Mie Potentials for Phase Equilibria: Application to Alkenes

Transferable united-atom force fields based on Mie potentials are presented for alkenes. Monte Carlo simulations in the grand canonical ensemble, combined with histogram reweighting, are used to determine vapor–liquid coexistence curves, vapor pressures, heats of vaporization, boiling points, and critical properties for 1-alkenes from ethene to 1-octene. To assess the transferability of the optimized parameters, additional calculations are performed for the cis and trans isomers of 2-butene and 2-pentene and the dienes 1,3-butadiene and 1,5-hexadiene. Saturated liquid densities for the 1-alkenes, 2-pentenes, and 1,5-hexadiene are predicted to within 1 % of experimental data, while deviations of (2 to 5) % from experiment were observed for <i>cis</i>-2-butene and 1,3-butadiene, respectively. Vapor pressures for the alkenes are predicted to within (2 to 15) % of experiment, with errors increasing with chain length and at lower temperatures. Critical temperatures are predicted to within 1 % of experiment for all molecules except for 1,3-butadiene, where the critical temperature is under-predicted by 3.5 %. Transferability is further evaluated through calculations of binary mixture vapor–liquid equilibria. Predictions of the Mie potentials for ethane + propene and 1-butane + 1-hexene are indistinguishable from experimental data

Elucidating Interactions Between Ionic Liquids and Polycyclic Aromatic Hydrocarbons by Quantum Chemical Calculations

Using quantum mechanical calculations performed at the density functional level of theory, the present study explores the binding energetics, orbital energies, and charge transfer behavior accompanying sorption of 12 different ionic liquids (ILs) onto 6 archetypal polyaromatic hydrocarbons (PAHs). The ILs were based on combinations of three different onium cations (i.e., 1-butyl-3-methylimidazolium, 1-butylpyridinium, 1-butyl-1-methylpyrrolidinium) paired with four common anions, that is, bromide, tetrafluoroborate, hexafluorophosphate, and bis­(trifluoromethylsulfonyl)­imide. In general, the size of the anion as well as interaction of the butyl side chain present on the cation with the paired anion exerted significant influence over the cation ring orientation with respect to the PAH surface. A smaller highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) energy band gap was observed for pyridinium-based ILs upon adsorption on the PAH surface in comparison to imidazolium and pyrrolidinium analogs, hinting at stronger interactions between PAHs and pyridinium ILs. Of the 12 ILs investigated, 1-butyl-3-methylimidazolium bis­(trifluoromethylsulfonyl)­imide displays the least favorable free energy of adsorption with PAHs whereas PAH interactions with 1-butyl-1-methylpyrrolidinium bis­(trifluoromethylsulfonyl)­imide are the most favored thermodynamically. Charges determined from a Mulliken population analysis were consistent with charge transfer (CT) from the IL to the PAH. On the contrary, charges determined via electrostatic potential using the more reliable grid based analysis method (i.e., CHELPG) suggested the reverse direction of CT from the PAH to the IL. The direction of the CT occurring from the HOMO of the PAH to the LUMO of the IL, as shown by CHELPG analysis, is consistent with the physical location of the orbitals and the negative shift in the Fermi energy level observed for the IL–PAH complex. A more favorable enthalpy of adsorption for ILs onto a PAH is observed with an increase in the size of the PAH considered. The free energy of adsorption, however, does not change significantly with an increase in the PAH surface area. The adsorption of an IL on the PAH surface leads to a small change in the entropy of the adsorbate/adsorbent system. The thermochemistry computed at variable temperature indicates a significant increase in the free energy of adsorption (i.e., a less favorable adsorption) as temperature rises. Additionally, decomposition of the entropic contribution suggests a greater contribution from translational and rotational entropies upon cooling, again consistent with stronger association at lower temperatures. Overall, the thermochemical analyses suggest an entropically driven process of desorption of an IL from the PAH surface, generally leading to fairly weak interactions between ILs and ordinary PAHs under normal laboratory conditions

Biomolecular Simulations with the Transferable Potentials for Phase Equilibria: Extension to Phospholipids

The Transferable Potentials for Phase Equilibria (TraPPE) is extended to zwitterionic and charged lipids including phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidylserine (PS), and phosphatidylglycerol (PG). The performance of the force field is validated through isothermal–isobaric ensemble (NPT) molecular dynamics simulations of hydrated lipid bilayers performed with the aforementioned head groups combined with saturated and unsaturated alkyl tails containing 12–18 carbon atoms. The effects of water model and sodium ion parameters on the performance of the lipid force field are determined. The predictions of the TraPPE force field for the area per lipid, bilayer thickness, and volume per lipid are within 1–5% of experimental values. Key structural properties of the bilayer, such as order parameter splitting in the sn-2 chain and X-ray form factors, are found to be in close agreement with experimental data

Meta-Hybrid Density Functional Theory Study of Adsorption of Imidazolium- and Ammonium-Based Ionic Liquids on Graphene Sheet

In this study, two types of ionic liquids (ILs) based on 1-butyl-3-methylimidazolium [Bmim]⁺ and butyltrimethylammonium [Btma]⁺ cations, paired to tetrafluoroborate [BF₄]⁻, hexafluorophosphate [PF₆]⁻, dicyanamide [DCA]⁻, and bis­(trifluoromethylsilfonyl)­imide [Tf₂N]⁻ anions, were chosen as adsorbates to investigate the influence of cation and anion type on the adsorption of ILs on the graphene surface. The adsorption process on the graphene surface (circumcoronene) was studied using M06-2X/cc-pVDZ level of theory. Empirical dispersion correction (D3) was also added to the M06-2X functional to investigate the effects of dispersion on the binding energy values. The graphene···IL configurations, binding energies, and thermochemistry of IL adsorption on the graphene surface were investigated. Orbital energies, charge transfer behavior, the influence of adsorption on the hydrogen bond strength between cation and anion of ILs, and the significance of noncovalent interactions on the adsorption of ILs on the graphene surface were also considered. ChelpG analysis indicated that upon adsorption of ILs on the graphene surface the overall charge on the cation, anion, and graphene surface changes, enabled by the charge transfer that occurs between ILs and graphene surface. Orbital energy and density of states calculations also show that the HOMO–LUMO energy gap of ILs decreases upon adsorption on the graphene surface. Quantum theory of atoms in molecules analysis indicates that the hydrogen-bond strength between cation and anion in ILs decreases upon adsorption on the graphene surface. Plotting the noncovalent interactions between ILs and graphene surface shows the role and significance of cooperative π···π, C–H···π, and X···π (X = N, O, F atoms from anions) interactions in the adsorption of ILs on the graphene surface. The thermochemical analysis also indicates that the free energy of adsorption (Δ<i>G</i>_ads) of ILs on the graphene surface is negative, and thus the adsorption occurs spontaneously

Kinetic Pathways To Control Hydrogen Evolution and Nanocarbon Allotrope Formation via Thermal Decomposition of Polyethylene

Polyethylene-based plastic materials are nonbiodegradable in nature and have a profound negative impact on our environment. Efficient disposal of plastic wastes in an efficient, environmental friendly fashion or chemical fixation of plastics into useful intermediates remains an outstanding problem. We employ temperature accelerated reactive molecular dynamics (TARMD) simulations to identify the kinetic pathways during thermal pyrolysis of polyethylene (PE). This allows for attainment of a dual objective <i>viz</i>. (1) clean fuel production via controlled hydrogen evolution and (2) formation of novel nanocarbon allotropes. Detailed atomistic picture of high temperature thermal decomposition that leads to partial or complete dehydrogenation of PE is presented. We identify the various reaction pathways for PE decomposition at high temperatures and demonstrate that a quenching-cooling strategy holds promise for tailoring the degree of graphitic order within the nanocarbon materials while simultaneously fine-tuning the evolution of clean fuel such as hydrogen gas. TARMD simulation trajectories elucidate the effect of simulated kinetic pathways on the reactive decomposition into hydrogen/flue gas/carbon, gas–liquid–solid phase separation of reaction products, interface dynamics, nucleation, and microstructural evolution of carbon particles. Depending on the quenching rate and the residual hydrogen content, we show that it is kinetically possible to control the reaction pathways and diffusion mechanisms and selectively produce a wide gamut of carbon allotropes (carbon onions, spheres, rods, graphene sheets to name a few). Suitable comparisons are made between simulation and our experimental results. Our simulations illustrate an environmental friendly strategy for controlled synthesis of nanocarbon materials and simultaneous clean energy production from nonbiodegradable products

Inverted funnel plot for randomized controlled trials of parenteral anticoagulation in cancer patients

<p><b>Copyright information:</b></p><p>Taken from "Parenteral anticoagulation may prolong the survival of patients with limited small cell lung cancer: a Cochrane systematic review"</p><p>http://www.jeccr.com/content/27/1/4</p><p>Journal of Experimental & Clinical Cancer Research : CR 2008;27(1):4-4.</p><p>Published online 15 May 2008</p><p>PMCID:PMC2438335.</p><p></p

Modulating Enzyme Activity by Altering Protein Dynamics with Solvent

Optimal enzyme activity depends on a number of factors, including structure and dynamics. The role of enzyme structure is well recognized; however, the linkage between protein dynamics and enzyme activity has given rise to a contentious debate. We have developed an approach that uses an aqueous mixture of organic solvent to control the functionally relevant enzyme dynamics (without changing the structure), which in turn modulates the enzyme activity. Using this approach, we predicted that the hydride transfer reaction catalyzed by the enzyme dihydrofolate reductase (DHFR) from <i>Escherichia coli</i> in aqueous mixtures of isopropanol (IPA) with water will decrease by ∼3 fold at 20% (v/v) IPA concentration. Stopped-flow kinetic measurements find that the pH-independent <i>k</i>_hydride rate decreases by 2.2 fold. X-ray crystallographic enzyme structures show no noticeable differences, while computational studies indicate that the transition state and electrostatic effects were identical for water and mixed solvent conditions; quasi-elastic neutron scattering studies show that the dynamical enzyme motions are suppressed. Our approach provides a unique avenue to modulating enzyme activity through changes in enzyme dynamics. Further it provides vital insights that show the altered motions of DHFR cause significant changes in the enzymeʼs ability to access its functionally relevant conformational substates, explaining the decreased <i>k</i>_hydride rate. This approach has important implications for obtaining fundamental insights into the role of rate-limiting dynamics in catalysis and as well as for enzyme engineering

Neural Network Corrections to Intermolecular Interaction Terms of a Molecular Force Field Capture Nuclear Quantum Effects in Calculations of Liquid Thermodynamic Properties

We incorporate nuclear quantum effects (NQE) in condensed matter simulations by introducing short-range neural network (NN) corrections to the ab initio fitted molecular force field ARROW. Force field NN corrections are fitted to average interaction energies and forces of molecular dimers, which are simulated using the Path Integral Molecular Dynamics (PIMD) technique with restrained centroid positions. The NN-corrected force field allows reproduction of the NQE for computed liquid water and methane properties such as density, radial distribution function (RDF), heat of evaporation (HVAP), and solvation free energy. Accounting for NQE through molecular force field corrections circumvents the need for explicit computationally expensive PIMD simulations in accurate calculations of the properties of chemical and biological systems. The accuracy and locality of pairwise NN NQE corrections indicate that this approach could be applicable to complex heterogeneous systems, such as proteins

Protein–Ligand Binding Free-Energy Calculations with ARROWA Purely First-Principles Parameterized Polarizable Force Field

Protein–ligand binding free-energy calculations using molecular dynamics (MD) simulations have emerged as a powerful tool for in silico drug design. Here, we present results obtained with the ARROW force field (FF)a multipolar polarizable and physics-based model with all parameters fitted entirely to high-level ab initio quantum mechanical (QM) calculations. ARROW has already proven its ability to determine solvation free energy of arbitrary neutral compounds with unprecedented accuracy. The ARROW FF parameterization is now extended to include coverage of all amino acids including charged groups, allowing molecular simulations of a series of protein–ligand systems and prediction of their relative binding free energies. We ensure adequate sampling by applying a novel technique that is based on coupling the Hamiltonian Replica exchange (HREX) with a conformation reservoir generated via potential softening and nonequilibrium MD. ARROW provides predictions with near chemical accuracy (mean absolute error of ∼0.5 kcal/mol) for two of the three protein systems studied here (MCL1 and Thrombin). The third protein system (CDK2) reveals the difficulty in accurately describing dimer interaction energies involving polar and charged species. Overall, for all of the three protein systems studied here, ARROW FF predicts relative binding free energies of ligands with a similar accuracy level as leading nonpolarizable force fields