AI Applied to Volatile Organic Compound (VOC) Profiles from Exhaled Breath Air for Early Detection of Lung Cancer.

Volatile organic compounds (VOCs) are an increasingly meaningful method for the early detection of various types of cancers, including lung cancer, through non-invasive methods. Traditional cancer detection techniques such as biopsies, imaging, and blood tests, though effective, often involve invasive procedures or are costly, time consuming, and painful. Recent advancements in technology have led to the exploration of VOC detection as a promising non-invasive and comfortable alternative. VOCs are organic chemicals that have a high vapor pressure at room temperature, making them readily detectable in breath, urine, and skin. The present study leverages artificial intelligence (AI) and machine learning algorithms to enhance classification accuracy and efficiency in detecting lung cancer through VOC analysis collected from exhaled breath air. Unlike other studies that primarily focus on identifying specific compounds, this study takes an agnostic approach, maximizing detection efficiency over the identification of specific compounds focusing on the overall compositional profiles and their differences across groups of patients. The results reported hereby uphold the potential of AI-driven techniques in revolutionizing early cancer detection methodologies towards their implementation in a clinical setting.

Exploring asymmetry induced entropy in tetraalkylammonium-urea DES systems: what can be learned from inelastic neutron scattering?

In this work, inelastic neutron scattering (INS) spectroscopy is used to investigate the impact of entropic factors on the behaviour of deep eutectic solvents (DES). Periodic density functional theory calculations (DFT) provide a reliable assignment of the vibrational modes of pure compounds. This assignment guides the analysis of INS spectra of binary mixtures - with particular attention to methyl torsional modes. Deviations from ideality in the mixtures of tetraalkylammonium salts with urea are readily determined through a simplified thermodynamic approach. This study reports and discusses the relationship between the cation's asymmetry, the INS spectra of the eutectic mixture and its deviation from ideality. Contrary to the majority of systems studied so far, the deep eutectic system comprised of [N2,2,2,1]Cl and urea appears to owe its deviation from ideality to entropic rather than enthalpic factors.

Intermolecular Interactions in 3-Aminopropyltrimethoxysilane, N-Methyl-3-aminopropyltrimethoxysilane and 3-Aminopropyltriethoxysilane: Insights from Computational Spectroscopy.

In this work, a computational spectroscopy approach was used to provide a complete assignment of the inelastic neutron scattering spectra of three title alkoxysilane derivatives-3-aminopropyltrimethoxysilane (APTS), N-methyl-3-aminopropyltrimethoxysilane (MAPTS), and 3-aminopropyltriethoxysilane (APTES). The simulated spectra obtained from density functional theory (DFT) calculations exhibit a remarkable match with the experimental spectra. The description of the experimental band profiles improves as the number of molecules considered in the theoretical model increases, from monomers to trimers. This highlights the significance of incorporating non-covalent interactions, encompassing classical NH···N, N-H···O, as well as C-H···N and C-H···O hydrogen bond contacts, to achieve a comprehensive understanding of the system. A distinct scenario emerges when considering optical vibrational techniques, infrared and Raman spectroscopy. In these instances, the monomer model provides a reasonable description of the experimental spectra, and no substantial alterations are observed in the simulated spectra when employing dimer and trimer models. This observation underscores the distinctive ability of neutron spectroscopy in combination with DFT calculations in assessing the structure and dynamics of molecular materials.

From PEF to PBF: What difference does the longer alkyl chain make a computational spectroscopy study of poly(butylene 2,5-furandicarboxylate).

This work explores the conformational preferences and the structure-property correlations of poly(butylene 2,5-furandicarboxylate) (PBF), a longer chain analogue of the most well-known biobased polyester from the furan family, poly(ethylene 2,5-furandicarboxylate) (PEF). A thorough computational spectroscopic study-including infrared, Raman and inelastic neutron scattering spectroscopy, combined with discrete and periodic density functional theory calculations-allowed the identification of dominant structural motifs in the amorphous and crystalline regions. Discrete calculations and vibrational spectroscopy of semi-crystalline and amorphous samples strongly support the predominance of gauche, trans, gauche conformations of the butylene glycol fragment in both the crystalline and amorphous domains. In what concerns the furandicarboxylate fragment, amorphous domains are dominated by syn,syn conformations, while in the crystalline domains the anti,anti forms prevail. A possible crystalline structure-built from these conformational preferences and including a network of C-H···O hydrogen bond contacts-was optimized using periodic density functional theory. This proposed crystal structure avoids the unrealistic structural features of the previously proposed X-ray structure, provides an excellent description of the inelastic neutron scattering spectrum of the semi-crystalline form, and allows the correlation between microscopic structure and macroscopic properties of the polymer.

Structural Dynamics of Chloromethanes through Computational Spectroscopy: Combining INS and DFT.

In this work, the structural dynamics of the chloromethanes CCl4, CHCl3 and CH2Cl2 were evaluated through a computational spectroscopy approach by comparing experimental inelastic neutron scattering (INS) spectra with the corresponding simulated spectra obtained from periodic DFT calculations. The overall excellent agreement between experimental and calculated spectra allows a confident assignment of the vibrational features, including not only the molecular fundamental modes but also lattice and combination modes. In particular, an impressive overtone sequence for CHCl3 is fully described by the simulated INS spectrum. In the CCl4 spectrum, the splitting of the ν3 mode at ca. 765-790 cm-1 is discussed on the basis of the Fermi resonance vs. crystal splitting controversy.

Vibrational Dynamics in crystalline 4-(dimethylamino) benzaldehyde: Inelastic Neutron Scattering and Periodic DFT Study.

The structure and dynamics of crystalline 4-(dimethylamino) benzaldehyde, 4DMAB, are assessed through INS spectroscopy combined with periodic DFT calculations. The excellent agreement between experimental and calculated spectra is the basis for a reliable assignment of INS bands. The external phonon modes of crystalline 4DMAB are quite well described by the simulated spectrum, as well as the modes involving low-frequency molecular vibrations. Crystal field splitting is predicted and observed for the modes assigned to the dimethylamino group. Concerning the torsional motion of methyl groups, four individual bands are identified and assigned to specific methyl groups in the asymmetric unit. The torsional frequencies of the four methyl groups in the asymmetric unit fall in a region of ca. 190 ± 20 cm-1, close to the range of values observed for methyl groups bonding to unsaturated carbon atoms. The hybridization state of the X atom in X-CH3 seems to play a key role in determining the methyl torsional frequency.

Melanin: Production from Cheese Bacteria, Chemical Characterization, and Biological Activities.

Pigments are compounds of importance to several industries, for instance, the food industry, where they can be used as additives, color intensifiers, and antioxidants. As the current trend around the world is shifting to the use of eco-friendly commodities, demand for natural dyes is increasing. Melanins are pigments that are produced by several microorganisms. Pseudomonas putida ESACB 191, isolated from goat cheese rind, was described as a brown pigment producer. This strain produces a brown pigment via the synthetic Müeller-Hinton Broth. This brown compound was extracted, purified, analyzed by FTIR and mass spectrometry, and identified as eumelanin. The maximum productivity was 1.57 mg/L/h. The bioactivity of eumelanin was evaluated as the capacity for scavenging free radicals (antioxidant activity), EC50 74.0 ± 0.2 µg/mL, and as an acetylcholinesterase inhibitor, with IC50 575 ± 4 µg/mL. This bacterial eumelanin did not show cytotoxicity towards A375, HeLa Kyoto, HepG2, or Caco2 cell lines. The effect of melanin on cholesterol absorption and drug interaction was evaluated in order to understand the interaction of melanin present in the cheese rind when ingested by consumers. However, it had no effect either on cholesterol absorption through an intestinal simulated barrier formed by the Caco2 cell line or with the drug ezetimibe.

New Insights on the Vibrational Dynamics of 2-Methoxy-, 4-Methoxy- and 4-Ethoxy-Benzaldehyde from INS Spectra and Periodic DFT Calculations.

The dynamics of 2-methoxybenzaldehyde, 4-methoxybenzaldehyde, and 4-ethoxybenzaldehyde in the solid state are assessed through INS spectroscopy combined with periodic DFT calculations. In the absence of experimental data for 4-ethoxybenzaldehyde, a tentative crystal structure, based on its similarity with 4-methoxybenzaldehyde, is considered and evaluated. The excellent agreement between calculated and experimental spectra allows a confident assignment of the vibrational modes. Several spectral features in the INS spectra are unambiguously assigned and torsional potential barriers for the methyl groups are derived from experimental frequencies. The intramolecular nature of the potential energy barrier for methyl rotation about O-CH3 bonds compares with the one reported for torsion about saturated C-CH3 bonds. On the other hand, the intermolecular contribution to the potential energy barrier may represent 1/3 of the barrier height in these systems.

Near Infrared Reflectance Spectroscopy Coupled to Chemometrics as a Cost-Effective, Rapid, and Non-Destructive Tool for Fish Fraud Control: Monitoring Source, Condition, and Nutritional Value of Five Common Whitefish Species.

Fish fraud is a problematic issue for the industry. For it to be properly addressed will require the use of accurate, rapid, and cost-effective tools. In this work, near infrared reflectance spectroscopy (NIRS) was used to predict nutritional values (protein, lipids, and moisture) as well as to discriminate between sources (farmed vs. wild fish) and conditions (fresh or defrosted fish). Samples of five whitefish species-Alaskan pollock (Gadus chalcogrammu), Atlantic cod (G. morhua), European plaice (Pleuronectes platessa), common sole (Solea solea), and turbot (Psetta maxima)-including farmed, wild, fresh, and frozen ones, were scanned by a low-cost handheld near infrared reflectance spectrometer with a spectral range between 900 and 1700 nm. Several machine learning algorithms were explored for both regression and classification tasks, achieving precisions and coefficients of determination higher than 88% and 0.78, respectively. Principal component analysis (PCA) was used to cluster samples according to classes where good linear discriminations were denoted. Loadings from PCA revealed bands at 1150, 1200, and 1400 nm as the most discriminative spectral regions regarding classification of both source and condition, suggesting the absorbance of OH, CH, CH2, and CH3 groups as the most important ones. This study shows the use of NIRS and both linear and non-linear learners as a suitable strategy to address fish fraud and fish QC.

Effect of Food Preparations on In Vitro Bioactivities and Chemical Components of Fucus vesiculosus.

Fucus vesiculosus is a brown macroalgae used in food and generally considered safe to be consumed, according to EU Directive (EC 258/97). The aim of this study is to analyze the effect of food preparation on F.vesiculosus of different origins on what concerns its chemical constituents and final bioactivities. The aqueous extract of the seaweeds were obtained at different temperatures, similar to food preparation and then purified by SPE. The compound identification was carried out by Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS/MS) and algae extracts microstructure were observed by Scanning Electron Microscopy (SEM). The activities were determined by using antioxidant activity, inhibition of acetylcholinesterase (AChE) and 3-hidroxi-3-methyl-glutaril-CoA (HMG-CoA) reductase (HMGR) together with Caco-2 cells line simulating the intestinal barrier. The activity of AChE and the HMGR were inhibited by the extracts giving IC50 values of 15.0 ± 0.1 µg/mL and 4.2 ± 0.1 µg/mL, respectively and 45% of the cholesterol permeation inhibition. The main compounds identified were phlorotannins and peptides derivatives. The mode of preparation significantly influenced the final bioactivities. Moreover, the in vitro results suggest that the preparation of F. vesiculosus as a soup could have hypercholesterolemia lowering effect.

Understanding the Structure and Dynamics of Nanocellulose-Based Composites with Neutral and ionic Poly(methacrylate) Derivatives using Inelastic Neutron Scattering and DFT Calculations.

Bacterial nanocellulose (BC)-based composites containing poly(2-hydroxyethyl methacrylate) (PHEMA), poly(methacroylcholine chloride) (PMACC) or poly(methacroylcholine hydroxide) (PMACH) were characterized by inelastic neutron scattering (INS) spectroscopy, combined with DFT (density functional theory) calculations of model systems. A reasonable match between calculated and experimental spectral lines and their intensities was used to support the vibrational assignment of the observed bands and to validate the possible structures. The differences between the spectra of the nanocomposites and the pure precursors indicate that interactions between the components are stronger for the ionic poly(methacrylate) derivatives than for the neutral counterpart. Displaced anions interact differently with cellulose chains, due to the different ability to compete with the O-H···O hydrogen bonds in cellulose. Hence, the INS is an adequate technique to delve deeper into the structure and dynamics of nanocellulose-based composites, confirming that they are true nanocomposite materials instead of simple mixtures of totally independent domains.

Vibrational Dynamics of Crystalline 4-Phenylbenzaldehyde from INS Spectra and Periodic DFT Calculations.

The present work emphasizes the value of periodic density functional theory (DFT) calculations in the assessment of the vibrational spectra of molecular crystals. Periodic calculations provide a nearly one-to-one match between the calculated and observed bands in the inelastic neutron scattering (INS) spectrum of crystalline 4-phenylbenzaldehyde, thus validating their assignment and correcting previous reports based on single molecule calculations. The calculations allow the unambiguous assignment of the phenyl torsional mode at ca. 118-128 cm-1, from which a phenyl torsional barrier of ca. 4000 cm-1 is derived, and the identification of the collective mode involving the antitranslational motion of CH···O bonded pairs, a hallmark vibrational mode of systems where C-H···O contacts are an important feature.

Understanding the vibrational spectra of crystalline isoniazid: Raman, IR and INS spectroscopy and solid-state DFT study.

This work presents a comprehensive spectroscopic analysis of crystalline isoniazid, one of the main drugs in tuberculosis chemotherapy, using a blend of spectroscopic and computational methods. Mid- and far-infrared, Raman, and inelastic neutron scattering spectroscopies, with contribution of isotopic substitution are combined with discrete and periodic DFT quantum chemical calculations. This combined approach successfully reproduces the whole spectral range, allowing a sound assignment of all the vibrational bands. Previous misassignments have been corrected and several spectral features of isoniazid crystal are reported for the first time. Virtues and limitations of the computational approach (periodic and discrete) are also discussed in light of the present state-of-the-art in the field.

Association of aescin with ß- and γ-cyclodextrins studied by DFT calculations and spectroscopic methods.

Background: Aescin, a natural mixture of saponins occurring in Aesculus hippocastanum, exhibits important flebotonic properties, being used in the treatment of chronic venous insufficiency in legs. The inclusion of aescin into cyclodextrins (CDs) is a technical solution for its incorporation into the textile of stockings, but details of the physicochemistry of these host-guest systems are lacking. This work investigates the inclusion of aescin into the cavities of two native cyclodextrins, ß-CD and γ-CD. Results: The continuous variation method applied to aqueous-phase 1H nuclear magnetic resonance (1H NMR) has demonstrated that the preferred CD/aescin inclusion stoichiometries are 2:1 with ß-CD and 1:1 with γ-CD. The affinity constant calculated for γ-CD·aescin was 894 M-1, while for 2ß-CD·aescin it was estimated to be 715 M-1. Density functional theory (DFT) calculations on the interaction of aescin Ib with CDs show that an inclusion can indeed occur and it is further demonstrated that the wider cavity of γ-CD is more adequate to accommodate this large guest. ROESY spectroscopy is consistent with the formation of a complex in which the triterpenic moiety of aescin is included into the cavity of γ-CD. The higher stability of this geometry was confirmed by DFT. Furthermore, DFT calculations were applied to determine the chemical shifts of the protons H3 and H5 of the CDs in the optimised structures of the inclusion complexes. The calculated values are very similar to the experimental data, validating the approach made in this study by NMR. Conclusion: The combination of experimental data from aqueous-state NMR measurements and theoretical calculations has demonstrated that γ-CD is the most suitable host for aescin, although the inclusion also occurs with ß-CD. The geometry of the γ-CD·aescin complex is characterised by the inclusion of the triterpene segment of aescin into the host cavity.

Layered Double Hydroxide Nanoclusters: Aqueous, Concentrated, Stable, and Catalytically Active Colloids toward Green Chemistry.

Increasing attention has been dedicated to the development of nanomaterials rendering green and sustainable processes, which occur in benign aqueous reaction media. Herein, we demonstrate the synthesis of another family of green nanomaterials, layered double hydroxide (LDH) nanoclusters, which are concentrated (98.7 g/L in aqueous solvent), stably dispersed (transparent sol for >2 weeks), and catalytically active colloids of nano LDHs (isotropic shape with the size of 7.8 nm as determined by small-angle X-ray scattering). LDH nanoclusters are available as colloidal building blocks to give access to meso- and macroporous LDH materials. Proof-of-concept applications revealed that the LDH nanocluster works as a solid basic catalyst and is separable from solvents of catalytic reactions, confirming the nature of nanocatalysts. The present work closely investigates the unique physical and chemical features of this colloid, the formation mechanism, and the ability to act as basic nanocatalysts in benign aqueous reaction systems.

Looking inside the pores of a MCM-41 based Mo heterogeneous styrene oxidation catalyst: an inelastic neutron scattering study.

Styrene oxidation mediated by a Mo-based mesoporous catalyst can yield selectively styrene oxide or benzaldehyde. Kinetic data evidenced that styrene oxide is the initial single-product formed by the catalytic Mo-mediated process. However, after some hours of reaction benzaldehyde yield rises while that of the epoxide decreases concomitantly. The mechanistic proposal pointed to a surface assisted acid-base mechanism by which styrene oxide is interconverted into benzaldehyde through over-oxidation and cleavage of the C-C bond and releases formaldehyde as well. In an attempt to gain some insight into whether this mechanistic proposal is realistic we have conducted a combined DRIFT and inelastic neutron scattering (INS) study to assess the adsorbed species at the catalyst's surface and confirm the mechanistic proposal. INS and DRIFT provided complementary insight into surface-adsorbed species by probing donor (INS) and acceptor (DRIFT) species. INS also allowed for an estimation of product selectivity by means of a Job method stressing the power of the technique.

Wittig Reaction: Domino Olefination and Stereoselectivity DFT Study. Synthesis of the Miharamycins' Bicyclic Sugar Moiety.

2-O-Acyl protected-d-ribo-3-uloses reacted with [(ethoxycarbonyl)methylene]triphenylphosphorane in acetonitrile to afford regio- and stereoselectively 2-(Z)-alkenes in 10-60 min under microwave irradiation. This domino reaction is proposed to proceed via tautomerization of 3-ulose to enol, acyl migration, tautomerization to the 3-O-acyl-2-ulose, and Wittig reaction. Alternatively, in chloroform, regioselective 3-olefination of 2-O-pivaloyl-3-uloses gave (E)-alkenes, key precursors for the miharamycins' bicyclic sugar moiety.

Vanadyl cationic complexes as catalysts in olefin oxidation.

Three new mononuclear oxovanadium(IV) complexes [VO(acac)(R-BIAN)]Cl (BIAN = 1,2-bis{(R-phenyl)imino}acenaphthene, R = H, 1; CH3, 2; Cl, 3) were prepared and characterized. They promoted the catalytic oxidation of olefins such as cyclohexene, cis-cyclooctene, and styrene with both tbhp (tert-butylhydroperoxide) and H2O2, and of enantiopure olefins (S(-)- and R(+)-pinene, and S(-)- and R(+)-limonene) selectively to their epoxides, with tbhp as the oxidant. The TOFs for styrene epoxidation promoted by complex 3 with H2O2 (290 mol mol(-1)V h(-1)) and for cis-cyclooctene epoxidation by 2 with tbhp (248 mol mol(-1)V h(-1)) are particularly good. Conversions reached 90% for several systems with tbhp, and were lower with H2O2. A preference for the internal C=C bond, rather than the terminal one, was found for limonene. Kinetic data indicate an associative process as the first step of the reaction and complex [VO(acac)(H-BIAN)](+) (1(+)) was isolated in an FTICR cell after adding tbhp to 1. EPR studies provide evidence for the presence of a V(IV) species in solution, until at least 48 hours after the addition of tbhp and cis-cyclooctene, and cyclic voltammetry studies revealed an oxidation potential above 1 V for complex 1. DFT calculations suggest that a [VO(H-BIAN)(MeOO)](+) complex is the likely active V(IV) species in the catalytic cycle from which two competitive mechanisms for the reaction proceed, an outer sphere path with an external attack of the olefin at the coordinated peroxide, and an inner sphere mechanism starting with a complex with the olefin coordinated to vanadium.

Can Semi-empirical Calculations Help Solve Mass Spectrometry Problems? Protonation Sites and Proton Affinities of Amino Acids.

Owing to the recent development of the PM6 and PM6-DH+ semi-empirical methodologies, which belong to the neglect of diatomic differential overlap (NDDO) family, it was decided to carry out a study to assess whether these inexpensive and fast methodologies could be used with confidence to help solve mass spectrometry problems. As such, a report on the feasibility of using semi-empirical calculations to identify probable protonation sites in amino acids is presented. The optimised geometries obtained by the semi-empirical calculations were compared to several structures reported in the literature (obtained through high-level theoretical calculations) and reasonable agreement was found. The proton affinities derived from semi-empirical calculations were also compared with experimental data and benchmarked as well with predicted values from the literature (also obtained through high-level theoretical calculations). Semi-empirical calculations accurately predicted the most probable protonation site for all amino acids considered; thus leading to results comparable to those obtained by high-level calculations at an extremely low computational cost. Regarding the proton affinity estimates, deviations from the available experimental values are greater for the semi-empirical proton affinities than for those observed for high-level calculations. A statistical analysis of the data, at a confidence level of 99 %, also showed that the semi-empirical proton affinities were different from experimental values and high-level proton affinities were equivalent to experimental values. Nevertheless, the overall correlation of the semi-empirical data with experimental values is, at least, satisfactory. We believe therefore that this paper shows that semi-empirical methodologies, which are fast and inexpensive, can indeed solve mass spectrometry problems, or at least, facilitate a quicker path to the solution.

On the way to understand antioxidants: chromanol and dimethoxyphenols gas-phase acidities.

Some antioxidant mechanisms displayed by several phenolic compounds relate with OH bond dissociation energy. One way for its determination, in the gas-phase, relies on acidity measurements. Gas-phase acidities were determined experimentally, applying the kinetic method, for chromanol and four dimethoxyphenols, and theoretically through quantum chemical DFT calculations for chromanol, six dimethoxyphenols and 3,4,5-trimethoxyphenol. The experimental acidity order, 2,3-dimethoxyphenol > 3,5-dimethoxyphenol > 2,6-dimethoxyphenol > 3,4-dimethoxyphenol ≈ phenol > chromanol shows good agreement with the theoretical acidity order, 2,5-dimethoxyphenol > 2,3-dimethoxyphenol > 3,4,5-trimethoxyphenol > 3,5-dimethoxyphenol ≈ 2,4-dimethoxyphenol > 2,6-dimethoxyphenol > 3,4-dimethoxyphenol > phenol > chromanol. These acidity trends were rationalized in terms of the substituent effects on the thermodynamic stabilities both of the parent phenols and the corresponding phenoxide ions. DFT calculations also evidenced the occurrence of intramolecular C-H···O hydrogen bonds whenever there are vicinal substituents (either OH, O(-) or OCH(3)) which induce further stabilization of the geometries.