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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Absorption Spectrum of Hydroperoxymethyl Thioformate: A Computational Chemistry Study

Molecules, Год журнала: 2025, Номер 30(2), С. 338 - 338

Опубликована: Янв. 16, 2025

Hydroperoxymethyl thioformate (or HPMTF) is a compound relevant to the chemistry of sulfur in marine atmosphere. The chemical cycling this molecule atmosphere still uncertain due part lack accurate knowledge its photolytic behavior. Only approximations based on properties chromophores are used previous studies. In work, we calculated absorption spectra gas and aqueous phases using Nuclear Ensemble Approach (NEA) CASPT2 method. Furthermore, such information obtain relative photolysis rates. We found that chromophore approximation overestimates rates phase by twice value obtained with NEA-CASPT2 protocol. for phase, predict lower role as compared phase.

Язык: Английский

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Advances in the Simulations of Enzyme Reactivity in the Dawn of the Artificial Intelligence Age

Wiley Interdisciplinary Reviews Computational Molecular Science, Год журнала: 2025, Номер 15(1)

Опубликована: Янв. 1, 2025

ABSTRACT The study of natural enzyme catalytic processes at a molecular level can provide essential information for rational design new enzymes, to be applied in more efficient and environmentally friendly industrial processes. use computational tools, combined with experimental techniques, is providing outstanding milestones the last decades. However, apart from complexity associated nature these large flexible biomolecular machines, full catalyzed process involves different physical chemical steps. Consequently, point view, deep understanding every single step requires selection proper technique get reliable, robust useful results. In this article, we summarize techniques their process, including conformational diversity, allostery those steps, as well enzymes. Because impact artificial intelligence all aspects science during years, special attention has been methods based on foundations some selected recent applications.

Язык: Английский

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Tensor Train Optimization for Conformational Sampling of Organic Molecules

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

Опубликована: Янв. 22, 2025

Exploring the conformational space of molecules remains a challenge fundamental importance to quantum chemistry: identification relevant conformers at ambient conditions enables predictive simulations almost arbitrary properties. Here, we propose novel approach, called TTConf, enable sampling large organic where combinatorial explosion possible prevents use brute-force systematic conformer search. We employ tensor trains as highly efficient dimensionality reduction algorithm, effectively reducing scaling from exponential polynomial. In our search is expressed global energy minimization task in high-dimensional grid dihedral angles. Dimensionality achieved through train representation torsion space. The performance approach assessed on variety drug-like direct comparison state-of-the-art metadynamics based implemented CREST. shows significant acceleration up an order magnitude, while maintaining comparable accuracy. More importantly, presented allows treatment larger than typically accessible with metadynamics.

Язык: Английский

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A Unique Case of ′in Situ’ Bifluoride Triggered Formation of Supramolecular Organogels Using Isophthalamide Hydrogen Bond Donating Receptors.

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

Опубликована: Янв. 23, 2025

Abstract A novel isopthalamide based receptor H 2 L2 featuring two p ‐benzoic acid units has been synthesised and its anion binding properties analysed by 1 H‐NMR spectroscopy in DMSO‐ d 6 /0.5 % O. As expected, the presence of tetrabutylammonium (TBA) fluoride deprotonation carboxylic moieties was observed. However, deprotonated 2− able to bind situ formed HF − via formation H‐bonds with amide NHs. When dissolved THF 4 equivalents TBAF were added CH 3 CN a unique sol‐gel transition occurred giving rise stable thixotropic supramolecular gel. Theoretical calculations elucidated gelation mechanism strongly support findings observed experimentally.

Язык: Английский

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DP4+-Based Stereochemical Reassignment and Total Synthesis of Polyenic Macrolactam Muanlactam

The Journal of Organic Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Янв. 31, 2025

The total synthesis of the stereoisomer muanlactam predicted by DP4+ calculations, which differed from that reported for natural product on relative configuration at C19, was completed, and structure polyenic macrolactam fully confirmed. Construction stereocenters involved iterative enantio- diastereoselective Krische's allylation reaction formal syn-1,3-diol addition a propargylic Grignard reagent to Ellman's chiral nonracemic tert-butylsulfinamide enantiopure amine fragment. conjugated triene diene units were constructed Suzuki–Miyaura cross-coupling reactions corresponding alkenylboronates alkenyl iodides. Formation tetraene Horner–Wadsworth–Emmons condensation functionalized partners followed challenging macrolactamization using hexafluorophosphate azabenzotriazole tetramethyluronium N,N-diisopropylethylamine. NMR data synthetic matched those product, thus correcting had previously been assigned DP4.

Язык: 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, Год журнала: 2025, Номер 79(2), С. 357 - 370

Опубликована: Фев. 3, 2025

Язык: Английский

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SpectroIBIS: Automated Data Processing for Multiconformer Quantum Chemical Spectroscopic Calculations

Journal of Natural Products, Год журнала: 2025, Номер unknown

Опубликована: Фев. 7, 2025

Quantum chemical spectroscopic calculations have grown increasingly popular in natural products research for aiding the elucidation of structures, especially their stereochemical configurations. These become faster with modern computational speeds, but subsequent data handling, inspection, and presentation remain key bottlenecks many researchers. In this article, we introduce SpectroIBIS computer program as a user-friendly tool to automate tedious tasks commonly encountered workflow. Through simple graphical user interface, researchers can drag drop Gaussian or ORCA output files produce Boltzmann-averaged ECD, VCD, UV–vis IR data, optical rotations, and/or 1H 13C NMR shifts seconds. Also produced are formatted, publication-quality supplementary tables containing conformer energies atomic coordinates, saved DOCX file compatible Microsoft Word LibreOffice. Importantly, assist finding common calculation issues by automatically checking redundant conformers imaginary frequencies. Additional useful features include recognition energy recalculations at higher theory level, automated generation input quantum chemistry programs optional exclusion high-energy conformers. Lastly, demonstrate applicability five products. is open-source software available free desktop application (https://github.com/bbulcock/SpectroIBIS).

Язык: Английский

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Predicting and Explaining Yields with Machine Learning for Carboxylated Azoles and Beyond

Journal of Chemical Information and Modeling, Год журнала: 2025, Номер unknown

Опубликована: Фев. 7, 2025

Carbon dioxide (CO2) can be transformed into valuable chemical building blocks, including C2-carboxylated 1,3-azoles, which have potential applications in pharmaceuticals, cosmetics, and pesticides. However, only a small fraction of the millions available 1,3-azoles are carboxylated at C2 position, highlighting significant opportunities for further research synthesis application these compounds. In this study, we utilized supervised machine learning approach to predict reaction yields data set amide-coupled 1,3-azoles. To facilitate molecular design, integrated an interpretable heat-mapping algorithm named PIXIE (Predictive Insights Xplainability Informed space Exploration). visualizes influence substructures on predicted by leveraging fingerprint bit importances, providing synthetic chemists with powerful tool rational design molecules. While heat mapping is established technique, its integration machine-learning model tailored represents advancement. This not enables targeted exploration underrepresented space, fostering discovery new bioactive compounds, but also demonstrates combining methods broader other domains.

Язык: Английский

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On the Stability Constants of Metal-Nitrate Complexes in Aqueous Solutions

Physical Chemistry Chemical Physics, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Stability constants of simple reactions involving addition the NO 3 − ion to hydrated metal complexes, [M(H 2 O) x ] n + are calculated with a computational workflow developed using cloud computing resources.

Язык: Английский

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