Search results for "molecular dynamics"

Visualizing Solubilization by a Realistic Particle Model in Chemistry Education

2019

An application for the visualization of the mixing process of two different types of structureless interacting particles is presented. The application allows to demonstrate on a qualitative basis, as well as by quantitatively monitoring the time evolution of the fractions of aggregates of different sizes, that the formation of a homogeneous mixture is the result of favorable solute-solvent interactions as well as by temperature. It is suggested that, along with the use of suitable macroscopic examples, visualizations by the present application are useful in elucidating concepts related to miscibility/solubility. The application is based on a two-dimensional realistic dynamic model where ato…

Assessment of the Potential Energy Hypersurfaces in Thymine within Multiconfigurational Theory: CASSCF vs. CASPT2

2016

The present study provides new insights into the topography of the potential energy hypersurfaces (PEHs) of the thymine nucleobase in order to rationalize its main ultrafast photochemical decay paths by employing two methodologies based on the complete active space self-consistent field (CASSCF) and the complete active space second-order perturbation theory (CASPT2) methods: (i) CASSCF optimized structures and energies corrected with the CASPT2 method at the CASSCF geometries and (ii) CASPT2 optimized geometries and energies. A direct comparison between these strategies is drawn, yielding qualitatively similar results within a static framework. A number of analyses are performed to assess t…

Revised Atomistic Models of the Crystal Structure of C–S–H with high C/S Ratio

2016

Abstract The atomic structure of calcium-silicate-hydrate (C1.67–S–H x ) has been studied. Atomistic C–S–H models suggested in our previous study have been revised in order to perform a direct comparison of energetic stability of the different structures. An extensive set of periodic structures of C–S–H with variation of water content was created, and then optimized using molecular dynamics with reactive force field ReaxFF and quantum chemical semiempirical method PM6. All models show organization of water molecules inside the structure of C–S–H. The new geometries of C–S–H, reported in this paper, show lower relative energy with respect to the geometries from the original definition of C–S…

Molecular Dynamics Simulations of SFG Librational Modes Spectra of Water at the Water–Air Interface

2016

At the water–air interface, the hydrogen-bond network of water molecules is interrupted, and accordingly, the structure and dynamics of the interfacial water molecules are altered considerably compared with the bulk. Such interfacial water molecules have been studied by surface-specific vibrational sum-frequency generation (SFG) spectroscopy probing high-frequency O–H stretch and H–O–H bending modes. In contrast, the low-frequency librational mode has been much less studied with SFG. Because this mode is sensitive to the hydrogen-bond connectivity, understanding the librational mode of the interfacial water is crucial for unveiling a microscopic view of the interfacial water. Here, we compu…

Computational strategies for the design of new enzymatic functions

2015

In this contribution, recent developments in the design of biocatalysts are reviewed with particular emphasis in the de novo strategy. Studies based on three different reactions, Kemp elimination, Diels–Alder and Retro-Aldolase, are used to illustrate different success achieved during the last years. Finally, a section is devoted to the particular case of designed metalloenzymes. As a general conclusion, the interplay between new and more sophisticated engineering protocols and computational methods, based on molecular dynamics simulations with Quantum Mechanics/Molecular Mechanics potentials and fully flexible models, seems to constitute the bed rock for present and future successful desig…

Activity mediated phase separation: Can we understand phase behavior of the nonequilibrium problem from an equilibrium approach?

2016

We present results for structure and dynamics of mixtures of active and passive particles, from molecular dynamics (MD) simulations and integral equation theory (IET) calculations, for a physically motivated model. The perfectly passive limit of the model corresponds to the phase-separating Asakura-Oosawa model for colloid-polymer mixtures in which, for the present study, the colloids are made self-propelling by introducing activity in accordance with the well known Vicsek model. Such activity facilitates phase separation further, as confirmed by our MD simulations and IET calculations. Depending upon the composition of active and passive particles, the diffusive motion of the active specie…

The effect of temperature on the internal dynamics of dansylated POPAM dendrimers

2011

The internal and rotational dynamics of the dansylated poly(propylene amine) dendrimers (POPAM) have been studied by time correlated single photon counting (TCSPC) and molecular dynamics (MD) simulations. The hydrodynamic volumes of the dendrimer generations from G1 to G4 were estimated by fluorescence anisotropy data. Experiments and simulations suggest that the volume and the shape of the dendrimers are temperature dependent. At low temperatures the dendrimer structure becomes more spacious and rigid and back-folding of the individual branches is slowed down. For the G3 and G4 generations the temperature effects are much stronger than for the smaller G1 and G2 generations, where back-fold…

Does glycosyl transfer involve an oxacarbenium intermediate? Computational simulation of the lifetime of the methoxymethyl cation in water

2011

2D free-energy surfaces for transfer of the methoxymethyl cation between two water molecules are constructed from molecular dynamics (MD) simulations in which these atoms are treated quantum-mechanically within a box of 1030 classical solvent water molecules at 300 K. This provides a simple model for glycosyl transfer in water. The AM1/TIP3P surfaces with 2D-spline corrections at either MPWB1K/6-31+G(d,p) or MP2/6-31+G(d,p) contain a shallow free-energy well corresponding to an oxacarbenium ion intermediate in a DN*AN mechanism. MD analysis at three temperatures leads to a classical estimate of the lifetime of the methoxymethyl cation in water; when quantum corrections for vibrational zero-…

2021

We report on the thermodynamic, structural, and dynamic properties of a recently proposed deep eutectic solvent, formed by choline acetate (ChAc) and urea (U) at the stoichiometric ratio 1:2, hereinafter indicated as ChAc:U. Although the crystalline phase melts at 36–38 °C depending on the heating rate, ChAc:U can be easily supercooled at sub-ambient conditions, thus maintaining at the liquid state, with a glass–liquid transition at about −50 °C. Synchrotron high energy x-ray scattering experiments provide the experimental data for supporting a reverse Monte Carlo analysis to extract structural information at the atomistic level. This exploration of the liquid structure of ChAc:U reveals th…

Oxide/water interfaces: how the surface chemistry modifies interfacial water properties

2012

The organization of water at the interface with silica and alumina oxides is analysed using density functional theory-based molecular dynamics simulation (DFT-MD). The interfacial hydrogen bonding is investigated in detail and related to the chemistry of the oxide surfaces by computing the surface charge density and acidity. We find that water molecules hydrogen-bonded to the surface have different orientations depending on the strength of the hydrogen bonds and use this observation to explain the features in the surface vibrational spectra measured by sum frequency generation spectroscopy. In particular, 'ice-like' and 'liquid-like' features in these spectra are interpreted as the result o…