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

The Journal of Chemical Physics, Год журнала: 2024, Номер 160(11)

Опубликована: Март 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.

Язык: Английский

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An atom-in-molecule adaptive polarized valence single-ζ atomic orbital basis for electronic structure calculations

The Journal of Chemical Physics, Год журнала: 2023, Номер 159(16)

Опубликована: Окт. 25, 2023

Many low-cost or semiempirical quantum mechanical-based electronic structure methods suffer from the use of unpolarized minimal atomic orbital (AO) basis sets. In this work, we overcome limitation by a fully DFT variationally optimized, adaptive set consistently available for elements up to radon (Z = 86). The new key feature is make linear coefficients primitive Gaussians in contracted AO dependent on effective charge atom molecule, i.e., each symmetry-unique obtains its "own" specifically adapted functions. way, physically important "breathing" AOs molecule with (a) (expansion/contraction anionic/cationic states) and (b) number close-lying bonded neighbor atoms accounted for. required charges are obtained specially developed extended Hückel type Hamiltonian coordination numbers geometry. Proper analytical derivatives resulting functions can easily be derived. Moreover, electric field-dependent, thus improving description of, e.g., dipole moments polarizabilities. termed q-vSZP (charge valence single-ζ, polarized) thoroughly benchmarked atomic/molecular thermochemical properties compared standard double-ζ sets at level accurate ωB97X-D4 functional. It shown that clearly superior existing sets, often reaching quality even better results. We expect it optimal choice future mechanical methods.

Язык: Английский

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Extension of the D3 and D4 London Dispersion Corrections to the full Actinides Series

Physical Chemistry Chemical Physics, Год журнала: 2024, Номер 26(32), С. 21379 - 21394

Опубликована: Янв. 1, 2024

Efficient dispersion corrections are an indispensable component of modern density functional theory, semi-empirical quantum mechanical, and even force field methods. In this work, we extend the well established D3 D4 London to full actinides series, francium, radium. To keep consistency with existing versions, original parameterization strategy model was only slightly modified. This includes improved reference Hirshfeld atomic partial charges at ωB97M-V/ma-def-TZVP level fit required electronegativity equilibration charge (EEQ) model. context, developed a new actinide data set called AcQM, which covers most common molecular compound space. Furthermore, efficient calculation dynamic polarizabilities that needed construct

Язык: Английский

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State-of-the-art local correlation methods enable affordable gold standard quantum chemistry for up to hundreds of atoms

Chemical Science, Год журнала: 2024, Номер 15(36), С. 14556 - 14584

Опубликована: Янв. 1, 2024

In this feature, we review the current capabilities of local electron correlation methods up to coupled cluster model with single, double, and perturbative triple excitations [CCSD(T)], which is a gold standard in quantum chemistry. The main computational aspects method types are assessed from perspective applications, but focus kept on how achieve chemical accuracy (

Язык: Английский

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Limiting factors in the accuracy of DFT calculation for redox potentials

Journal of Computational Chemistry, Год журнала: 2024, Номер 45(14), С. 1177 - 1186

Опубликована: Фев. 4, 2024

Abstract In the present study, we have investigated factors affecting accuracy of computational chemistry calculation redox potentials, namely gas‐phase ionization energy (IE) and electron affinity (EA), continuum solvation effect. general, double‐hybrid density functional theory methods yield IEs EAs that are on average within ~0.1 eV our high‐level W3X‐L benchmark, with best performing method being DSD‐BLYP/ma‐def2‐QZVPP. For lower‐cost methods, errors ~0.2–0.3 eV, ω B97X‐3c most accurate (~0.15 eV). component, essentially all an error ~0.3 which shows limitation model. Curiously, directly calculated potentials show for methods. These notably smaller than what can be expected from propagation two components (IE EA, effect). Such a discrepancy attributed to cancellation errors, lowest‐cost GFN2‐xTB benefiting most, least. organometallic species, large deviations exceeding ~0.5 even DSD‐BLYP. The those EAs, represents major barrier such systems.

Язык: Английский

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N‐Hydroxyphthalimide/TiO2 Catalyzed Addition of Ethers, Alkylarenes and Aldehydes to Azodicarboxylates under Visible Light

Chemistry - A European Journal, Год журнала: 2025, Номер unknown

Опубликована: Янв. 31, 2025

The addition of carbon-centered radicals to double bonds is one the most atom-efficient approaches formation new C-C or C-heteroatom bonds. Existing for generation often require elevated temperatures, UV radiation expensive transition metal catalysts. In this work, a photocatalytic system based on heterogeneous TiO2 catalyst and redox organocatalyst N-hydroxyphthalimide proposed from C(sp3)-H substrates aldehydes at room temperature under visible light irradiation. developed approach was successfully applied ethers, alkylarenes azodicarboxylates. Titanium oxide acts as photocatalyst, producing phthalimide-N-oxyl N-hydroxyphthalimide, thereby enabling organocatalytic process in solution. Phthalimide-N-oxyl act catalytically active species that cleave C-H form radicals.

Язык: Английский

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Do Optimally Tuned Range-Separated Hybrid Functionals Require a Reparametrization of the Dispersion Correction? It Depends

Journal of Chemical Theory and Computation, Год журнала: 2023, Номер 19(22), С. 8097 - 8107

Опубликована: Ноя. 13, 2023

For ground- and excited-state studies of large molecules, it is the state art to combine (time-dependent) DFT with dispersion-corrected range-separated hybrid functionals (RSHs), which ensures an asymptotically correct description exchange effects London dispersion. Specifically for studying excited states, common practice tune range-separation parameter ω (optimal tuning), can further improve accuracy. However, since optimal tuning essentially changes functional, unclear if how much parameters used dispersion correction depend on chosen value. To answer this question, we explore interdependency by refitting DFT-D4 model six established RSHs over a wide range values (0.05-0.45 a0-1) using set noncovalently bound molecular complexes. The results reveal some surprising differences among investigated functionals: While PBE-based ωB97M-D4 generally exhibit weak robust performance values, B88-based RSHs, specifically LC-BLYP, are strongly affected. these, even minor reduction from default value manifests in strong systematic overbinding poor typical optimally tuned values. Finally, discuss strategies mitigate these issues reflect context employed D4 optimization algorithm fit set, outlining future improvements.

Язык: Английский

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Sorting drug conformers in enzyme active sites: the XTB way

Physical Chemistry Chemical Physics, Год журнала: 2024, Номер 26(16), С. 12610 - 12618

Опубликована: Янв. 1, 2024

An assessment of low-cost computational chemistry methods reveals the outstanding performance XTB1 for calculating relative binding energies chemically similar systems, notably conformers substrates in enzyme active sites.

Язык: Английский

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Quantum chemical package Jaguar: A survey of recent developments and unique features

The Journal of Chemical Physics, Год журнала: 2024, Номер 161(5)

Опубликована: Авг. 2, 2024

This paper is dedicated to the quantum chemical package Jaguar, which commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar’s scientific features that are relevant research as well describe those aspects of program pertinent user interface, organization computer code, its maintenance testing. Among topics feature prominently in this methods grounded pseudospectral approach. A number multistep workflows dependent on Jaguar covered: prediction protonation equilibria aqueous solutions (particularly calculations tautomeric stability pKa), reactivity predictions based automated transition state search, assembly Boltzmann-averaged spectra such vibrational electronic circular dichroism, nuclear magnetic resonance. Discussed also oriented toward materials science applications, particular, properties optoelectronic organic semiconductors, molecular catalyst design. The topic treatment conformations inevitably comes up real world projects considered part all mentioned above. In addition, we examine role machine learning performed from auxiliary functions return approximate calculation runtime a actual properties. current work second series reviews first having been published more than ten years ago. Thus, serves rare milestone path being traversed development thirty existence.

Язык: Английский

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Accurate QM/MM Molecular Dynamics for Periodic Systems in GPU4PySCF with Applications to Enzyme Catalysis

Journal of Chemical Theory and Computation, Год журнала: 2025, Номер unknown

Опубликована: Янв. 15, 2025

We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation electrostatics, and pseudobond treatment QM/MM boundary. demonstrate that our has well-controlled errors, stable self-consistent convergence, energy-conserving dynamics. further describe application to catalytic kinetics chorismate mutase. Using accurate hybrid functional reparametrized coupled cluster energetics, simulations highlight sensitivity in calculated rate choice method, region selection, local protein conformation. Our work is provided through open-source PySCF package acceleration from GPU4PySCF module.

Язык: Английский

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