Electrostatic Polarization Energies of Charge Carriers in Organic Molecular Crystals: A Comparative Study with Explicit State-Specific Atomic Polarizability Based AMOEBA Force Field and Implicit Solvent Method

2018 ◽  
Vol 14 (7) ◽  
pp. 3728-3739 ◽  
Author(s):  
Tao Xu ◽  
Wenliang Wang ◽  
Shiwei Yin
Keyword(s):  
Comparative Study ◽  
Force Field ◽  
Molecular Crystals ◽  
Charge Carriers ◽  
Implicit Solvent ◽  
Solvent Method ◽  
Organic Molecular Crystals ◽  
Atomic Polarizability ◽  
Electrostatic Polarization ◽  
Amoeba Force Field

scholarly journals An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

2016 ◽  
Vol 72 (4) ◽  
pp. 477-487 ◽  
Author(s):  
Edward O. Pyzer-Knapp ◽  
Hugh P. G. Thompson ◽  
Graeme M. Day
Keyword(s):  
Force Field ◽  
Crystal Structures ◽  
Force Fields ◽  
Molecular Crystals ◽  
Intermolecular Force ◽  
Organic Molecular Crystals ◽  
Organic Solid ◽  
Lattice Energies ◽  
Validation Set ◽  
Unit Cell Dimensions

We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.

scholarly journals Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

2020 ◽  
Author(s):  
Rae Corrigan ◽  
Guowei Qi ◽  
Andrew Thiel ◽  
Jack Lynn ◽  
Brandon Walker ◽  
...  
Keyword(s):  
Force Field ◽  
Protein Design ◽  
Numerical Solutions ◽  
Target Function ◽  
Model Parameters ◽  
Implicit Solvent ◽  
Electrostatic Model ◽  
Implicit Solvents ◽  
Poisson Boltzmann Equation ◽  
Amoeba Force Field

Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br>

scholarly journals Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

2020 ◽  
Author(s):  
Rae Corrigan ◽  
Guowei Qi ◽  
Andrew Thiel ◽  
Jack Lynn ◽  
Brandon Walker ◽  
...  
Keyword(s):  
Force Field ◽  
Protein Design ◽  
Numerical Solutions ◽  
Target Function ◽  
Model Parameters ◽  
Implicit Solvent ◽  
Electrostatic Model ◽  
Implicit Solvents ◽  
Poisson Boltzmann Equation ◽  
Amoeba Force Field

Computational protein design, ab initio protein/RNA folding, and protein-ligand screening can be too computationally demanding for explicit treatment of solvent. For these applications, implicit solvent offers a compelling alternative, which we describe here for the polarizable atomic multipole AMOEBA force field based on three treatments of continuum electrostatics: numerical solutions to the Poisson-Boltzmann equation (PBE), the domain-decomposition Conductor-like Screening Model (ddCOSMO) approximation to the PBE, and the analytic generalized Kirkwood (GK) approximation. The continuum electrostatic models are combined with a nonpolar estimator based on novel cavitation and dispersion terms. Electrostatic model parameters are numerically optimized using a least squares style target function based on a library of 103 small molecule solvation free energy differences. Mean signed errors for the APBS, ddCOSMO, and GK models are 0.05, 0.00, and 0.00 kcal/mol, respectively, while the mean unsigned errors are 0.70, 0.63, and 0.51 kcal/mol, respectively. Validation of the electrostatic response of the resulting implicit solvents, which are available in the Tinker (or Tinker-HP), OpenMM, and Force Field X software packages, is based on comparisons to explicit solvent simulations for a series of proteins and nucleic acids. Overall, the emergence of performative implicit solvent models for polarizable force fields will open the door to their use for folding and design applications.<br>

Solid state amorphization of organic molecular crystals using a vibrating mill

1995 ◽  
Vol 94 (12) ◽  
pp. 1013-1018 ◽  
Author(s):  
Itaru Tsukushi ◽  
Osamu Yamamuro ◽  
Takasuke Matsuo
Keyword(s):  
Solid State ◽  
Molecular Crystals ◽  
Organic Molecular Crystals ◽  
State Amorphization

scholarly journals Role of Conical Intersections on the Efficiency of Fluorescent Organic Molecular Crystals

2021 ◽  
Vol 125 (4) ◽  
pp. 1012-1024
Author(s):  
Miguel Rivera ◽  
Ljiljana Stojanović ◽  
Rachel Crespo-Otero
Keyword(s):  
Molecular Crystals ◽  
Conical Intersections ◽  
Organic Molecular Crystals
Sign in / Sign up

Export Citation Format

Share Document