9 research outputs found
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
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
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 bisÂ(trifluoromethylsulfonyl)Âimide.
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 bisÂ(trifluoromethylsulfonyl)Âimide
displays the least favorable free energy of adsorption with PAHs whereas
PAH interactions with 1-butyl-1-methylpyrrolidinium bisÂ(trifluoromethylsulfonyl)Âimide
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
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]<sup>+</sup> and butyltrimethylammonium [Btma]<sup>+</sup> cations,
paired to tetrafluoroborate [BF<sub>4</sub>]<sup>−</sup>, hexafluorophosphate
[PF<sub>6</sub>]<sup>−</sup>, dicyanamide [DCA]<sup>−</sup>, and bisÂ(trifluoromethylsilfonyl)Âimide [Tf<sub>2</sub>N]<sup>−</sup> 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><sub>ads</sub>) 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><sub>hydride</sub> 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><sub>hydride</sub> 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