Literature DB >> 26588959

Convergence of Electronic Structure with the Size of the QM Region: Example of QM/MM NMR Shieldings.

Denis Flaig1, Matthias Beer1, Christian Ochsenfeld1.   

Abstract

The influence of the chemical environment on NMR shifts of a central molecular region is studied for several biomolecular and supramolecular systems. To investigate the long-range effects, we systematically increase the QM region until the changes of the NMR shielding tensor are negligible for the considered nuclei; that is, convergence with the selected QM size is reached. To reach size convergence, QM regions with up to about 1500 atoms and 15 000 basis functions are treated by our density matrix-based linear-scaling coupled perturbed self-consistent field methods. The results also provide insights into the locality and convergence of the electronic structure. Furthermore, we demonstrate to what extent the inclusion of the chemical environment as partial point charges within a hybrid QM/MM approach improves the convergence behavior. In addition, some benchmark data on NMR accuracies are provided using various ab initio methods.

Year:  2012        PMID: 26588959     DOI: 10.1021/ct300036s

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  18 in total

1.  Converging nuclear magnetic shielding calculations with respect to basis and system size in protein systems.

Authors:  Joshua D Hartman; Thomas J Neubauer; Bethany G Caulkins; Leonard J Mueller; Gregory J O Beran
Journal:  J Biomol NMR       Date:  2015-05-21       Impact factor: 2.835

2.  Revealing quantum mechanical effects in enzyme catalysis with large-scale electronic structure simulation.

Authors:  Zhongyue Yang; Rimsha Mehmood; Mengyi Wang; Helena W Qi; Adam H Steeves; Heather J Kulik
Journal:  React Chem Eng       Date:  2018-11-29       Impact factor: 4.239

3.  Large-scale QM/MM free energy simulations of enzyme catalysis reveal the influence of charge transfer.

Authors:  Heather J Kulik
Journal:  Phys Chem Chem Phys       Date:  2018-08-08       Impact factor: 3.676

Review 4.  Chemical shifts in biomolecules.

Authors:  David A Case
Journal:  Curr Opin Struct Biol       Date:  2013-02-17       Impact factor: 6.809

5.  Electronic Absorption Spectra from MM and ab initio QM/MM Molecular Dynamics: Environmental Effects on the Absorption Spectrum of Photoactive Yellow Protein.

Authors:  Christine M Isborn; Andreas W Götz; Matthew A Clark; Ross C Walker; Todd J Martínez
Journal:  J Chem Theory Comput       Date:  2012-10-06       Impact factor: 6.006

6.  AFNMR: automated fragmentation quantum mechanical calculation of NMR chemical shifts for biomolecules.

Authors:  Jason Swails; Tong Zhu; Xiao He; David A Case
Journal:  J Biomol NMR       Date:  2015-08-02       Impact factor: 2.835

7.  Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

Authors:  Qiang Cui; Tanmoy Pal; Luke Xie
Journal:  J Phys Chem B       Date:  2021-01-06       Impact factor: 2.991

8.  Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.

Authors:  Mark A Hix; Emmett M Leddin; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2021-06-04       Impact factor: 6.578

9.  A base-independent repair mechanism for DNA glycosylase--no discrimination within the active site.

Authors:  Iris D Blank; Keyarash Sadeghian; Christian Ochsenfeld
Journal:  Sci Rep       Date:  2015-05-27       Impact factor: 4.379

10.  Current and emerging opportunities for molecular simulations in structure-based drug design.

Authors:  Julien Michel
Journal:  Phys Chem Chem Phys       Date:  2014-03-14       Impact factor: 3.676

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