25 research outputs found
OH-Stretching Overtone Induced Dynamics in HSO<sub>3</sub>F from Reactive Molecular Dynamics Simulations
The OH-stretch induced dynamics in
fluorosulfonic acid (HSO<sub>3</sub>F) is characterized from a statistically
significant number
of trajectories using multisurface adiabatic reactive molecular dynamics
(MS-ARMD) simulations. The global reactive potential energy surface,
which describes H-transfer and HF-elimination, is parametrized at
the MP2/6-311G++(2p,2d) level of theory with an accuracy of better
than 1 kcal/mol. Excitation along the OH-local mode leads to H-transfer
dynamics but elimination of HF is only observed for excitations with
Μ ℠6 for 1 out of 5000 trajectories. This finding differs
fundamentally from the situation for vibrationally induced photodissociation
of H<sub>2</sub>SO<sub>4</sub> and HSO<sub>3</sub>Cl, for which, even
with excitations of 4 quanta along the OH-stretch mode, elimination
of H<sub>2</sub>O and HCl, respectively, is readily observed on the
subnanosecond time scale. RRKM rates for HX-elimination in HSO<sub>3</sub>X (X = F, Cl) only differ by a factor of 5. The findings from
the reactive molecular dynamics simulations together with the RRKM
results thus indicate that the origin for a closed HF-production channel
is dynamical. This is also consistent with experimental findings for
hydrofluoroethanes in shock tubes, which found pronounced non-RRKM
behavior
Dynamics of Water/Methanol Mixtures at Functionalized Chromatographic Interfaces
Fully atomistic simulations of water/methanol mixtures
of varying
compositions (80/20 and 50/50) at chromatographic interfaces with
different functionalizations are presented. The dynamical properties
in terms of equilibration times and solvent exchange dynamics are
characterized and found to depend on the different systems on the
nanosecond time scale. The solvent density profile and the structuring
of the stationary phase differ for derivatizations including (âCN,
NO<sub>2</sub>, âNH<sub>2</sub>, âC<sub>6</sub>H<sub>5</sub>) of the C<sub>18</sub> chain. The time scale and intensity
of the water exchange dynamics differs for the different realizations
of the chromatographic systems and ranges from 200 to 500 ps. Water
exchange rates depend on solvent composition as well as on the functionalization
of alkyl chains. Simulations with acridine as a probe molecule provide
atomistic insight into the slot model
Toolkit for the Construction of Reproducing Kernel-Based Representations of Data: Application to Multidimensional Potential Energy Surfaces
In the early days of computation,
slow processor speeds limited
the amount of data that could be generated and used for scientific
purposes. In the age of big data, the limiting factor usually is the
method with which large amounts of data are analyzed and useful information
is extracted. A typical example from chemistry are high-level ab initio
calculations for small systems, which have nowadays become feasible
even if energies at many different geometries are required. Molecular
dynamics simulations often require several thousand distinct trajectories
to be run. Under such circumstances suitable analytical representations
of potential energy surfaces (PESs) based on ab initio calculations
are required to propagate the dynamics at an acceptable cost. In this
work we introduce a toolkit which allows the automatic construction
of multidimensional PESs from gridded ab initio data based on reproducing
kernel Hilbert space (RKHS) theory. The resulting representations
require no tuning of parameters and allow energy and force evaluations
at ab initio quality at the same cost as empirical force fields. Although
the toolkit is primarily intended for constructing multidimensional
potential energy surfaces for molecular systems, it can also be used
for general machine learning purposes. The software is published under
the MIT license and can be downloaded, modified, and used in other
projects for free
Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate
The dynamics and
infrared spectroscopic signatures of proton transfer
in protonated oxalate (<i>p</i>âOxa) are studied
using classical and quantum dynamics. The intermolecular interactions
are described by a force field suitable to follow proton transfer.
This allows to carry out multiple extended classical molecular dynamics
(MD) and ring polymer MD simulations from which the infrared spectrum
is determined. Simulations at 600 K sample the quantum mechanical
ground state probability distribution and best reproduce the experimentally
observed maximum absorption wavelength and part of the line shape.
Comparison with the experimentally measured spectrum provides an estimate
for the barrier height for proton transfer which can not be determined
directly from experiment. A barrier of 4.2 kcal/mol is found to best
reproduce the position and width of the infrared absorption of the
transferring proton in <i>p</i>âOxa and also leads
to an infrared (IR) spectrum in good agreement with experiment for
the deuterated species <i>d</i>âOxa. A novel means
to capture the two resonance forms of oxalate depending on the localization
of the excess proton on either CO moiety is found to yield improved
results for the spectroscopy in the framework region between 1000
and 2000 cm<sup>â1</sup>
Dihedral probability distributions for Phe<sup>E15</sup>.
<p>2-dimensional probability distributions <i>p</i>(<i>Ï</i><sub>1</sub>, <i>Ï</i><sub>2</sub>) of <i>Ï</i><sub>1</sub> and <i>Ï</i><sub>2</sub> dihedral angles upon Xe1aâXe2 transitions, compared to the equilibrium distribution. A single Phe is reported in the left upper corner, along with the definition of angles <i>Ï</i><sub>1</sub> and <i>Ï</i><sub>2</sub>. <i>p</i>(<i>Ï</i><sub>1</sub>, <i>Ï</i><sub>2</sub>) in panels B and C are different from the equilibrium distribution. Distributions also differ depending on where Xe came from before the transition. Characteristic examples are Xe2âXe1aâXe2 vs Xe1bâXe1aâXe2 events from panel B and Xe1aâXe2âXe1a vs Xe1bâXe2âXe1a events from panel C.</p
Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations
Multipole (MTP) electrostatics
provides the means to describe anisotropic
interactions in a rigorous and systematic manner. A number of earlier
molecular dynamics (MD) implementations have increasingly relied on
the use of molecular symmetry to reduce the (possibly large) number
of MTP interactions. Here, we present a CHARMM implementation of MTP
electrostatics in terms of spherical harmonics. By relying on a systematic
set of reference-axis systems tailored to various chemical environments,
we obtain an implementation that is both efficient and scalable for
(bio)Âmolecular systems. We apply the method to a series of halogenated
compounds to show (i) energy conservation; (ii) improvements in reproducing
thermodynamic properties compared to standard point-charge (PC) models;
(iii) performance of the code; and (iv) better stabilization of a
brominated ligand in a target protein, compared to a PC force field.
The implementation provides interesting perspectives toward a dual
PC/MTP resolution, aÌ la QM/MM
Xe position probability distributions, short vs long residence times.
<p>Comparison of probability distributions <i>P</i>(<i>x</i>, <i>y</i>) from many short dwell times (left, 5 ps) with <i>P</i>(<i>x</i>, <i>y</i>) of a simulation with a 1.2 ns dwell time (right) in the Xe1a state. The two distributions differ in shape and size because for short dwell times, Xe samples the available volume with little protein adaptation taking place whereas for long dwell times the protein is able to pack more closely around the Xe atom which typically leads to reduction of the volume of the sampled space.</p
Molecular Dynamics with Conformationally Dependent, Distributed Charges
Accounting for geometry-induced changes in the electronic
distribution
in molecular simulation is important for capturing effects such as
charge flow, charge anisotropy, and polarization. Multipolar force
fields have demonstrated their ability to correctly represent chemically
significant features such as anisotropy and sigma holes. It has also
been shown that off-center point charges offer a compact alternative
with similar accuracy. Here, it is demonstrated that allowing relocation
of charges within a minimally distributed charge model (MDCM) with
respect to their reference atoms is a viable route to capture changes
in the molecular charge distribution depending on geometry, i.e.,
intramolecular polarization. The approach, referred to as âflexible
MDCMâ (fMDCM), is validated on a number of small molecules
and provides accuracies in the electrostatic potential (ESP) of 0.5
kcal/mol on average compared with reference data from electronic structure
calculations, whereas MDCM and point charges have root mean squared
errors of a factor of 2 to 5 higher. In addition, MD simulations in
the NVE ensemble using fMDCM for a box of flexible
water molecules with periodic boundary conditions show a width of
0.1 kcal/mol for the fluctuation around the mean at 300 K on the 10
ns time scale. For water, the equilibrium valence angle in the gas
phase is found to increase by 2° for simulations in the condensed
phase which is consistent with experiment. The accuracy in capturing
the geometry dependence of the ESP together with the long-time stability
in energy conserving simulations makes fMDCM a promising tool to introduce
advanced electrostatics into atomistic simulations
Migration of small ligands in globins: Xe diffusion in truncated hemoglobin N
<div><p>In heme proteins, the efficient transport of ligands such as NO or O<sub>2</sub> to the binding site is achieved via ligand migration networks. A quantitative assessment of ligand diffusion in these networks is thus essential for a better understanding of the function of these proteins. For this, Xe migration in truncated hemoglobin N (trHbN) of <i>Mycobacterium Tuberculosis</i> was studied using molecular dynamics simulations. Transitions between pockets of the migration network and intra-pocket relaxation occur on similar time scales (10 ps and 20 ps), consistent with low free energy barriers (1-2 kcal/mol). Depending on the pocket from where Xe enters a particular transition, the conformation of the side chains lining the transition region differs which highlights the coupling between ligand and protein degrees of freedom. Furthermore, comparison of transition probabilities shows that Xe migration in trHbN is a non-Markovian process. Memory effects arise due to protein rearrangements and coupled dynamics as Xe moves through it.</p></div
Xe1aâXe2 transition region.
<p>Xe1a and Xe2 pockets (orange and gray sphere, respectively), together with surrounding residues Val<sup>B6</sup> (cyan), Phe<sup>B9</sup> (green), Phe<sup>E15</sup> (magenta), Gln<sup>E11</sup> (red), and Leu<sup>G12</sup>(blue). The minimum energy transition path (in blue cylinder) and one particular transition path (small black spheres) are shown between the two pockets. In grey (background) the ribbon structure of the protein and in licorice the heme-unit.</p