TY - CHAP
T1 - Chapter 1
T2 - QM/MM with Auxiliary DFT in deMon2k
AU - Samaniego-Rojas, Juan D.
AU - Hernández-Segura, Luis Ignacio
AU - López-Sosa, Luis
AU - Delgado-Venegas, Rogelio I.
AU - Gomez, Badhin
AU - Lambry, Jean Christophe
AU - De La Lande, Aurelien
AU - Mineva, Tzonka
AU - Alejandre, José
AU - Zúñiga-Gutiérrez, Bernardo A.
AU - Flores-Moreno, Roberto
AU - Calaminici, Patrizia
AU - Geudtner, Gerald
AU - Köster, Andreas M.
N1 - Publisher Copyright:
© The Royal Society of Chemistry 2022.
PY - 2022/1/1
Y1 - 2022/1/1
N2 - This chapter describes the theoretical background of the quantum mechanical/molecular mechanical (QM/MM) implementation in deMon2k within the framework of auxiliary density functional theory (ADFT). It aims to give the reader an overview of the current state of the art of this QM/MM implementation and perspectives for its future development. To this end, we first derive the ADFT working equations for the QM and QM/MM energy and gradient expressions. Based on the joint QM/MM gradient expression, we present algorithms for QM/MM structure optimizations, transition-state searches and molecular dynamics simulations. The use of auxiliary density perturbation theory (ADPT) in the framework of QM/MM is discussed using illustrative implementations including analytic second-order ADFT energy derivatives, nuclear magnetic resonance chemical shift calculations and excited state calculations using time-dependent ADFT. The chapter closes with the description of a transformation program used to generate deMon2k QM/MM inputs.
AB - This chapter describes the theoretical background of the quantum mechanical/molecular mechanical (QM/MM) implementation in deMon2k within the framework of auxiliary density functional theory (ADFT). It aims to give the reader an overview of the current state of the art of this QM/MM implementation and perspectives for its future development. To this end, we first derive the ADFT working equations for the QM and QM/MM energy and gradient expressions. Based on the joint QM/MM gradient expression, we present algorithms for QM/MM structure optimizations, transition-state searches and molecular dynamics simulations. The use of auxiliary density perturbation theory (ADPT) in the framework of QM/MM is discussed using illustrative implementations including analytic second-order ADFT energy derivatives, nuclear magnetic resonance chemical shift calculations and excited state calculations using time-dependent ADFT. The chapter closes with the description of a transformation program used to generate deMon2k QM/MM inputs.
UR - https://www.scopus.com/pages/publications/85116403247
U2 - 10.1039/9781839164668-00001
DO - 10.1039/9781839164668-00001
M3 - Chapter
AN - SCOPUS:85116403247
T3 - RSC Theoretical and Computational Chemistry Series
SP - 1
EP - 54
BT - Multiscale Dynamics Simulations Nano and Nano-bio Systems in Complex Environments
A2 - Salahub, Dennis R.
A2 - Wei, Dongqing
PB - Royal Society of Chemistry
ER -