4 research outputs found
General Charge Transfer Dipole Model for AMOEBA-Like Force Fields
The development of highly accurate
force fields is always
an importance
aspect in molecular modeling. In this work, we introduce a general
damping-based charge transfer dipole (D-CTD) model to describe the
charge transfer energy and the corresponding charge flow for H, C,
N, O, P, S, F, Cl, and Br elements in common bio-organic systems.
Then, two effective schemes to evaluate the charge flow from the corresponding
induced dipole moment between the interacting molecules were also
proposed and discussed. The potential applicability of the D-CTD model
in ion-containing systems was also demonstrated in a series of ionâwater
complexes including Li+, Na+, K+,
Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, Fâ, Clâ, Brâ, and Iâ ions. In general, the D-CTD
model demonstrated good accuracy and good transferability in both
charge transfer energy and the corresponding charge flow for a wide
range of model systems. By distinguishing the intermolecular charge
redistribution (charge transfer) under the influence of an external
electric field from the accompanying intramolecular charge redistribution
(polarization), the D-CTD model is theoretically consistent with current
induced dipole-based polarizable dipole models and hence can be easily
implemented and parameterized. Along with our previous work in charge
penetration-corrected electrostatics, a bottom-up approach constructed
water model was also proposed and demonstrated. The structure-maker
and structure-breaker roles of cations and anions were also correctly
reproduced using Na+, K+, Clâ, and Iâ ions in the new water model, respectively.
This work demonstrates a cost-effective approach to describe the charge
transfer phenomena. The water and ion models also show the feasibility
of a modulated development approach for future force fields
Capturing Many-Body Interactions with Classical Dipole Induction Models
The
nonadditive many-body interactions are significant for structural
and thermodynamic properties of condensed phase systems. In this work
we examined the many-body interaction energy of a large number of
common organic/biochemical molecular clusters, which consist of 18
chemical species and cover nine common organic elements, using the
MøllerâPlesset perturbation theory to the second order
(MP2) [Møller et al. Phys. Rev. 1934, 46, 618.]. We evaluated the capability of Thole-based
dipole induction models to capture the many-body interaction energy.
Three models were compared: the original model and parameters used
by the AMOEBA force field, a variation of this original model where
the damping parameters have been reoptimized to MP2 data, and a third
model where the damping function form applied to the permanent electric
field is modified. Overall, we find the simple classical atomic dipole
models are able to capture the 3- and 4-body interaction energy across
a wide variety of organic molecules in various intermolecular configurations.
With modified Thole models, it is possible to further improve the
agreement with MP2 results. These models were also tested on systems
containing metal/halogen ions to examine the accuracy and transferability.
This work suggests that the form of damping function applied to the
permanent electrostatic field strongly affects the distance dependence
of polarization energy at short intermolecular separations
General Charge Transfer Dipole Model for AMOEBA-Like Force Fields
The development of highly accurate
force fields is always
an importance
aspect in molecular modeling. In this work, we introduce a general
damping-based charge transfer dipole (D-CTD) model to describe the
charge transfer energy and the corresponding charge flow for H, C,
N, O, P, S, F, Cl, and Br elements in common bio-organic systems.
Then, two effective schemes to evaluate the charge flow from the corresponding
induced dipole moment between the interacting molecules were also
proposed and discussed. The potential applicability of the D-CTD model
in ion-containing systems was also demonstrated in a series of ionâwater
complexes including Li+, Na+, K+,
Mg2+, Ca2+, Fe2+, Zn2+, Pt2+, Fâ, Clâ, Brâ, and Iâ ions. In general, the D-CTD
model demonstrated good accuracy and good transferability in both
charge transfer energy and the corresponding charge flow for a wide
range of model systems. By distinguishing the intermolecular charge
redistribution (charge transfer) under the influence of an external
electric field from the accompanying intramolecular charge redistribution
(polarization), the D-CTD model is theoretically consistent with current
induced dipole-based polarizable dipole models and hence can be easily
implemented and parameterized. Along with our previous work in charge
penetration-corrected electrostatics, a bottom-up approach constructed
water model was also proposed and demonstrated. The structure-maker
and structure-breaker roles of cations and anions were also correctly
reproduced using Na+, K+, Clâ, and Iâ ions in the new water model, respectively.
This work demonstrates a cost-effective approach to describe the charge
transfer phenomena. The water and ion models also show the feasibility
of a modulated development approach for future force fields
Polarizable Multipole-Based Force Field for Dimethyl and Trimethyl Phosphate
Phosphate groups are commonly observed
in biomolecules such as
nucleic acids and lipids. Due to their highly charged and polarizable
nature, modeling these compounds with classical force fields is challenging.
Using quantum mechanical studies and liquid-phase simulations, the
AMOEBA force field for dimethyl phosphate (DMP) ion and trimethyl
phosphate (TMP) has been developed. On the basis of <i>ab initio</i> calculations, it was found that ion binding and the solution environment
significantly impact both the molecular geometry and the energy differences
between conformations. Atomic multipole moments are derived from MP2/cc-pVQZ
calculations of methyl phosphates at several conformations with their
chemical environments taken into account. Many-body polarization is
handled via a Thole-style induction model using distributed atomic
polarizabilities. van der Waals parameters of phosphate and oxygen
atoms are determined by fitting to the quantum mechanical interaction
energy curves for water with DMP or TMP. Additional stretch-torsion
and angle-torsion coupling terms were introduced in order to capture
asymmetry in PâO bond lengths and angles due to the generalized
anomeric effect. The resulting force field for DMP and TMP is able
to accurately describe both the molecular structure and conformational
energy surface, including bond and angle variations with conformation,
as well as interaction of both species with water and metal ions.
The force field was further validated for TMP in the condensed phase
by computing hydration free energy, liquid density, and heat of vaporization.
The polarization behavior between liquid TMP and TMP in water is drastically
different