The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization

Nakamura, Taiji; Fedorov, Dmitri G.

doi:10.1039/d1cp05851g

Cited by 11 publications

(6 citation statements)

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“…One reason for choosing DFTB in this work is the availability of partition analysis (PA) [ 51 ], which has been applied to identify solvent molecules strongly bound to residues in protein crystals [ 52 ] and to clarify the transition state stabilization in solid state catalysis [ 53 ]. Conceptually, PA resembles partial methods [ 54 ].…”

Section: Methodsmentioning

confidence: 99%

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

Sládek

Fedorov

2022

IJMS

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Quantum mechanical (QM) calculations at the level of density-functional tight-binding are applied to a protein–DNA complex (PDB: 2o8b) consisting of 3763 atoms, averaging 100 snapshots from molecular dynamics simulations. A detailed comparison of QM and force field (Amber) results is presented. It is shown that, when solvent screening is taken into account, the contributions of the backbones are small, and the binding of nucleotides in the double helix is governed by the base–base interactions. On the other hand, the backbones can make a substantial contribution to the binding of amino acid residues to nucleotides and other residues. The effect of charge transfer on the interactions is also analyzed, revealing that the actual charge of nucleotides and amino acid residues can differ by as much as 6 and 8% from the formal integer charge, respectively. The effect of interactions on topological models (protein -residue networks) is elucidated.

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Section: Methodsmentioning

confidence: 99%

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

Sládek

Fedorov

2022

IJMS

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“…The cost of quantum-mechanical (QM) calculations of properties of molecular systems can be reduced by using fragmentation methods 1 developed for both ground 2−9 and excited states. 10−15 The fragment molecular orbital (FMO) method 16−18 is used for performing low-scaling QM calculations of organic, 19,20 inorganic, 21,22 and biochemical 23,24 molecular systems. Analyses based on FMO provide rich physicochemical insight into binding of macromolecules 25−27 and chemical reactions.…”

Section: Introductionmentioning

confidence: 99%

“…Analyses based on FMO provide rich physicochemical insight into binding of macromolecules 25−27 and chemical reactions. 28,29 FMO methods for excited states have been developed for multiconfiguration self-consistent field (MCSCF), 30 timedependent (TD) density functional theory (TD-DFT), 31 TD density-functional tight-binding (TD-DFTB), 32 configuration interaction (CI), 33 and GW approximation. 34 Analytic gradients are available for FMO-TDDFT, 35 and excitonic coupling can be analyzed.…”

Section: Introductionmentioning

confidence: 99%

“…The fragment molecular orbital (FMO) method − is used for performing low-scaling QM calculations of organic, , inorganic, , and biochemical , molecular systems. Analyses based on FMO provide rich physicochemical insight into binding of macromolecules − and chemical reactions. , FMO methods for excited states have been developed for multiconfiguration self-consistent field (MCSCF), time-dependent (TD) density functional theory (TD-DFT), TD density-functional tight-binding (TD-DFTB), configuration interaction (CI), and GW approximation . Analytic gradients are available for FMO-TDDFT, and excitonic coupling can be analyzed. , …”

Section: Introductionmentioning

confidence: 99%

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Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level

Fedorov

2023

J. Phys. Chem. A

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A many-body expansion of ionization potentials and electron affinities is developed based on a combination of the fragment molecular orbital method and equation-of-motion coupled-cluster (EOM-CC). In addition to site-specific values, obtained as one-body properties, pair and triple corrections are added to account for nonlocal EOM-CC contributions of the molecular environment of a chromophore. The developed method is applied to carboxylic acids, alkyl cations, a protein ubiquitin (Protein Data Bank ID 1UBQ), and a nano ribbon of white graphene elucidating the effect of environment on ionization potential and electron affinity.

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“…It can be combined with pair interaction energy decomposition analysis (PIEDA) 89,90 We note that in all FMO calculations, the Ca 2+ ion was merged into one fragment with residues Asp106 and Glu107, which is a conventional and convenient way to ensure better charge transfer among metal ions and surrounding residues. 91 This is unnecessary in PA, 70,71,92 and Ca 2+ , Asp106, and Glu107 were kept as individual segment.…”

Section: ■ Introductionmentioning

confidence: 99%

How E-, L-, and P-Selectins Bind to sLe^x and PSGL-1: A Quantification of Critical Residue Interactions

Sládek

Šmak

Tvaroŝka

2023

J. Chem. Inf. Model.

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Selectins and their ability to interact with specific ligands are a cornerstone in cell communication. Over the last three decades, a considerable wealth of experimental and molecular modeling insights into their structure and modus operandi were gathered. Nonetheless, explaining the role of individual selectin residues on a quantitative level remained elusive, despite its importance in understanding the structure–function relationship in these molecules and designing their inhibitors. This work explores essential interactions of selectin–ligand binding, employing a multiscale approach that combines molecular dynamics, quantum-chemical calculations, and residue interaction network models. Such an approach successfully reproduces most of the experimental findings. It proves to be helpful, with the potential for becoming an established tool for quantitative predictions of residue contribution to the binding of biomolecular complexes. The results empower us to quantify the importance of particular residues and functional groups in the protein–ligand interface and to pinpoint differences in molecular recognition by the three selectins. We show that mutations in the E-, L-, and P-selectins, e.g., different residues in positions 46, 85, 97, and 107, present a crucial difference in how the ligand is engaged. We assess the role of sulfation of tyrosine residues in PSGL-1 and suggest that TyrSO3 – in position 51 interacting with Arg85 in P-selectin is a significant factor in the increased affinity of P-selectin to PSGL-1 compared to E- and L-selectins. We propose an original pharmacophore targeting five essential PSGL-binding sites based on the analysis of the selectin···PSGL-1 interactions.

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The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization

Abstract: Adsorption and chemical reactions occurring on industrially important ZSM-5 and faujasite zeolite catalysts are investigated with the quantum-mechanical fragment molecular orbital method combined with periodic boundary conditions. Suitable fragmentation patterns...

Cited by 11 publications

References 60 publications

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level

How E-, L-, and P-Selectins Bind to sLe^x and PSGL-1: A Quantification of Critical Residue Interactions

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The catalytic activity and adsorption in faujasite and ZSM-5 zeolites: the role of differential stabilization and charge delocalization

Abstract: Adsorption and chemical reactions occurring on industrially important ZSM-5 and faujasite zeolite catalysts are investigated with the quantum-mechanical fragment molecular orbital method combined with periodic boundary conditions. Suitable fragmentation patterns...

Cited by 11 publications

References 60 publications

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides

Site-Specific Ionization Potentials and Electron Affinities in Large Molecular Systems at Coupled Cluster Level

How E-, L-, and P-Selectins Bind to sLex and PSGL-1: A Quantification of Critical Residue Interactions

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How E-, L-, and P-Selectins Bind to sLe^x and PSGL-1: A Quantification of Critical Residue Interactions