We estimated the accuracy of the theoretical predictions for the structure of liquid n-butanol resulting from the model calculations implemented by various force fields: GROMOS96-54a7, CHARMM27, OPLS-AA, AMBER03, and TraPPE-UA. For this purpose we performed extensive molecular dynamic simulations of model alcohol and measurements of small- and wide-angle X-ray scattering of liquid n-butanol. Utilizing the Complemented system approach method developed for the calculation of X-ray scattering from simulation data scattering intensities of model n-butanol resulting from simulations were calculated and compared to the experimental scattering data. The simulation results show that all the tested models reproduce the basic characteristics of the experimental scattering curves of n-butanol. However, minor qualitative to considerable quantitative discrepancies in the shape of the scattering functions referring to different force fields are still observed and assigned to different model parametrizations. Simulation results were presented and discussed also via the radial and spatial distribution functions and through the H-bonding data.
COBISS.SI-ID: 1537336771
A detailed data analysis utilizing the string-of-beads model was performed on experimental small-angle X-ray scattering data in a targeted structural study of three very important industrial polysaccharides. The results demonstrate the quality of performance for this model on three polymers with quite different thermal structural behavior. Furthermore, they show the advantages of the model used by way of excellent fits in the ranges where the classic approach to the small-angle scattering data interpretation fails and an additional 3D visualization of the model’s molecular conformations and anticipated polysaccharide supramolecular structure. The importance of this study is twofold: firstly, the methodology used and, secondly, the structural details of important biopolymers that are widely applicable in practice.
COBISS.SI-ID: 1537414339
We introduce a statistical mechanical model (CageWater) of water's hydrogen bonding and Lennard-Jones interactions. It predicts the energetic and volumetric and anomalous properties accurately. Yet, because the model is analytical, it is essentially instantaneous to compute. This model advances our understanding beyond current molecular simulations and experiments.
COBISS.SI-ID: 1538049987
We performed structural and rheological studies of terminal 1,n-diols from ethane-1,2-diol to pentane-1,5-diol using a combination of the experimental small- and wide-angle x-ray scattering (SWAXS) technique and theoretical TraPPE-UA force-field model-based molecular dynamics (MD) simulations. Our well-established complemented-system approach was used to calculate the SWAXS intensities from the simulation data needed to validate the accuracy of the theoretical results by comparing them with the experimental SWAXS data. Next, a simulated analogue of the contrast-matching method was used to reveal the supra-molecular structural details of the studied diols, which were then further discussed in a comparison with those of the basic primary mono-ols from our previous study (Tomšič M., et al., 2007). This revealed the important structural differences arising from the influence of an additional –OH group in the molecule and an increasing diol alkyl chain length. The additional –OH group enhances the H-bonding and leads to a more compact supra-molecular structure that is increasingly locally inhomogeneous with an increasing diol alkyl chain length. Furthermore, the shear-rate-dependent viscosities were calculated for the modelled 1,n-diols using the non-equilibrium MD periodic perturbation method and the extrapolated zero-shear viscosities were compared with the experimental data. In this way we directly related the effect of the structure to the viscosity of diols. Allowing the modelled system to occupy a higher degree of stretched molecular conformations was in turn reflected in the greatly increased viscosity of the system. Terminal 1,n-diols exhibit much higher viscosities than the basic mono-ols due to a more rigid cross-linking between the sequentially H-bonded OH-aggregates in the system.
COBISS.SI-ID: 1538077635
A statistical model was developed which describes the thermal and volumetric properties of water-like molecules. A molecule is presented as a three-dimensional sphere with four hydrogen bonding arms. Each water molecule interacts with its neighboring waters through a van der Waals interaction and an orientation-dependent hydrogen bonding interaction. This model, which is largely analytical, is a variant of a model developed before for a two-dimensional Mercedes- Benz model of water. Properties such as molar volume, density, heat capacity, thermal expansion coefficient, and isothermal compressibility were explored as a function of temperature and pressure. It was found that the volumetric and thermal properties follow the same trends with temperature as in real water and are in good general agreement with Monte Carlo simulations, including the density anomaly, the minimum in the isothermal compressibility, and the decreased number of hydrogen bonds upon increasing the temperature.
COBISS.SI-ID: 1537232067