@article{D2CP00698G,
author = {Pavlov, Sergey and Danilova, Valentina and
Sivakov, Vyacheslav and Kislenko, Sergey},
journal = {Phys. Chem. Chem. Phys.},
number = {27},
pages = {16746--16754},
publisher = {The Royal Society of Chemistry},
title = {{The effect of a mixture of an ionic liquid and
organic solvent on oxygen reduction reaction
kinetics}},
volume = {24},
year = {2022},
abstract = {Li–O2 batteries attract great attention due to
their promising theoretical energy density. One of
the main obstacles on the way to achieving high
energy density and good cyclability is positive
electrode passivation by the Li2O2 discharge product
as well as the presence of parasitic reactions that
degrade electrode and electrolyte materials. To
overcome these issues new electrolytes are being
extensively searched for to ensure the bulk-mediated
mechanism of the oxygen reduction reaction and
inhibition of parasitic reactions. Different
additives to organic solvents can significantly
change the properties of electrolytes. This work is
devoted to the effect of ionic liquids (ILs){,} which
are proposed as an additive to the solvent due to
their excellent solvation properties{,} high
stability{,} low volatility and flammability. Using
molecular dynamics simulations we investigate
mixtures of the Pyr14TFSI ionic liquid and
dimethoxyethane (DME) with different volume fractions
of the IL. Our calculations show that the presence of
the ionic liquid in the electrolyte stabilises
solvation shells around the ions{,} both involved in
the oxygen reduction and parasitic reactions{,}
slowing down the kinetics of Li+ and O2−
association. This makes the usage of such mixtures
promising for electrolyte design for Li–O2
batteries.},
doiurl = {10.1039/D2CP00698G},
url = {http://dx.doi.org/10.1039/D2CP00698G},
}
@article{gao2022,
author = {{Zhiyi Gao, Zongjing Lu, Yining Zhang, Jing Xia, Xuejing
Zhang, Chao Sun, Yijun Yang, Yong Xu, Ke Wang, Xi Wang}, Jiannian Yao},
journal = {Chem. Eng. Sci.},
pages = {117633},
title = {{Regulating interfacial desolvation via a weakly
coordinating solvent molecule enhances Li-ion storage
at subzero temperatures}},
volume = {254},
year = {2022},
}
@article{organic_diff_my,
author = {Orekhov, M A},
journal = {J. Mol. Liq.},
pages = {117647},
publisher = {Elsevier B.V.},
title = {{Effect of divalent ion coordination on ion diffusion
in organic liquids}},
volume = {343},
year = {2021},
doiurl = {10.1016/j.molliq.2021.117647},
issn = {0167-7322},
url = {https://doi.org/10.1016/j.molliq.2021.117647},
}
@article{Orekhov2017b,
author = {Orekhov, M A},
journal = {Phys. Chem. Chem. Phys},
pages = {32398--32403},
publisher = {Royal Society of Chemistry},
title = {{Fluctuation enhancement of ion diffusivity in
liquids}},
volume = {19},
year = {2017},
doiurl = {10.1039/C7CP07170A},
issn = {1463-9076},
url = {http://dx.doi.org/10.1039/C7CP07170A},
}
@article{Liu2013,
author = {Liu, Hongjun and Maginn, Edward},
journal = {J. Chem. Phys.},
number = {11},
pages = {114508},
title = {{Effect of ion structure on conductivity in
lithium-doped ionic liquid electrolytes: A molecular
dynamics study}},
volume = {139},
year = {2013},
abstract = {Molecular dynamics simulations were performed to
examine the role cation and anion structure have on
the performance of ionic liquid (IL) electrolytes for
lithium conduction over the temperature range of
320-450 K. Two model ionic liquids were studied:
1-butyl-3-methylimidazolium
bis[(trifluoromethyl)sulfonyl]imide ([bmim][Tf2N])
and 1-butyl-4-methylpyridinium pyrrolide
([bmpyr][pyl]) doped with Li[Tf2N] and Li[pyl],
respectively. The results have demonstrated that the
Li(+) doped IL containing the planar [bmpyr] cation
paired with the planar [pyl] anion significantly
outperformed the [bmim][Tf2N] IL. The different
coordination of Li(+) with the [Tf2N](-) or [pyl](-)
anions produces a remarkable change in IL structure
with a concomitant effect on the transport of all
ions. For the doped [bmim][Tf2N], each Li(+) is
coordinated by four oxygen atoms from [Tf2N](-)
anions. Formation of a rigid structure between Li(+)
and [Tf2N](-) induces a decrease in the mobility of
all ions. In contrast, for the doped [bmpyr][pyl],
each Li(+) is coordinated by two nitrogen atoms from
[pyl](-) anions. The original alternating structure
cation∣anion∣cation in the neat [bmpyr][pyl] is
replaced by another alternating structure
cation∣anion∣Li(+)∣anion∣cation in the doped
[bmpyr][pyl]. Increases of Li(+) mole fraction in
doped [bmpyr][pyl] affects the dynamics to a much
lesser extent compared with [bmim][Tf2N] and leads to
reduced diffusivities of cations and anions, but
little change in the dynamics of Li(+). More
importantly, the calculations predict that the Li(+)
ion conductivity of doped [bmpyr][pyl] is comparable
to that observed in organic liquid electrolytes and
is about an order of magnitude higher than that of
doped [bmim][Tf2N]. Such Li(+) conductivity
improvement suggests that this and related ILs may be
promising candidates for use as electrolytes in
lithium ion batteries and capacitors.},
doiurl = {10.1063/1.4821155},
isbn = {0021-9606},
issn = {00219606},
}
@article{diffusion_jml,
author = {Dai, Jian-xing and Zhang, Wei and Ren, Cui-lan and
Guo, Xiao-jing},
journal = {J. Mol. Liq.},
pages = {114059},
publisher = {Elsevier B.V},
title = {{Prediction of dynamics properties of ThF4-based
fluoride molten salts by molecular dynamic
simulation}},
year = {2020},
doiurl = {10.1016/j.molliq.2020.114059},
issn = {0167-7322},
url = {https://doi.org/10.1016/j.molliq.2020.114059},
}
@article{Kislenko2019,
author = {Smirnov, Vladimir and Kislenko, Sergey},
journal = {ChemPhysChem},
pages = {1960--1966},
title = {{Effect of Cation Size on Solvation and Association
with Superoxide Anion in Aprotic Solvents}},
volume = {20},
year = {2019},
doiurl = {10.1002/cphc.201900389},
issn = {1439-4235},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/
cphc.201900389},
}
@article{Kumar2019,
author = {Kumar, Parveen and Yashonath, S.},
journal = {J. Mol. Liq.},
pages = {506--515},
publisher = {Elsevier B.V},
title = {{Ionic conductivity in aqueous electrolyte solutions:
Insights from computer simulations}},
volume = {277},
year = {2019},
abstract = {There exist a large amount of data on conductivity of
various ions in aqueous and non-aqueous solvents as a
function of ionic radius, pressure, temperature,
ionic concentration, etc. Because of its importance
in chemistry, biology, electrochemistry and a number
of other areas, a consistent picture of how the
various factors influence the conductivity is
essential. We present detailed molecular dynamics
simulations of ions in water in order to understand
the influence of three factors: (i) ionic radius (ii)
temperature and (iii) pressure. We propose an
alternative explanation for the variation of ionic
conductivity as a function of ionic radius for ions
in water. The explanation is based on the Levitation
Effect which arises from mutual cancellation of
forces on the diffusant or ions when the ions are of
the same radius as the bottleneck present in the
solvent. This theoretical framework not only accounts
for the variation of conductivity with ionic radius
but also its variation with pressure. Experimental
data on variation of ionic conductivity shows
contrasting dependence on pressure for ions of
different radius. We show that the proposed
theoretical framework also accounts for the variation
of ionic conductivity as a function of pressure for
ions of different radius. Thus, we have been able to
propose a theoretical framework which unifies our
understanding of three different factors, namely,
ionic radius, temperature and pressure.},
doiurl = {10.1016/j.molliq.2018.12.090},
issn = {01677322},
url = {https://doi.org/10.1016/j.molliq.2018.12.090},
}
@article{Borodin2015,
author = {Borodin, Oleg and Olguin, Marco and Spear, Carrie E. and
Leiter, Kenneth W. and Knap, Jaroslaw},
journal = {Nanotechnology},
number = {35},
pages = {354003},
publisher = {IOP Publishing},
title = {{Towards high throughput screening of electrochemical
stability of battery electrolytes}},
volume = {26},
year = {2015},
abstract = {High throughput screening of solvents and additives
with potential applications in lithium batteries is
reported. The initial test set is limited to
carbonate and phosphate-based compounds and focused
on their electrochemical properties. Solvent
stability towards first and second reduction and
oxidation is reported from density functional theory
(DFT) calculations performed on isolated solvents
surrounded by implicit solvent. The reorganization
energy is estimated from the difference between
vertical and adiabatic redox energies and found to be
especially important for the accurate prediction of
reduction stability. A majority of tested compounds
had the second reduction potential higher than the
first reduction potential indicating that the second
reduction reaction might play an important role in
the passivation layer formation. Similarly, the
second oxidation potential was smaller for a
significant subset of tested molecules than the first
oxidation potential. A number of potential sources of
errors introduced during screening of the electrolyte
electrochemical properties were examined. The
formation of lithium fluoride during reduction of
semifluorinated solvents such as fluoroethylene
carbonate and the H-transfer during oxidation of
solvents were found to shift the electrochemical
potential by 1.5-2 V and could shrink the
electrochemical stability window by as much as 3.5 V
when such reactions are included in the screening
procedure. The initial oxidation reaction of ethylene
carbonate and dimethyl carbonate at the surface of
the completely de-lithiated
LiNi0.5Mn1.5O4 high
voltage spinel cathode was examined using DFT.
Depending on the molecular orientation at the cathode
surface, a carbonate molecule either exhibited
deprotonation or was found bound to the transition
metal via its carbonyl oxygen.},
doiurl = {10.1088/0957-4484/26/35/354003},
issn = {13616528},
url = {http://dx.doi.org/10.1088/0957-4484/26/35/354003},
}
@article{Martinez-Crespo2022,
author = {Mart{\'{i}}nez-Crespo, Pablo and
Otero-Lema, Mart{\'{i}}n and Cabeza, Oscar and
Montes-Campos, Hadri{\'{a}}n and Varela, Luis M.},
journal = {J. Mol. Liq.},
pages = {119188},
title = {{Structure, dynamics and ionic conductivities of
ternary ionic liquid/lithium salt/DMSO mixtures}},
volume = {359},
year = {2022},
abstract = {In this paper we report classical Molecular Dynamics
and ab initio Density Functional Theory simulations
of the structure and single particle dynamics of
ternary mixtures of a protic (ethylammonium nitrate,
EAN) and an aprotic (1-Ethyl-3-methylimidazolium
tetrafluoroborate, EMIMBF4) ionic liquid, lithium
salts with common anion and a molecular cosolvent,
dimethyl sulfoxide (DMSO). The coordination numbers
and electrical conductivities of the different
mixtures have been calculated throughout the whole
concentration range, and the differences between
mixtures with the protic and aprotic ionic liquids
were analyzed. In both cases, the evolution of the
electrical conductivity is seen to correlate well
with the formation of mixed tetrahedral solvation
complexes of lithium cations with ionic liquid anions
and cosolvent molecules. The differences in the
solvation and charge transport mechanisms in hydrogen
bonded mixtures and those based in the aprotic ionic
liquid are analyzed. Our conclusions indicate that
the major feature behind the electrical conductivity
of the ternary mixtures is the composition of the
solvation shell of the metal cations in the mixtures
and the rate at which anions in it are replaced by
DMSO molecules.},
doiurl = {10.1016/j.molliq.2022.119188},
issn = {01677322},
}
@article{Bakulin2021,
author = {Bakulin, I. K. and Kondratyuk, N. D. and
Lankin, A. V. and Norman, G. E.},
journal = {J. Phys.: Conf. Ser.},
number = {1},
title = {{Molecular dynamics simulation of ion binding in
aqueous solution of 18-crown-6 ether}},
volume = {1787},
year = {2021},
abstract = {Crown ethers are unique compounds with exceptional
ion binding properties. We investigate the 18-crown-6
ether molecule binding selectivity for a set of
alkali ions (K+, Rb+, Cs+). We employ combination of
umbrella sampling technique with the weighted
histogram analysis method to derive free energies of
ion-ether association. The obtained results are in a
good agreement with experimental values available and
represent the ion selectivity feature of the
18-crown-6 ether.},
doiurl = {10.1088/1742-6596/1787/1/012010},
issn = {17426596},
}
@article{Kondratyuk2016,
author = {Kondratyuk, N D and Norman, G E and Stegailov, V V},
journal = {Polymer Science Series A},
number = {5},
pages = {825--836},
title = {{Microscopic Mechanisms of Diffusion of Higher
Alkanes}},
volume = {56},
year = {2016},
doiurl = {10.1134/S0965545X16050072},
issn = {0965-545X},
}
@article{Kondratyuk2016a,
author = {Kondratyuk, Nikolay D. and Norman, Genri E. and
Stegailov, Vladimir V.},
journal = {J. Chem. Phys.},
number = {20},
pages = {204504},
title = {{Self-consistent molecular dynamics calculation of
diffusion in higher n -alkanes}},
volume = {145},
year = {2016},
doiurl = {10.1063/1.4967873},
issn = {00219606},
url = {http://dx.doi.org/10.1063/1.4967873},
}
@article{Garkul2022,
author = {Garkul, Anastasiia and Stegailov, Vladimir},
journal = {Sci. Rep.},
pages = {13325},
publisher = {Nature Publishing Group UK},
title = {{Molecular dynamics analysis of elastic properties
and new phase formation during amorphous ices
transformations}},
volume = {12},
year = {2022},
abstract = {Unlike conventional first-order phase transitions,
the kinetics of amorphous-amorphous transitions has
been much less studied. The ultrasonic experiments on
the transformations between low-density and
high-density amorphous ice induced by pressure or
heating provided the pressure and temperature
dependencies of elastic moduli. In this article, we
make an attempt to build a microscopic picture of
these experimentally studied transformations using
the molecular dynamics method with the TIP4P/Ice
water model. We study carefully the dependence of the
results of elastic constants calculations on the
deformation rates. The system size effects are
considered as well. The comparison with the
experimental data enriches our understanding of the
transitions observed. Our modeling gives new
information about the formation mechanisms of new
phase clusters during the transition between
low-density and high-density amorphous ices. We
analyse the applicability of the term
“nucleation” for these processes.},
doiurl = {10.1038/s41598-022-17666-2},
isbn = {0123456789},
issn = {20452322},
url = {https://doi.org/10.1038/s41598-022-17666-2},
}
@article{Kuksin2005,
author = {Kuksin, A. Y. and Morozov, I. V. and Norman, G. E. and
Stegailov, V. V. and Valuev, I. A.},
journal = {Mol Simul},
number = {14-15},
pages = {1005--1017},
title = {{Standards for molecular dynamics modelling and
simulation of relaxation}},
volume = {31},
year = {2005},
abstract = {An attempt is made to formulate a set of requirements
for simulation and modelling of relaxation in dense
media. Each requirement is illustrated by examples of
numerical simulation of particles with different
types of interaction given by soft-sphere,
Lennard-Jones, embedded atom method or Coulomb
potential. The approaches developed are expected to
be universal for some classes of relaxation processes
in liquids, fluids, crystals and plasmas.},
doiurl = {10.1080/08927020500375259},
issn = {08927022},
}
@article{Lankin2015,
author = {Lankin, A V and Norman, G E and Orekhov, M A},
journal = {Journal of Physics: Conference Series},
pages = {12155},
title = {{Temporal and spatial properties of ion solvation in
simple liquids}},
volume = {653},
year = {2015},
doiurl = {10.1088/1742-6596/653/1/012155},
issn = {1742-6588},
url = {http://stacks.iop.org/1742-6596/653/i=1/a=012155?
key=crossref.305acae7afb24a721902f0c5f935e109},
}
@article{2021,
author = {Орехов, М. А.},
journal = {ЖФХ},
number = {10},
pages = {1538--1543},
title = {{Координационные Числа
Двухвалентных Ионов В
Органических Растворителях}},
volume = {95},
year = {2021},
doiurl = {10.31857/s0044453721100204},
issn = {0044-4537},
language = {russian},
}
@article{Reddy2012,
author = {Reddy, Sandeep K. and Balasubramanian, Sundaram},
journal = {J. Phys. Chem. B},
number = {51},
pages = {14892--14902},
title = {{Liquid dimethyl carbonate: A quantum chemical and
molecular dynamics study}},
volume = {116},
year = {2012},
abstract = {A density functional theory based Car-Parrinello
molecular dynamics simulation of liquid dimethyl
carbonate, an environmentally benign solvent, has
been carried out to study its structure and dynamics.
Conformational excitations of the molecule have been
probed in both its gas and liquid phases. While the
cis-cis conformer is the global energy minimum and,
thus, the most predominant, at ambient conditions a
few percent of molecules are present in the cis-trans
conformation as well. The latter possesses a dipole
moment of around 4.5 D in the liquid state, a value
that is nearly five times as large as that for the
cis-cis conformer. Dipole-dipole interactions play a
crucial role in the formation of small hydrogen
bonded clusters of cis-trans conformers in the
liquid. The vibrational spectrum of liquid dimethyl
carbonate has been obtained from the trajectory and
is shown to agree quite well with available
experimental data. {\textcopyright} 2012 American
Chemical Society.},
doiurl = {10.1021/jp309374m},
issn = {15205207},
}
@article{Klasczyk2010,
author = {Klasczyk, Benjamin and Knecht, Volker},
journal = {J. Chem. Phys.},
number = {2},
pages = {0--12},
title = {{Kirkwood-Buff derived force field for alkali
chlorides in simple point charge water}},
volume = {132},
year = {2010},
abstract = {Solvated ions are a fundamental constituent of many
biological systems. An important class consists of
the alkali cations. In particular, potassium (K +) is
the most abundant ion in the cytoplasm, whereas
lithium (Li+), rubidium (Rb+), and cesium (Cs+) are
of fundamental physicochemical and medical relevance.
A powerful tool to understand ion specificity and
cellular systems on a microscopic level is provided
by molecular dynamics simulations. Previously,
reliable force field parameters for Li+, K+, Rb+, and
Cs+ in aqueous solution have not been available for
the simple point charge (SPC) water model widely used
in conjunction with the GROMOS force field. We used
the Kirkwood-Buff theory to develop force fields for
Li+, K+, Rb+, and Cs+ in SPC water to reproduce
experimental data on respective aqueous alkali
chloride solutions (LiCl, KCl, RbCl, CsCl). The force
field developed reproduces many of the known
properties of alkali metal chlorides solutions
including densities and partial molar volumes. Our
force field is shown to be superior to other common
alkali chloride force fields in terms of reproducing
the activity derivative, as a prerequisite for a
realistic measure of ion-solute association
underlying ion-specific phenomena (Hofmeister
effects). For lithium and potassium, the ionic radii
from cation-water oxygen pair correlation functions
and hydration numbers are well reproduced. The force
field developed will be useful for modeling
physiological conditions and ion-specific phenomena
for biomolecular systems. {\textcopyright} 2010
American Institute of Physics.},
doiurl = {10.1063/1.3273903},
issn = {00219606},
}
@article{E.V.Kuzminaa,
author = {Kuzmina, E. V. and Karaseva, E. V. and
Kolosnitsyn, V. S.},
journal = {Russ. J. Phys. Chem. A},
number = {1},
pages = {115--124},
title = {{Molecular Dynamics Studies of the Physicochemical
Properties and Structure of the 1 M LiClO4 Solution
in Sulfolane}},
volume = {96},
year = {2022},
abstract = {Abstract: The effect of the force field, atomic
charges of sulfolane and perchlorate anion, and scale
of ionic charges on the results of molecular dynamics
(MD) simulation of the physicochemical properties of
a 1 M LiClO4 solution in sulfolane was evaluated. The
simulation was performed using the OPLS-AA, Amber
(GAFF), Charmm, and Gromos force fields. The best
correlation between the calculated and experimental
physicochemical properties of the solution was
obtained using the OPLS-AA force field, the atomic
charges calculated by the B3LYP/aug-cc-pVTZ method,
and with ionic charges scaled by 80% as default
charges (±1.0). The coordination number of the
lithium cation with respect to sulfolane was
calculated: 5.3 with ionic charges scaled by 100% and
4.7 for 80%. It was shown that sulfolane is
coordinated to the lithium cation by one oxygen atom
of the sulfone group.},
doiurl = {10.1134/S0036024422010174},
issn = {1531863X},
}
@article{GROMACS,
author = {Berendsen, H.J.C. and van der Spoel, D and
van Drunen, R},
journal = {Comput. Phys. Commun.},
number = {1-3},
pages = {43--56},
title = {{GROMACS: A message-passing parallel molecular
dynamics implementation}},
volume = {91},
year = {1995},
}
@article{Jorgensen1996,
author = {Jorgensen, William L. and Maxwell, David S. and
Tirado-Rives, Julian},
journal = {J. Am. Chem. Soc.},
number = {45},
pages = {11225--11236},
title = {{Development and testing of the OPLS all-atom force
field on conformational energetics and properties of
organic liquids}},
volume = {118},
year = {1996},
abstract = {The parametrization and testing of the OPLS all-atom
force field for organic molecules and peptides are
described. Parameters for both torsional and
nonbonded energetics have been derived, while the
bond stretching and angle bending parameters have
been adopted mostly from the AMBER all-atom force
field. The torsional parameters were determined by
fitting to rotational energy profiles obtained from
ab initio molecular orbital calculations at the
RHF/6-31G*//RHF/6-31G* level for more than 50 organic
molecules and ions. The quality of the fits was high
with average errors for conformational energies of
less than 0.2 kcal/mol. The force-field results for
molecular structures are also demonstrated to closely
match the ab initio predictions. The nonbonded
parameters were developed in conjunction with Monte
Carlo statistical mechanics simulations by computing
thermodynamic and structural properties for 34 pure
organic liquids including alkanes, alkenes, alcohols,
ethers, acetals, thiols, sulfides, disulfides,
aldehydes, ketones, and amides. Average errors in
comparison with experimental data are 2% for heats of
vaporization and densities. The Monte Carlo
simulations included sampling all internal and
intermolecular degrees of freedom. It is found that
such non-polar and monofunctional systems do not show
significant condensed-phase effects on internal
energies in going from the gas phase to the pure
liquids.},
doiurl = {10.1021/ja9621760},
issn = {00027863},
}
@article{Malde2011,
author = {Malde, Alpeshkumar K and Zuo, Le and Breeze, Matthew and
Stroet, Martin and Poger, David and Nair, Pramod C and
Oostenbrink, Chris and Mark, Alan E},
journal = {J. Chem. Theory Comput.},
number = {12},
pages = {4026--4037},
title = {{An Automated Force Field Topology Builder (ATB) and
Repository: Version 1.0}},
volume = {7},
year = {2011},
abstract = {The Automated force field Topology Builder (ATB,
http://compbio.biosci.uq.edu.au/atb) is a
Web-accessible server that can provide topologies and
parameters for a wide range of molecules appropriate
for use in molecular simulations, computational drug
design, and X-ray refinement. The ATB has three
primary functions: (1) to act as a repository for
molecules that have been parametrized as part of the
GROMOS family of force fields, (2) to act as a
repository for pre-equilibrated systems for use as
starting configurations in molecular dynamics
simulations (solvent mixtures, lipid systems
pre-equilibrated to adopt a specific phase, etc.),
and (3) to generate force field descriptions of novel
molecules compatible with the GROMOS family of force
fields in a variety of formats (GROMOS, GROMACS, and
CNS). Force field descriptions of novel molecules are
derived using a multistep process in which results
from quantum mechanical (QM) calculations are
combined with a knowledge-based approach to ensure
compatibility (as far as possible) with a specific
parameter set of the GROMOS force field. The ATB has
several unique features: (1) It requires that the
user stipulate the protonation and tautomeric states
of the molecule. (2) The symmetry of the molecule is
analyzed to ensure that equivalent atoms are assigned
identical parameters. (3) Charge groups are assigned
automatically. (4) Where the assignment of a given
parameter is ambiguous, a range of possible
alternatives is provided. The ATB also provides
several validation tools to assist the user to assess
the degree to which the topology generated may be
appropriate for a given task. In addition to
detailing the steps involved in generating a force
field topology compatible with a specific GROMOS
parameter set (GROMOS 53A6), the challenges involved
in the automatic generation of force field parameters
for atomic simulations in general are discussed.},
}
@article{LigPar,
author = {Dodda, Leela S. and Cabeza de Vaca, Israel and
Tirado-Rives, Julian and Jorgensen, William L.},
journal = {Nucleic Acids Research},
month = {04},
number = {W1},
pages = {W331-W336},
title = {{LigParGen web server: an automatic OPLS-AA parameter
generator for organic ligands}},
volume = {45},
year = {2017},
abstract = {{The accurate calculation of protein/nucleic
acid–ligand interactions or condensed phase
properties by force field-based methods require a
precise description of the energetics of
intermolecular interactions. Despite the progress
made in force fields, small molecule parameterization
remains an open problem due to the magnitude of the
chemical space; the most critical issue is the
estimation of a balanced set of atomic charges with
the ability to reproduce experimental properties. The
LigParGen web server provides an intuitive interface
for generating OPLS-AA/1.14*CM1A(-LBCC) force field
parameters for organic ligands, in the formats of
commonly used molecular dynamics and Monte Carlo
simulation packages. This server has high value for
researchers interested in studying any phenomena
based on intermolecular interactions with ligands via
molecular mechanics simulations. It is free and open
to all at jorgensenresearch.com/ligpargen, and has no
login requirements.}},
doiurl = {10.1093/nar/gkx312},
issn = {0305-1048},
url = {https://doi.org/10.1093/nar/gkx312},
}
@article{Yeh2004,
author = {Yeh, In-Chul and {and Gerhard Hummer}},
journal = {J. Phys. Chem. B},
number = {40},
pages = {15873},
title = {{System-Size Dependence of Diffusion Coefficients and
Viscosities from Molecular Dynamics Simulations with
Periodic Boundary Conditions}},
volume = {108},
year = {2004},
doiurl = {10.1021/jp0477147},
url = {http://dx.doi.org/10.1021/jp0477147},
}
@article{Yeh2004a,
author = {Yeh, In-Chul and Hummer, Gerhard},
journal = {Biophys. J.},
number = {2},
pages = {681--689},
publisher = {Elsevier},
title = {{Diffusion and electrophoretic mobility of
single-stranded RNA from molecular dynamics
simulations.}},
volume = {86},
year = {2004},
abstract = {Hydrodynamic properties of small single-stranded RNA
homopolymers with three and six nucleotides in free
solution are determined from molecular dynamics
simulations in explicit solvent. We find that the
electrophoretic mobility increases with increasing
RNA length, consistent with experiment. Diffusion
coefficients of RNA, corrected for finite-size
effects and solvent viscosity, agree well with those
estimated from experiments and hydrodynamic
calculations. The diffusion coefficients and
electrophoretic mobilities satisfy a Nernst-Einstein
relation in which the effective charge of RNA is
reduced by the charge of transiently bound
counterions. Fluctuations in the counterion
atmosphere are shown to enhance the diffusive spread
of RNA molecules drifting along the direction of the
external electric field. As a consequence, apparent
diffusion coefficients measured by capillary zone
electrophoresis can be significantly larger than the
actual values at certain experimental conditions.},
doiurl = {10.1016/S0006-3495(04)74147-8},
isbn = {0006-3495},
issn = {00063495},
url = {http://dx.doi.org/10.1016/S0006-3495(04)74147-8},
}
@article{Dunweg1993,
author = {D{\"{u}}nweg, Burkhard and Kremer, Kurt},
journal = {J. Chem. Phys.},
number = {9},
pages = {6983--6997},
title = {{Molecular dynamics simulation of a polymer chain in
solution}},
volume = {99},
year = {1993},
abstract = {Results of a molecular dynamics simulation of a
single polymer chain in a good solvent are presented.
The latter is modeled explicitly as a bath of
particles. This system provides a first‐principles
microscopic test of the hydrodynamic Kirkwood–Zimm
theory of the chain's Brownian motion. A 30 monomer
chain is studied in 4066 solvent particles as well as
40/4056 and 60/7940 systems. The density was chosen
rather high, in order to come close to the ideal
situation of incompressible flow, and to ensure that
diffusive momentum transport is much faster than
particle motions. In order to cope with the numerical
instability of microcanonical algorithms, we generate
starting states by a Langevin simulation that
includes a coupling to a heat bath, which is switched
off for the analysis of the dynamics. The long range
of the hydrodynamic interaction induces a large
effect of finite box size on the diffusive
properties, which is observable for the diffusion
constants of both the chain and the solvent
particles. The Kirkwood theory of the diffusion
constant, as well as the Akcasu et al. theory of the
initial decay rate in dynamic light scattering are
generalized for the finite box case, replacing the
Oseen tensor by the corresponding Ewald sum. In
leading order, the finite‐size corrections are
inversely proportional to the linear box dimensions.
With this modification of the theory taken into
account, the Kirkwood formula for the diffusion
constant is verified. Moreover, the monomer motions
exhibit a scaling that is much closer to Zimm than to
Rouse exponents (t2/3 law in the mean square
displacement; decay rate of the dynamic structure
factor ∝k3). However, the prefactors are not
consistent with the theory, indicating that (on the
involved short length scales) the dynamics is more
complex than the simple hydrodynamic description
suggests.},
doiurl = {10.1063/1.465445},
isbn = {0021-9606},
issn = {00219606},
}
@article{Orekhov2021,
author = {Orekhov, M. A.},
journal = {J. Mol. Liq.},
pages = {114554},
title = {{Improving molecular dynamics calculation of
diffusivity in liquids with theoretical models}},
volume = {322},
year = {2021},
abstract = {An effect of the collective motions on the variance
of diffusivity in liquids is considered. It is shown
theoretically and with simulation that collective
fluctuations increase statistical uncertainty of
diffusivity in liquids. On this basis we develop
approach that combines molecular dynamics and
theoretical models to calculate diffusion coefficient
in liquids. We decompose diffusivity into a low scale
molecular part and a large scale hydrodynamic part.
The low scale term is calculated with the molecular
dynamics. It is performed using a small simulation
box with less than 100 particles. Local molecular
motions appear in such simulations while collective
hydrodynamical fluctuations are absent. The large
scale hydrodynamics is included with a theoretical
model. Thus, molecular dynamics term includes only
molecular processes such as rearrangements of
molecules, and hydrodynamical term includes
collective processes. This approach provides lower
statistical uncertainty compared with simulations of
large systems. The improvement in statistical
accuracy is shown theoretically and confirmed with
simulations. It is connected to the relation between
diffusivity due to local molecular processes and
diffusivity due to hydrodynamics. To illustrate the
application of this approach, we compute the
self-diffusion coefficient in Lennard-Jones liquid
and liquid water, diffusivity of divalent ions in
aqueous solutions.},
doiurl = {10.1016/j.molliq.2020.114554},
issn = {01677322},
}
@article{Smirnov2017,
author = {Smirnov, Vladimir S. and Kislenko, Sergey A.},
journal = {Chem. Phys. Chem.},
number = {1},
pages = {75--81},
title = {{Effect of Solvents on the Behavior of Lithium and
Superoxide Ions in Lithium-Oxygen Battery
Electrolytes}},
volume = {19},
year = {2017},
doiurl = {10.1002/cphc.201700980},
issn = {14394235},
url = {http://doi.wiley.com/10.1002/cphc.201700980},
}