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Title: The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein

The calculation of spectral properties for photoactive proteins is challenging because of the large cost of electronic structure calculations on large systems. Mixed quantum mechanical (QM) and molecular mechanical (MM) methods are typically employed to make such calculations computationally tractable. This study addresses the connection between the minimal QM region size and the method used to model the MM region in the calculation of absorption properties—here exemplified for calculations on the green fluorescent protein. We find that polarizable embedding is necessary for a qualitatively correct description of the MM region, and that this enables the use of much smaller QM regions compared to fixed charge electrostatic embedding. Furthermore, absorption intensities converge very slowly with system size and inclusion of effective external field effects in the MM region through polarizabilities is therefore very important. Furthermore, this embedding scheme enables accurate prediction of intensities for systems that are too large to be treated fully quantum mechanically.
Authors:
ORCiD logo [1] ; ORCiD logo [1] ; ORCiD logo [2] ; ORCiD logo [1]
  1. Univ. of Southern Denmark (Denmark)
  2. Stanford Univ., Stanford, CA (United States); SLAC National Accelerator Lab., Menlo Park, CA (United States)
Publication Date:
Grant/Contract Number:
CF15-0823; AC02-76SF00515
Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 13; Journal Issue: 12; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Research Org:
SLAC National Accelerator Lab., Menlo Park, CA (United States)
Sponsoring Org:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
OSTI Identifier:
1471082

Nåbo, Lina J., Olsen, Jógvan Magnus Haugaard, Martínez, Todd J., and Kongsted, Jacob. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. United States: N. p., Web. doi:10.1021/acs.jctc.7b00528.
Nåbo, Lina J., Olsen, Jógvan Magnus Haugaard, Martínez, Todd J., & Kongsted, Jacob. The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein. United States. doi:10.1021/acs.jctc.7b00528.
Nåbo, Lina J., Olsen, Jógvan Magnus Haugaard, Martínez, Todd J., and Kongsted, Jacob. 2017. "The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein". United States. doi:10.1021/acs.jctc.7b00528. https://www.osti.gov/servlets/purl/1471082.
@article{osti_1471082,
title = {The Quality of the Embedding Potential Is Decisive for Minimal Quantum Region Size in Embedding Calculations: The Case of the Green Fluorescent Protein},
author = {Nåbo, Lina J. and Olsen, Jógvan Magnus Haugaard and Martínez, Todd J. and Kongsted, Jacob},
abstractNote = {The calculation of spectral properties for photoactive proteins is challenging because of the large cost of electronic structure calculations on large systems. Mixed quantum mechanical (QM) and molecular mechanical (MM) methods are typically employed to make such calculations computationally tractable. This study addresses the connection between the minimal QM region size and the method used to model the MM region in the calculation of absorption properties—here exemplified for calculations on the green fluorescent protein. We find that polarizable embedding is necessary for a qualitatively correct description of the MM region, and that this enables the use of much smaller QM regions compared to fixed charge electrostatic embedding. Furthermore, absorption intensities converge very slowly with system size and inclusion of effective external field effects in the MM region through polarizabilities is therefore very important. Furthermore, this embedding scheme enables accurate prediction of intensities for systems that are too large to be treated fully quantum mechanically.},
doi = {10.1021/acs.jctc.7b00528},
journal = {Journal of Chemical Theory and Computation},
number = 12,
volume = 13,
place = {United States},
year = {2017},
month = {11}
}