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Dominik Horinek

Publications and source records attributed to Dominik Horinek.

6 recordsLinked to original sources
PubMed2006

Interaction of carboranes with biomolecules: formation of dihydrogen bonds.

Noncovalent interactions of the polyhedral carborane 1-carba-closo-dodecaborane (CB(11)H(12))(-) with building blocks of biomolecules, modelled by glycine (GLY), serine (SER), phenylalanine (PHE), glutamic acid (GLU), lysine (LYS) and arginine (ARG), were investigated in vacuo by molecular dynamics simulations with the UFF empirical potential. Selected structures were further studied by accurate ab initio quantum chemical procedures. Interactions with a peptide bond (GLY-SER dipeptide) and a nucleic acid building block (guanine) were also considered. The RESP and NPA charges of carboranes and small model systems are compared and their use is discussed. The dominant interaction between carboranes and biomolecules is the formation of unconventional proton-hydride hydrogen bonds (dihydrogen bonds) characterized by a short distance between hydrogen atoms (as close as 1.8 A) and an average strength in the range of 4.2-5.8 kcal mol(-1). The total stabilization energy of complexes investigated is rather large, and the largest value (approximately 15 kcal mol(-1)) was found for the carborane complexes with ARG and the GLY-SER dipeptide. These interactions are ubiquitous under geometrical constraints influencing the strength of the interaction. The carborane forms dihydrogen bonds with biomolecules preferably with the hydrogen atoms of its lower hemisphere (i.e. the part of the cage opposite to the carbon atom). These two geometrical factors can be used to explain the specificity of inhibition of HIV protease by carboranes.

Biophysics↗
PubMed2006

How the stabilization of INK4 tumor suppressor 3D structure evaluated by quantum chemical and molecular mechanics calculations corresponds well with experimental results: interplay of association enthalpy, entropy, and solvation effects.

The folding free energy of the INK4c tumor suppressor core, consisting of 10 helices, was determined as the sum of gas-phase interaction enthalpy, gas-phase interaction entropy, and dehydration and hydration free energy. The interaction energy and the hydration free energy were determined using the nonempirical density functional theory (DFT) method, augmented by a dispersion-energy correction term, the semiempirical density-functional tight-binding method covering the dispersion energy, and the density functional theory/conductor-like screening model (DFT/COSMO) procedure, whereas the interaction entropy was calculated with the empirical Cornell et al. force field. Alternatively, all contributions were evaluated consistently using empirical methods. All the values of the interaction energy of helix pairs are stabilizing, and the dominant stabilizing terms stem from the London dispersion energy and, in the case of charged systems, the electrostatic energy. The stabilization energy of the core, determined as the difference of the energy of the core and 10 separate helices, amounts to approximately 450 kcal/mol. Systematically, the difference in the hydration free energy of a helix pair and its separate components is smaller in magnitude than the interaction energy, and it is negative for some pairs while positive for others. The average total free energy of a core formation amounts to -29.6 kcal/mol (yielded by scaled quantum-chemical methods) and +13.9 kcal/mol (resulting from empirical methods). These values are considerably smaller than their single components, which are dominated by the interaction energy. The computationally predicted interval encloses the experimental value of the folding free energy (-2.8 kcal/mol).

Amino Acid Motifs↗
PubMed2005

Surface-mounted altitudinal molecular rotors in alternating electric field: single-molecule parametric oscillator molecular dynamics.

Molecular dynamics simulations of the response to oscillating electric field elicited from an altitudinal dipolar molecular rotor mounted on the Au(111) surface and previously studied experimentally in static fields show unidirectional rotation in one of the three pairs of conformational enantiomers. The simulations are based on the universal force field and take into account electronic friction in the metal through its effect on the image charges. The rotor consists of two cobalt sandwich posts whose upper decks carry a biphenyl-like rotator with a dipole moment perpendicular to the rotation axle, mounted parallel to the surface. A phase diagram of rotor performance at 10 K as a function of field frequency and amplitude contains five unidirectional rotation regions: synchronous, half-synchronous (every other cycle skipped), quarter-synchronous (only indistinctly), asynchronous, and essentially no response. The nature of the subharmonic "single-molecule parametric oscillator" behavior is understood in mechanistic detail. Simulations at higher temperatures distinguish the thermal ("Brownian") and driven regimes of rotation, elucidated in terms of time-dependent potential energy surfaces for the rotation.

Journal Article↗
PubMed2004

Dipolar and nonpolar altitudinal molecular rotors mounted on an Au(111) surface.

We describe the preparation of a compound whose molecules consist of two metal sandwich stands carrying tentacles with affinity to metal surfaces and holding an axle that carries a dipolar or a nonpolar rotator. The dipolar rotor exists as three pairs of enantiomers, rapidly interconverting at room temperature. When mounted on a gold surface, each molecule represents a chiral altitudinal rotor, with the rotator axle parallel to the surface. The surface-mounted rotor molecules are characterized by several spectroscopic and imaging techniques. At any one time, in about one-third of the dipolar rotors the rotator is free to turn and the direction of its dipole can be flipped by the electric field applied by an STM tip, as revealed by differential barrier height imaging. Molecular dynamics calculations suggest that electric field normal to the surface causes members of one pair of enantiomers to rotate unidirectionally.

Journal Article↗
PubMed2003

Molecular dynamics simulation of an electric field driven dipolar molecular rotor attached to a quartz glass surface.

Molecular dynamics simulations of the response of a dipolar azimuthal 3-chloroprop-1-ynyl rotor mounted on the surface of quartz glass to a rotating electric field were performed. The rotor motion was classified as synchronous, asynchronous, random, or hindered, based on the value of the average lag of the rotor behind the field and a comparison of the intrinsic rotational barrier V(b) with kT. A phase diagram of rotor behavior was deduced at 10, 300, and 500 K as a function of field strength and frequency. A simple model for the rotor motion was developed, containing the driving force, the temperature, the height of the torsional barrier, and the friction constant of the rotor. Defining E(bo) to be the electric field strength necessary to get rotational response from the rotor ("breakoff field") and mu to be the rotor dipole moment component in the plane of rotation, we find that E(bo) is frequency independent when 2 microE(bo) is less than either V(b) or kT (the driving force needs to overcome the more important of the two, the intrinsic barrier or random thermal motion). At higher frequencies, E(bo) is a quadratic function of the frequency and the driving force fights friction, which is dictated by intramolecular vibrational redistribution (IVR) from the pumped rotational mode to all others. Fitting the simple model to simulation data, we derived a friction constant of 0.26 ps eV x (nu - 0.5)/THz between 500 and 1000 GHz.

Journal Article↗