ωB97X-3c: A composite range-separated hybrid DFT method with a molecule-optimized polarized valence double-ζ basis set

The Journal of Chemical Physics, Journal Year: 2022, Volume and Issue: 158(1)

Published: Dec. 12, 2022

A new composite density functional theory (DFT) method is presented. It based on ωB97X-V as one of the best-performing functionals for GMTKN55 thermochemistry database and completes family "3c" methods toward range-separated hybrid DFT. This consistently available all elements up to Rn (Z = 1-86). Its further key ingredients are a polarized valence double-ζ (vDZP) Gaussian basis set, which was fully optimized in molecular DFT calculations, combination with large-core effective core potentials specially adapted D4 dispersion correction. Unlike most existing atomic orbital sets, vDZP shows only small set superposition errors (BSSEs) can compete standard sets triple-ζ quality. Small residual BSSE effects efficiently absorbed by damping scheme, overall eliminates need an explicit treatment or empirical corrections BSSE. Thorough tests variety benchmark show that method, dubbed ωB97X-3c, par even outperforms quadruple-zeta at fraction computational cost. Particular strengths this description non-covalent interactions barrier heights, it among overall.

Language: Английский

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Autonomous Reaction Network Exploration in Homogeneous and Heterogeneous Catalysis

Topics in Catalysis, Journal Year: 2022, Volume and Issue: 65(1-4), P. 6 - 39

Published: Jan. 13, 2022

Autonomous computations that rely on automated reaction network elucidation algorithms may pave the way to make computational catalysis a par with experimental research in field. Several advantages of this approach are key catalysis: (i) Automation allows one consider orders magnitude more structures systematic and open-ended fashion than what would be accessible by manual inspection. Eventually, full resolution terms structural varieties conformations as well respect type number potentially important elementary steps (including decomposition reactions determine turnover numbers) achieved. (ii) Fast electronic structure methods uncertainty quantification warrant high efficiency reliability order not only deliver results quickly, but also allow for predictive work. (iii) A degree autonomy reduces amount human work, processing errors, bias. Although being inherently unbiased, it is still steerable specific regions an emerging addition new reactant species. This fidelity formalization some catalytic process surprising silico discoveries. In we first review state art embed autonomous explorations into general field from which draws its ingredients. We then elaborate conceptual issues arise context procedures, discuss at example system.

Language: Английский

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Exploring Cuneanes as Potential Benzene Isosteres and Energetic Materials: Scope and Mechanistic Investigations into Regioselective Rearrangements from Cubanes

Journal of the American Chemical Society, Journal Year: 2023, Volume and Issue: 145(30), P. 16355 - 16364

Published: July 24, 2023

Cuneane is a strained hydrocarbon that can be accessed via metal-catalyzed isomerization of cubane. The carbon atoms cuneane define polyhedron the C2v point group with six faces─two triangular, two quadrilateral, and pentagonal. rigidity, strain, unique exit vectors skeleton make it potential scaffold interest for synthesis functional small molecules materials. However, limited previous synthetic efforts toward cuneanes have focused on monosubstituted or redundantly substituted systems such as permethylated, perfluorinated, bis(hydroxymethylated) cuneanes. Such compounds, particularly rotationally symmetric cuneanes, building blocks complex molecules. Reliable, predictable, selective syntheses polysubstituted bearing more substitution patterns would facilitate study this ring system in myriad applications. Herein, we report regioselective, AgI-catalyzed asymmetrically 1,4-disubstituted cubanes to In-depth DFT calculations provide charge-controlled regioselectivity model, direct dynamics simulations indicate nonclassical carbocation invoked short-lived dynamic effects augment charge model.

Language: Английский

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

Physical Chemistry Chemical Physics, Journal Year: 2024, Volume and Issue: 26(32), P. 21379 - 21394

Published: Jan. 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

Language: Английский

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Modeling Zinc Complexes Using Neural Networks

Journal of Chemical Information and Modeling, Journal Year: 2024, Volume and Issue: 64(8), P. 3140 - 3148

Published: April 8, 2024

Understanding the energetic landscapes of large molecules is necessary for study chemical and biological systems. Recently, deep learning has greatly accelerated development models based on quantum chemistry, making it possible to build potential energy surfaces explore space. However, most this work focused organic due simplicity their electronic structures as well availability data sets. In work, we a architecture model energetics zinc organometallic complexes. To achieve this, have compiled configurationally conformationally diverse set complexes using metadynamics overcome limitations traditional sampling methods. terms neural network potentials, our results indicate that complexes, partial charges play an important role in modeling long-range interactions with network. Our developed outperforms semiempirical methods predicting relative conformers, yielding mean absolute error (MAE) 1.32 kcal/mol reference double-hybrid PWPB95 method.

Language: Английский

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Sorting drug conformers in enzyme active sites: the XTB way

Physical Chemistry Chemical Physics, Journal Year: 2024, Volume and Issue: 26(16), P. 12610 - 12618

Published: Jan. 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.

Language: Английский

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Accurate Enthalpies of Formation for Bioactive Compounds from High-Level Ab Initio Calculations with Detailed Conformational Treatment: A Case of Cannabinoids

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

Published: Jan. 9, 2025

Our recently developed approach based on the local coupled-cluster with single, double, and perturbative triple excitation [LCCSD(T)] model gives very efficient means to compute ideal-gas enthalpies of formation. The expanded uncertainty (95% confidence) method is about 3 kJ·mol–1 for medium-sized compounds, comparable typical experimental measurements. Larger compounds interest often exhibit many conformations that can significantly differ in intramolecular interactions. Although present capabilities allow processing even a few hundred distinct conformer structures given compound, systems numbers well excess 1000. In this study, we investigate how reduce number expensive LCCSD(T) calculations large ensembles while controlling error approximation. best strategy found was correct results lower-level, surrogate (density functional theory, DFT) systematic manner. It also conformational contribution introduced by mainly driven (bias) rather than random component DFT energy deviation from target. This distinction usually overlooked benchmarking studies. As result work, formation 20 cannabinoid cannabinoid-related were obtained. Comprehensive analysis suggests uncertainties obtained values are below 4 kJ·mol–1.

Language: Английский

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Potent SARS-CoV-2 3C-like protease inhibitor ( +)-eupenoxide-3,6-diketone (IC50: 0.048 μM) was synthesized based on ( +)-eupenoxide; lead from ( +)-eupenoxide analogs study by endophytic fermentation

Journal of Natural Medicines, Journal Year: 2025, Volume and Issue: 79(2), P. 357 - 370

Published: Feb. 3, 2025

Language: Английский

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Conformational Energy Benchmark for Longer n-Alkane Chains

The Journal of Physical Chemistry A, Journal Year: 2022, Volume and Issue: 126(22), P. 3521 - 3535

Published: May 26, 2022

We present the first benchmark set focusing on conformational energies of highly flexible, long n-alkane chains, termed ACONFL. Unbranched alkanes are ubiquitous building blocks in nature, so goal is to be able calculate their properties most accurately improve modeling of, e.g., complex (biological) systems. Very accurate DLPNO-CCSD(T1)/CBS reference values provided, which allow for a statistical meaningful evaluation even best available density functional methods. The performance established and modern (dispersion corrected) functionals comprehensively assessed. recently introduced r2SCAN-V shows excellent performance, similar efficient composite DFT methods like B97-3c r2SCAN-3c, provide an better cost-accuracy ratio, while almost reaching accuracy much more computationally demanding hybrid or double with large QZ AO basis sets. In addition, we investigated common wave function methods, where MP2/CBS surprisingly performs worse compared simple D4 dispersion corrected Hartree-Fock. Furthermore, investigate several semiempirical force field commonly used generation ensembles multilevel workflows scale molecular dynamics studies. Outstanding obtained by general field, GFN-FF, other applied universal yield errors. recommend ACONFL as helpful parametrization new machine learning potentials well validation newly developed

Language: Английский

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Temperature and indoor environments

Indoor Air, Journal Year: 2022, Volume and Issue: 32(5)

Published: May 1, 2022

From the thermodynamic perspective, term temperature is clearly defined for ideal physical systems: A unique can be assigned to each black body via its radiation spectrum, and of an gas given by velocity distribution molecules. While indoor environment not system, fundamental chemical processes, such as diffusion, partitioning equilibria, reactions, are predictably temperature-dependent. For example, logarithm reaction rate equilibria constants proportional reciprocal absolute temperature. It therefore possible have non-linear, very steep changes in phenomena over a relatively small range. On contrary, transport processes more influenced spatial temperature, momentum, pressure gradients well density, porosity, composition materials. Consequently, emergent phenomena, emission rates or dynamic air concentrations, result complex temperature-dependent relationships that require empirical approach. Indoor environmental conditions further thermal comfort needs occupants. Not only do occupants create serve maintain their core which usually accomplished wearing appropriate clothing, but also surroundings must adapted so they feel comfortable. This includes interaction living space with ambient environment, vary greatly region season. Design houses, apartments, commercial buildings, schools generally utility driven, requiring energy balance, sometimes considering ventilation rarely including impact on contaminant levels. In our article, we start review variables discuss influence typical processes. Then, describe heat balance people environment. An extensive literature study devoted release pollutants from materials various interior compartments aspects chemistry. Finally, assess need consider holistically regard expected global emergencies climate change.

Language: Английский

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