Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
unknown
Опубликована: Сен. 16, 2024
We
report
the
formulation
and
implementation
of
an
extended
Frenkel
exciton
model
(EFEM)
designed
for
simulating
dynamics
multichromophoric
systems,
taking
into
account
possible
presence
interchromophore
charge
transfer
states,
as
well
other
states
in
which
two
chromophores
are
simultaneously
excited.
Our
approach
involves
constructing
a
Hamiltonian
based
on
calculations
performed
monomers
selected
dimers
within
aggregate.
Nonadiabatic
molecular
is
addressed
using
surface
hopping
approach,
while
electronic
wave
functions
energies
required
EFEM
computed
utilizing
semiempirical
floating
occupation
orbitals-configuration
interaction
(FOMO-CI)
structure
method.
To
validate
our
we
simulate
singlet
fission
process
trimer
2,5-bis(fluorene-9-ylidene)-2,5-dihydrothiophene
(ThBF)
molecules,
embedded
their
crystal
environment,
comparing
results
to
standard
"supermolecule"
approach.
Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
20(3), С. 1193 - 1213
Опубликована: Янв. 25, 2024
Machine
learning
(ML)
is
increasingly
becoming
a
common
tool
in
computational
chemistry.
At
the
same
time,
rapid
development
of
ML
methods
requires
flexible
software
framework
for
designing
custom
workflows.
MLatom
3
program
package
designed
to
leverage
power
enhance
typical
chemistry
simulations
and
create
complex
This
open-source
provides
plenty
choice
users
who
can
run
with
command-line
options,
input
files,
or
scripts
using
as
Python
package,
both
on
their
computers
online
XACS
cloud
computing
service
at
XACScloud.com.
Computational
chemists
calculate
energies
thermochemical
properties,
optimize
geometries,
molecular
quantum
dynamics,
simulate
(ro)vibrational,
one-photon
UV/vis
absorption,
two-photon
absorption
spectra
ML,
mechanical,
combined
models.
The
choose
from
an
extensive
library
containing
pretrained
models
mechanical
approximations
such
AIQM1
approaching
coupled-cluster
accuracy.
developers
build
own
various
algorithms.
great
flexibility
largely
due
use
interfaces
many
state-of-the-art
packages
libraries.
Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
20(2), С. 614 - 624
Опубликована: Янв. 11, 2024
This
study
investigates
velocity
adjustment
directions
after
hopping
in
surface
dynamics.
Using
fulvene
and
a
protonated
Schiff
base
(PSB4)
as
case
studies,
we
investigate
the
population
decay
reaction
yields
of
different
sets
dynamics
with
adjusted
either
nonadiabatic
coupling,
gradient
difference,
or
momentum
directions.
For
latter,
addition
to
conventional
algorithm,
investigated
performance
reduced
kinetic
energy
reservoir
approach
recently
proposed.
Our
evaluation
also
considered
approximate
coupling
vectors.
While
results
for
are
susceptible
approach,
PSB4
is
not.
We
correlated
this
dependence
topography
near
conical
intersections.
When
vectors
unavailable,
difference
direction
best
option.
If
semiempirical
vector
becomes
an
excellent
option
prevent
artificial
excess
back
hoppings.
The
precise
less
crucial
describing
than
reservoir's
size.
Journal of Chemical Theory and Computation,
Год журнала:
2023,
Номер
19(22), С. 8273 - 8284
Опубликована: Ноя. 8, 2023
The
field
of
nonadiabatic
dynamics
has
matured
over
the
last
decade
with
a
range
algorithms
and
electronic
structure
methods
available
at
moment.
While
community
currently
focuses
more
on
developing
benchmarking
new
algorithms,
underlying
controls
outcome
simulations.
Yet,
electronic-structure
sensitivity
analysis
is
typically
neglected.
In
this
work,
we
present
cyclopropanone
to
algorithms.
particular,
compare
wave
function-based
CASSCF,
FOMO-CASCI,
MS-
XMS-CASPT2,
density-functional
REKS,
semiempirical
MRCI-OM3
Landau-Zener
surface
hopping,
fewest
switches
ab
initio
multiple
spawning
informed
stochastic
selection
results
clearly
demonstrate
that
choice
significantly
influences
accuracy
for
even
when
potential
energy
surfaces
exhibit
qualitative
quantitative
similarities.
Thus,
selecting
solely
basis
mapping
can
be
misleading.
Conversely,
observe
no
discernible
differences
in
performance
across
various
methods.
Based
above
results,
discuss
present-day
practice
computational
photodynamics.
The Journal of Chemical Physics,
Год журнала:
2024,
Номер
160(15)
Опубликована: Апрель 16, 2024
This
research
examines
the
nonadiabatic
dynamics
of
cyclobutanone
after
excitation
into
n
→
3s
Rydberg
S2
state.
It
stems
from
our
contribution
to
Special
Topic
Journal
Chemical
Physics
test
predictive
capability
computational
chemistry
against
unseen
experimental
data.
Decoherence-corrected
fewest-switches
surface
hopping
was
used
simulate
with
full
and
approximated
couplings.
Several
simulation
sets
were
computed
different
electronic
structure
methods,
including
a
multiconfigurational
wavefunction
[multiconfigurational
self-consistent
field
(MCSCF)]
specially
built
describe
dissociative
channels,
multireference
semiempirical
approach,
time-dependent
density
functional
theory,
algebraic
diagrammatic
construction,
coupled
cluster.
MCSCF
predicts
slow
deactivation
state
(10
ps),
followed
by
an
ultrafast
population
transfer
S1
S0
(<100
fs).
CO
elimination
(C3
channel)
dominates
over
C2H4
formation
(C2
channel).
These
findings
radically
differ
other
which
predicted
lifetimes
10-250
times
shorter
C2
channel
predominance.
results
suggest
that
routine
methods
may
hold
low
power
for
outcome
dynamics.
Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
20(12), С. 5043 - 5057
Опубликована: Июнь 5, 2024
We
present
an
open-source
MLatom@XACS
software
ecosystem
for
on-the-fly
surface
hopping
nonadiabatic
dynamics
based
on
the
Landau–Zener–Belyaev–Lebedev
algorithm.
The
can
be
performed
via
Python
API
with
a
wide
range
of
quantum
mechanical
(QM)
and
machine
learning
(ML)
methods,
including
ab
initio
QM
(CASSCF
ADC(2)),
semiempirical
methods
(e.g.,
AM1,
PM3,
OMx,
ODMx),
many
types
ML
potentials
KREG,
ANI,
MACE).
Combinations
also
used.
While
user
build
their
own
combinations,
we
provide
AIQM1,
which
is
Δ-learning
used
out-of-the-box.
showcase
how
AIQM1
reproduces
isomerization
yield
trans-azobenzene
at
low
cost.
example
scripts
that,
in
dozens
lines,
enable
to
obtain
final
population
plots
by
simply
providing
initial
geometry
molecule.
Thus,
those
perform
optimization,
normal
mode
calculations,
condition
sampling,
parallel
trajectories
propagation,
analysis,
result
plotting.
Given
capabilities
MLatom
training
different
models,
this
seamlessly
integrated
into
protocols
building
models
dynamics.
In
future,
deeper
more
efficient
integration
Newton-X
will
vast
functionalities
dynamics,
such
as
fewest-switches
hopping,
facilitate
similar
workflows
API.
Journal of Chemical Theory and Computation,
Год журнала:
2023,
Номер
19(9), С. 2430 - 2445
Опубликована: Апрель 18, 2023
We
tested
the
effect
of
different
ways
sampling
initial
conditions
in
surface
hopping
simulations,
with
a
focus
on
energy
distributions
and
treatment
zero
point
(ZPE).
As
test
case,
we
chose
gas
phase
photodynamics
azomethane,
which
features
processes
occurring
overlapping
time
scales:
geometry
relaxation
excited
state,
internal
conversion,
photoisomerization,
fast
slow
dissociation.
The
based
semiempirical
method,
had
sufficiently
long
duration
(10
ps)
to
encompass
all
above
processes.
several
variants
methods
quantum
mechanical
(QM)
nuclear
coordinates
q
momenta
p,
yield,
at
least
average
over
large
set,
correct
QM
energy,
namely
ZPE
when
starting
from
ground
vibrational
state.
compared
samplings
classical
Boltzmann
(CB)
distribution
obtained
by
thermostated
trajectory,
whereby
thermal
effects
are
taken
into
account,
but
is
utterly
ignored.
found
that
most
CB
approaches
yield
similar
results
as
short
dynamics
decay
lifetimes,
whereas
rate
state
dissociation
reaction
CH3NNCH3
→
CH3NN
+
CH3
sharply
affected
method.
With
fraction
trajectories
dissociate
promply
(<1
after
rates
order
10-1
ps-1
first
ps.
Instead,
much
smaller
prompt
dissociations
lower
times.
provided
evidence
"leaks"
high
frequency
modes
reactive
ones
(N-C
bond
elongations),
therefore
unphysically
increasing
samplings.
show
an
effective
way
take
account
avoid
"leaking"
problem
add
potential
surfaces
function
relevant
coordinates.
Then,
can
be
done
usual,
so
this
approach
suitable
also
for
condensed
dynamics.
In
tests
present
here,
correction
method
yields
intermediate
between
uncorrected
Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
20(11), С. 4396 - 4426
Опубликована: Май 31, 2024
We
reconsider
recent
methods
by
which
direct
dynamics
calculations
of
electronically
nonadiabatic
processes
can
be
carried
out
while
requiring
only
adiabatic
potential
energies
and
their
gradients.
show
that
these
understood
in
terms
a
new
generalization
the
well-known
semiclassical
Ehrenfest
method.
This
is
convenient
because
it
eliminates
need
to
evaluate
electronic
wave
functions
matrix
elements
along
mixed
quantum-classical
trajectories.
The
approximations
procedures
enabling
this
advance
are
curvature-driven
approximation
time-derivative
coupling,
generalized
method,
gradient
correction
scheme
called
(TDM)
scheme.
When
spin–orbit
coupling
present,
one
carry
fully
basis
using
gradients
calculated
without
plus
elements.
Even
when
neglected,
method
useful
allows
structure
for
vectors
unavailable.
In
order
place
considerations
context,
article
starts
with
review
background
material
on
trajectory
surface
hopping,
scheme,
incorporating
decoherence.
consider
both
internal
conversion
intersystem
crossing.
also
several
examples
from
our
group
successful
applications
approximation.
Chemical Communications,
Год журнала:
2024,
Номер
60(24), С. 3240 - 3258
Опубликована: Янв. 1, 2024
This
article
gives
a
perspective
on
the
progress
of
AI
tools
in
computational
chemistry
through
lens
author's
decade-long
contributions
put
wider
context
trends
this
rapidly
expanding
field.
over
last
decade
is
tremendous:
while
ago
we
had
glimpse
what
was
to
come
many
proof-of-concept
studies,
now
witness
emergence
AI-based
that
are
mature
enough
make
faster
and
more
accurate
simulations
increasingly
routine.
Such
turn
allow
us
validate
even
revise
experimental
results,
deepen
our
understanding
physicochemical
processes
nature,
design
better
materials,
devices,
drugs.
The
rapid
introduction
powerful
rise
unique
challenges
opportunities
discussed
too.
The Journal of Chemical Physics,
Год журнала:
2024,
Номер
160(13)
Опубликована: Апрель 4, 2024
Computer
simulation
has
long
been
an
essential
partner
of
ultrafast
experiments,
allowing
the
assignment
microscopic
mechanistic
detail
to
low-dimensional
spectroscopic
data.
However,
ability
theory
make
a
priori
predictions
experimental
results
is
relatively
untested.
Herein,
as
part
community
challenge,
we
attempt
predict
signal
upcoming
photochemical
experiment
using
state-of-the-art
in
context
preexisting
Specifically,
employ
ab
initio
Ehrenfest
with
collapse
block
mixed
quantum-classical
simulations
describe
real-time
evolution
electrons
and
nuclei
cyclobutanone
following
excitation
3s
Rydberg
state.
The
gas-phase
electron
diffraction
(GUED)
simulated
for
direct
comparison
at
Stanford
Linear
Accelerator
Laboratory.
Following
initial
ring-opening,
dissociation
via
two
distinct
channels
observed:
C3
channel,
producing
cyclopropane
CO,
C2
CH2CO
C2H4.
Direct
calculations
GUED
indicate
how
ring-opened
intermediate,
products,
products
can
be
discriminated
signal.
We
also
report
analysis
anticipated
errors
our
predictions:
without
knowledge
result,
which
features
spectrum
do
feel
confident
have
predicted
correctly,
might
wrong?