Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
20(12), С. 5291 - 5305
Опубликована: Июнь 4, 2024
The
significance
of
soil
organic
matter
(SOM)
in
environmental
contexts,
particularly
its
role
pollutant
adsorption,
has
prompted
an
increased
utilization
molecular
simulations
to
understand
microscopic
interactions.
This
study
introduces
a
coarse-grained
SOM
model,
parametrized
within
the
framework
versatile
Martini
3
force
field.
Utilizing
models
generated
by
Vienna
Soil
Organic
Matter
Modeler
2,
which
constructs
humic
substance
systems
from
fragment
database,
we
employed
Swarm-CG
parametrize
fragments
and
subsequently
assembled
them
into
macromolecules.
Direct
Boltzmann
inversion
(DBI)
facilitated
determination
bonded
parameters
between
fragments.
parametrization
yielded
favorable
agreement
radius
gyration
solvent-accessible
surface
area.
Transfer
free
energies
exhibited
strong
correlation
with
hexadecane–water
chloroform–water
values,
albeit
deviations
were
noted
for
octanol–water
values.
Comparing
densities
modeled
Leonardite
acid
at
atomistic
levels
revealed
promising
agreement,
higher
water
concentrations.
DBI
approach
effectively
reproduced
average
values
interactions
Radial
distribution
functions
carboxylate
groups
calcium
ions
showed
partial
however,
reproducing
certain
peaks
was
challenging
due
fixed
bead
sizes.
Detailed
analysis
different
configurations
groups,
explaining
discrepancies.
present
contribution
provides
comprehensive
insight
properties,
strengths,
weaknesses
serving
as
foundation
future
investigations
encompassing
varied
compositions.
Journal of Plant Nutrition and Soil Science,
Год журнала:
2025,
Номер
unknown
Опубликована: Апрель 26, 2025
ABSTRACT
In
soil
studies,
the
current
definition
of
microplastics
as
particles
<5
mm
was
adopted
directly
from
marine
research.
To
our
opinion,
a
more
precise
and
differentiated
size
is
needed
to
focus
studies
on
specific
challenges
plastics
cause
for
ecosystems.
As
relevant
functions
such
water,
carbon,
nutrient
retention
provision
are
mainly
controlled
by
structure,
biota,
chemical
processes
dominantly
appearing
in
micro‐
nanoscale,
we
suggest
adapting
ranges
respective
process
scales
ecosystem
studies.
Even
more,
expect
that
larger
will
not
be
incorporated
into
until
they
reach
threshold
compatible
structure
(<1000
µm,
depending
properties).
Redefining
plastic
sizes
accordance
with
International
System
Units
(SI)
should
implemented
A
unified
(1–1000
µm)
nanoplastics
nm)
set
standard
further
allow
relating
across
research
disciplines.
Journal of Chemical Theory and Computation,
Год журнала:
2024,
Номер
20(12), С. 5291 - 5305
Опубликована: Июнь 4, 2024
The
significance
of
soil
organic
matter
(SOM)
in
environmental
contexts,
particularly
its
role
pollutant
adsorption,
has
prompted
an
increased
utilization
molecular
simulations
to
understand
microscopic
interactions.
This
study
introduces
a
coarse-grained
SOM
model,
parametrized
within
the
framework
versatile
Martini
3
force
field.
Utilizing
models
generated
by
Vienna
Soil
Organic
Matter
Modeler
2,
which
constructs
humic
substance
systems
from
fragment
database,
we
employed
Swarm-CG
parametrize
fragments
and
subsequently
assembled
them
into
macromolecules.
Direct
Boltzmann
inversion
(DBI)
facilitated
determination
bonded
parameters
between
fragments.
parametrization
yielded
favorable
agreement
radius
gyration
solvent-accessible
surface
area.
Transfer
free
energies
exhibited
strong
correlation
with
hexadecane–water
chloroform–water
values,
albeit
deviations
were
noted
for
octanol–water
values.
Comparing
densities
modeled
Leonardite
acid
at
atomistic
levels
revealed
promising
agreement,
higher
water
concentrations.
DBI
approach
effectively
reproduced
average
values
interactions
Radial
distribution
functions
carboxylate
groups
calcium
ions
showed
partial
however,
reproducing
certain
peaks
was
challenging
due
fixed
bead
sizes.
Detailed
analysis
different
configurations
groups,
explaining
discrepancies.
present
contribution
provides
comprehensive
insight
properties,
strengths,
weaknesses
serving
as
foundation
future
investigations
encompassing
varied
compositions.
