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

2018 ◽  
Author(s):  
Heather Kulik
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Large Scale ◽  
Active Site Residues ◽  
Functional Theory ◽  
Energy Simulations ◽  
Electrostatic Embedding

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if <i>ab initio </i>QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of <i>ab initio </i>QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.<br>

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

2018 ◽  
Author(s):  
Heather Kulik
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Large Scale ◽  
Active Site Residues ◽  
Functional Theory ◽  
Energy Simulations ◽  
Electrostatic Embedding

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if <i>ab initio </i>QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying 200 ps of <i>ab initio </i>QM/MM dynamics for each of five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that important aspects of enzymatic rate enhancement in methyltransferases are identified with large-scale electronic structure.<br>

Charge Transfer Effects in Enzyme Catalysis Observed with Large-Scale QM/MM Free Energy Simulations

2018 ◽  
Author(s):  
Heather Kulik
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Ab Initio ◽  
Density Functional ◽  
Large Scale ◽  
Active Site Residues ◽  
Functional Theory ◽  
Energy Simulations ◽  
Electrostatic Embedding

Hybrid quantum mechanical-molecular mechanical (QM/MM) simulations provide key insights into enzyme structure–function relationships. Numerous studies have demonstrated that large QM regions are needed to systematically converge ground state, zero temperature properties with electrostatic embedding QM/MM. However, it is not well known if ab initio QM/MM free energy simulations have this same dependence, in part due to the hundreds of thousands of energy evaluations required for free energy estimations that in turn limit QM region size. Here, we leverage recent advances in electronic structure efficiency and accuracy to carry out range-separated hybrid density functional theory free energy simulations in a representative methyltransferase. By studying for 200 ps each of ab initio QM/MM dynamics in five QM regions from minimal (64 atoms) to one-sixth of the protein (544 atoms), we identify critical differences between large and small QM region QM/MM in charge transfer between substrates and active site residues as well as in geometric structure and dynamics that coincide with differences in predicted free energy barriers. Distinct geometric and electronic structure features in the largest QM region indicate that fundamental aspects of enzymatic rate enhancement are identified with large-scale electronic structure.

Electronic Structure Of (AgSb)xPbn-2xTen

2003 ◽  
Vol 793 ◽  
Author(s):  
Daniel I Bilc ◽  
S.D. Mahanti ◽  
M.G. Kanatzidis
Keyword(s):  
Electronic Structure ◽  
Ab Initio ◽  
Density Functional ◽  
Full Potential ◽  
Generalized Gradient ◽  
Two Component System ◽  
Functional Theory ◽  
Covalent Interaction ◽  
Salt Structure ◽  
Linearized Augmented Plane Wave

ABSTRACTComplex quaternary chalcogenides (AgSb)xPbn-2xTen (0<x<n/2) are thought to be narrow band-gap semiconductors which are very good candidates for room and high temperature thermoelectric applications. These systems form in the rock-salt structure similar to the well known two component system PbTe (x=0). In these systems Ag and Sb occupy Pb sites randomly although there is some evidence of short-range order. To gain insights into the electronic structure of these compounds, we have performed electronic structure calculations in AgSbTe2 (x=n/2). These calculations were carried out within ab initio density functional theory (DFT) using full potential linearized augmented plane wave (LAPW) method. The generalized gradient approximation (GGA) was used to treat the exchange and correlation potential. Spinorbit interaction (SOI) was incorporated using a second variational procedure. Since it is difficult to treat disorder in ab initio calculations, we have used several ordered structures for AgSbTe2. All these structures show semimetallic behavior with a pseudogap near the Fermi energy. Te and Sb p orbitals, which are close in energy, hybridize rather strongly indicating a covalent interaction between Te and Sb atoms.

scholarly journals Thermodynamic Parameters of PbTe Crystals: DFT-Calculations

2015 ◽  
Vol 16 (1) ◽  
pp. 28-33
Author(s):  
D. M. Freik ◽  
B. P. Volochanska ◽  
T. O. Parashchuk
Keyword(s):  
Density Functional Theory ◽  
Free Energy ◽  
Electronic Structure ◽  
Thermodynamic Parameters ◽  
Quantum Chemical ◽  
Density Functional ◽  
Cubic Phase ◽  
Functional Theory ◽  
Temperature Dependences ◽  
Analytical Expressions

Based on the analysis of the crystal NaCl type and electronic structure of cubic phase CdS crystals the cluster models have been built for calculation of the geometric and thermodynamic parameters. According to density functional theory (DFT) and using the hybrid valence base set B3LYP the temperature dependence of the energy ΔE and the enthalpy ΔH of formation, Gibbs free energy ΔG, entropy ΔS, specific heat at constant volume CV and pressure CP of the crystals have been found. The analytical expressions of the temperature dependences of presented thermodynamic parameters which was approximated from the quantum- chemical calculations data and with using mathematical package Maple 14 have been received.

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