Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces

Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller–Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers’ stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm−1–1700 cm−1 and 2300 cm−1–3400 cm−1 in the gas phase and 600 cm−1–1800 cm−1 and 2200 cm−1–3400 cm−1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm−1–1700 cm−1 and 2300 cm−1–3300 cm−1 for the gas phase and one broad absorption region in the solid state between 700 cm−1 and 3100 cm−1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.     

Fluorescent Liquid Tetrazines

Tetrazines with branched alkoxy substituents are liquids at ambient temperature that despite the high chromophore density retain the bright orange fluorescence that is characteristic of this exceptional fluorophore. Here, we study the photophysical properties of a series of alkoxy-tetrazines in solution and as neat liquids. We also correlate the size of the alkoxy substituents with the viscosity of the liquids. We show using time-resolved spectroscopy that intersystem crossing is an important decay pathway competing with fluorescence, and that its rate is higher for 3,6-dialkoxy derivatives than for 3-chloro-6-alkoxytetrazines, explaining the higher fluorescence quantum yields for the latter. Quantum chemical calculations suggest that the difference in rate is due to the activation energy required to distort the tetrazine core such that the nπ*S1 and the higher-lying ππ*T2 states cross, at which point the spin-orbit coupling exceeding 10 cm−1 allows for efficient intersystem crossing to occur. Femtosecond time-resolved anisotropy studies in solution allow us to measure a positive relationship between the alkoxy chain lengths and their rotational correlation times, and studies in the neat liquids show a fast decay of the anisotropy consistent with fast exciton migration in the neat liquid films.     

Data-Driven and Multiscale Modeling of DNA-Templated Dye Aggregates

Dye aggregates are of interest for excitonic applications, including biomedical imaging, organic photovoltaics, and quantum information systems. Dyes with large transition dipole moments (μ) are necessary to optimize coupling within dye aggregates. Extinction coefficients (ε) can be used to determine the μ of dyes, and so dyes with a large ε (>150,000 M⁻¹cm⁻¹) should be engineered or identified. However, dye properties leading to a large ε are not fully understood, and low-throughput methods of dye screening, such as experimental measurements or density functional theory (DFT) calculations, can be time-consuming. In order to screen large datasets of molecules for desirable properties (i.e., large ε and μ), a computational workflow was established using machine learning (ML), DFT, time-dependent (TD-) DFT, and molecular dynamics (MD). ML models were developed through training and validation on a dataset of 8802 dyes using structural features. A Classifier was developed with an accuracy of 97% and a Regressor was constructed with an R2 of above 0.9, comparing between experiment and ML prediction. Using the Regressor, the ε values of over 18,000 dyes were predicted. The top 100 dyes were further screened using DFT and TD-DFT to identify 15 dyes with a μ relative to a reference dye, pentamethine indocyanine dye Cy5. Two benchmark MD simulations were performed on Cy5 and Cy5.5 dimers, and it was found that MD could accurately capture experimental results. The results of this study exhibit that our computational workflow for identifying dyes with a large μ for excitonic applications is effective and can be used as a tool to develop new dyes for excitonic applications.     

Interaction Energy Analysis of Monovalent Inorganic Anions in Bulk Water Versus Air/Water Interface

Soft anions exhibit surface activity at the air/water interface that can be probed using surface-sensitive vibrational spectroscopy, but the structural implications of this surface activity remain a matter of debate. Here, we examine the nature of anion–water interactions at the air/water interface using a combination of molecular dynamics simulations and quantum-mechanical energy decomposition analysis based on symmetry-adapted perturbation theory. Results are presented for a set of monovalent anions, including Cl⁻, Br⁻, I⁻, CN⁻, OCN⁻, SCN⁻, NO2−, NO3−, and ClOn− (n=1,2,3,4), several of which are archetypal examples of surface-active species. In all cases, we find that average anion–water interaction energies are systematically larger in bulk water although the difference (with respect to the same quantity computed in the interfacial environment) is well within the magnitude of the instantaneous fluctuations. Specifically for the surface-active species Br⁻(aq), I⁻(aq), ClO4−(aq), and SCN⁻(aq), and also for ClO⁻(aq), the charge-transfer (CT) energy is found to be larger at the interface than it is in bulk water, by an amount that is greater than the standard deviation of the fluctuations. The Cl⁻(aq) ion has a slightly larger CT energy at the interface, but NO3−(aq) does not; these two species are borderline cases where consensus is lacking regarding their surface activity. However, CT stabilization amounts to <20% of the total induction energy for each of the ions considered here, and CT-free polarization energies are systematically larger in bulk water in all cases. As such, the role of these effects in the surface activity of soft anions remains unclear. This analysis complements our recent work suggesting that the short-range solvation structure around these ions is scarcely different at the air/water interface from what it is in bulk water. Together, these observations suggest that changes in first-shell hydration structure around soft anions cannot explain observed surface activities.     

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.     

Studies of the Formation of Inclusion Complexes Derivatives of Cinnamon Acid with α-Cyclodextrin in a Wide Range of Temperatures Using Conductometric Methods

The electrical conductivities of aqueous solutions of sodium salts of trans-4-hydroxycinnamic acid (trans-p-coumaric acid), trans-3,4-dihydroxycinnamic acid (trans-caffeic acid), trans-4-hydroxy-3-methoxycinnamic acid, (trans-ferulic acid) and trans-3-phenylacrylic acid (trans-cinnamic acid) with α-cyclodextrin were measured in the temperature range of 288.15 K–318.15 K. For the first time in the literature, using the limiting molar conductivity (Λmo) obtained from conductivity measurements, the values of the complexation constants (K_f) of the salts of phenolic acid derivatives with α-cyclodextrin were determined using a modified low concentration chemical model (IcCM). An attempt was also made to analyze the individual thermodynamic functions ΔGo, ΔHo and ΔSo describing the complexation process as a function of temperature changes. The obtained results show that the process of formation of inclusion complexes is exothermic and is spontaneous.     

Anharmonic Vibrational Frequencies of Water Borane and Associated Molecules

Water borane (BH3OH2) and borinic acid (BH2OH) have been proposed as intermediates along the pathway of hydrogen generation from simple reactants: water and borane. However, the vibrational spectra for neither water borane nor borinic acid has been investigaged experimentally due to the difficulty of isolating them in the gas phase, making accurate quantum chemical predictions for such properties the most viable means of their determination. This work presents theoretical predictions of the full rotational and fundamental vibrational spectra of these two potentially application-rich molecules using quartic force fields at the CCSD(T)-F12b/cc-pCVTZ-F12 level with additional corrections included for the effects of scalar relativity. This computational scheme is further benchmarked against the available gas-phase experimental data for the related borane and HBO molecules. The differences are found to be within 3 cm−1 for the fundamental vibrational frequencies and as close as 15 MHz in the B0 and C0 principal rotational constants. Both BH2OH and BH3OH2 have multiple vibrational modes with intensities greater than 100 km mol−1, namely ν2 and ν4 in BH2OH, and ν1, ν3, ν4, ν9, and ν13 in BH3OH2. Finally, BH3OH2 has a large dipole moment of 4.24 D, which should enable it to be observable by rotational spectroscopy, as well.     

Theoretical Analysis on Absorption of Carbon Dioxide (CO2) into Solutions of Phenyl Glycidyl Ether (PGE) Using Nonlinear Autoregressive Exogenous Neural Networks

In this paper, we analyzed the mass transfer model with chemical reactions during the absorption of carbon dioxide (CO2) into phenyl glycidyl ether (PGE) solution. The mathematical model of the phenomenon is governed by a coupled nonlinear differential equation that corresponds to the reaction kinetics and diffusion. The system of differential equations is subjected to Dirichlet boundary conditions and a mixed set of Neumann and Dirichlet boundary conditions. Further, to calculate the concentration of CO2, PGE, and the flux in terms of reaction rate constants, we adopt the supervised learning strategy of a nonlinear autoregressive exogenous (NARX) neural network model with two activation functions (Log-sigmoid and Hyperbolic tangent). The reference data set for the possible outcomes of different scenarios based on variations in normalized parameters (α1,α2,β1,β2,k) are obtained using the MATLAB solver “pdex4”. The dataset is further interpreted by the Levenberg–Marquardt (LM) backpropagation algorithm for validation, testing, and training. The results obtained by the NARX-LM algorithm are compared with the Adomian decomposition method and residual method. The rapid convergence of solutions, smooth implementation, computational complexity, absolute errors, and statistics of the mean square error further validate the design scheme’s worth and efficiency.     

Photochemistry of Thymine in Protic Polar Nanomeric Droplets Using Electrostatic Embeding TD-DFT/MM

Thymine photochemistry is important for understanding DNA photodamage. In the gas phase, thymine undergoes a fast non-radiative decay from S 2 to S 1 . In the S 1 state, it gets trapped for several picoseconds until returning to the ground-state S 0 . Here, we explore the electrostatic effects of nanomeric droplets of methanol and water on the excited states of thymine. For this purpose, we develop and implement an electrostatic embedding TD-DFT/MM method based on a QM/MM coupling defined through electrostatic potential fitting charges. We show that both in methanol and water, the mechanism is similar to the gas phase. The solvent molecules participate in defining the branching plane of S 0 /S 1 intersection and have a negligible effect on the S 1 /S 2 intersection. Despite the wrong topology of the ground/excited state intersections, electrostatic embedding TD-DFT/MM allows for a fast exploration of the potential energy surfaces and a qualitative picture of the photophysics of thymine in solvent droplets.     

Metastable Kitaev Magnets

Nearly two decades ago, Alexei Kitaev proposed a model for spin-1/2 particles with bond-directional interactions on a two-dimensional honeycomb lattice which had the potential to host a quantum spin-liquid ground state. This work initiated numerous investigations to design and synthesize materials that would physically realize the Kitaev Hamiltonian. The first generation of such materials, such as Na2IrO3, α-Li2IrO3, and α-RuCl3, revealed the presence of non-Kitaev interactions such as the Heisenberg and off-diagonal exchange. Both physical pressure and chemical doping were used to tune the relative strength of the Kitaev and competing interactions; however, little progress was made towards achieving a purely Kitaev system. Here, we review the recent breakthrough in modifying Kitaev magnets via topochemical methods that has led to the second generation of Kitaev materials. We show how structural modifications due to the topotactic exchange reactions can alter the magnetic interactions in favor of a quantum spin-liquid phase.     

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.     

Removal of Carbamazepine in Aqueous Solution by CoS2/Fe2+/PMS Process

Carbamazepine (CBZ), as a typical pharmaceutical and personal care product (PPCP), cannot be efficiently removed by the conventional drinking water and wastewater treatment process. In this work, the CoS₂/Fe²⁺/PMS process was applied for efficient elimination of CBZ. The CBZ removal efficiency of CoS₂/Fe²⁺/PMS was 2.5 times and 23 times higher than that of CoS₂/PMS and Fe²⁺/PMS, respectively. The intensity of DMPO-HO• and DMPO-SO4•− followed the order of Fe²⁺/PMS < CoS₂/PMS < CoS₂/Fe²⁺/PMS, also suggesting the CoS₂/Fe²⁺/PMS process has the highest oxidation activity. The effects of reaction conditions (e.g., CoS₂ dosage, Fe²⁺ concentration, PMS concentration, initial CBZ concentration, pH, temperature) and water quality parameters (e.g., SO42−, NO3−, H2PO4−, Cl−, NH4+, humic acid) on the degradation of CBZ were also studied. Response surface methodology analysis was carried out to obtain the best conditions for the removal of CBZ, which are: Fe²⁺ = 70 µmol/L, PMS = 240 µmol/L, CoS₂ = 0.59 g/L. The sustainability test demonstrated that the repeated use of CoS₂ for 8 successive cycles resulted in little function decrease (<10%). These findings suggest that CoS₂/Fe²⁺/PMS may be a promising method for advanced treatment of tailwater from sewage treatment plant.     

Optical Dynamic Nuclear Polarization of 13C Spins in Diamond at a Low Field with Multi-Tone Microwave Irradiation

Majority of dynamic nuclear polarization (DNP) experiments have been requiring helium cryogenics and strong magnetic fields for a high degree of nuclear polarization. In this work, we instead demonstrate an optical hyperpolarization of naturally abundant 13C nuclei in a diamond crystal at a low magnetic field and the room temperature. It exploits continuous laser irradiation for polarizing electronic spins of nitrogen vacancy centers and microwave irradiation for transferring the electronic polarization to 13C nuclear spins. We have studied the dependence of 13C polarization on laser and microwave powers. For the first time, a triplet structure corresponding to the 14N hyperfine splitting has been observed in the 13C polarization spectrum. By simultaneously exciting three microwave frequencies at the peaks of the triplet, we have achieved 13C bulk polarization of 0.113 %, leading to an enhancement of 90,000 over the thermal polarization at 17.6 mT. We believe that the multi-tone irradiation can be extended to further enhance the 13C polarization at a low magnetic field.     

Galvano-Fenton Engineering Solution with Spontaneous Catalyst’s Generation from Waste: Experimental Efficiency,Parametric Analysis and Modeling Interpretation Applied to a Clean Technology for Dyes Degradation in Water

In this paper, the degradation of the diazo dye naphthol blue black (NBB) using the Galvano-Fenton process is studied experimentally and numerically. The simulations are carried out based on the anodic, cathodic, and 34 elementary reactions evolving in the electrolyte, in addition to the oxidative attack of NBB by HO• at a constant rate of 3.35×107 mol−1·m3·s−1 during the initiation stage of the chain reactions. The selection of the operating conditions including the pH of the electrolyte, the stirring speed, and the electrodes disposition is performed by assessing the kinetics of NBB degradation; these parameters are set to 3, 350 rpm and a parallel disposition with a 3 cm inter-electrode distance, respectively. The kinetics of Fe(III) in the electrolyte were monitored using the principles of Fricke dosimetry and simulated numerically. The model showed more than a 96% correlation with the experimental results in both the blank test and the presence of the dye. The effects of H2O2 and NBB concentrations on the degradation of the dye were examined jointly with the evolution of the simulated H2O2, Fe2+, and HO• concentrations in the electrolyte. The model demonstrated a good correlation with the experimental results in terms of the initial degradation rates, with correlation coefficients exceeding 98%.     

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.     

Deposition of Hybrid Photocatalytic Layers for Air Purification Using Commercial TiO2 Powders

Photocatalytic nanomaterials, using only light as the source of excitation, have been developed for the breakdown of volatile organic compounds (VOCs) in air for a long time. It is a tough challenge to immobilize these powder photocatalysts and prevent their entrainment with the gas stream. Conventional methods for making stable films typically require expensive deposition equipment and only allow the deposition of very thin layers with limited photocatalytic performance. The present work presents an alternative approach, using the combination of commercially available photocatalytic nanopowders and a polymer or inorganic sol–gel-based matrix. Analysis of the photocatalytic degradation of ethanol was studied for these layers on metallic substrates, proving a difference in photocatalytic activity for different types of stable layers. The sol–gel-based TiO2 layers showed an improved photocatalytic activity of the nanomaterials compared with the polymer TiO2 layers. In addition, the used preparation methods require only a limited amount of photocatalyst, little equipment, and allow easy upscaling.     

Does Hamiltonian Replica Exchange via Lambda-Hopping Enhance the Sampling in Alchemical Free Energy Calculations?

In the context of computational drug design, we examine the effectiveness of the enhanced sampling techniques in state-of-the-art free energy calculations based on alchemical molecular dynamics simulations. In a paradigmatic molecule with competition between conformationally restrained E and Z isomers whose probability ratio is strongly affected by the coupling with the environment, we compare the so-called λ-hopping technique to the Hamiltonian replica exchange methods assessing their convergence behavior as a function of the enhanced sampling protocols (number of replicas, scaling factors, simulation times). We found that the pure λ-hopping, commonly used in solvation and binding free energy calculations via alchemical free energy perturbation techniques, is ineffective in enhancing the sampling of the isomeric states, exhibiting a pathological dependence on the initial conditions. Correct sampling can be restored in λ-hopping simulation by the addition of a “hot-zone” scaling factor to the λ-stratification (FEP⁺ approach), provided that the additive hot-zone scaling factors are tuned and optimized using preliminary ordinary replica-exchange simulation of the end-states.     

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.