Hydrogen atom transfer (HAT) processes promoted by the quinolinimide-N-oxyl radical: a kinetic and theoretical study

A kinetic study of the hydrogen atom transfer (HAT) reactions from a series of organic compounds to the quinolinimide-N-oxyl radical (QINO) was performed in CH3CN. The HAT rate constants are significantly higher than those observed with the phthalimide- N-oxyl radical (PINO) as a result of enthalpic and polar effects due to the presence of the N-heteroaromatic ring in QINO. The relevance of polar effects is supported by theoretical calculations conducted for the reactions of the two N-oxyl radicals with toluene, which indicate that the HAT process is characterized by a significant degree of charge transfer permitted by the π-stacking that occurs between the toluene and the N-oxyl aromatic rings in the transition state structures. An increase in the HAT reactivity of QINO was observed in the presence of 0.15 M HClO4 and 0.15 M Mg(ClO4)2 due to the protonation or complexation with the Lewis acid of the pyridine nitrogen that leads to a further decrease in the electron density in the N-oxyl radical. These results fully support the use of N-hydroxyquinolinimide as a convenient substitute for N-hydroxyphthalimide in the catalytic aerobic oxidations of aliphatic hydrocarbons characterized by relatively high C–H bond dissociation energies

Development of atom-centered potentials for efficient and accurate electronic structure modeling of large molecular systems

Accurate quantum mechanical (QM) modeling of large molecular systems is computationally challenging due to the dramatic increase in the demand for computational resources with increasing system size. To tackle this problem, atom-centered potentials (ACPs) were developed to mitigate the errors of Hartree–Fock (HF) and density-functional theory (DFT) methods, particularly when used with small basis sets. The objective behind developing ACPs for such methods was to improve their accuracy in predicting various molecular properties without impacting their low computational cost. ACPs are optimized one-electron Gaussian-type functions that share the same mathematical form as generally used effective-core potentials, except they do not replace any electrons, making them easily usable with many quantum chemistry software packages. Besides, ACPs allow for a convenient means to simultaneously correct the absence of correlation (or deficiencies in exchange-correlation density functionals), basis set incompleteness, and other shortcomings in HF or DFT methods with small basis sets. The overall research conducted for this dissertation demonstrates the gradual transition from the development of proof-of-concept ACPs to final ACPs with more general applicability. In particular, the final ACPs are presented for ten elements in the first and second rows (H, B, C, N, O, F, Si, P, S, Cl), extending the applicability to various organic and biochemical molecules. The ACP-corrected methods have been shown to predict the target molecular properties with slightly less accuracy than very computationally expensive QM methods but at a much lower computational cost. It is anticipated that the methods presented in this dissertation will assist in applications such as supramolecular host-guest complexation, enzymatic catalysis, drug-target binding, protein folding, and others. This dissertation also contributes towards filling the gap in the literature regarding benchmark data sets by presenting new diverse data sets of molecular properties such as polypeptide conformational energies (PEPCONF), bond separation energies (BSE49), barrier height energies (BH9), and reaction energies (BH9-RE). These data sets have been generated using a significant amount of manual and computational effort to address the need for reference data in the ACP development process and other applications.Science, Irving K. Barber Faculty of (Okanagan)Chemistry, Department of (Okanagan)Graduat

Fast and accurate quantum mechanical modeling of large molecular systems using small basis set Hartree–Fock methods corrected with atom-centered potentials

There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine-learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bio-organic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*), and the HF-3c method. The new ACPs are trained on a very large set (73832 data points) of non-covalent properties (interaction and conformational energies) and validated additionally on a set of 32048 data points. All reference data is of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for non-covalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set DFT but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and non-covalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms

Small basis set density-functional theory methods corrected with atom-centered potentials

Density-functional theory (DFT) is currently the most popular method for modeling non-covalent interactions and thermochemistry. The accurate calculation of non-covalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of non-covalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M062X and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118,655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include non-covalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42,567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M062X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of non-covalent, thermochemical, and kinetic properties in large molecular systems

BH9, a New Comprehensive Benchmark Dataset for Barrier Heights and Reaction Energies: Assessment of Density Functional Approximations and Basis Set Incompleteness Potentials

The calculation of accurate reaction energies and barrier heights is essential in computational studies of reaction mechanisms and thermochemistry. In order to assess methods regarding their ability to predict these two properties, high-quality benchmark sets are required that comprise a reasonably large and diverse set of organic reactions. Due to the time-consuming nature of both locating transition states and computing accurate reference energies for reactions involving large molecules, previous benchmark sets have been limited in scope, the number of reactions considered, and the size of the reactant and product molecules. Recent advances in coupled-cluster theory, in particular local correlation methods like DLPNO-CCSD(T), now allow the calculation of reaction energies and barrier heights for relatively large systems. In this work, we present a comprehensive, and diverse benchmark set of barrier heights and reaction energies based on DLPNO-CCSD(T)/CBS, called BH9. BH9 comprises 449 chemical reactions belonging to nine types common in organic chemistry and biochemistry. We examine the accuracy of DLPNO-CCSD(T) vis-a-vis canonical CCSD(T) for a subset of BH9 and conclude that, although there is a penalty in using the DLPNO approximation, the reference data are accurate enough to serve as benchmark for density-functional theory (DFT) methods. We then present two applications of the BH9 set. First, we examine the performance of several density functional approximations commonly used in thermochemical and mechanistic studies. Second, we assess our basis set incompleteness potentials regarding their ability to mitigate basis set incompleteness error. The number of data points, the diversity of the reactions considered, and the relatively large size of the reactant molecules make BH9 the most comprehensive thermochemical benchmark set to date, and a useful tool for the development and assessment of computational methods

Atom-Centered Potentials with Dispersion-Corrected Minimal-Basis-Set Hartree–Fock: An Efficient and Accurate Computational Approach for Large Molecular Systems

We present a computational methodology based on atom-centered potentials (ACPs) for the efficient and accurate structural modeling of large molecular systems. ACPs are atom-centered one-electron potentials that have the same functional form as effective-core potentials. In recent works, we showed that ACPs can be used to produce a correction to the ground-state wave function and electronic energy to alleviate shortcomings in the underlying model chemistry. In this work, we present ACPs for H, C, N, and O atoms that are specifically designed to predict accurate non-covalent binding energies and inter- and intramolecular geometries when combined with dispersion-corrected Hartree–Fock (HF-D3) and a minimal basis-set (scaled MINI or MINIs). For example, the combined HF-D3/MINIs-ACP method demonstrates excellent performance, with mean absolute errors of 0.36 and 0.28 kcal/mol for the S22x5 and S66x8 benchmark sets, respectively, relative to highly correlated complete-basis-set data. The application of ACPs results in a significant decrease in error compared to uncorrected HF-D3/MINIs for all benchmark sets examined. In addition, HF-D3/MINIs-ACP, has a cost only slightly higher than a minimal-basis-set HF calculation and can be used with any electronic structure program for molecular quantum chemistry that uses Gaussian basis sets and effective-core potentials

Atom-Centered Potentials with Dispersion-Corrected Minimal-Basis-Set Hartree–Fock: An Efficient and Accurate Computational Approach for Large Molecular Systems

We present a computational methodology based on atom-centered potentials (ACPs) for the efficient and accurate structural modeling of large molecular systems. ACPs are atom-centered one-electron potentials that have the same functional form as effective-core potentials. In recent works, we showed that ACPs can be used to produce a correction to the ground-state wave function and electronic energy to alleviate shortcomings in the underlying model chemistry. In this work, we present ACPs for H, C, N, and O atoms that are specifically designed to predict accurate non-covalent binding energies and inter- and intramolecular geometries when combined with dispersion-corrected Hartree–Fock (HF-D3) and a minimal basis-set (scaled MINI or MINIs). For example, the combined HF-D3/MINIs-ACP method demonstrates excellent performance, with mean absolute errors of 0.36 and 0.28 kcal/mol for the S22x5 and S66x8 benchmark sets, respectively, relative to highly correlated complete-basis-set data. The application of ACPs results in a significant decrease in error compared to uncorrected HF-D3/MINIs for all benchmark sets examined. In addition, HF-D3/MINIs-ACP, has a cost only slightly higher than a minimal-basis-set HF calculation and can be used with any electronic structure program for molecular quantum chemistry that uses Gaussian basis sets and effective-core potentials

Hydrogen atom transfer (HAT) processes promoted by the quinolinimide-N-oxyl radical: a kinetic and theoretical study

A kinetic study of the hydrogen atom transfer (HAT) reactions from a series of organic compounds to the quinolinimide-N-oxyl radical (QINO) was performed in CH3CN. The HAT rate constants are significantly higher than those observed with the phthalimide- N-oxyl radical (PINO) as a result of enthalpic and polar effects due to the presence of the N-heteroaromatic ring in QINO. The relevance of polar effects is supported by theoretical calculations conducted for the reactions of the two N-oxyl radicals with toluene, which indicate that the HAT process is characterized by a significant degree of charge transfer permitted by the π-stacking that occurs between the toluene and the N-oxyl aromatic rings in the transition state structures. An increase in the HAT reactivity of QINO was observed in the presence of 0.15 M HClO4 and 0.15 M Mg(ClO4)2 due to the protonation or complexation with the Lewis acid of the pyridine nitrogen that leads to a further decrease in the electron density in the N-oxyl radical. These results fully support the use of N-hydroxyquinolinimide as a convenient substitute for N-hydroxyphthalimide in the catalytic aerobic oxidations of aliphatic hydrocarbons characterized by relatively high C–H bond dissociation energies

Molecular Engineering of Triphenylamine Based Aggregation Enhanced Emissive Fluorophore: Structure-Dependent Mechanochromism and Self-Reversible Fluorescence Switching

Triphenylamine (TPA), a propeller-shaped optoelectronic molecule, has been used to generate stimuli-responsive smart fluorescent organic materials and correlate the effect of subtle structural changes on the molecular packing and mechanochromic fluorescence (MCF). The substituent (OCH₃) position in the TPA phenyl ring and acceptors (malononitrile, cyanoacetamide, cyanoacetic acid, ethyl cyanoacetate, and diethylmalonate) strongly influenced the solid state and mechanochromic fluorescence as well as the molecular packing. The structure–property studies revealed that (i) TPA derivatives without the OCH₃ substituent exhibit strong fluorescence (Φ_f = 85% (TCAAD-1, 55% (TDEM)), (ii) higher dihedral angle (τ) between donor (aminophenyl) and acceptor lead to weak/non fluorescent material, (iii) substituent at the ortho position to acceptor increased the dihedral angle (τ = 26.49 (TCAAD-2), τ = 27.14 (TDMM)), and (iv) the increase of alkyl groups produced self-reversible high contrast off-on fluorescence switching materials (TDEM). Powder X-ray diffraction studies indicate that stimuli induced reversible phase transformation from crystalline to amorphous and vice versa was responsible for fluorescence switching. The computational studies also supported that OCH₃ substitution at ortho to acceptor increased the dihedral angle and optical band gap. Thus, the present studies provide a structural insight for designing TPA based organic molecules for developing new smart organic materials

Effects of hospital facilities on patient outcomes after cancer surgery: an international, prospective, observational study

© 2022 The Author(s). Published by Elsevier Ltd. This is an Open Access article under the CC BY 4.0 licenseBackground: Early death after cancer surgery is higher in low-income and middle-income countries (LMICs) compared with in high-income countries, yet the impact of facility characteristics on early postoperative outcomes is unknown. The aim of this study was to examine the association between hospital infrastructure, resource availability, and processes on early outcomes after cancer surgery worldwide. Methods: A multimethods analysis was performed as part of the GlobalSurg 3 study—a multicentre, international, prospective cohort study of patients who had surgery for breast, colorectal, or gastric cancer. The primary outcomes were 30-day mortality and 30-day major complication rates. Potentially beneficial hospital facilities were identified by variable selection to select those associated with 30-day mortality. Adjusted outcomes were determined using generalised estimating equations to account for patient characteristics and country-income group, with population stratification by hospital. Findings: Between April 1, 2018, and April 23, 2019, facility-level data were collected for 9685 patients across 238 hospitals in 66 countries (91 hospitals in 20 high-income countries; 57 hospitals in 19 upper-middle-income countries; and 90 hospitals in 27 low-income to lower-middle-income countries). The availability of five hospital facilities was inversely associated with mortality: ultrasound, CT scanner, critical care unit, opioid analgesia, and oncologist. After adjustment for case-mix and country income group, hospitals with three or fewer of these facilities (62 hospitals, 1294 patients) had higher mortality compared with those with four or five (adjusted odds ratio [OR] 3·85 [95% CI 2·58–5·75]; p<0·0001), with excess mortality predominantly explained by a limited capacity to rescue following the development of major complications (63·0% vs 82·7%; OR 0·35 [0·23–0·53]; p<0·0001). Across LMICs, improvements in hospital facilities would prevent one to three deaths for every 100 patients undergoing surgery for cancer. Interpretation: Hospitals with higher levels of infrastructure and resources have better outcomes after cancer surgery, independent of country income. Without urgent strengthening of hospital infrastructure and resources, the reductions in cancer-associated mortality associated with improved access will not be realised. Funding: National Institute for Health and Care Research