Journal of Chemical Information and Modeling,
Journal Year:
2024,
Volume and Issue:
64(9), P. 3767 - 3778
Published: April 15, 2024
In
this
work,
we
introduce
the
Solvate
Suite,
a
comprehensive
and
modular
command-line
interface
designed
for
molecular
simulation
microsolvation
modeling.
The
suite
interfaces
with
widely
used
scientific
software,
streamlining
computational
experiments
liquid
systems
through
automated
creation
of
boxes
topology
adjustable
parameters.
Furthermore,
it
has
features
graphical
statistical
analysis
simulated
properties
extraction
trajectory
configurations
various
filters.
Additionally,
introduces
innovative
strategies
modeling
multiscale
approach,
employing
equilibrated
dynamics
to
identify
favorable
solute–solvent
interactions
enabling
full
cluster
optimization
free-energy
calculations
without
imaginary
frequency
contamination.
Journal of Computational Chemistry,
Journal Year:
2025,
Volume and Issue:
46(11)
Published: April 24, 2025
ABSTRACT
Within
this
work,
we
present
the
derivation
and
implementation
of
analytical
gradients
for
Gaussian‐switching
(SwiG)
Conductor‐like
Polarizable
Continuum
Model
(CPCM)
with
general
nuclear
coordinate‐dependent
non‐static
radii
used
creation
van
der
Waals‐type
cavities.
This
is
done
using
recently
presented
dynamic
adjustment
continuum
solvation
(
Draco
)
scheme.
allows
efficient
geometry
optimization
reasonable
numerical
Hessian
calculations.
The
derived
gradient
implemented
in
ORCA,
therefore
easily
applicable.
validated
by
comparing
testing
optimizations
on
a
diverse
test
set,
including
small
organic
compounds,
metal‐organic
complexes,
highly
charged
species.
We
additionally
continuity
potential
energy
surface
an
example
where
very
strong
changes
occur.
computational
efficiency
investigated.
ACS Materials Letters,
Journal Year:
2024,
Volume and Issue:
6(7), P. 2905 - 2918
Published: June 10, 2024
Research
on
electrochemical
water
splitting
has
experienced
significant
growth
in
interest
transition
metal
borides,
carbides,
pnictides,
and
chalcogenides,
owing
to
their
notable
catalytic
performance.
These
materials,
collectively
called
X-ides,
are
often
considered
promising
electrocatalysts
for
the
oxygen
evolution
reaction
(OER).
However,
under
strongly
oxidizing
conditions
of
OER,
X-ides
act
as
precatalysts,
undergoing
situ
reconstruction
a
different,
catalytically
active
phase.
Discrepancies
exist
literature,
with
some
studies
claiming
absence
such
transformations.
Building
upon
previous
efforts
elucidate
performance
trends
community,
this
Perspective
discusses
more
nuanced
approach
X-ide
research,
emphasizing
need
reassess
our
understanding
chemical
stability
significance
process.
By
discussing
role
experimental
computational
databases,
we
present
strategies
predicting
stress
importance
thorough
validation.
Moreover,
highlight
use
machine
learning
extract
meaningful
insights
from
these
data
urge
community
adopt
standardized,
systematic
reporting
Finally,
provide
strategic
guidelines
directions
advance
ultimately
enhancing
future
application
sustainable
hydrogen
economy.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: July 27, 2024
Abstract
We
investigate
solvent
effects
in
the
hydrodeoxygenation
of
4-propylguaiacol
(4PG,
166
amu),
a
key
lignin-derived
monomer,
over
Ru/C
catalyst
by
combined
operando
synchrotron
photoelectron
photoion
coincidence
(PEPICO)
spectroscopy
and
molecular
dynamics
simulations.
With
without
isooctane
co-feeding,
ring-hydrogenated
2-methoxy-4-propylcyclohexanol
(172
amu)
is
first
product,
due
to
favorable
flat
adsorption
configuration
4PG
on
surface.
In
contrast,
tetrahydrofuran
(THF)—a
polar
aprotic
that
representative
those
used
for
lignin
solubilization
upgrading—strongly
coordinates
surface
at
oxygen
atom.
This
induces
local
steric
hindrance,
blocking
more
effectively,
as
it
needs
Ru
sites
than
tilted
revealed
Therefore,
THF
suppresses
benzene
ring
hydrogenation,
favoring
demethoxylation
route
yields
4-propylphenol
(136
followed
dehydroxylation
propylbenzene
(120
amu).
Solvent
selection
may
provide
new
avenues
controlling
catalytic
selectivity.
Journal of Chemical Information and Modeling,
Journal Year:
2024,
Volume and Issue:
64(9), P. 3767 - 3778
Published: April 15, 2024
In
this
work,
we
introduce
the
Solvate
Suite,
a
comprehensive
and
modular
command-line
interface
designed
for
molecular
simulation
microsolvation
modeling.
The
suite
interfaces
with
widely
used
scientific
software,
streamlining
computational
experiments
liquid
systems
through
automated
creation
of
boxes
topology
adjustable
parameters.
Furthermore,
it
has
features
graphical
statistical
analysis
simulated
properties
extraction
trajectory
configurations
various
filters.
Additionally,
introduces
innovative
strategies
modeling
multiscale
approach,
employing
equilibrated
dynamics
to
identify
favorable
solute–solvent
interactions
enabling
full
cluster
optimization
free-energy
calculations
without
imaginary
frequency
contamination.
