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Dominik Marx

Publications and source records attributed to Dominik Marx.

30 records · Page 2Linked to original sources
PubMed2004

Quantum and thermal fluctuation effects on the photoabsorption spectra of clusters.

A first principles approach for the calculation of photoabsorption cross sections of clusters and molecules is presented which includes both quantum and thermal fluctuations. The method relies on an ab initio path integral representation of the nuclear quantum motion in conjunction with time-dependent density-functional theory for electronic excitations. It is shown that quantum fluctuations of cold lithium clusters, such as Li8 below 50 K, affect significantly their photoabsorption spectra.

Journal Article↗
PubMed2004

Folding and unfolding of an elastinlike oligopeptide: "inverse temperature transition," reentrance, and hydrogen-bond dynamics.

The temperature-dependent behavior of a solvated oligopeptide, GVG(VPGVG), is investigated. Spectroscopic measurements, thermodynamic measurements, and molecular dynamics simulations find that this elastinlike octapeptide behaves as a two-state system that undergoes an "inverse temperature" folding transition and reentrant unfolding close to the boiling point of water. A molecular picture of these processes is presented, emphasizing changes in the dynamics of hydrogen bonding at the protein/water interface and peptide backbone librational entropy.

Elastin↗
PubMed2004

Temperature-dependent conformational transitions and hydrogen-bond dynamics of the elastin-like octapeptide GVG(VPGVG): a molecular-dynamics study.

A joint experimental/theoretical investigation of the elastin-like octapeptide GVG(VPGVG) was carried out. In this article a comprehensive molecular-dynamics study of the temperature-dependent folding and unfolding of the octapeptide is presented. The current study, as well as its experimental counterpart (see companion article in this issue) find that this peptide undergoes an inverse temperature transition (ITT), leading to a folding at approximately 40-60 degrees C. In addition, an unfolding transition is identified at unusually high temperatures approaching the normal boiling point of water. Due to the small size of the system, two broad temperature regimes are found: the ITT regime at approximately 10-60 degrees C and the unfolding regime at approximately T > 60 degrees C, where the peptide has a maximum probability of being folded at T approximately 60 degrees C. A detailed molecular picture involving a thermodynamic order parameter, or reaction coordinate, for this process is presented along with a time-correlation function analysis of the hydrogen-bond dynamics within the peptide as well as between the peptide and solvating water molecules. Correlation with experimental evidence and ramifications on the properties of elastin are discussed.

Biomimetic Materials↗
PubMed2003

Glycine on a wet pyrite surface at extreme conditions.

We present ab initio molecular dynamics (MD) simulations of the simplest amino acid, glycine, at the water/pyrite interface under extreme pressure/temperature conditions. These simulations are aimed to contribute to the discussion of the "iron-sulfur world" (ISW) scenario, an intriguing proposal in the controversial field of "Origin of Life" research. The simulations show that glycine easily desorbs from a water/pyrite interface through hydrogen-bond assistance. The retention time is only of the order of a picosecond, and the surface bonding is best understood as a relatively weak electrostatic interaction. However, we have found indications of glycine activation due to the interaction with the surface, and thus for a possible reaction with a suitable anchor molecule.

Journal Article↗
PubMed2003

Glycosidic bond formation in aqueous solution: on the oxocarbenium intermediate.

The mechanism of specific acid-catalyzed glycosidic bond formation between methanol and alpha-d-glucopyranoside in aqueous solution at 300 K was studied using Car-Parrinello molecular dynamics. The reaction was found to proceed through a non-solvent equilibrated oxocarbenium cation intermediate characterized by the loss of a hydrogen-bonding interaction between the ring oxygen and solvating water. The mechanism, which was found to be D(N)A(N) in nature, is discussed in detail.

Glycosides↗
PubMed2002

Fast anomalous diffusion of small hydrophobic species in water.

Using Car-Parrinello molecular dynamics a structural diffusion mechanism for the simplest hydrophobic species in water, an H atom, is proposed. The hydrophobic solvation cavity is a highly dynamical aggregate that actually drives, by its own hydrogen-bond fluctuations, the diffusion of the enclosed solute. This makes possible an anomalously fast diffusion that falls only short of that of "Grotthuss structural diffusion" of H+ in water. Here, the picture of a static, i.e., "iceberglike," clathrate cage is a misleading concept. The uncovered scenario is similar to the "dynamical hole mechanism" found in a very different context, that is, large molecules moving in hot polymeric melts.

Diffusion↗
PubMed2002

Pulling monatomic gold wires with single molecules: an Ab initio simulation.

Car-Parrinello molecular dynamics simulations demonstrate that pulling a single thiolate molecule anchored on a stepped gold surface does not preferentially break the sulfur-gold chemical bond. Instead, it is found that this process leads to the formation of a monoatomic gold nanowire, followed by breaking a gold-gold bond with a rupture force of about 1.2 nN. The simulations also indicate that previous single-molecule thiolate-gold and gold-gold rupture experiments both probe the same phenomenon, namely, the breaking of a gold-gold bond within a gold nanowire.

Journal Article↗
PubMed2002

Reassigning hydrogen-bond centering in dense ice.

Hydrogen bonds in H2O ice change dramatically upon compression. Thereby a hydrogen-bonded molecular crystal, ice VII, is transformed to an atomic crystal, ice X. Car-Parrinello simulations reproduce the features of the x-ray diffraction spectra up to about 170 GPa but allow for analysis in real space. Starting from molecular ice VII with static orientational disorder, dynamical translational disordering occurs first via creation of ionic defects, which results in a systematic violation of the ice rules. As a second step, the transformation to an atomic solid and thus hydrogen-bond centering occurs around 110 GPa at 300 K and no novel phase is found up to at least 170 GPa.

Freezing↗
PubMed2002

The nature and transport mechanism of hydrated hydroxide ions in aqueous solution.

Compared to other ions, protons (H(+)) and hydroxide ions (OH(-)) exhibit anomalously high mobilities in aqueous solutions. On a qualitative level, this behaviour has long been explained by 'structural diffusion' the continuous interconversion between hydration complexes driven by fluctuations in the solvation shell of the hydrated ions. Detailed investigations have led to a clear understanding of the proton transport mechanism at the molecular level. In contrast, hydroxide ion mobility in basic solutions has received far less attention, even though bases and base catalysis play important roles in many organic and biochemical reactions and in the chemical industry. The reason for this may be attributed to the century-old notion that a hydrated OH(-) can be regarded as a water molecule missing a proton, and that the transport mechanism of such a 'proton hole' can be inferred from that of an excess proton by simply reversing hydrogen bond polarities. However, recent studies have identified OH(-) hydration complexes that bear little structural similarity to proton hydration complexes. Here we report the solution structures and transport mechanisms of hydrated hydroxide, which we obtained from first-principles computer simulations that explicitly treat quantum and thermal fluctuations of all nuclei. We find that the transport mechanism, which differs significantly from the proton hole picture, involves an interplay between the previously identified hydration complexes and is strongly influenced by nuclear quantum effects.

Journal Article↗
PubMed2002

Nonadiabatic Car-Parrinello molecular dynamics.

An extension of Car-Parrinello (CP) molecular dynamics for efficient treatment of electronically nonadiabatic processes is presented. The current approach couples the S1 restricted open-shell Kohn-Sham excited state to the S0 ground state using a surface hopping scheme. Efficient evaluation of the nonadiabatic couplings is achieved by exploiting the available wave function time derivatives. Since the computational cost scales linearly with the number of excited states, the technique makes possible nonadiabatic ab initio simulations of systems of similar complexity to those typically studied by standard CP methods. It is thus ideally suited to study the photochemistry of large molecules, particularly in condensed phases.

Journal Article↗