A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase

Bennie, Simon J.; Kamp, Marc W. van der; Pennifold, Robert C. R.; Stella, Martina; Manby, Frederick R.; Mulholland, Adrian J.

doi:10.1021/acs.jctc.6b00285

Cited by 75 publications

(125 citation statements)

References 106 publications

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“…Accurate molecular energies can be obtained in an unbiased, systematically correctable manner [72–74] to get the desired accuracy. However, the computational resource required is very expensive, and is usually unacceptable because resource must be apportioned to adequate conformational sampling.…”

Section: Computational Analyses Of Mfx Complexesmentioning

confidence: 99%

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

2017

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The phosphoryl group, PO3 –, is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by “nuclear mutation,” by substitution of PO3 – by MgF3 – or AlF4 –, has underpinned the application of metal fluoride (MFx) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis. Protein crystallography in the solid state and 19F NMR in solution have enabled direct observation of ternary and quaternary protein complexes embracing MFx transition state models with precision. These studies have underpinned a radically new mechanistic approach to enzyme catalysis for a huge range of phosphoryl transfer processes, as varied as kinases, phosphatases, phosphomutases, and phosphohydrolases. The results, without exception, have endorsed trigonal bipyramidal geometry (tbp) for concerted, “in-line” stereochemistry of phosphoryl transfer. QM computations have established the validity of tbp MFx complexes as reliable models for true transition states, delivering similar bond lengths, coordination to essential metal ions, and virtually identical hydrogen bond networks. The emergence of protein control of reactant orbital overlap between bond-forming species within enzyme transition states is a new challenging theme for wider exploration.

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Section: Computational Analyses Of Mfx Complexesmentioning

confidence: 99%

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

2017

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“…In He, for example, important correlation effects can be accomplished by the polarizations, ( ) Many very accurate configuration interaction calculations have been carried out on atoms, molecules and clusters using large basis sets that include higher spherical harmonic functions. [1][2][3][4][5][6][7][8][9][10][11] As systems increase in size, the additional functions required for angular correlation cause a rapid increase in the number of configurations, limiting the applicability of the method.…”

Section: Methodsmentioning

confidence: 99%

“…If the p-shell is occupied by n electrons, the correlation contributions for an s-excitation is reduced to (6 ) 6 n E δ − . Since there are no d-electrons in the virtual space in the atoms and molecules considered, there is no reduction in δ E for pp dd ′ ′ → excitations.…”

Section: Methodsmentioning

confidence: 99%

“…There is a vast literature on ways to do this ranging from perturbation methods that generate configurations and evaluate energies efficiently to methods for partitioning large systems into localized electronic subspaces or ways to balance errors in systems that are being compared. [1][2][3][4][5][6][7][8][9][10][11] Relatively few configurations are required to dissociate molecules correctly or to create proper spin states. However, dynamical correlation effects, particularly those associated with angular correlation, require higher spherical harmonic basis functions and this leads to a rapid increase in number of interacting configurations.…”

Section: Introductionmentioning

confidence: 99%

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Electron correlation by polarization of interacting densities

Whitten

2017

The Journal of Chemical Physics

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Coulomb interactions that occur in electronic structure calculations are correlated by allowing basis function components of the interacting densities to polarize dynamically, thereby reducing the magnitude of the interaction. Exchange integrals of molecular orbitals are not correlated. The modified Coulomb interactions are used in single-determinant or configuration interaction calculations. The objective is to account for dynamical correlation effects without explicitly introducing higher spherical harmonic functions into the molecular orbital basis. Molecular orbital densities are decomposed into a distribution of spherical components that conserve the charge and each of the interacting components is considered as a two-electron wavefunction embedded in the system acted on by an average field Hamiltonian plus 1 12 − r . A method of avoiding redundancy is described. Applications to atoms, negative ions and molecules representing different types of bonding and spin states are discussed.

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“…Accurate molecular energies can be obtained in an unbiased, systematically correctable manner [72][73][74] to get the desired accuracy. However, the computational resource required is very expensive, and is usually unacceptable because resource must be apportioned to adequate conformational sampling.…”

Section: Tradeoff In Accuracy Of Energy/structure: Parameterization Smentioning

confidence: 99%

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

Jin

Molt

Blackburn

2017

Phosphate Labeling and Sensing in Chemical Biology

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The phosphoryl group, PO 3 -, is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by ''nuclear mutation,'' by substitution of PO 3 -by MgF 3 -or AlF 4 -, has underpinned the application of metal fluoride (MF x ) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis. Protein crystallography in the solid state and 19 F NMR in solution have enabled direct observation of ternary and quaternary protein complexes embracing MF x transition state models with precision. These studies have underpinned a radically new mechanistic approach to enzyme catalysis for a huge range of phosphoryl transfer processes, as varied as kinases, phosphatases, phosphomutases, and phosphohydrolases. The results, without

show abstract

A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase

Cited by 75 publications

References 106 publications

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

Electron correlation by polarization of interacting densities

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

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