Lorenzo Gontrani

Structural properties of 1-alkyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}amide ionic liquids: X-ray diffraction data and molecular dynamics simulations.

X-ray diffraction data for 1-alkyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}amides are reported as a function of the length of the alkyl chain on the imidazolium ring. The measured diffraction patterns have been compared with the theoretical patterns calculated (from the geometries obtained) with molecular dynamics simulations. This provides a detailed description (at the atomistic level) of the morphology in the liquid state of these salts, highlighting the role played by the alkyl chain length. An analysis of the behavior of the hydrogen bonds that are formed between the imidazolium acidic protons and the anion is presented.

Glycine and alanine: a theoretical study of solvent effects upon energetics and molecular response properties

Abstract In the present work, we show that polarisable continuum model is able to reproduce the stability of zwitterionic forms of amino acids alanine and glycine in water solution at B3-LYP/6-31G (d) level of theory. The model is then extended to the calculation of vibrational frequencies, Vibrational circular dichroism spectra and nuclear magnetic resonance chemical shifts. The agreement with experimental data is good, except in the case of vibrations where specific hydrogen bond interactions are involved. In the latter case, a supermolecular approach may help in the predictions of some vibrational frequencies of the groups which form hydrogen bonds.

Liquid Structure of Trihexyltetradecylphosphonium Chloride at Ambient Temperature: An X-ray Scattering and Simulation Study

We report on an experimental and simulation study done on a representative room temperature ionic liquid, namely tetradecyltrihexylphosphonium chloride, at ambient conditions. The study was conducted using small and wide angle X-ray scattering and molecular dynamics simulations. Both approaches converge in indicating that this material is characterized by the existence of strong P-Cl interactions (with characteristic distances between 3.5 and 5.0 A) and by the occurrence of nanoscale segregation, despite the symmetric nature of the cation and similarly to other room temperature ionic liquids. A good agreement is found between the structure factor and pair correlation functions obtained from MD simulations and the corresponding experimental observables, thus strongly validating the interaction potential used in the simulations.

Liquid structure of 1-alkyl-3-methylimidazolium-hexafluorophosphates by wide angle x-ray and neutron scattering and molecular dynamics

We report for the first time joined energy dispersed x-ray and neutron diffraction experiments on a series of (both protiated and selectively deuteriated) 1-alkyl-3-methylimidazolium hexafluorophosphate salts (alkyl = butyl, hexyl, octyl) at ambient conditions. The x-ray experimental data are used to optimize the interaction potential used for running molecular dynamics simulations on these systems. Such a potential leads to a good description of neutron scattering data from the samples without additional refinement, thus further validating the potential definition. The molecular dynamics simulations were used to access microscopic information on the morphology of the proposed systems, thus probing the role played by alkyl chain length on the structure. The comparison of x-ray weighted and neutron-weighted computed diffraction patterns allows the rationalization of several diffraction features. Further insight into cation-anion coordination and alkyl chain conformational equilibrium is provided on the basis of the MD-derived snapshots, confirming and extending previously obtained results on these issues.

The interpretation of diffraction patterns of two prototypical protic ionic liquids: a challenging task for classical molecular dynamics simulations.

In this study, we discuss the performance of classical molecular dynamics in predicting the experimental X-ray diffraction patterns of liquid ethylammonium nitrate (one of the simplest protic room-temperature ionic liquid showing amphiphilic behavior) and of its hydroxy derivative (2-ethanolammonium nitrate, 2-HOEAN). Newly recorded energy-dispersive X-ray diffraction structure factors are compared with the corresponding quantities extracted from molecular dynamics simulations. Other useful theoretical and experimental indicators are used as a probe of the local structure of the title ionic liquids. We shall show that the use of a general purpose, two-body terms only, force field, such as OPLS/AA is able to describe most of the structural experimental data. However, we shall also point out that an improved description of some key structural features observed in the X-ray radial distribution function, can be obtained very easily by adding a general three-body potential energy term instead of changing the two-body potential parameters, in order to optimize the agreement with experimental data. This three-body term turns out to be naturally able to describe the complex polarization effects due to hydrogen bonding without requiring a quanto-mechanical treatment or a polarizable force field. In addition the present model turns out to be able to account for the presence of a low-Q peak in the scattering patterns of EAN, which has been commonly interpreted as a manifestation of the amphiphilic nature of this compound.

An energy dispersive x-ray scattering and molecular dynamics study of liquid dimethyl carbonate

In this work, we report on the first x-ray diffraction study on liquid dimethyl carbonate. Diffraction spectra were collected with an energy-dispersive instrument, whose wide Q-range allows the structure determination of weakly ordered systems (such as liquids). The structural correlation in this liquid ranges up to about 20 A. The observed patterns are interpreted with a structural model derived from classical molecular dynamics simulations. The simulations were run using OPLS force field, only slightly modified to restrain bond distances to the experimental values. The model structure function and radial distribution functions, averaged among the productive trajectory frames, are in very good agreement with the corresponding experimental ones. Molecular dynamics results show that the deviations from C(2v) cis-cis structure, predicted by ab initio calculations and observed by electron diffraction in the gas phase, are small. By analyzing the intra- and intermolecular pair distribution functions, it was possible to assign the peaks of the experimental radial distribution function to specific structural correlations, and to compute the different average intermolecular coordination numbers. The intermolecular methyl-carbonyl oxygen distance is thoroughly discussed to assess the presence of weak C-H...O hydrogen bonds.

Hydrogen bonding in barbituric and 2-thiobarbituric acids: a theoretical and FT-IR study

Abstract The effects of intermolecular hydrogen bonding on the molecular properties of barbituric acid (BA) and thiobarbituric acid are discussed on the basis of density functional theory calculations. B3LYP methods were applied to monomers and cyclic dimers. Trimer and hexamer of BA were studied as examples where several CO and NH groups are involved in hydrogen bonding. The theoretical IR spectra of monomers and all oligomers here considered are compared with the FT-IR spectra measured in Ar and nitrogen matrices at different concentrations.

UV-Vis Spectra of the Anticancer Campothecin Family Drugs in Aqueous Solution: Specific Spectroscopic Signatures Unraveled by a Combined Computational and Experimental Study

The ultraviolet-visible absorption spectrum of camptothecin (CPT) has been been recorded in aqueous solution at pH 5.3, where the equilibrium among the different CPT forms is shifted toward the lactonic one. Time-dependent density functional theory (TD-DFT) computations lead to a remarkable reproduction of the experimental spectrum only upon addition of explicit water molecules in interaction with specific moieties of the camptothecin molecule. Molecular dynamics (MD) simulations enforcing boundary periodic conditions for CPT embedded with 865 water molecules, with a force field derived from DFT computations, show that the experimental spectrum is due to the contributions of CPT molecules with different solvation patterns. A similar solvent effect is observed for several CPT derivatives, including the clinically relevant SN-38 and topotecan drugs. The quantitative agreement between TD-DFT/MD computations and experimental data allow us to identify specific spectroscopic signatures diagnostic of the drug environment and to develop procedures that can be used to monitor the drug-DNA/protein interaction.

Liquid structure of 1-ethyl-3-methylimidazolium alkyl sulfates by x-ray scattering and molecular dynamics

We report a joined X-ray diffraction and molecular dynamics study on the series of 1-ethyl-3-methylimidazolium alkyl sulfates (alkyl = ethyl, butyl, hexyl, octyl) ionic liquids. A general good agreement between experimental and theoretical structure functions has been found for each term of the series in all ranges of q values. Once the quality of the employed force field in reproducing structural data was tested, we used dynamics simulations to access information on morphology and properties of these systems. The series of ionic liquids presents nanoscale structural heterogeneity, whose size depends on the anion alkyl chain size. Analyzing our simulation data on the basis of alkyl chain length, we propose a structural model consistent with the presence of low q peaks.

NMR Investigation of Imidazolium-Based Ionic Liquids and Their Aqueous Mixtures

(1)H and (13)C NMR spectroscopy is employed to investigate the interaction of water with two imidazolium-based ionic liquids (ILs), 1-hexyl-3-methylimidazolium bromide ([C(6)mim]Br) and 1-octyl-3-methylimidazolium bromide ([C(8)mim]Br), at IL concentrations well above the critical aggregation concentration (CAC). The results are compared with those of the neat samples. To this aim, a detailed analysis of the changes in the (1)H chemical shifts, (13)C relaxation parameters, and 2D ROESY data due to the presence of water is performed. The results for both neat ILs are consistent with a packed structure where head-to-head, head-to-tail, and tail-to-tail contacts occur and where the site of maximal mobility restriction is at the polar head. At the lowest investigated water content, the presence of water influences mainly the environment around the IL polar head, slowing down the motional dynamics of the aromatic ring with respect to the alkyl chain. At higher water contents this difference diminishes, the motional freedom of the whole molecule increasing. The presence of ROESY cross-peaks between protons in the polar and apolar IL regions, as well as between protons in non-neighboring alkyl groups, at all investigated water contents suggests that the alkyl tails are not fully segregated in hydrophobic domains, as expected for micelle-like structures.