Relative Cooperativity in Neutral and Charged Molecular Clusters Using QM/MM Calculations DOI Creative Commons
Jorge Nochebuena, Shubin Liu, G. Andrés Cisneros

et al.

Published: Oct. 31, 2023

QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body involving three or more particles. contrast, polarizable fields account partially for effects polarization, but still handle van der Waals permanent electrostatic pairwise. We despite those limitations, can reproduce relative cooperativity achieved using Density Functional Theory, due error compensation mechanisms. this contribution, assess the performance of reproducing these phenomena. Our highlights significance QM region size field choice simulations, emphasizing importance parameter validation obtain accurate interaction energy predictions.

Language: Английский

Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites DOI
Paige E. Bowling, Saswata Dasgupta, John M. Herbert

et al.

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(9), P. 3912 - 3922

Published: April 22, 2024

In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads undesirable artifacts in form small imaginary frequencies. These preclude evaluation finite-temperature free-energy corrections, limiting thermochemical calculations enthalpies only. Full-dimensional vibrational frequency are possible by replacing constraints with harmonic confining potentials. Here, we compare that an alternative strategy which contributions Hessian simply omitted. While latter does eliminate frequencies, it tends underestimate both zero-point energy and entropy while introducing artificial rigidity. Harmonic potentials frequencies provide a flexible means construct active-site can used unconstrained relaxations, affording better convergence reaction energies barrier heights respect size, as compared constraints.

Language: Английский

Citations

8
SCINE—Software for chemical interaction networks DOI Creative Commons
Thomas Weymuth, Jan P. Unsleber, Paul L. Türtscher

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(22)

Published: June 10, 2024

The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum calculations on molecular structures to a new level. While individual as well simple relations between them have become routine in chemistry, developments pushed field high-throughput calculations. Chemical may be created by search specific properties design attempt, or they can defined set elementary reaction steps that form network. modules SCINE been designed facilitate such studies. features are (i) general applicability applied methodologies ranging from electronic structure (no restriction elements periodic table) microkinetic modeling (with little restrictions molecularity), full modularity so also stand-alone programs exchanged external packages fulfill similar purpose (to increase options computational campaigns and provide alternatives case tasks hard impossible accomplish with certain programs), (ii) high stability autonomous operations control steering an operator easy possible, (iii) embedding into complex heterogeneous environments taken individually context A graphical user interface unites all ensures interoperability. All components made available open source free charge.

Language: Английский

Citations

8
Nanoscale chemical reaction exploration with a quantum magnifying glass DOI Creative Commons
Katja‐Sophia Csizi, Miguel Steiner, Markus Reiher

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: June 22, 2024

Abstract Nanoscopic systems exhibit diverse molecular substructures by which they facilitate specific functions. Theoretical models of them, aim at describing, understanding, and predicting these capabilities, are difficult to build. Viable quantum-classical hybrid come with challenges regarding atomistic structure construction quantum region selection. Moreover, if their dynamics mapped onto a state-to-state mechanism such as chemical reaction network, its exhaustive exploration will be impossible due the combinatorial explosion space. Here, we introduce “quantum magnifying glass” that allows one interactively manipulate nanoscale structures level. The glass seamlessly combines autonomous model parametrization, ultra-fast mechanical calculations, automated exploration. It represents an approach investigate complex sequences in physically consistent manner unprecedented effortlessness real time. We demonstrate features for reactions bio-macromolecules metal-organic frameworks, highlight general applicability.

Language: Английский

Citations

4
How Accurate Are QM/MM Models? DOI
Junming Ho, Haibo Yu, Yihan Shao

et al.

The Journal of Physical Chemistry A, Journal Year: 2024, Volume and Issue: unknown

Published: Dec. 4, 2024

Despite the success and widespread use of QM/MM methods in modeling (bio)chemically important processes, their accuracy is still not well understood. A key reason because these are ultimately approximations to direct QM calculations very large systems, which impractical perform most cases. We highlight recent progress toward development realistic model systems where it possible obtain full reference data directly systematically evaluate effectiveness different generation schemes. These highly flexible can be tailored probe sensitivity a reaction types simulation parameters such as pairing MM potentials, region size, composition. It envisaged that this strategy could used validate schemes spur more robust models future.

Language: Английский

Citations

3
Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations DOI Open Access
Jorge Nochebuena, Shubin Liu, G. Andrés Cisneros

et al.

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(13)

Published: April 1, 2024

QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body involving three or more particles. contrast, polarizable fields account partially for effects polarization, but still handle van der Waals permanent electrostatic pairwise. We despite those limitations, can reproduce relative cooperativity achieved using density functional theory due error compensation mechanisms. this contribution, assess the performance of reproducing these phenomena. Our highlights significance QM region size field choice calculations, emphasizing importance parameter validation obtain accurate interaction energy predictions.

Language: Английский

Citations

0
Relative Cooperativity in Neutral and Charged Molecular Clusters Using QM/MM Calculations DOI Creative Commons
Jorge Nochebuena, Shubin Liu, G. Andrés Cisneros

et al.

Published: Oct. 31, 2023

QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body involving three or more particles. contrast, polarizable fields account partially for effects polarization, but still handle van der Waals permanent electrostatic pairwise. We despite those limitations, can reproduce relative cooperativity achieved using Density Functional Theory, due error compensation mechanisms. this contribution, assess the performance of reproducing these phenomena. Our highlights significance QM region size field choice simulations, emphasizing importance parameter validation obtain accurate interaction energy predictions.

Language: Английский

Citations

1