1H NMR Mixture Design-Fingerprints and ASCA Analysis in Ilex paraguariensis: Model Stability in Search of a Global Metabolome.

The effects of experimental repetitions and solvent extractors on the 1H NMR fingerprinting of yerba mate extracts, obtained from two genders and two light environments, were analyzed in-depth by ANOVA-simultaneous component analysis (ASCA). Different solvents were used according to a mixture design based on ethanol, dichloromethane, and hexane and their combinations. The number of experimental repetitions significantly affected the ASCA results. Increasing repetitions led to decreases in the percentage effect variance values and an increase in the percentage residual variance. However, secondary sexual dimorphism, light availability, and their interaction effects became more significant with decreasing p-values at or above the 95% confidence level. The choice of a solvent extractor significantly affects the chemical profile and can lead to distinct conclusions regarding the significance of effect values. Pure solvents yielded different conclusions about the significance of factorial design effects, with each solvent extracting unique metabolites and maximizing information for specific effects. However, the use of binary solvent mixtures, such as ethanol-dichloromethane, proved more efficient in extracting sets of compounds that simultaneously differentiate between different experimental conditions. The mixture design-fingerprint strategy provided satisfactory results expanding the range of extracted metabolites with high percentage of residual variances and low explained percentage effect variances in the ASCA models. Ternary and even higher-ordered mixtures could be good alternative extracting media for work-intensive procedures. Our study underscores the significance of experimental design and solvent selection in metabolomic analysis, improving the accuracy, robustness, and interpretability of metabolomic models, leading to a better understanding of the chemical composition and biological implications of plant extracts.

Characteristic Substituent Effect Model for the Infrared Intensities of the X2CY (X = H, F, Cl, Br; Y = O, S) Molecules.

Many years ago, the gas-phase infrared fundamental intensities of Cl2CS were determined within experimental error from the experimental intensities and frequencies of F2CO, Cl2CO, and F2CS. An additive characteristic substituent shift relationship between atomic polar tensors of these molecules formed the basis for these calculations. Here, QCISD/cc-pVTZ-level Quantum Theory of Atoms In Molecules (QTAIM) individual charge, charge transfer, and polarization contributions to these atomic polar tensor elements are shown to obey the same basic relationship for the extended X2CY (Y = O, S; X = H, F, Cl, Br) family of molecules. QTAIM charge and polarization contributions, as well as the total equilibrium dipole moments of the X2CY molecules, also follow this characteristic substituent shift model. The root-mean-sqaure error for the 231 estimates of these parameters is 0.14 e or only about 1% of the total 10 e range of the Atomic Polar Tensor (APT) contributions determined from the wave functions. The substituent effect APT contribution estimates were used to calculate the infrared intensities of the X2CY molecules. Although one serious discrepancy was observed for one of the CH stretching vibrations of H2CS, accurate values were within 45 km·mol-1 or about 7% of the 656 km·mol-1 intensity range predicted by the QCISD/cc-pVTZ wave functions. Hirshfeld charge, charge transfer, and polarization contributions are also found to follow this model, although their charge parameters do not follow electronegativity expectations.

Energetic Origins of Force Constants: Adding a New Dimension to the Hessian Matrix via Interacting Quantum Atoms.

The Interacting Quantum Atoms (IQA) energy decomposition scheme divides the total energy of a molecule into intra- and interatomic contributions. While the former relates to the kinetic and potential energies of electrons inside a unique individual atomic basin, the latter contains the Coulomb and exchange-correlation potentials between electrons from two atomic basins. Considering that the molecular energy is a sum of IQA contributions, the Hessian matrix can also be written as a sum of "IQA Hessian" matrices, whose elements are second derivatives of IQA terms. Herein, we present a mathematical formalism for the IQA decomposition of force constants revealing their energetic origins. The method consists of adding a new dimension to the Hessian matrix, which becomes 3N × 3N × N2, with N being the number of atoms in the molecule and N2 the number of IQA terms. Since there is no analytical method that produces the IQA second derivatives, the three-dimensional IQA Hessian is numerically calculated. When studying molecular vibrations, force constants, providing information about the nature of chemical bond and related to infrared frequencies, can be obtained by Wilson's FG method, which involves detailed manipulations of the Hessian matrix. In this paper, the methodology is reported and validated for a set of 30 molecules and more than 200 force constants and their interactions. Energetic origins of force constants are presented for diatomics and small molecules containing carbon-carbon, oxygen-oxygen, and carbon-oxygen bonds with different bond orders. It is found that bond stability and stiffness can have strikingly different energetic origins.

Infrared intensities of [Formula: see text]: a true challenge for DFT methods.

Absolute infrared intensities of [Formula: see text] were evaluated with a great variety of DFT and ab initio methods and basis sets. It is shown that the intensities calculated by different levels of theory may not agree with each other even in the qualitative (weak/strong) sense. Geometrical parameters, as well as net atomic charges evaluated from multiple partition schemes, did not vary as much as the intensities and thus cannot explain the tremendous differences found for the latter. As there are no experimental estimates for the intensities to guide the theoretical evaluation, deciding on the best level of theory is reduced to comparisons between the different DFT methods and QCISD or CCSD, believed to be the best theoretical estimates in the set. The differences found among the various DFT methods suggest the development of new methods, instead of converging to a focal point, is rather diverging.

An Interacting Quantum Atoms (IQA) and Relative Energy Gradient (REG) Analysis of the Anomeric Effect.

The explanation of the anomeric effect in terms of underlying quantum properties is still controversial almost 70 years after its introduction. Here, we use a method called Relative Energy Gradient (REG), which is able to compute chemical insight with a view to explaining the anomeric effect. REG operates on atomic energy contributions generated by the quantum topological energy decomposition Interacting Quantum Atoms (IQA). Based on the case studies of dimethoxymethane and 2-fluorotetrahydropyran, we show that the anomeric effect is electrostatic in nature rather than governed by hyperconjugation.

Towards an atomistic understanding of polymorphism in molecular solids.

Understanding and controlling polymorphism in molecular solids is a major unsolved problem in crystal engineering. While the ability to calculate accurate lattice energies with atomistic modelling provides valuable insight into the associated energy scales, existing methods cannot connect energy differences to the delicate balances of intra- and intermolecular forces that ultimately determine polymorph stability ordering. We report herein a protocol for applying Quantum Chemical Topology (QCT) to study the key intra- and intermolecular interactions in molecular solids, which we use to compare the three known polymorphs of succinic acid including the recently-discovered γ form. QCT provides a rigorous partitioning of the total energy into contributions associated with topological atoms, and a quantitative and chemically intuitive description of the intra- and intermolecular interactions. The newly-proposed Relative Energy Gradient (REG) method ranks atomistic energy terms (steric, electrostatic and exchange) by their importance in constructing the total energy profile for a chemical process. We find that the conformation of the succinic acid molecule is governed by a balance of large and opposing electrostatic interactions, while the H-bond dimerisation is governed by a combination of electrostatics and sterics. In the solids, an atomistic energy balance emerges that governs the contraction, towards the equilibrium geometry, of a molecular cluster representing the bulk crystal. The protocol we put forward is as general as the capabilities of the underlying quantum-mechanical model and it can provide novel perspectives on polymorphism in a wide range of chemical systems.

Electronic Distribution of SN2 IRC and TS Structures: Infrared Intensities of Imaginary Frequencies.

A novel IRC-TS-CCTDP method to investigate transition states (TS) is proposed in which changes in the molecular geometry follow atomic displacements corresponding to the imaginary frequency normal coordinate. Electronic charge structure changes can be analyzed using the charge-charge-transfer-dipolar polarization (CCTDP) model. An application is presented for the gas-phase SN2 reaction transition state structures for nine NuCX3LG- systems, with Nu and LG = H, F, Cl and X = H, F. Using quantum theory of atoms in molecules (QTAIM) at the QCISD/aug-cc-pVTZ level, atomic charges and atomic dipoles were obtained and applied to calculate the CCTDP contributions to their imaginary normal mode intensities. The results show that the imaginary bands are exceptionally strong, ranging from 1217 to 16 086 km·mol-1, much higher than the stretching intensities found in the methyl halides (that are all less than 100 km·mol-1). For all systems, the CT contributions are responsible for 63% of the total dipole moment derivatives. The charge contributions are slightly higher for transition states where X = F. Dipolar polarization contributions are always small and only reflect the molecular orientation change when the nucleophile displaces the leaving group and, therefore, can be neglected. The same occurs for contributions from the X atoms. Only atoms aligned with the reaction axis Nu--C-LG contribute to the total intensity. Almost all of the infrared intensities are determined by electron transfers from the nucleophile to carbon and subsequently from carbon to the leaving group. The mechanism of charge transfer revealed by the CCTDP model is consistent with the well-accepted reaction mechanism. Open-access codes for performing the IRC-TS-CCTDP analysis are described and provided for potential users in the Supporting Information.

Short-chain fatty acid acetate triggers antiviral response mediated by RIG-I in cells from infants with respiratory syncytial virus bronchiolitis.

BACKGROUND: Gut microbiota-derived short-chain fatty-acid (SFCA) acetate protects mice against RSV A2 strain infection by increasing interferon-ß production and expression of interferon-stimulated genes (ISGs). However, the role of SFCA in RSV infection using strains isolated from patients is unknown. METHODS: We first used RSV clinical strains isolated from infants hospitalized with RSV bronchiolitis to investigate the effects of in vitro SCFA-acetate treatment of human pulmonary epithelial cells. We next examined whether SCFA-acetate treatment is beneficial in a mouse model of RSV infection using clinical isolates. We sought to investigate the relationship of gut microbiota and fecal acetate with disease severity among infants hospitalized with RSV bronchiolitis, and whether treating their respiratory epithelial cells with SCFA-acetate ex-vivo impacts viral load and ISG expression. We further treated epithelial cells from SARS-CoV-2 infected patients with SCFA-acetate. FINDINGS: In vitro pre-treatment of A549 cells with SCFA-acetate reduced RSV infection with clinical isolates and increased the expression of RIG-I and ISG15. Animals treated with SCFA-acetate intranasally recovered significantly faster, with reduction in the RSV clinical isolates viral load, and increased lung expression of IFNB1 and the RIG-I. Experiments in RIG-I knockout A549 cells demonstrated that the protection relies on RIG-I presence. Gut microbial profile was associated with bronchiolitis severity and with acetate in stool. Increased SCFA-acetate levels were associated with increasing oxygen saturation at admission, and shorter duration of fever. Ex-vivo treatment of patients' respiratory cells with SCFA-acetate reduced RSV load and increased expression of ISGs OAS1 and ISG15, and virus recognition receptors MAVS and RIG-I, but not IFNB1. These SCFA-acetate effects were not found on cells from SARS-CoV-2 infected patients. INTERPRETATION: SCFA-acetate reduces the severity of RSV infection and RSV viral load through modulation of RIG-I expression. FUNDING: FAPERGS (FAPERGS/MS/CNPq/SESRS no. 03/2017 - PPSUS 17/2551-0001380-8 and COVID-19 20/2551-0000258-6); CNPq 312504/2017-9; CAPES) - Finance Code 001.

Unavoidable failure of point charge descriptions of electronic density changes for out-of-plane distortions.

Population analyses based on point charge approximations accurately estimating the equilibrium dipole moment will systematically fail when predicting infrared intensities of out-of-plane vibrations of planar molecules, whereas models based on both charges and dipoles will always succeed. It is not a matter of how the model is devised but rather how many degrees of freedom are available for the calculation. Population analyses based on point charges are very limited in terms of the amount of meaningful chemical information they provide, whereas models employing both atomic charges and atomic dipoles should be preferred for molecular distortions. A good model should be able to correctly describe not only static, equilibrium structures but also distorted geometries in order to correctly assess information from vibrating molecules. The limitations of point charge models also hold for distortions much larger than those encountered vibrationally.

Electrostatics Explains the Reverse Lewis Acidity of BH3 and Boron Trihalides: Infrared Intensities and a Relative Energy Gradient (REG) Analysis of IQA Energies.

The reaction path for the formation of BX3-NH3 (X = H, F, Cl, Br) complexes was divided into two processes: (i) rehybridization of the acid while adopting a pyramidal geometry, and (ii) the complex formation from the pyramidal geometries of the acid and base. The interacting quantum atom (IQA) method was used to investigate the Lewis acidity trend of these compounds. This topological analysis suggests that the boron-halogen bond exhibits a considerable degree of ionicity. A relative energy gradient (REG) analysis on IQA energies indicates that the acid-base complex formation is highly dependent on electrostatic energy. With increasing halogen electronegativity, a higher degree of ionicity of the B-X is observed, causing an increase in the absolute value of X and B charges. This increases not only the attractive electrostatic energy between the acid and base but also enhances the repulsive energy. The latter is the main factor behind the acidity trend exhibited by trihalides. Changes in geometry are relevant only for complexes where BH3 acts as an acid, where lower steric hindrance facilitates the adoption of the pyramidal geometry observed in the complex. The CCTDP analysis shows that infrared intensities of BX3-NH3 are determined mostly by the atomic charges and not by the charge transfer or polarization. The opposite is observed in covalent analogues.

Are "GAPT Charges" Really Just Charges?

Generalized atomic polar tensor (GAPT) has turned into a very popular charge model since it was proposed three decades ago. During this period, several works aiming to compare different partition schemes have included it among their tested models. Nonetheless, GAPT exhibits a set of unique features that prevent it from being directly comparable to "standard" partition schemes. We take this opportunity to explore some of these features, mainly related to the need of evaluating multiple geometries and the dynamic character of GAPT, and show how to obtain the static and dynamic parts of GAPT from any static charge model in the literature. We also present a conceptual evaluation of charge models that aims to explain, at least partially, why GAPT and quantum theory of atoms in molecules (QTAIM) charges are strongly correlated with one another, even though they seem to be constructed under very different frameworks. Similar to GAPT, infrared charges (also derived from atomic polar tensors of planar molecules) are also shown to provide an improved interpretation if they are described as a combination of static charges and changing atomic dipoles rather than just experimental static atomic charges.

AC/DC Analysis: Broad and Comprehensive Approach to Analyze Infrared Intensities at the Atomic Level.

We present a complete theoretical protocol to partition infrared intensities into terms owing to individual atoms by two different but related approaches: the atomic contributions (ACs) show how the entire molecular vibrational motion affects the electronic structure of a single atom and the total infrared intensity. On the other hand, the dynamic contributions (DCs) show how the displacement of a single atom alters the electronic structure of the entire molecule and the total intensity. The two analyses are complementary ways of partitioning the same total intensity and conserve most of the features of the total intensity itself. Combined, they are called the AC/DC analysis. These can be further partitioned following the CCTDP (or CCT) models according to the population analysis chosen by the researcher. The main conceptual features of the equations are highlighted, and representative numerical results are shown to support the interpretation of the equations. The results are invariant to rotation and translation and can readily be extended to molecules of any size, shape, or symmetry. Although the AC/DC analysis requires the choice of a charge model, all charge models that correctly reproduce the total molecular dipole moment can be used. A fully automated protocol managed by the Placzek program is made available, free of charge and with input examples.

Atomic charge and atomic dipole modeling of gas-phase infrared intensities of fundamental bands for out-of-plane CH and CF bending vibrations.

Out-of-plane CH group bending vibrational bands have long been known to be more intense than those for CF groups in similar molecular environments. This contrasts with expectations derived from charge models for which equilibrium atomic charge displacements are considered dominant contributions to dipole moment change on vibration. For this reason, the Charge, Charge Transfer, Dipolar Polarization (CCTDP) model based on the Quantum Theory for Atoms in Molecules (QTAIM) has been applied to the ethylene, tetrafluoroethylene and difluoro- and dichloroethylene molecules. Atomic charges and atomic dipoles from QTAIM and infrared intensities were calculated at the M06-2X/aug-cc-pVTZ level. The CH out-of-plane bending vibrations with relatively high intensities between 48.0 and 82.1 km/mol are characterized by small atomic charge and large polarization contributions having the same sign resulting in large net dipole moment contributions. Large charge and polarization dipole moment derivative contributions with opposite signs cancel each other producing very small intensities between 0.3 and 12.7 km/mol for the CF bends. Intensity variations can be successfully modeled by only their carbon atomic contributions with smaller contributions from the terminal atoms. Both CH and CF bending vibrations have large polarization contributions. Their charge contributions are usually small except for carbon atoms bonded to two fluorine atoms. The terminal atoms as well as the carbons have charge and polarization contributions of opposite sign. Comparison to benzene and hexafluorobenzene reveals that changes in these molecules' electronic densities caused by the out-of-plane atomic displacements are characteristic for each bond. In conclusion, successful modeling of the ethylene intensities must include atomic dipole parameters.Models based only on charges are doomed to failure.

A Video-Based Framework for Automatic 3D Localization of Multiple Basketball Players: A Combinatorial Optimization Approach.

Sports complexity must be investigated at competitions; therefore, non-invasive methods are essential. In this context, computer vision, image processing, and machine learning techniques can be useful in designing a non-invasive system for data acquisition that identifies players' positions in official basketball matches. Here, we propose and evaluate a novel video-based framework to perform automatic 3D localization of multiple basketball players. The introduced framework comprises two parts. The first stage is player detection, which aims to identify players' heads at the camera image level. This stage is based on background segmentation and on classification performed by an artificial neural network. The second stage is related to 3D reconstruction of the player positions from the images provided by the different cameras used in the acquisition. This task is tackled by formulating a constrained combinatorial optimization problem that minimizes the re-projection error while maximizing the number of detections in the formulated 3D localization problem.

QTAIM Atomic Charge and Polarization Parameters and Their Machine-Learning Transference among Boron-Halide Molecules.

Atomic charges are invariant for out-of-plane distortions, making their molecular vibrations enticing for electronic structure studies. Of planar molecules, the boron trihalides contain some of the most polar bonds known to chemistry, although their out-of-plane bending intensities are very small contrary to expectations from atomic charge models. Here, the out-of-plane infrared intensities of the BX(2)X(3)X(4) (X(2), X(3), X(4) = H, F, Cl, Br) molecules are investigated using quantum theory of atoms in molecules atomic charges and atomic dipoles within the formulism of the charge, charge transfer, dipolar polarization model at the QCISD/aug-cc-pVTZ quantum level. Dipole moments induced by equilibrium charge displacement of atoms perpendicular to the molecular plane are almost completely cancelled by their electronic density polarizations. The calculated boron trihalide intensities are small for molecules with such polar bonds ranging from 0.6 to 106.1 km mol-1. Even though the Cl atomic charge of -0.72 e in BCl3 is more negative than the hydrogen values of -0.67 e in BH3, the hydride out-of-plane intensity of 82.0 km mol-1 is an order of magnitude larger than that of the trichloride, 6.3 km mol-1. Owing to their diverse electronic structures, transference of atomic charges and dipole parameters among the boron trihalides is extremely challenging and does not result in accurate intensity values. For this reason, a machine-learning decision-tree algorithm was used to perform the transference procedure. Decision trees were optimized using quantum-level intensity values. Atomic charge and dipole parameters were estimated for a set of 12 test set molecules. These parameters provided intensity estimates with a root-mean-square error of 2.1 km mol-1 compared with QCISD/aug-cc-pVTZ reference values.

Quantum chemical intensity determinations of overlapped gas phase infrared bands.

The largest source of experimental error in determining gas phase fundamental infrared intensities arises from the separation of overlapped bands. Quantum chemical calculations at the QCISD/cc-pVTZ and QCISD/aug-cc-pVTZ levels were carried out on four simple hydrocarbons and the fluoro- and chloromethanes with the aim of accurate overlapped band separation. Fundamental vibrational intensity results were compared with individual empirical intensity estimates reported for overlapped band systems. Root mean square differences of 3.7 km mol-1 are found between the experimental and QCISD/cc-pVTZ values for nine overlapped bands of the hydrocarbons and 11.8 km mol-1 for the QCISD/aug-cc-pVTZ values for 12 overlapped bands of the fluoro- and chloromethanes. These values correspond to 14% and 18% of the average hydrocarbon and halomethane intensity values. Previous experimental separation errors were estimated to be quite larger, between 20% and 50%. As quantum calculations are continuously being refined one can expect more accurate band separation results in the future.

Orthokeratology on patient with ectasic cornea / Ortoceratologia no paciente com córnea ectásica

Abstract A 26-year-old man, single, business student, reveals a ectasic cornea during corneal topography exam. Among some procedures, the patient chose Orthokeratology to do a corneal reshape and got successfully a good visual acuity, going against the most authors guidance.

Resumo Estudante de 26 anos, masculino, estudante de economia, apresentou ao exame topográfico de córneas, ectasia corneal. Dentre todos os procedimentos apresentados, optou pela ortoceratologia para o remodelamento corneal, e obteve sucesso com melhora da acuidade visual, indo contra a orientação da maioria dos autores.

Complex Networks Models and Spectral Decomposition in the Analysis of Swimming Athletes' Performance at Olympic Games.

This study aims to present complex network models which analyze professional swimmers of 50-m freestyle Olympic competitions, comparing characteristics and variables that are considered performance determinants. This comparative research includes Olympic medalists' versus non-medalists' behavior. Using data from 40 athletes with a mean age, weight and height of 26 ± 2.9 years, 87 ± 5.59 kg, 193 ± 3.85 cm, respectively, at the Olympics of 2000, 2004, 2008, 2012, and 2016 (16-year interval), we built two types of complex networks (graphs) for each edition, using mathematical correlations, metrics and the spectral decomposition analysis. It is possible to show that complex metrics behave differently between medalists and non-medalists. The spectral radius (SR) proved to be an important form of evaluation since in all 5 editions it was higher among medalists (SR results: 3.75, 3.5, 3.39, 2.91, and 3.66) compared to non-medalists (2.18, 2.51, 2.23, 2.07, and 2.04), with significantly differences between. This study introduces a remarkable tool in the evaluation of the performance of groups of swimming athletes by complex networks, and is relevant to athletes, coaches, and even amateurs, regarding how individual variables relate to competition results and are reflected in the SR for the best performance. In addition, this is a general method and may, in the future, be developed in the analysis of other competitive sports.

Infrared Intensification and Hydrogen Bond Stabilization: Beyond Point Charges.

Infrared band intensification of the A-H bond stretching mode of A-H···B acid-base systems has long been known to be the most spectacular spectral change occurring on hydrogen bonding. A QTAIM/CCTDP model is reported here to quantitatively explain the electronic structure origins of intensification and investigate the correlation between experimental enthalpies of formation and infrared hydrogen bond stretching intensifications amply reported in the literature. Augmented correlation-consistent polarized triple-zeta quantum calculations at the MP2 level were performed on complexes with HF and HCl electron acceptors and HF, HCl, NH3, H2O, HCN, acetonitrile, formic acid, acetaldehyde, and formaldehyde electron donor molecules. The A-H stretching band intensities are calculated to be 3 to 40 times larger than their monomer values. Although the acidic hydrogen atomic charge is important for determining the intensities of HF complexes relative to HCl complexes with the same electron donor, they are not important for infrared intensifications occurring on hydrogen bond formation for a series of bases with a common acid. Charge transfers are found to be the most important factor resulting in the intensifications, but dipolar polarization effects are also significant for each series of complexes. A mechanism involving intra-acid and intermolecular electron transfers as well as atomic polarizations is proposed for understanding the intensifications. The calculated sums of the intermolecular electron transfer and acid dipolar polarization contributions to the dipole moment derivatives for each series of complexes are highly correlated with their enthalpies of formation and H-bond intensifications. This could be related to increasing electron transfer from base to acid that correlates with the calculated hydrogen bonding energies and may be a consequence of the A-H bond elongation on complex formation having amplitudes similar to those expected for the A-H vibration.

FTIR and dispersive gas phase absolute infrared intensities of hydrocarbon fundamental bands.

New experimental intensity results obtained by band integration from the PNNL (Pacific Northwest National Laboratory) spectral library are reported for 26 CH vibrations of methane, acetylene, ethylene, ethane, allene, propyne and cyclopropane. The PNNL intensity values range from 3.1 to 185.4 km mol-1 and are in excellent agreement, rms difference of 3.1 km mol-1, with earlier low resolution intensity results. QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ theoretical results are in good agreement with the PNNL intensity values with rms differences of 4.4 and 4.9 km mol-1, respectively. Charge-charge transfer-dipolar polarization model parameters at both quantum levels indicate that the charge transfer-dipolar polarization contributions to the intensities are much larger than those owing to the movements of static equilibrium charges on hydrogen for these vibrations except for the CH vibrations of acetylene that is known to contain very acidic hydrogen atoms. The main effect of the static charge movement comes from its interaction with charge transfer-dipolar polarization owing to the relatively large parameter values of this dynamic electronic contribution. The sum of the charge transfer-dipolar polarization parameters with their interaction with the charge accurately describes the variations in the intensity values of these hydrocarbon vibrations.