Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry**

Angewandte Chemie International Edition, Journal Year: 2022, Volume and Issue: 61(42)

Published: Sept. 14, 2022

Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share these quantum-chemical applies density functional theory (DFT) evaluated in atomic-orbital basis sets. This work provides best-practice guidance on the numerous methodological technical aspects DFT three parts: Firstly, we set stage introduce a step-by-step decision tree to choose computational protocol that models experiment as closely possible. Secondly, present recommendation matrix guide choice depending task at hand. A particular focus is achieving an optimal balance between accuracy, robustness, efficiency through multi-level approaches. Finally, discuss selected representative examples illustrate recommended protocols effect choices.

Language: Английский

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CREST—A program for the exploration of low-energy molecular chemical space

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(11)

Published: March 21, 2024

Conformer–rotamer sampling tool (CREST) is an open-source program for the efficient and automated exploration of molecular chemical space. Originally developed in Pracht et al. [Phys. Chem. Phys. 22, 7169 (2020)] as driver calculations at extended tight-binding level (xTB), it offers a variety molecular- metadynamics simulations, geometry optimization, structure analysis capabilities. Implemented algorithms include procedures conformational sampling, explicit solvation studies, calculation absolute entropy, identification protonation deprotonation sites. Calculations are set up to run concurrently, providing single-node parallelization. CREST designed require minimal user input comes with implementation GFNn-xTB Hamiltonians GFN-FF force-field. Furthermore, interfaces any quantum chemistry force-field software can easily be created. In this article, we present recent developments code show selection applications most important features program. An novelty refactored backend, which provides significant speed-up small or medium-sized drug molecules allows more sophisticated setups, example, mechanics/molecular mechanics minimum energy crossing point calculations.

Language: Английский

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Best‐Practice DFT Protocols for Basic Molecular Computational Chemistry**

Angewandte Chemie, Journal Year: 2022, Volume and Issue: 134(42)

Published: Sept. 14, 2022

Abstract Nowadays, many chemical investigations are supported by routine calculations of molecular structures, reaction energies, barrier heights, and spectroscopic properties. The lion's share these quantum‐chemical applies density functional theory (DFT) evaluated in atomic‐orbital basis sets. This work provides best‐practice guidance on the numerous methodological technical aspects DFT three parts: Firstly, we set stage introduce a step‐by‐step decision tree to choose computational protocol that models experiment as closely possible. Secondly, present recommendation matrix guide choice depending task at hand. A particular focus is achieving an optimal balance between accuracy, robustness, efficiency through multi‐level approaches. Finally, discuss selected representative examples illustrate recommended protocols effect choices.

Language: Английский

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Automated Molecular Cluster Growing for Explicit Solvation by Efficient Force Field and Tight Binding Methods

Journal of Chemical Theory and Computation, Journal Year: 2022, Volume and Issue: 18(5), P. 3174 - 3189

Published: April 28, 2022

An automated and broadly applicable workflow for the description of solvation effects in an explicit manner is introduced. This method, termed quantum cluster growth (QCG), based on semiempirical GFN2-xTB/GFN-FF methods, enabling efficient geometry optimizations MD simulations. Fast structure generation provided using intermolecular force field xTB-IFF. Additionally, approach uses implicit model electrostatic embedding growing clusters. The novel QCG procedure presents a robust tool subsequent application higher-level (e.g., DFT) methods to study molecular geometries explicitly or average spectroscopic properties over ensembles. Furthermore, computation free energy with supermolecular can be carried out QCG. underlying process physically motivated by computing leading-order solute-solvent interactions first account conformational chemical changes due low-energy barrier processes. space explored NCI-MTD algorithm as implemented CREST program, combination metadynamics GFN2-xTB yields realistic solution reasonable energies various systems without introducing many empirical parameters. Computed IR spectra some solutes show better match experimental data compared well-established models.

Language: Английский

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Interfacing single-atom catalysis with continuous-flow organic electrosynthesis

Chemical Society Reviews, Journal Year: 2022, Volume and Issue: 51(10), P. 3898 - 3925

Published: Jan. 1, 2022

This manuscript reviews for the first time developments at interface between organic electrosynthesis and single-atom catalysis, highlighting advantages in shifting from a batch to flow production.

Language: Английский

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High-entropy hybrid perovskites with disordered organic moieties for perovskite solar cells

Nature Photonics, Journal Year: 2024, Volume and Issue: 18(9), P. 960 - 966

Published: July 1, 2024

Language: Английский

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Convergent Protocols for Computing Protein–Ligand Interaction Energies Using Fragment-Based Quantum Chemistry

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 2, 2025

Fragment-based quantum chemistry methods offer a means to sidestep the steep nonlinear scaling of electronic structure calculations so that large molecular systems can be investigated using high-level methods. Here, we use fragmentation compute protein-ligand interaction energies in with several thousand atoms, new software platform for managing fragment-based implements screened many-body expansion. Convergence tests minimal-basis semiempirical method (HF-3c) indicate two-body calculations, single-residue fragments and simple hydrogen caps, are sufficient reproduce obtained conventional supramolecular within 1 kcal/mol at about 1% computational cost. We also demonstrate HF-3c results illustrative trends density functional theory basis sets up augmented quadruple-ζ quality. Strategic deployment facilitates converged biomolecular model alongside high-quality sets, bringing

Language: Английский

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Free and open source software for computational chemistry education

Wiley Interdisciplinary Reviews Computational Molecular Science, Journal Year: 2022, Volume and Issue: 12(5)

Published: March 23, 2022

Abstract After decades of waiting, computational chemistry for the masses is finally here. Our brief review on free and open source software (FOSS) packages points out existence offering a wide range functionality, all way from approximate semiempirical calculations with tight‐binding density functional theory to sophisticated ab initio wave function methods such as coupled‐cluster theory, covering both molecular solid‐state systems. Combined remarkable increase in computing power personal devices, which now rivals that fastest supercomputers world 1990s, we demonstrate decentralized model teaching possible thanks FOSS packages, enabling students perform reasonable modeling their own devices bring your device (BYOD) scheme. can be made trivially simple install keep up date, eliminating need departmental support, also enables comprehensive strategies, various algorithms' actual implementations used teaching. We exemplify what kinds are feasible four electronic structure programs, assuming only extremely modest resources, illustrate how enable approaches education within BYOD has further benefits driving its adoption: access code democratizes science chemistry, without limitation beyond education, academic industrial applications, example. This article categorized under: Software > Quantum Chemistry

Language: Английский

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Probing London Dispersion in Proton-Bound Onium Ions: Are Alkyl–Alkyl Steric Interactions Reliably Modeled?

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 28, 2025

We report spectroscopic and spectrometric experiments that probe the London dispersion interaction between tert-butyl substituents in three series of covalently linked, protonated bis-pyridines gas phase. Molecular ions test series, along with several reference molecules for control, were electrosprayed from solution into phase then probed by infrared multiphoton dissociation spectroscopy trapped ion mobility spectrometry. The observed N-H stretching frequencies provided an experimental readout diagnostic ground-state geometry each ion, which could be furthermore compared to a second, independent structural via collision cross section. In strength modulated systematically progressive increase size H Me tert-Bu. Parallel study, extensive dispersion-corrected density functional theory (DFT-D3BJ) calculations performed range exchange correlation functionals. A full analysis conformational space flexible members vibrational spectra context general double-well potential, finds DFT-D3BJ appears significantly overbind alkyl-alkyl interactions, specifically interactions tert-Bu groups, even failing predict minimum energy structures reliably case competes other noncovalent such as hydrogen bonding.

Language: Английский

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Understanding Conformational Entropy in Small Molecules

Journal of Chemical Theory and Computation, Journal Year: 2021, Volume and Issue: 17(4), P. 2099 - 2106

Published: March 24, 2021

The calculation of the entropy flexible molecules can be challenging, since number possible conformers grow exponentially with molecule size and many low-energy may thermally accessible. Different methods have been proposed to approximate contribution conformational molecular standard entropy, including performing thermochemistry calculations all stable conformations developing empirical corrections from experimental data. We performed conformer sampling on over 120,000 small generating some 12 million conformers, develop models predict across a wide range molecules. Using insight into nature disorder, our cross-validated physically motivated statistical model gives mean absolute error ∼4.8 J/mol·K or under 0.4 kcal/mol at 300 K. Beyond predicting entropies free energies, implies high degree correlation between torsions in most molecules, often assumed independent. While individual dihedral rotations low energetic barriers, shape chemical functionality necessarily correlate their torsional degrees freedom hence restrict immensely. Our simple capture these correlations advance understanding entropy.

Language: Английский

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