Sandro L. Fornili

Water interaction with α,α-trehalose: molecular dynamics simulation

This paper reports on simulations of a rather large water–trehalose system, based on the AMBER compatible GLYCAM force-field (R. J. Woods, R. A. Dwek, C. J. Edge and B. Fraser-Reid, J. Phys. Chem., 1995, 99, 3832), whose applicability to trehalose has been carefully examined using abinitio quantum mechanical calculations to optimize the molecular geometry and to evaluate the net atomic charges. Statistical analyses of the simulation trajectories show that the structure and dynamics of the solvent are remarkably affected by the presence of trehalose. In particular, ca. 36 water molecules are found to reside in the first hydration shell, 19 of which are hydrogen bonded to trehalose. The water mobility within the first hydration shell is ca. 25% smaller than that of pure water.

Molecular dynamics simulation of aqueous solutions of trimethylamine-N-oxide and tert-butyl alcohol

In this work we have investigated hydration properties of aqueous solutions up to a solute molar fraction X2 = 0.125 of two isosteric molecules – the bioprotectant trimethylamine-N-oxide (TMAO) and the denaturant tert-butyl alcohol (TBA) – using molecular dynamics simulation at 298 K. Statistical analyses of the trajectories show in particular that as the solute concentration increases the number of the water molecules in the first hydration shell decreases uniformly for TMAO, while for TBA it decreases more rapidly in a concentration range where experiments indicate that TBA starts to self-aggregate. No appreciable solute segregation occurs for TMAO even in the most concentrated solution, where on the average each water molecule is shared by two solutes. This result parallels what has been recently found for glycine betaine, an organic osmolyte closely related to TMAO.

Molecular Dynamics Simulation of Aqueous Solutions of 26-Unit Segments of p(NIPAAm) and of p(NIPAAm) “Doped” with Amino Acid Based Comonomers

We have performed 75-ns molecular dynamics (MD) simulations of aqueous solutions of a 26-unit NIPAAm oligomer at two temperatures, 302 and 315 K, below and above the experimentally determined lower critical solution temperature (LCST) of p(NIPAAm). We have been able to show that at 315 K the oligomer assumes a compact form, while it keeps a more extended form at 302 K. A similar behavior has been demonstrated for a similar NIPAAm oligomer, where two units had been substituted by methacryloyl-l-valine (MAVA) comonomers, one of them being charged and one neutral. For another analogous oligomer, where the same units had been substituted by methacryloyl-l-leucine (MALEU) comonomers, no transition from the extended to the more compact conformation has been found within the same simulation time. Statistical analysis of the trajectories indicates that this transition is related to the dynamics of the oligomer backbone, and to the formation of intramolecular hydrogen bonds and water-bridges between distant units of the solute. In the MAVA case, we have also evidenced an important role of the neutral MAVA comonomer in stabilizing the compact coiled structure. In the MALEU case, the corresponding comonomer is not equally efficacious and, possibly, is even hindering the readjustment of the oligomer backbone. Finally the self-diffusion coefficient of water molecules surrounding the oligomers at the two temperatures for selected relevant times is observed to characteristically depend on the distance from the solute molecules.

Ab initio study on the photoisomers of a nitro-substituted spiropyran

Structural and spectroscopic properties of the photoisomers of a nitro-substituted spiropyran have been investigated by performing ab initio molecular orbital (MO) calculations both in vacuo and in hexafluoro-2-propanol solution. Full geometry optimisation of the closed form and of the transoid conformations of the open form has been carried out. Dipole moments of both photoisomers have been determined, the ratio of which agrees with recent experimental results. Net atomic charges have also been determined according to three different approaches.

A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates in vacuo

Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and n(c) additional sodium ions, i.e. [AOT(n)Na(n+n(c))](n(c)), have been investigated by molecular dynamics (MD) simulations for n = 1-20 and n(c) = 0-5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for n(c) = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alkyl chains. Moreover, the aggregate shapes may be approximated by rather flat and elongated ellipsoids whose longer axis increases with n and n(c). The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. In one particular case, for which experimental findings are available in the literature, a good agreement is found with the present fragmentation data.

Molecular dynamics simulation of aqueous solutions of glycine betaine

Molecular dynamics simulation is used to investigate hydration properties of glycine betaine in a large range of solute concentrations. Statistical analyses of the system trajectories evidence microscopic details suggesting an interpretation of experimental results recently obtained for aqueous solutions of trimethylamine-N-oxide, a bioprotectant closely related to glycine betaine.

Molecular dynamics of electrosprayed water nanodroplets containing sodium bis(2-ethylhexyl)sulfosuccinate

The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) subject to electrospray ionization (ESI) has been investigated by molecular dynamics (MD) simulations at three temperatures (350, 500 and 800 K). We consider several types of water nanodroplets containing AOTNa molecules and composed of a fixed number of water molecules (1000), N(AOT)(0) AOT(-) anions (N(AOT)(0) =  0, 5, 10) and N(Na)(0) sodium ions (N(Na)(0) =  0, 5, 10, 15, 20): in a short time scale (less than 1 ns), the AOTNa molecules, initially forming direct micelles in the interior of the water nanodroplets, are observed in all cases to diffuse nearby the nanodroplet surface, so that the hydrophilic heads and sodium ions become surrounded by water molecules, whereas the alkyl chains lay at the droplet surface. Meanwhile, evaporation of water molecules and of solvated sodium ions occurs, leading to a decrease of the droplet size and charge. At 350 K, no ejection of neutral or charged surfactant molecules is observed, whereas at 500 K, some fragmentation occurs, and at 800 K, this event becomes more frequent. The interplay of all these processes, which depend on the values of temperature, N(AOT)(0) and N(Na)(0) eventually leads to anhydrous charged surfactant aggregates with prevalence of monocharged ones, in agreement with experimental results of ESI mass spectrometry. The quantitative analysis of the MD trajectories allows to evidence molecular details potentially useful in designing future ESI experimental conditions.

Water interaction with glycine betaine: A hybrid QM/MM moleculardynamics simulation

Experiments suggest that under conditions of water stress the preservation of functional stereodynamics of biomolecules by so-called ‘compatible solutes ’ is related to their interaction with water. In the present work, the interaction of water with glycine betaine, which is one of the osmoprotectants most effective and widespread in nature, is investigated using quantum mechanical calculations and QM/MM molecular dynamics simulation. Its effects on structure and dynamics of the surrounding water are compared with those exerted by two other remarkable bioprotectants: the disaccharide trehalose and the quaternary ammonium compound TMAO (trimethylamine-N-oxide). In particular, statistical analysis of a 500 ps simulation trajectory evidences common features of the 3D water distributions around glycine betaine and TMAO.

Structure, Stability, and Fragmentation of Sodium bis(2-ethylhexyl)Sulfosuccinate Negatively Charged Aggregates In Vacuo by MD Simulations

AbstractNegatively charged supramolecular aggregates formed in vacuo by n bis(2-ethylhexyl)sulfosuccinate (AOT–) anions and n + nc sodium counterions (i.e., [AOTnNan+nc]nc) have been investigated by molecular dynamics (MD) simulations for n = 1 to 20 and nc = –1 to –5. By comparing the maximum excess charge values of negatively and positively charged AOTNa aggregates, it is found that the charge storage capability is higher for the latter systems, the difference decreasing as the aggregation number increases. Statistical analysis of physical properties like gyration radii and moment of inertia tensors of aggregates provides detailed information on their structural properties. Even for nc = –5, all stable aggregates show a reverse micelle-like structure with an internal core, including sodium counterions and surfactant polar heads, surrounded by an external layer consisting of the surfactant alkyl chains. Interestingly, the reverse micelle-like structure is retained also in proximity of fragmentation. Moreover, the aggregate shapes may be approximated by elongated ellipsoids whose longer axis increases with n and |nc|. The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. The simulated fragmentation patterns of a representative aggregate show good agreement with experimental data obtained using low collision voltages. Figureᅟ

Molecular dynamics and metadynamics simulations of electrosprayed water nanodroplets including sodium bis(2-ethylhexyl)sulfosuccinate micelles

The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) under conditions of electrospray ionization (ESI) has been investigated by molecular dynamics (MD) and well-tempered metadynamics (WTM) simulations at 300 K and 400 K. We have examined water droplets with initial fixed numbers of water molecules (1000) and AOT- anions (100), and with sodium cations in the range of 70-130. At 300 K, all charged droplets show the water evaporation rate increasing with the absolute value of the initial droplet charge state (Z), accompanied by ejection of an increasing number of solvated sodium ions or by expulsion of AOT- anions depending on the sign of Z and by fragmentation in the case of high |Z|. At 400 K, the water evaporation becomes more rapid and the fission process more extensive. In all cases, the AOTNa molecules, arranged as a direct micelle inside the aqueous system, undergo a rapid inversion in vacuo so that the hydrophilic heads and sodium ions surrounded by water molecules move toward the droplet interior. At the end of the 100-ns MD simulations, some water molecules remain within the aggregates at both temperatures. The subsequent metadynamics simulations accelerate the droplet evolution and show that all systems become anhydrous, in agreement with the experimental results of ESI mass spectrometry. This complete water loss is accompanied by sodium counterion emission for positively charged aggregates at 300 K. The analysis shows how the temperature and droplet charge state affect the populations of the generated surfactant aggregates, providing information potentially useful in designing future ESI experimental conditions.