Preprocessing Strategies for Sparse Infrared Spectroscopy: A Case Study on Cartilage Diagnostics

The aim of the study was to optimize preprocessing of sparse infrared spectral data. The sparse data were obtained by reducing broadband Fourier transform infrared attenuated total reflectance spectra of bovine and human cartilage, as well as of simulated spectral data, comprising several thousand spectral variables into datasets comprising only seven spectral variables. Different preprocessing approaches were compared, including simple baseline correction and normalization procedures, and model-based preprocessing, such as multiplicative signal correction (MSC). The optimal preprocessing was selected based on the quality of classification models established by partial least squares discriminant analysis for discriminating healthy and damaged cartilage samples. The best results for the sparse data were obtained by preprocessing using a baseline offset correction at 1800 cm⁻¹, followed by peak normalization at 850 cm⁻¹ and preprocessing by MSC.     

Millimeter-Wave Spectroscopy of Methylfuran Isomers: Local vs. Global Treatments of the Internal Rotation

Methylfurans are methylated aromatic heterocyclic volatile organic compounds and primary or secondary pollutants in the atmosphere due to their capability to form secondary organic aerosols in presence of atmospheric oxidants. There is therefore a significant interest to monitor these molecules in the gas phase. High resolution spectroscopic studies of methylated furan compounds are generally limited to pure rotational spectroscopy in the vibrational ground state. This lack of results might be explained by the difficulties arisen from the internal rotation of the methyl group inducing non-trivial patterns in the rotational spectra. In this study, we discuss the benefits to assign the mm-wave rotational-torsional spectra of methylfuran with the global approach of the BELGI-Cs code compared to local approaches such as XIAM and ERHAM. The global approach reproduces the observed rotational lines of 2-methylfuran and 3-methylfuran in the mm-wave region at the experimental accuracy for the ground vt=0 and the first torsional vt=1 states with a unique set of molecular parameters. In addition, the V3 and V6 parameters describing the internal rotation potential barrier may be determined with a high degree of accuracy with the global approach. Finally, a discussion with other heterocyclic compounds enables the study of the influence of the electronic environment on the hindered rotation of the methyl group.     

Give or Take: Effects of Electron-Accepting/-Withdrawing Groups in Red-Fluorescent BODIPY Molecular Rotors

Mapping microviscosity, temperature, and polarity in biosystems is an important capability that can aid in disease detection. This can be achieved using fluorescent sensors based on a green-emitting BODIPY group. However, red fluorescent sensors are desired for convenient imaging of biological samples. It is known that phenyl substituents in the β position of the BODIPY core can shift the fluorescence spectra to longer wavelengths. In this research, we report how electron-withdrawing (EWG) and -donating (EDG) groups can change the spectral and sensory properties of β-phenyl-substituted BODIPYs. We present a trifluoromethyl-substituted (EWG) conjugate with moderate temperature sensing properties and a methoxy-substituted (EDG) molecule that could be used as a lifetime-based polarity probe. In this study, we utilise experimental results of steady-state and time-resolved fluorescence, as well as quantum chemical calculations using density functional theory (DFT). We also explain how the energy barrier height (Ea) for non-radiative relaxation affects the probe’s sensitivity to temperature and viscosity and provide appropriate Ea ranges for the best possible sensitivity to viscosity and temperature.     

Application of the generalised SAFT-VR approach for long-ranged square-well potentials to model the phase behaviour of real fluids

In a recent generalisation of the SAFT-VR equation of state the method was extended so as to deal with short as well as long square-well ranges, namely, 1.2≤λ≤3.0$1.2\le \lambda \le 3.0$ [B.H. Patel, H. Docherty, S. Varga, A. Galindo, G.C. Maitland., Mol. Phys. 103 (1) (2005) 129–139]. Here, we confirm the accuracy of the approach by comparison with numerical calculations of the first perturbation term and with vapour pressure and coexistence density computer simulation data. The approach is then used to model a number of real substances, from non-polar to strongly polar. We discuss in particular the values of the square-well potential model found. For this purpose we construct a relative least squares objective function and the percentage absolute average deviation (%AAD) to determine the intermolecular model parameters (m  , λ$\lambda$, σ$\sigma$, ?/_kB$?/k_B$, _?hb/_kB${?}_{hb}/k_B$ and _rc$r_c$) by comparison to experimental vapour-pressure and saturated liquid density data. In order to ensure in each case that the global minimum is identified, the dimensionality of the problem is reduced by discretising the parameter-space [G.N.I. Clark, A.J. Haslam, A. Galindo, G. Jackson., Mol. Phys. 104 (22–24) (2006) 3561–3581]. Applying this method to the study of argon, n  -alkanes, nitrogen, benzene, carbon dioxide, carbon monoxide, the refrigerant R1270, hydrogen chloride hydrogen bromide and water we find that the optimal models always present square-well ranges λ<1.8$\lambda <1.8$, meaning that an upper bound value of λ=1.8$\lambda =1.8$ set in the original approach is sufficient to model real fluids; even polar ones. This finding is explained in terms of the averaged dipole–dipole interaction and of the long-range mean-field limit of the square-well potential.     

Dehydration performance of a hydrophobic DD3R zeolite membrane

The all silica DDR membrane turns out to be well suited to separate water from organic solvents under pervaporation conditions, despite its hydrophobic character. All-silica zeolites are chemically and hydrothermally more stable than aluminum containing ones and are therefore preferred for membrane applications, including for dehydration, even though these type of membranes are hydrophobic. Permeation of water, ethanol and methanol through an all-silica DDR membrane has been measured at temperatures ranging from 344 to 398 K. The hydrophobic membrane shows high water fluxes (up to 20 kg m⁻² h⁻¹). The pure water permeance is insensitive to temperature and is well described assuming weak adsorption. Excellent performance in dewatering ethanol (N=2$N=2$ kg m⁻² h⁻¹and _αw=1500${\alpha }_{\text{w}}=1500$ at 373 K and _xw=0.18$x_{\text{w}}=0.18$) is observed and the membrane is also able to selectively remove water from methanol (N=5$N=5$ kg m⁻² h⁻¹ and _αw=9${\alpha }_{\text{w}}=9$). Water could also be removed from methanol/ethanol/water (_αwater_/EtOH=1500${\alpha }_{\text{water}/\text{EtOH}}=1500$, _αMeOH_/EtOH=70${\alpha }_{\text{MeOH}/\text{EtOH}}=70$ at 373 K) mixtures, even at water feed concentrations below 1.5 mol%.     

Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations including Charge Transfer States

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence {"type":"entrez-nucleotide","attrs":{"text":"T30695","term_id":"612793"}}T30695 (5′TGGGTGGGTGGGTGGG3′), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.     

Structure of M-X-ray satellite and hypersatellite lines of thorium

Very extensive multiconfiguration Dirac–Fock calculations with the inclusion of the transverse (Breit) interaction and QED corrections have been carried out on thorium to elucidate the structure of various satellite (additional vacancies in N and/or O shells) and hypersatellite (additional vacancies in M or M and N shells) $M{\alpha }_{1,2}$ ($M_5{N}_{6,7}$) and $M{\beta }_1$ ($M_4{N}_6$) lines in its X-ray spectra. For each type of lines two theoretical spectra have been synthesized: one being a sum of the Lorentzian natural line shapes and the other one being a convolution of the sum of the Lorentzian natural line shapes with the Gaussian instrumental response. The obtained theoretical results will be very helpful in reliable and quantitative interpretation of various experimental M-X-ray spectra of thorium target bombarded by different light and heavy projectiles (such as O and Ne ions).     

Addendum to “Volumetric properties of binary liquid-phase mixture of (water + glycerol) at temperatures of (278.15 to 323.15) K and pressures of (0.1 to 100) MPa” [J. Chem. Thermodyn. 79 (2014) 135–158]: Effect of pressure on excess thermodynamic characteristics of mixture water + glycerol

Experimentally determined volumetric properties of the liquid binary mixture of {water (1) + glycerol (2)} were processed to calculate the changes of the following thermodynamic parameters with pressure: excess molar Gibbs free energy, ${\mathrm{\Delta }}_{P_o\to P}{G}_m^E$, excess molar entropy, ${\mathrm{\Delta }}_{P_o\to P}{S}_m^E$, excess molar enthalpy, ${\mathrm{\Delta }}_{P_o\to P}{H}_m^E$, as well as the enthalpy of mixing of water and glycerol, $H_m^E$, at 100 MPa. The mixing enthalpies of water and glycerol, $H_m^E$, became more exothermic with pressure increasing at all temperatures studied.     

Identification of Stingless Bee Honey Adulteration Using Visible-Near Infrared Spectroscopy Combined with Aquaphotomics

Honey is a natural product that is considered globally one of the most widely important foods. Various studies on authenticity detection of honey have been fulfilled using visible and near-infrared (Vis-NIR) spectroscopy techniques. However, there are limited studies on stingless bee honey (SBH) despite the increase of market demand for this food product. The objective of this work was to present the potential of Vis-NIR absorbance spectroscopy for profiling, classifying, and quantifying the adulterated SBH. The SBH sample was mixed with various percentages (10–90%) of adulterants, including distilled water, apple cider vinegar, and high fructose syrup. The results showed that the region at 400–1100 nm that is related to the color and water properties of the samples was effective to discriminate and quantify the adulterated SBH. By applying the principal component analysis (PCA) on adulterants and honey samples, the PCA score plot revealed the classification of the adulterants and adulterated SBHs. A partial least squares regression (PLSR) model was developed to quantify the contamination level in the SBH samples. The general PLSR model with the highest coefficient of determination and lowest root means square error of cross-validation (RCV2=0.96 and RMSECV=5.88 %) was acquired. The aquaphotomics analysis of adulteration in SBH with the three adulterants utilizing the short-wavelength NIR region (800–1100 nm) was presented. The structural changes of SBH due to adulteration were described in terms of the changes in the water molecular matrix, and the aquagrams were used to visualize the results. It was revealed that the integration of NIR spectroscopy with aquaphotomics could be used to detect the water molecular structures in the adulterated SBH.     

Operando Raman Shift Replaces Current in Electrochemical Analysis of Li-ion Batteries: A Comparative Study

Li-rich and catalytically active γ-LixV2O5 (x = 1.48) was investigated as a cathode for its heterogeneous charge transfer kinetics. Using a specially designed two-electrode system lithium half cell, Butler–Volmer analysis was performed, and Raman spectra were acquired in 18 mV intervals. A direct correlation was observed between the Raman shift of the active modes Ag,Bg, Au, and Bu, and the development of the Faraday current at the working electrode. The Raman intensity and the Raman shift were implemented to replace the current in a Tafel plot used for the analysis of Butler–Volmer kinetics. Striking similarities in the charge transfer proportionality constants α were found for current and Raman-based analysis. The potential of this new method of Raman-aided electrochemical detection at the diffraction limit is discussed.     

Influence of Liquid Crystallinity and Mechanical Deformation on the Molecular Relaxations of an Auxetic Liquid Crystal Elastomer

Liquid Crystal Elastomers (LCEs) combine the anisotropic ordering of liquid crystals with the elastic properties of elastomers, providing unique physical properties, such as stimuli responsiveness and a recently discovered molecular auxetic response. Here, we determine how the molecular relaxation dynamics in an acrylate LCE are affected by its phase using broadband dielectric relaxation spectroscopy, calorimetry and rheology. Our LCE is an excellent model system since it exhibits a molecular auxetic response in its nematic state, and chemically identical nematic or isotropic samples can be prepared by cross-linking. We find that the glass transition temperatures (Tg) and dynamic fragilities are similar in both phases, and the T-dependence of the α relaxation shows a crossover at the same T* for both phases. However, for T>T*, the behavior becomes Arrhenius for the nematic LCE, but only more Arrhenius-like for the isotropic sample. We provide evidence that the latter behavior is related to the existence of pre-transitional nematic fluctuations in the isotropic LCE, which are locked in by polymerization. The role of applied strain on the relaxation dynamics and mechanical response of the LCE is investigated; this is particularly important since the molecular auxetic response is linked to a mechanical Fréedericksz transition that is not fully understood. We demonstrate that the complex Young’s modulus and the α relaxation time remain relatively unchanged for small deformations, whereas for strains for which the auxetic response is achieved, significant increases are observed. We suggest that the observed molecular auxetic response is coupled to the strain-induced out-of-plane rotation of the mesogen units, in turn driven by the increasing constraints on polymer configurations, as reflected in increasing elastic moduli and α relaxation times; this is consistent with our recent results showing that the auxetic response coincides with the emergence of biaxial order.     

Deuterium Isotope Effects on Acid-Base Equilibrium of Organic Compounds

Deuterium isotope effects on acid–base equilibrium have been investigated using a combined path integral and free-energy perturbation simulation method. To understand the origin of the linear free-energy relationship of ΔpKa=pKaD2O−pKaH2O versus pKaH2O, we examined two theoretical models for computing the deuterium isotope effects. In Model 1, only the intrinsic isotope exchange effect of the acid itself in water was included by replacing the titratable protons with deuterons. Here, the dominant contribution is due to the difference in zero-point energy between the two isotopologues. In Model 2, the medium isotope effects are considered, in which the free energy change as a result of replacing H₂O by D₂O in solute–solvent hydrogen-bonding complexes is determined. Although the average ΔpKa change from Model 1 was found to be in reasonable agreement with the experimental average result, the pKaH2O dependence of the solvent isotope effects is absent. A linear free-energy relationship is obtained by including the medium effect in Model 2, and the main factor is due to solvent isotope effects in the anion–water complexes. The present study highlights the significant roles of both the intrinsic isotope exchange effect and the medium solvent isotope effect.     

Spectral Signatures of Hydrogen Thioperoxide (HOSH) and Hydrogen Persulfide (HSSH): Possible Molecular Sulfur Sinks in the Dense ISM

For decades, sulfur has remained underdetected in molecular form within the dense interstellar medium (ISM), and somewhere a molecular sulfur sink exists where it may be hiding. With the discovery of hydrogen peroxide (HOOH) in the ISM in 2011, a natural starting point may be found in sulfur-bearing analogs that are chemically similar to HOOH: hydrogen thioperoxide (HOSH) and hydrogen persulfide (HSSH). The present theoretical study couples the accuracy in the anharmonic fundamental vibrational frequencies from the explicitly correlated coupled cluster theory with the accurate rotational constants provided by canonical high-level coupled cluster theory to produce rovibrational spectra for use in the potential observation of HOSH and HSSH. The ν6 mode for HSSH at 886.1 cm−1 is within 0.2 cm−1 of the gas-phase experiment, and the B0 rotational constant for HSSH of 6979.5 MHz is within 9.0 MHz of the experimental benchmarks, implying that the unknown spectral features (such as the first overtones and combination bands) provided herein are similarly accurate. Notably, a previous experimentally-attributed 2ν1 mode, at 7041.8 cm−1, has been reassigned to the ν1+ν5 combination band based on the present work’s ν1+ν5 value at 7034.3 cm−1. The most intense vibrational transitions for each molecule are the torsions, with HOSH having a more intense transition of 72 km/mol compared to HSSH’s intensity of 14 km/mol. Furthermore, HOSH has a larger net dipole moment of 1.60 D compared to HSSH’s 1.15 D. While HOSH may be the more likely candidate of the two for possible astronomical observation via vibrational spectroscopy due to the notable difference in their intensities, both HSSH and HOSH have large enough net dipole moments to be detectable by rotational spectroscopy to discover the role these molecules may have as possible molecular sulfur sinks in the dense ISM.