Reaction mechanisms of C(3PJ) and C+(2PJ) with benzene in the interstellar medium from quantum mechanical molecular dynamics simulations.

While spectroscopic data on small hydrocarbons in interstellar media in combination with crossed molecular beam (CMB) experiments have provided a wealth of information on astrochemically relevant species, much of the underlying mechanistic pathways of their formation remain elusive. Therefore, in this work, the chemical reaction mechanisms of C(3PJ) + C6H6 and C+(2P) + C6H6 systems using the quantum mechanical molecular dynamics (QMMD) technique at the PBE0-D3(BJ) level of theory is investigated, mimicking a CMB experiment. Both the dynamics of the reactions as well as the electronic structure for the purpose of the reaction network are evaluated. The method is validated for the first reaction by comparison to the available experimental data. The reaction scheme for the C(3PJ) + C6H6 system covers the literature data, e.g. the major products are the 1,2-didehydrocycloheptatrienyl radical (C7H5) and benzocyclopropenyl radical (C6H5-CH), and it reveals the existence of less common pathways for the first time. The chemistry of the C+(2PJ) + C6H6 system is found to be much richer, and we have found that this is because of more exothermic reactions in this system in comparison to those in the C(3PJ) + C6H6 system. Moreover, using the QMMD simulation, a number of reaction paths have been revealed that produce three distinct classes of reaction products with different ring sizes. All in all, at all the collision energies and orientations, the major product is the heptagon molecular ion for the ionic system. It is also revealed that the collision orientation has a dominant effect on the reaction products in both systems, while the collision energy mostly affects the charged system. These simulations both prove the applicability of this approach to simulate crossed molecular beams, and provide fundamental information on reactions relevant for the interstellar medium.

Reactive molecular dynamics simulation for isotope-exchange reactions in H/D systems: ReaxFFHD development.

To investigate the chemical isotope-exchange reactions within a system composed of a mixture of hydrogen and deuterium (H/D) in the plasma media, the ReaxFFHD potential was parameterized against an appropriate quantum mechanics (QM)-based training set. These QM data involve structures and energies related to bond dissociation, angle distortion, and an exchange reaction of the tri-atomic molecular ions, H3 +, D3 +, H2D+, and D2H+, produced in the hydrogen plasma. Using the ReaxFFHD potential, a range of reactive molecular dynamics simulations were performed on different mixtures of H/D systems. Analysis of the reactions involved in the production of these tri-atomic molecular ions was carried out over 1 ns simulations. The results show that the ReaxFFHD potential can properly model isotope-exchange reactions of tri-atomic molecular ions and that it also has a perfect transferability to reactions taking place in these systems. In our simulations, we observed some intermediate molecules (H2, D2, and HD) that undergo secondary reactions to form the tri-atomic molecular ions as the most likely products in the hydrogen plasma. Moreover, there remains a preference for D in the produced molecular ions, which is related to the lower zero-point energy of the D-enriched species, showing the isotope effects at the heart of the ReaxFFHD potential.

4He/3He separation using oxygen-functionalized nanoporous graphene.

First-principles density functional calculations have been used to model various oxygen-functionalized graphene nanopores, and quantum tunneling corrected transition state theory was used to investigate their 4He/3He separation performances under both kinetic competition and thermally driven steady-state conditions at the temperature range of 10-120 K. It is found that the two quantum effects, zero-point energy and quantum tunneling, which act in opposite directions, show different levels of participation in each set of process conditions. Under the kinetic competition conditions, the selectivity in helium isotope transmission is more affected by zero-point energy differences at the transition state structure, while the steady state separation factor is more affected by quantum tunneling. As a result of the present study, the efficiencies of all model pores are compared under both process conditions and the best pore structures are introduced.

Interaction mechanism of insulin with ZnO nanoparticles by replica exchange molecular dynamics simulation.

The interaction of ZnO nanoparticles with biological molecules such as proteins is one of the most important and challenging problems in molecular biology. Molecular dynamics (MD) simulations are useful technique for understating the mechanism of various interactions of proteins and nanoparticles. In the present work, the interaction mechanism of insulin with ZnO nanoparticles was studied. Simulation methods including MD and replica exchange molecular dynamics (REMD) and their conditions were surveyed. According to the results obtained by REMD simulation, it was found that insulin interacts with ZnO nanoparticle surface via its polar and charged amino acids. Unfolding insulin at ZnO nanoparticle surface, the terminal parts of its chains play the main role. Due to the linkage between chain of insulin and chain of disulfide bonds, opposite directional movements of N terminal part of chain A (toward nanoparticle surface) and N termini of chain B (toward solution) make insulin unfolding. In unfolding of insulin at this condition, its helix structures convert to random coils at terminal parts chains.

Interaction of insulin with colloidal ZnS quantum dots functionalized by various surface capping agents.

Interaction of quantum dots (QDs) and proteins strongly influenced by the surface characteristics of the QDs at the protein-QD interface. For a precise control of these surface-related interactions, it is necessary to improve our understanding in this field. In this regard, in the present work, the interaction between the insulin and differently functionalized ZnS quantum dots (QDs) were studied. The ZnS QDs were functionalized with various functional groups of hydroxyl (OH), carboxyl (COOH), amine (NH2), and amino acid (COOH and NH2). The effect of surface hydrophobicity was also studied by changing the alkyl-chain lengths of mercaptocarboxylic acid capping agents. The interaction between insulin and the ZnS QDs were investigated by fluorescence quenching, synchronous fluorescence, circular dichroism (CD), and thermal aggregation techniques. The results reveal that among the studied QDs, mercaptosuccinic acid functionalized QDs has the strongest interaction (∆G°=-51.50kJ/mol at 310K) with insulin, mercaptoethanol functionalized QDs destabilize insulin by increasing the beta-sheet contents, and only cysteine functionalized QDs improves the insulin stability by increasing the alpha-helix contents of the protein, and. Our results also indicate that by increasing the alkyl-chain length of capping agents, due to an increase in hydrophobicity of the QDs surface, the beta-sheet contents of insulin increase which results in the enhancement of insulin instability.

Unfolding of insulin at the surface of ZnO quantum dots.

ZnO quantum dots (QDs) have been used in many biomedical applications such as bioimaging, cancer treatments and etc. Crystallinity, particle size, optical absorption and photoluminescence spectra of ZnO QDs were analyzed by X-ray diffraction (XRD), transmission electron microscopy (TEM), UV-vis absorption spectroscopy and fluorescence spectroscopy respectively. Interaction of ZnO QDs with insulin was investigated by fluorescence quenching, circular dichroism (CD), isothermal titration calorimetry (ITC) and thermal aggregation tests. The fluorescence quenching results showed a static type quenching along with red shift in synchronize fluorescence (a sign of protein unfolding). CD spectroscopy results also confirmed this unfolding and show a reduction in alpha helices content of insulin in contact with ZnO QDs and their conversion to random coils. According to ITC results, the ΔG, ΔH and binding constant of this interaction are -32.35 kJ/mol, -43.21 kJ/mol and 4.69 × 10(5) M(-1), respectively. Thermal aggregation test showed fast aggregation of insulin in the presence of ZnO QDs. Therefore in biological application of ZnO QDs such as bioimaging, presence of such QDs in vicinity of insulin could unfold this protein.

Hydrogen bonding motifs in a hydroxy-bisphosphonate moiety: revisiting the problem of hydrogen bond identification.

Bisphosphonates are important therapeutic agents in bone-related diseases and exhibit complex H-bonding networks. To assess the role of H-bonds in biophosphonate stability, a full conformational search was performed for methylenebisphosphonate (MBP) and 1-hydroxyethylidene-1,1-diphosphonate (HEDP) using the MP2 method in conjunction with the continuum solvation model. The most stable structures and their equilibrium populations were analyzed at two protonation states via assignment of H-bonding motifs to each conformer. Geometrical and topological approaches for the identification and characterization of H-bonds were compared with each other, and some of the important correlations between H-bond features were described over the entire conformational space of a hydroxy-bisphosphonate moiety. The topologically derived H-bond energy obtained from the local density of potential energy at bond critical points shows consistent correlations with other measures such as H-bond frequency shift. An inverse power form without an intercept predicts topological H-bond energies from hydrogen-acceptor distances with an RMS error of less than 1 kcal mol(-1). The consistency of this measure was further checked by building a model that reasonably reproduces the relative stabilities of different conformers from their hydrogen-acceptor distances. In all systems, the predictions of this model are improved by the consideration of weak H-bonds that have no bond critical point.

Relaxation of a steep density gradient in a simple fluid: comparison between atomistic and continuum modeling.

We compare dynamical nonequilibrium molecular dynamics and continuum simulations of the dynamics of relaxation of a fluid system characterized by a non-uniform density profile. Results match quite well as long as the lengthscale of density nonuniformities are greater than the molecular scale (~10 times the molecular size). In presence of molecular scale features some of the continuum fields (e.g., density and momentum) are in good agreement with atomistic counterparts, but are smoother. On the contrary, other fields, such as the temperature field, present very large difference with respect to reference (atomistic) ones. This is due to the limited accuracy of some of the empirical relations used in continuum models, the equation of state of the fluid in the present example.

Binding of noble metal clusters with rare gas atoms: theoretical investigation.

Binding of noble metal clusters (M(n), M = Cu, Ag, and Au; n = 2-4) with rare gas atoms (Rg = Kr, Xe, and Rn) has been investigated at the density functional (CAM-B3LYP) and ab initio (MP2) levels of theory. The calculation shows significant affinity of neutral metal clusters for interaction with rare gas atoms. The binding energies indicate that gold clusters have the highest and silver clusters have the lowest affinity for interaction with rare gas atoms, and for the same metal clusters, there is a continuous increase in E(b) from Kr to Rn. The M-Rg bonding mechanism have been interpreted by means of the quantum theory of atoms in molecules (QTAIM), natural bond orbital (NBO), and energy decomposition analysis (EDA). According to these theories, the M-Rg bonds are found to be partially electrostatic and partially covalent. EDA results identify that these bonds have less than 40% covalent character and more than 60% electrostatic, and also NBO calculations predict the amount of charge transfer from the lone pair of rare gas to σ* and n*orbitals of metal clusters.

An ab initio intermolecular potential energy surface for the F(2) dimer.

Two analytical representations for the potential energy surface of the F(2) dimer were constructed on the basis of ab initio calculations up to the fourth-order of Møller-Plesset (MP) perturbation theory. The best estimate of the complete basis set limit of interaction energy was derived for analysis of basis set incompleteness errors. At the MP4/aug-cc-pVTZ level of theory, the most stable structure of the dimer was obtained at R = 6.82 au, theta(a) = 12.9 degrees , theta(b) = 76.0 degrees , and phi = 180 degrees , with a well depth of 716 microE(h). Two other minima were found for canted and X-shaped configurations with potential energies around -596 and -629 microE(h), respectively. Hexadecapole moments of monomers play an important role in the anisotropy of interaction energy that is highly R-dependent at intermediate intermolecular distances. The quality of potentials was tested by computing values of the second virial coefficient. The fitted MP4 potential has a more reasonable agreement with experimental values.

Translocation and interactions of L-arabinose in OmpF porin: A molecular dynamics study.

The passage of a natural substrate, L-arabinose (L-ARA) through Escherichia coli porin embedded in an artificial bilayer, is studied by equilibrium molecular dynamics simulations. We investigate the early stage of translocation process of L-ARA from intra-cellular to extra-cellular side (Int-to-Ext) across the bilayer. The average trajectory path over all L-ARA molecules along with quantum-mechanical configuration-optimizations at PM3 level predict the existence of at least three trapping zones. The common feature within all these zones is that L-ARA remains perpendicular to the channel axis. It is remarkable how the orientation and translational-rotational motion of L-ARA molecule play a role in its transport through OmpF channel. These simulations are important for better understanding of permeation process in OmpF channel. They also provide an insight into the chiral recognition of translocation process in protein nanochannels from substrate and protein prospects and help interpret experiments on permeation process of small dipolar molecules across biological membranes.