Adsorption of HCN at the Surface of Ice : A Grand Canonical Monte Carlo Simulation Study

Adsorption of HCN molecules at the surface of hexagonal (I-h) ice is studied under tropospheric conditions by a set of grand canonical Monte Carlo simulations. Although the adsorption isotherm is of Langmuir shape and the saturated adsorption layer is practically monomolecular, lateral interactions are found to have a non-negligible effect on the adsorption. The Langmuir shape of the isotherm can be rationalized by the fact that the interaction energy for HCN-water and HCN-HCN pairs is rather close to each other, and hence, monomolecular adsorption even in the presence of lateral interactions turns into a special case. At low surface coverages the HCN molecules prefer a tilted orientation, pointing by the N atom flatly toward the ice surface, in which they can form a strong O-H center dot center dot center dot N-type hydrogen bond with the surface water molecules. At high surface coverages, an opposite tilted orientation is preferred, in which the H atom points toward the ice phase and the HCN molecule can form only a weak C-H center dot center dot center dot O-type hydrogen bond with a surface water molecule. This orientational change is dictated by the smaller surface area occupied by a H than a N atom, and the corresponding energy loss is (over)compensated by formation of C-H center dot center dot center dot N-type hydrogen bonds between neighboring HCN molecules. The obtained results have several consequences both on the atmospheric effect of HCN and also on the possible prebiotic formation of precursor molecules of adenine. These consequences are also discussed in the paper

Analyses of the Large Subunit Histidine-Rich Motif Expose an Alternative Proton Transfer Pathway in [NiFe] Hydrogenases

A highly conserved histidine-rich region with unknown function was recognized in the large subunit of [NiFe] hydrogenases. The HxHxxHxxHxH sequence occurs in most membrane-bound hydrogenases, but only two of these histidines are present in the cytoplasmic ones. Site-directed mutagenesis of the His-rich region of the T. roseopersicina membrane-attached Hyn hydrogenase disclosed that the enzyme activity was significantly affected only by the replacement of the His104 residue. Computational analysis of the hydrogen bond network in the large subunits indicated that the second histidine of this motif might be a component of a proton transfer pathway including Arg487, Asp103, His104 and Glu436. Substitutions of the conserved amino acids of the presumed transfer route impaired the activity of the Hyn hydrogenase. Western hybridization was applied to demonstrate that the cellular level of the mutant hydrogenases was similar to that of the wild type. Mostly based on theoretical modeling, few proton transfer pathways have already been suggested for [NiFe] hydrogenases. Our results propose an alternative route for proton transfer between the [NiFe] active center and the surface of the protein. A novel feature of this model is that this proton pathway is located on the opposite side of the large subunit relative to the position of the small subunit. This is the first study presenting a systematic analysis of an in silico predicted proton translocation pathway in [NiFe] hydrogenases by site-directed mutagenesis

Glutathione as a Prebiotic Answer to alpha-Peptide Based Life.

The energetics of peptide bond formation is an important factor not only in the design of chemical peptide synthesis, but it also has a role in protein biosynthesis. In this work, quantum chemical calculations at 10 different levels of theory including G3MP2B3 were performed on the energetics of glutathione formation. The strength of the peptide bond is found to be closely related to the acid strength of the to-be N-terminal and the basicity of the to-be C-terminal amino acid. It is shown that the formation of the first peptide activates the amino acid for the next condensation step, manifested in bacterial protein synthesis where the first step is the formation of an N-formylmethionine dipeptide. The possible role of glutathione in prebiotic molecular evolution is also analyzed. The implications of the thermodynamics of peptide bond formation in prebiotic peptide formation as well as in the preference of alpha- instead of beta- or gamma-amino acids are discussed. An empirical correction is proposed for the compensation of the error due to the incapability of continuum solvation models in describing the change of the first solvation shell when a peptide bond is formed from two zwitterions accompanied by the disappearance of one ion pair

Molecular Dynamics and Metadynamics Insights of 1,4-Dioxane-Induced Structural Changes of Biomembrane Models

1,4-dioxane is a cytotoxic B2 type human carcinogen, a serious water pollutant produced solely by industrial activity. The effect of 1,4-dioxane on phospholipid membrane models composed by DPPC and its branched isomer (IPPC) was investigated using MD simulations. Clear and polluted membranes were compared by membrane parameters such as APL, VPL, compressibility modulus, membrane thickness and orderliness of lipid tails. While neat systems significantly differ from each other, the presence of the pollutant has the same effect on both types of lipid membranes: high density of dioxane appears at the vicinity of ester groups which pushes away lipid headgroups from each other, leading to an overall change in lipid structure: APL and VPL grows, while the orderliness of lipid tails, membrane thickness and compressibility modulus decreases. Orientational preferences of water and dioxane molecules were also investigated and different membrane regions have been specified according to the stance of water molecules. Free energy profile for 1,4-dioxane penetration mechanism into DPPC membranes was carried out using metadynamics for two different concentrations of the pollutant (c1=7.51 g/dm3 , c2=75.10 g/dm3 ), which showed that the higher the concentration is, the lower the free energy of penetration gets. Only a small free energy barrier was found in the headgroup region and accumulation of dioxane is thermodynamically unfavored in the middle of the bilayer. The penetration mechanism has been described in detail based on the orientational preference of 1,4-dioxane molecules and the free energy profiles

Adsorption of Formamide at the Surface of Amorphous and Crystalline Ices under Interstellar and Tropospheric Conditions. A Grand Canonical Monte Carlo Simulation Study

International audienceThe adsorption of formamide is studied both at the surface of crystalline (Ih) ice at 200 K and at the surface of low density amorphous (LDA) ice in the temperature range of 50–200 K by grand canonical Monte Carlo (GCMC) simulation. These systems are characteristic of the upper troposphere and of the interstellar medium (ISM), respectively. Our results reveal that while no considerable amount of formamide is dissolved in the bulk ice phase in any case, the adsorption of formamide at the ice surface under these conditions is a very strongly preferred process, which has to be taken into account when studying the chemical reactivity in these environments. The adsorption is found to lead to the formation of multimolecular adsorption layer, the occurrence of which somewhat precedes the saturation of the first molecular layer. Due to the strong lateral interaction acting between the adsorbed formamide molecules, the adsorption isotherm does not follow the Langmuir shape. Adsorption is found to be slightly stronger on LDA than Ih ice under identical thermodynamic conditions, due to the larger surface area exposed to the adsorption. Indeed, the monomolecular adsorption capacity of the LDA and Ih ice surfaces is found to be 10.5 ± 0.7 μmol/m2 and 9.4 μmol/m2, respectively. The first layer formamide molecules are very strongly bound to the ice surface, forming typically four hydrogen bonds with each other and the surface water molecules. The heat of adsorption at infinitely low surface coverage is found to be −105.6 kJ/mol on Ih ice at 200 K

Adsorption of Methylamine on Amorphous Ice under Interstellar Conditions. A Grand Canonical Monte Carlo Simulation Study

The adsorption of methylamine at the surface of amorphous ice is studied at various temperatures, ranging from 20 to 200 K, by grand canonical Monte Carlo simulations under conditions that are characteristic to the interstellar medium (ISM). The results are also compared with those obtained earlier on crystalline (<i>I_h</i>) ice. We found that methylamine has a strong ability of being adsorbed on amorphous ice, involving also multilayer adsorption. The decrease of the temperature leads to a substantial increase of this adsorption ability; thus, considerable adsorption is seen at 20–50 K even at bulk gas phase concentrations that are comparable with that of the ISM. Further, methylamine molecules can also be dissolved in the bulk amorphous ice phase. Both the adsorption capacity of amorphous ice and the strength of the adsorption on it are found to be clearly larger than those corresponding to crystalline (<i>I_h</i>) ice, due to the molecular scale roughness of the amorphous ice surface as well as to the lack of clear orientational preferences of the water molecules at this surface. Thus, the surface density of the saturated adsorption monolayer is estimated to be 12.6 ± 0.4 μmol/m², 20% larger than the value of 10.35 μmol/m², obtained earlier for <i>I_h</i> ice, and at low enough surface coverages the adsorbed methylamine molecules are found to easily form up to three hydrogen bonds with the surface water molecules. The estimated heat of adsorption at infinitely low surface coverage is calculated to be −69 ± 5 kJ/mol, being rather close to the estimated heat of solvation in the bulk amorphous ice phase of −74 ± 7 kJ/mol, indicating that there are at least a few positions at the surface where the adsorbed methylamine molecules experience a bulk-like local environment

Miscibility and Thermodynamics of Mixing of Different Models of Formamide and Water in Computer Simulation

The thermodynamic changes that occur upon mixing five models of formamide and three models of water, including the miscibility of these model combinations itself, is studied by performing Monte Carlo computer simulations using an appropriately chosen thermodynamic cycle and the method of thermodynamic integration. The results show that the mixing of these two components is close to the ideal mixing, as both the energy and entropy of mixing turn out to be rather close to the ideal term in the entire composition range. Concerning the energy of mixing, the OPLS/AA_mod model of formamide behaves in a qualitatively different way than the other models considered. Thus, this model results in negative, while the other ones in positive energy of mixing values in combination with all three water models considered. Experimental data supports this latter behavior. Although the Helmholtz free energy of mixing always turns out to be negative in the entire composition range, the majority of the model combinations tested either show limited miscibility, or, at least, approach the miscibility limit very closely in certain compositions. Concerning both the miscibility and the energy of mixing of these model combinations, we recommend the use of the combination of the CHARMM formamide and TIP4P water models in simulations of water–formamide mixtures