Physical Chemistry Chemical Physics,
Год журнала:
2023,
Номер
25(20), С. 14005 - 14015
Опубликована: Янв. 1, 2023
A
systematic
study
of
the
entropic
penalty
for
associative
reactions
is
presented.
It
shown
that
computed
solution-phase
Gibbs
free
energies
typically
overestimate
contributions.
This
in
solution,
i.e.,
if
number
particles
decreases
along
reaction
coordinate
(sum
stoichiometric
numbers
),
originates
from
insufficient
treatment
effects
by
implicit
solvent
models.
We
propose
an
additive
correction
scheme
to
suitable
routine
applications
non-expert
users.
based
on
Garza's
formalism
entropy
[A.
J.
Garza,
Chem.
Theory
Comput.,
2019,
15,
3204.]
physically
sound
and
embedded
into
efficient
black-box
type
algorithm.
To
critically
evaluate
its
proposed
treatment,
we
compiled
experimental
benchmark
set
31
ΔrG
22
15
different
solvents.
Using
a
representative
best-practice
computational
protocol
(at
wave
function
theory
(WFT)
DLPNO-CCSD(T)
density
functional
(DFT)
revDSD-PBEP86-D4
level
with
model),
determined
sizeable
ranging
2-11
kcal
mol-1.
presented
herein,
corrected
chemical
accuracy
≤1
mol-1
(WFT
DFT).
The
same
applies
at
WFT
level.
Barriers
DFT
are
overestimated
2
(classic)
underestimated
(corrected).
effect
attributed
finding
barriers
systematically
2-3
lower
than
obtained
WFT.
Angewandte Chemie International Edition,
Год журнала:
2022,
Номер
61(42)
Опубликована: Сен. 14, 2022
Nowadays,
many
chemical
investigations
are
supported
by
routine
calculations
of
molecular
structures,
reaction
energies,
barrier
heights,
and
spectroscopic
properties.
The
lion's
share
these
quantum-chemical
applies
density
functional
theory
(DFT)
evaluated
in
atomic-orbital
basis
sets.
This
work
provides
best-practice
guidance
on
the
numerous
methodological
technical
aspects
DFT
three
parts:
Firstly,
we
set
stage
introduce
a
step-by-step
decision
tree
to
choose
computational
protocol
that
models
experiment
as
closely
possible.
Secondly,
present
recommendation
matrix
guide
choice
depending
task
at
hand.
A
particular
focus
is
achieving
an
optimal
balance
between
accuracy,
robustness,
efficiency
through
multi-level
approaches.
Finally,
discuss
selected
representative
examples
illustrate
recommended
protocols
effect
choices.
The Journal of Chemical Physics,
Год журнала:
2024,
Номер
160(11)
Опубликована: Март 21, 2024
Conformer–rotamer
sampling
tool
(CREST)
is
an
open-source
program
for
the
efficient
and
automated
exploration
of
molecular
chemical
space.
Originally
developed
in
Pracht
et
al.
[Phys.
Chem.
Phys.
22,
7169
(2020)]
as
driver
calculations
at
extended
tight-binding
level
(xTB),
it
offers
a
variety
molecular-
metadynamics
simulations,
geometry
optimization,
structure
analysis
capabilities.
Implemented
algorithms
include
procedures
conformational
sampling,
explicit
solvation
studies,
calculation
absolute
entropy,
identification
protonation
deprotonation
sites.
Calculations
are
set
up
to
run
concurrently,
providing
single-node
parallelization.
CREST
designed
require
minimal
user
input
comes
with
implementation
GFNn-xTB
Hamiltonians
GFN-FF
force-field.
Furthermore,
interfaces
any
quantum
chemistry
force-field
software
can
easily
be
created.
In
this
article,
we
present
recent
developments
code
show
selection
applications
most
important
features
program.
An
novelty
refactored
backend,
which
provides
significant
speed-up
small
or
medium-sized
drug
molecules
allows
more
sophisticated
setups,
example,
mechanics/molecular
mechanics
minimum
energy
crossing
point
calculations.
Angewandte Chemie,
Год журнала:
2022,
Номер
134(42)
Опубликована: Сен. 14, 2022
Abstract
Nowadays,
many
chemical
investigations
are
supported
by
routine
calculations
of
molecular
structures,
reaction
energies,
barrier
heights,
and
spectroscopic
properties.
The
lion's
share
these
quantum‐chemical
applies
density
functional
theory
(DFT)
evaluated
in
atomic‐orbital
basis
sets.
This
work
provides
best‐practice
guidance
on
the
numerous
methodological
technical
aspects
DFT
three
parts:
Firstly,
we
set
stage
introduce
a
step‐by‐step
decision
tree
to
choose
computational
protocol
that
models
experiment
as
closely
possible.
Secondly,
present
recommendation
matrix
guide
choice
depending
task
at
hand.
A
particular
focus
is
achieving
an
optimal
balance
between
accuracy,
robustness,
efficiency
through
multi‐level
approaches.
Finally,
discuss
selected
representative
examples
illustrate
recommended
protocols
effect
choices.
The Journal of Physical Chemistry A,
Год журнала:
2025,
Номер
unknown
Опубликована: Фев. 27, 2025
The
extended
tight
binding
(xTB)
family
of
methods
opened
many
new
possibilities
in
the
field
computational
chemistry.
Within
just
5
years,
GFN2-xTB
parametrization
for
all
elements
up
to
Z
=
86
enabled
more
than
a
thousand
applications,
which
were
previously
not
feasible
with
other
electronic
structure
methods.
xTB
provide
robust
and
efficient
way
apply
quantum
mechanics-based
approaches
obtaining
molecular
geometries,
computing
free
energy
corrections
or
describing
noncovalent
interactions
found
applicability
targets.
A
crucial
contribution
success
is
availability
within
simulation
packages
frameworks,
supported
by
open
source
development
its
program
library
packages.
We
present
comprehensive
summary
applications
capabilities
different
fields
Moreover,
we
consider
main
software
calculations,
covering
their
current
ecosystem,
novel
features,
usage
scientific
community.
Journal of Chemical Information and Modeling,
Год журнала:
2024,
Номер
64(3), С. 749 - 760
Опубликована: Янв. 11, 2024
Accurately
determining
the
global
minima
of
a
molecular
structure
is
important
in
diverse
scientific
fields,
including
drug
design,
materials
science,
and
chemical
synthesis.
Conformational
search
engines
serve
as
valuable
tools
for
exploring
extensive
conformational
space
molecules
identifying
energetically
favorable
conformations.
In
this
study,
we
present
comparison
Auto3D,
CREST,
Balloon,
ETKDG
(from
RDKit),
which
are
freely
available
engines,
to
evaluate
their
effectiveness
locating
minima.
These
employ
distinct
methodologies,
machine
learning
(ML)
potential-based,
semiempirical,
force
field-based
approaches.
To
validate
these
methods,
propose
use
collisional
cross-section
(CCS)
values
obtained
from
ion
mobility–mass
spectrometry
studies.
We
hypothesize
that
experimental
gas-phase
CCS
can
provide
evidence
likely
have
minimum
given
molecule.
facilitate
effort,
used
our
conformation
library
(GPCL)
currently
consists
full
ensembles
20
small
be
by
community
any
engine.
Further
members
GPCL
readily
created
molecule
interest
using
standard
workflow
compute
values,
expanding
ability
validation
exercises.
innovative
techniques
enhance
understanding
landscape
insights
into
performance
generation
engines.
Our
findings
shed
light
on
strengths
limitations
each
engine,
enabling
informed
decisions
utilization
various
where
accurate
determination
crucial
biological
activity
designing
targeted
interventions.
By
facilitating
identification
reliable
conformations,
study
significantly
contributes
enhancing
efficiency
accuracy
determination,
with
particular
focus
metabolite
elucidation.
The
research
also
developing
effective
workflows
predicting
structures
unknown
compounds
high
precision.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Май 1, 2024
Abstract
Autonomous
reaction
network
exploration
algorithms
offer
a
systematic
approach
to
explore
mechanisms
of
complex
chemical
processes.
However,
the
resulting
networks
are
so
vast
that
an
all
potentially
accessible
intermediates
is
computationally
too
demanding.
This
renders
brute-force
explorations
unfeasible,
while
with
completely
pre-defined
or
hard-wired
constraints,
such
as
element-specific
coordination
numbers,
not
flexible
enough
for
systems.
Here,
we
introduce
STEERING
WHEEL
guide
otherwise
unbiased
automated
exploration.
The
algorithm
intuitive,
generally
applicable,
and
enables
one
focus
on
specific
regions
emerging
network.
It
also
allows
guiding
data
generation
in
context
mechanism
exploration,
catalyst
design,
other
optimization
challenges.
demonstrated
elucidation
transition
metal
catalysts.
We
highlight
how
catalytic
cycles
reproducible
way.
objectives
fully
adjustable,
allowing
harness
both
structure-specific
(accurate)
calculations
well
broad
high-throughput
screening
possible
intermediates.
Visual,
sensitive,
and
selective
detection
of
carcinogenic
substances
is
highly
desired
in
portable
health
protection
practical
medicine
production.
However,
achieving
this
goal
presents
significant
challenges
with
the
traditional
single-mode
sensors
reported
so
far,
as
they
have
limited
sensing
mechanisms
provide
only
a
single
output
signal.
Here,
we
report
an
effective
optical
electrical
dual-mode
sensor
for
visual,
