecular complex via an intermediate that can be trapped and characterized.
HIGHLY EXCITED VIBRATIONAL STATES OF CYCLIC MOLECULES INVESTIGATED BY I.C.L.A SPECTROSCOPY WITH PHOTOACOUSTIC DETECTION
1991
The spectra of the fourth and fifth CH stretching overtones of cyclohexene and cyclopentene molecules and of some of their selectively deuterated derivatives have been measured by dye laser intracavity spectroscopy with photoacoustic detection. The intramolecular relaxation of the vibrational energy occurs principally through Fermi resonances with CH2 bending combinations in cyclohexene and through a coupling between the stretching and the ring puckering motions in cyclopentene.
Elastic properties of DNA linked flexible magnetic filaments.
2011
Elastic properties of magnetic filaments linked by DNA in solutions of univalent and bivalent salts with different pH values are investigated through their deformation in an external field. A strong dependence of the bending modulus in bivalent salt solution on the pH is shown. Experimental results are interpreted on the basis of the magnetic elastica.
Influence of Dynamics on The Analysis of Solid-State NMR Data From Membrane-bound Peptides
2009
By isotope labeling of membrane-bound peptides, typically with 2H, 19F, or 15N, solid-state NMR experiments can yield data from which the orientation of peptides in a native membrane environment can be determined. Such an orientation is defined by a tilt angle and an azimuthal rotation angle.Here we show that to obtain correct values of the orientation angles, it is important to include dynamics in the analysis of the NMR data. Nevertheless the effects of dynamics are different depending on the type of isotope labeling and NMR experiment considered.To analyze the influence of dynamics in detail, we generated virtual NMR observables using a model peptide undergoing explicit Gaussian fluctuat…
Homopolymer adsorption on periodically structured surfaces in systems with incommensurable lengths
2013
Surface-induced selective adsorption of homopolymers on a generic level is numerically analyzed for freely jointed chains (with a fixed bond length) whose monomers are attracted by the sites of regular periodic patterns. In particular, the behavior of the specific heat, the gyration tensor, and the bond order tensor are investigated as functions of the temperature. The properties of the transition are related to the interplay of the characteristic lengths. The adsorption proceeds in two steps for certain incommensurabilities of the bond length and the lattice constant. The corresponding adsorption mechanisms are elucidated by looking at the evolution of the inter bond angle distribution upo…
Difficulties of density functional theory in predicting the torsional potential of 2,2?-bithiophene
1998
The internal rotation of 2,2′-bithiophene was investigated within the density functional theory (DFT) approach. Fully optimized DFT torsional potentials are compared with Moller–Plesset (MP2) results which predict a fourfold potential with s-cis- and s-trans-gauche minima. DFT calculations fail in describing the energetics of the internal rotation because they favor planar vs. perpendicular conformers. Gradient-corrected functionals provide torsional potentials where the gauche minima have almost vanished and the s-ciss-trans interconversion barriers are twice as high as the barriers obtained at the MP2 level. The use of local functionals augments the shortcomings of the DFT approach. The g…
Mechanical unfolding pathway of a model β-peptide foldamer.
2015
Foldamers constructed from oligomers of β-peptides form stable secondary helix structures already for small chain lengths, which makes them ideal candidates for the investigation of the (un)folding of polypeptides. Here, the results of molecular simulations of the mechanical unfolding of a β-heptapeptide in methanol solvent revealing the detailed unfolding pathway are reported. The unfolding process is shown to proceed via a stable intermediate even for such a small system. This result is arrived at performing non-equilibrium force ramp simulations employing different pulling velocities and also using standard calculations of the potential of mean force, i.e., the free energy as a function …
How Well Can Coarse-Grained Models of Real Polymers Describe Their Structure? The Case of Polybutadiene
2015
Coarse-graining of chemical structure of macromolecules in the melt is investigated using extensive molecular dynamics simulation data which are based on a united atom force-field model of polybutadiene. Systematically increasing the number, n, of the united atoms approximated by an effective coarse-grained monomer, we study the influence of degree of coarse-graining on the structure functions such as the segment-segment intermolecular and intramolecular correlation functions. These results are compared to Monte Carlo simulations of the corresponding coarse-grained bead-spring model and Chen-Kreglewski potential for chain molecules. In contrast to the atomistic chemically realistic model of…
Single-molecule FRET studies of counterion effects on the free energy landscape of human mitochondrial lysine tRNA.
2011
The folding energy landscape of RNA is greatly affected by interactions between the RNA and counterions that neutralize the backbone negative charges and may also participate in tertiary contacts. Valence, size, coordination number, and electron shell structure can all contribute to the energetic stabilization of specific RNA conformations. Using single-molecule fluorescence resonance energy transfer (smFRET), we have examined the folding properties of the RNA transcript of human mitochondrial tRNA(Lys), which possesses two different folded states in addition to the unfolded one under conditions of thermodynamic equilibrium. We have quantitatively analyzed the degree of RNA tertiary structu…
Incoherent elastic and quasi-elastic neutron scattering investigation of hemoglobin dynamics.
2005
In this work we investigate the dynamic properties of hemoglobin in glycerolD(8)/D(2)O solution using incoherent elastic (ENS) and quasi-elastic (QENS) neutron scattering. Taking advantage of complementary energy resolutions of backscattering spectrometers at ILL (Grenoble), we explore motions in a large space-time window, up to 1 ns and 14 A; moreover, in order to cover the harmonic and anharmonic protein dynamics regimes, the elastic experiments have been performed over the wide temperature interval of 20-300 K. To study the dependence of the measured dynamics upon the protein quaternary structure, both deoxyhemoglobin (in T quaternary conformation) and carbonmonoxyhemoglobin (in R quater…