An insight into structure and stability of DNA in ionic liquids from molecular dynamics simulation and experimental studies

Molecular dynamics simulation and biophysical analysis were employed to reveal the characteristics and the influence of ionic liquids (ILs) on the structural properties of DNA. Both computational and experimental evidence indicate that DNA retains its native B-conformation in ILs. Simulation data show that the hydration shells around the DNA phosphate group were the main criteria for DNA stabilization in this ionic media. Stronger hydration shells reduce the binding ability of ILs' cations to the DNA phosphate group, thus destabilizing the DNA. The simulation results also indicated that the DNA structure maintains its duplex conformation when solvated by ILs at different temperatures up to 373.15 K. The result further suggests that the thermal stability of DNA at high temperatures is related to the solvent thermodynamics, especially entropy and enthalpy of water. All the molecular simulation results were consistent with the experimental findings. The understanding of the properties of IL–DNA could be used as a basis for future development of specific ILs for nucleic acid technology

Short-Range Order in Polyethylene Melts: Identification and Characterization

Experimental results by Fisher et al. [Faraday Discuss. Chem. Soc. 1979, 68, 26] showed the existence of local orientational correlations of segments of the <i>n</i>-alkane molecules in the liquid state. Since the estimated correlation volume is below 10³ ų, molecular dynamics simulations appear to be a suitable method for their identification and characterization. We used molecular dynamics to fully characterize short-range order in polyethylene melts. The characterization started by identifying sequences of aligned segments in chains, each one having at least one Kuhn monomer in length. Afterward, a search was made for interactions of a tagged aligned chain segment with others fulfilling the same condition, laying within a limiting separation distance (18 Å) and making a limiting orientation angle (40°). When, at least, four interactions are counted, a short-range ordered region is defined. Chain placement in these regions has similarities to that of the unit cell at the solid phase, although with different separation distances and angle. Overall, short-range order resembles a dynamic uniaxial nematic phase, the local order parameter increasing with the chain length in agreement with experimental results. Segments at the ordered regions persist over time, for times longer than the Rouse relaxation time of the chain. Those in random conformational sequences between the ordered regions have a mass distribution in agreement with the Flory distribution, with a number-average value comparable to experimental results for the molecular mass between entanglements

Solvation free energies in [bmim]-based ionic liquids: anion effect toward solvation of amino acid side chain analogues

Stochastic molecular dynamics simulations were performed to investigate the solvation free energy of 15 neutral amino acid side chain analogues in aqueous and five, 1-butyl-3-methylimidazolium ([BMIM])-based ionic liquids. The results in aqueous were found highly correlated with previous experimental and simulation data. Meanwhile, [BMIM]-based RTILs showed better solvation thermodynamics than water to an extent that they were capable of solvating molecules immiscible in water. Non-polar analogues showed stronger solvation in hydrophobic RTIL anions such as [PF6]− and [Tf2N]− while polar analogues showed stronger solvation in the more hydrophilic RTIL anions such as [Cl]−, [TfO]− and [BF4]−

Solvation free energies of nucleic acid bases in ionic liquids

<p>The solvation free energies of five nucleic acid bases in [C_nbim]Br (where <i>n</i> = 2, 4, 6) ionic liquids (ILs) were computed using the Bennett acceptance ratio (BAR) method employing molecular dynamics simulations. The computed free energies using BAR were in agreement with other methods. The large and negative predicted free energies of the bases in ILs indicated that the bases were better solvated in the ILs rather than in water. Hydrogen bonding interactions between polar sites of the bases and ILs’ ions significantly contributed to the solvation mechanism.</p

Generalised Kelvin contact models for DEM modelling of asphalt mixtures

Rigid particle models based on the discrete element method (DEM) have been adopted to model creep, fracture, and the viscoelastic behaviour of asphalt mixtures considering an irregular micro-structure and particle contacts. Within a DEM framework, the Burgers contact model, which is known to have a narrow frequency and temperature range, is usually adopted to model viscoelastic properties. In this study, a new explicit three-dimensional generalised Kelvin (GK) contact model formulation for the DEM model is proposed for asphalt materials. The model is implemented following two different methodologies (GK (Formula presented.) and GK (Formula presented.)). The models are validated in uniaxial tension-compression sinusoidal tests for predicting the dynamic modulus ((Formula presented.)) and phase angle (ϕ) of these composites at a frequency range of 1–10 Hz at (Formula presented.) C. Four mixtures are investigated based on the modelling of their mastic. The influence of the GK contact parameters on the dynamic response of mastics is assessed. Results show that (Formula presented.) has an important influence on both rheological properties and that (Formula presented.) can be used for small adjustments focussing on the predicted phase angle. Moreover, it is shown that a viscoelastic contact model should be adopted to simulate aggregate-to-mastic contacts in mixtures. As expected, the response obtained for both GK models is the same but the simulations with the GK (Formula presented.) are 14% faster. In addition, the response predicted with the proposed GK contact model is compared with the response predicted with a Burgers contact model. The DEM predictions obtained for the GK model are more accurate. For mastics, the average errors for (Formula presented.) and ϕ when adopting the GK model (Burgers) are 2.40% (3.46%) and 3.64% (4.17%), respectively. For mixtures, the average errors for (Formula presented.) for the GK model (Burgers) are 7.00% (7.92%). The proposed contact model greatly enhances the DEM ability to simulate the viscoelasticity of asphalt materials.This work is part of the research activity carried out at Civil Engineering Research and Innovation for Sustainability (CERIS) and has been funded by Fundacao para a Ciencia e a Tecnologia (FCT) in the framework of [project number UIDB/04625/2020]

Functional and conformational changes in the aspartic protease cardosin A induced by TFE

Conformational and functional changes of cardosin A, an aspartic protease of vegetal origin, in the presence of 2,2,2-trifluoroethanol (TFE), were assessed. TFE induced alterations of cardosin activity and conformation that differed with the solvent concentration. MD simulations showed that there are significant local alterations in protein flexibility and TFE molecules were found to replace several hydration molecules in the active site of the enzyme. This may explain some of the activity loss observed in the presence of TFE, especially at low TFE concentrations, as well as the recovery of enzyme activity upon aqueous dilution, indicating the release of the TFE molecules from the active site.publishe

Water Dependent Properties of Cutinase in Nonaqueous Solvents: A Computational Study of Enantioselectivity

The catalytic properties of enzymes in nonaqueous solvents are known to be dependent on the nature of the solvent. Here we present a molecular modeling study of the enantioselective properties of the enzyme cutinase in hexane under varying hydration conditions. Previous simulation studies have shown that for this model enzyme in hexane, the structural and dynamical properties are affected by the amount of water associated with the protein, being more similar to the aqueous simulation at 5–10% of water content. The implications of the hydration levels on the enzyme resolution of (R,S)-1-phenylethanol and (R,S)-2-phenyl-1-propanol are investigated using free energy calculations of the tetrahedral intermediate (TI) model. With this model system we show that the enzyme enantioselective properties are under the control of the amount of water present in the organic media. Maximum enantioselectivity is achieved at 10% water content. The stabilizing effects of the catalytic histidine on the TI are evaluated at different water contents and shown to be correlated. The correlation between the amount of water present in the media and the structural, dynamical, and thermodynamic properties of the enzyme are examined as well as the active site discriminative power

Short-Range Order in Polyethylene Melts: Identification and Characterization

Experimental results by Fisher et al. [Faraday Discuss. Chem. Soc. 1979, 68, 26] showed the existence of local orientational correlations of segments of the n-alkane molecules in the liquid state. Since the estimated correlation volume is below 10(3) angstrom(3), molecular dynamics simulations appear to be a suitable method for their identification and characterization. We used molecular dynamics to fully characterize short-range order in polyethylene melts. The characterization started by identifying sequences of aligned segments in chains, each one having at least one Kuhn monomer in length. Afterward, a search was made for interactions of a tagged aligned chain segment with others fulfilling the same condition, laying within a limiting separation distance (18 angstrom) and making a limiting orientation angle (40 degrees). When, at least, four interactions are counted, a short-range ordered region is defined. Chain placement in these regions has similarities to that of the unit cell at the solid phase, although with different separation distances and angle. Overall, short-range order resembles a dynamic uniaxial nematic phase, the local order parameter increasing with the chain length in agreement with experimental results. Segments at the ordered regions persist over time, for times longer than the Rouse relaxation time of the chain. Those in random conformational sequences between the ordered regions have a mass distribution in agreement with the Flory distribution, with a number-average value comparable to experimental results for the molecular mass between entanglements