Designing one-compartment H2O2 fuel cell using electroactive phenalenyl-based [Fe2(hnmh-PLY)3] complex as the cathode material

The sustainable chemical energy of H2O2 as a fuel and an oxidant in an advantageous single-compartment fuel cell design can be converted into electric energy, which requires molecular engineering to design suitable cathodes for lowering the high overpotential associated with H2O2 reduction. The present work covers the synthesis and structural characterization of a novel cathode material, [FeIII2(hnmh-PLY)3] complex, 1, designed from a PLY-derived Schiff base ligand (E)-9-(2-((2-hydroxynaphthalen-1-yl)methylene)hydrazineyl)-1H-phenalen-1-one, hnmh-PLYH2. Complex 1, when coated on the surface of a glassy carbon electrode (GC-1) significantly catalyzed the reduction of H2O2 in an acidic medium. Therefore, a complex 1 modified glassy carbon electrode was employed in a one-compartment H2O2 fuel cell operated in 0.1 M HCl with Ni foam as the corresponding anode to produce a high open circuit potential (OCP) of 0.65 V and a peak power density (PPD) of 2.84 mW cm-2. CV studies of complex 1 revealed the crucial participation of two Fe(III) centers for initiating H2O2 reduction, and the role of coordinated redox-active PLY units is also highlighted. In the solid state, the π-conjugated network of coordinating (hnmh-PLY) ligands in complex 1 has manifested interesting face-to-face π-π stacking interactions, which have helped the reduction of the complex and facilitated the overall catalytic performance.

Revealing the Structure and Noncovalent Interactions of Isolated Molecules by Laser-Desorption/Ionization-Loss Stimulated Raman Spectroscopy and Quantum Calculations

The structural and dynamical characteristics of isolated molecules are essential, yet obtaining this information is difficult. We demonstrate laser-desorption jet-cooling/ionization-loss stimulated Raman spectroscopy to obtain Raman spectral signatures of nonvolatile molecules in the gas phase. The vibrational features of a test substance, the most abundant conformer of tryptamine, are compared and found to match those resulting from the scaled harmonic Raman spectrum obtained by density functional theory calculations. The vibrational signatures serve to identify the most prominent gauche conformer and evaluate its predicted electronic structure. These findings, together with noncovalent interaction (NCI) analysis, provide new insights into electron densities and reduced density gradients, assessing the hydrogen bonds (N-H···π and C-H···H-C) and interplay between attractive and repulsive NCIs affecting the structure. This approach accesses vibrational signatures of isolated nonvolatile molecules by tabletop lasers at uniform resolution and in a broad frequency range, promising great benefit to future studies.

On the rearrangements of biologically-relevant vinyl allene oxides to cis-cyclopentenones, ketols, and Favorskii-type carboxylic acids

In addition to stereodefined cis-cyclopentenones, the rearrangement of naturally-occurring vinyl allene oxides can provide ketols, cyclopropylcarbinols, and Favorskii-type bis-(Z)-but-2-en-1-yl acetic acids. These processes have been studied by DFT computations using (Z)-but-1-en-1-yl allene oxides as model systems. Prior studies on the stepwise cascade process starting from (Z)-but-1-en-1-yl allene oxides established as key steps the ring opening of the oxirane to give oxidopentadienyl biradicals, and their isomerization through formation of alkenylcyclopropanone intermediates prior to the conrotatory electrocyclic ring closure to cis-configured cyclopentenones. Under neutral or under acidic conditions, the corresponding ketols and cyclopropylcarbinols have been computationally characterized as resulting from SN2, SN1 and SN1'-type processes, showing that the rearrangement of vinyl allene oxides is pH-dependent. Moreover, stereoconvergent base-induced Favorskii-type rearrangements to provide bis-(Z)-but-1-en-1-yl substituted acetic acids have also been justified. Since the model system captures the structural features of the vinyl allene oxides of biological relevance, our computations provide the most comprehensive overview of the complex reactivity of these natural species.

Some opinions on MD-based vibrational spectroscopy of gas phase molecules and their assembly: An overview of what has been achieved and where to go

We hereby review molecular dynamics simulations for anharmonic gas phase spectroscopy and provide some of our opinions of where the field is heading. With these new directions, the theoretical IR/Raman spectroscopy of large (bio)-molecular systems will be more easily achievable over longer time-scale MD trajectories for an increase in accuracy of the MD-IR and MD-Raman calculated spectra. With the new directions presented here, the high throughput 'decoding' of experimental IR/Raman spectra into 3D-structures should thus be possible, hence advancing e.g. the field of MS-IR for structural characterization by spectroscopy. We also review the assignment of vibrational spectra in terms of anharmonic molecular modes from the MD trajectories, and especially introduce our recent developments based on Graph Theory algorithms. Graph Theory algorithmic is also introduced in this review for the identification of the molecular 3D-structures sampled over MD trajectories.

UV-Vis, Raman spectroscopic and density functional theoretical studies on microsolvation 1, 2, 4-triazole-3-thione clusters

Photophysical and photochemical reactions of microsolvation clusters are attracting an increasing attention due to their wide applications in materials science and biology. In this paper, 1, 2, 4-triazole-3-thione (3TT) is investigated in solid, protic, and aprotic solvents using FT-Raman, resonance Raman and electronic absorption spectroscopic experiments. The structures of microsolvation clusters in solvents were confirmed by 488 nm Raman spectroscopy combining with density functional theory (DFT) calculation. Steady-state absorption and resonance Raman spectra of 3TT in different environments indicate that the intermolecular hydrogen bonding may reveal important insights in the photophysical and photochemical process. With the aid of DFT and time-dependent density functional theory (TDDFT) calculations, we assigned the observed Raman spectra to the microsolvation clusters in acetonitrile, water and methanol, and carried out preliminary investigations on spectrum shifts of UV and Raman spectra due to the hydrogen bonding with the solvent molecules. The intermolecular >NH···O and >=S···H hydrogen bonding interactions, which are the key constituents of stable thione structure of 3TT, revealed the obvious spectrum shifts of 3TT, including Raman and absorption shifts in CH₃CN, CH₃OH and H₂O. The hydrogen bond sites were further confirmed to be located on the functional group SCNH of 3TT with CH₃CN, H₂O and CH₃OH.

Water clusters as bifunctional catalysts in organic chemistry: the hydrolysis of oxirane and its methyl derivatives

This contribution explores the bifunctional catalytic activity of water clusters ((H₂O)_n with n = 1-5) in organic chemistry similar to that observed in the formation of H₂SO₄ in acid rain (Chem. Commun., 53, 3516, (2017)). We considered for this purpose the Hydrolysis of Epoxides (HE), in particular, that of oxirane and its methyl derivatives. Surrounding water molecules with H-bond cooperative effects decrease the activation energy of the rate-limiting step of HE in condensed phase, especially when they lead to an anti-periplanar attack on the alkoxide leaving group. Furthermore, the water molecules have a bifunctional catalytic role in HE by (i) increasing the nucleophilic and electrophilic character of the attacking oxygen atom and the leaving group of the reaction, respectively, and (ii) placing the reactants in a suitable disposition for the substitution to occur. Overall, this investigation provides relevant insights into the collective action of water molecules on organic reactions in neutral, basic and acid media.

Ultra-broadband terahertz fingerprint spectrum of melatonin with vibrational mode analysis

Melatonin (MLT), as a neurotransmitter and an endogenous neurohormone, plays an important role in physiological functions through interactions with specific receptors. The conformations of MLT are closely related to its biological activities and functions. However, the internal relationship between the structure and interaction of MLT and its allosteric transition remains unclear. In this work, we obtain the broadband fingerprint terahertz (THz) spectrum of MLT in the range of 0.5-18 THz using the air-plasma terahertz time-domain spectroscopy (THz-TDS) system. DFT calculations are employed to analyze the vibration characteristics of MLT. The result shows that the low-frequency vibrations mainly come from the strong coupling between inter- and intramolecular vibrations, and the contribution of intramolecular vibrations gradually dominates with increasing frequency. Meanwhile, the local vibrations of the different functional groups distribute widely in the THz low-frequency band, relating to the diversity of conformational changes in the molecule. The intermolecular hydrogen bonds (HBs) have distinct resonant responses and play critical roles in the THz low-frequency vibrations. The study reveals the complex characteristics of the resonant coupling of MLT with THz electromagnetic waves. The results will help to understand the conformational preferences of MLT in neural signal transmission processes.

Accurate location of hydrogen atoms in hydrogen bonds of tizoxanide from the combination of experimental and theoretical models

To obtain detailed information about the position of hydrogen atoms in hydrogen bonds, HBs, of crystalline organic molecular compounds is not an easy task. In this work we propose a combination of ssNMR experimental data with theoretical procedures to get such information. Furthermore, the combination of experimental and theoretical models provides us with well-defined grounds to analyse the strength of π-stacking interactions between layers of hydrogen bonded molecules. Two different theoretical models were considered, both approaches being quite different. The first one is a solid-state model, so that the periodicity of a crystalline system underlies calculations of the electronic energy, the electronic density and NMR parameters. The other one is a molecular model in which molecules are taken as isolated monomers, dimers and tetramers. These two models were applied to the tizoxanide, TIZ, molecular crystal though it can widely be applied to any other molecular crystal. By the application of the quantum molecular model it was possible to learn about the way the intermolecular HBs affect the position of hydrogen atoms that belong to HBs in TIZ. This molecule has two intermolecular HBs that stabilize the structure of a basic dimer, but it also has an intramolecular HB in each monomer whose position should be optimized together with the other ones. We found that by doing this it is possible to obtain reliable results of calculations of NMR spectroscopic parameters. Working with the solid-state model we found that any local variation of the TIZ crystalline structure is correlated with the variation of the values of the NMR parameters of each nucleus. The excellent agreement between experimental and calculated chemical shifts leads to the conclusion that the N10-H10 bond distance should be (1.00 ± 0.02) Å.

Carbonyl stretch of CH⋯O hydrogen-bonded methyl acetate in supercritical trifluoromethane

Infrared spectroscopy in the gas phase was used to study the formation reaction of the CH⋯O hydrogen bonding complex involving the CH group of trifluoromethane, as a hydrogen donor, and the carbonyl group of methyl acetate, as a hydrogen acceptor, under different (T, p) conditions. The hydrogen-bonded carbonyl stretch of the molecular pair was monitored in dilute mixtures of methyl acetate in trifluoromethane at near-critical temperatures, from gas- to liquid-like densities. In the gas region, it was possible to discriminate the carbonyl signal of the hydrogen-bonded complex from that of the free ester and have access to their relative concentration. The equilibrium constant of the hydrogen bonding reaction and the standard enthalpy and entropy changes in the process were determined using the spectroscopic data. CH⋯O bonding was favored by lowering temperature or pressurizing F₃CH in the mixture, remaining essentially no free carbonyl groups about the critical density. The carbonyl band of the hydrogen-bonded pair appeared as a single symmetric peak up to liquid-like densities, suggesting that the 1:1 methyl acetate-trifluoromethane complex has the most abundant stoichiometry. Spectral features as frequency shift and bandwidth of the hydrogen-bonded carbonyl were studied as a function of temperature and solvent-density. A bathochromic (red) vibrational shift was registered for the bound carbonyl band against density, with a sudden change in behavior in the near-critical region, while the width of this band remains mostly unresponsive.

Time-Dependent Perspective for the Intramolecular Couplings of the N–H Stretches of Protonated Tryptophan

Quasi-classical direct dynamics simulations, performed with the B3LYP-D3/cc-pVDZ electronic structure theory, are reported for vibrational relaxation of the three NH stretches of the −NH₃⁺ group of protonated tryptophan (TrpH⁺), excited to the n = 1 local mode states. The intramolecular vibrational energy relaxation (IVR) rates determined for these states, from the simulations, are in good agreement with the experiment. In accordance with the experiment, IVR for the free NH stretch is slowest, with faster IVR for the remaining two NH stretches which have intermolecular couplings with an O atom and a benzenoid ring. For the free NH and the NH coupled to the benzenoid ring, there are beats (i.e., recurrences) in their relaxations versus time. For the free NH stretch, 50% of the population remained in n = 1 when the trajectories were terminated at 0.4 ps. IVR for the free NH stretch is substantially slower than for the CH stretch in benzene. The agreement found in this study between quasi-classical direct dynamics simulations and experiments indicates the possible applicability of this simulation method to larger biological molecules. Because IVR can drive or inhibit reactions, calculations of IVR time scales are of interest, for example, in unimolecular reactions, mode-specific chemistry, and many photochemical processes.

Gas-Phase Infrared Spectroscopy of Neutral Peptides: Insights from the Far-IR and THz Domain

Gas-phase, double resonance IR spectroscopy has proven to be an excellent approach to obtain structural information on peptides ranging from single amino acids to large peptides and peptide clusters. In this review, we discuss the state-of-the-art of infrared action spectroscopy of peptides in the far-IR and THz regime. An introduction to the field of far-IR spectroscopy is given, thereby highlighting the opportunities that are provided for gas-phase research on neutral peptides. Current experimental methods, including spectroscopic schemes, have been reviewed. Structural information from the experimental far-IR spectra can be obtained with the help of suitable theoretical approaches such as dynamical DFT techniques and the recently developed Graph Theory. The aim of this review is to underline how the synergy between far-IR spectroscopy and theory can provide an unprecedented picture of the structure of neutral biomolecules in the gas phase. The far-IR signatures of the discussed studies are summarized in a far-IR map, in order to gain insight into the origin of the far-IR localized and delocalized motions present in peptides and where they can be found in the electromagnetic spectrum.

Probing the selectivity of Li+ and Na+ cations on noradrenaline at the molecular level

Although several mechanisms concerning the biological function of lithium salts, drugs having tranquilizing abilities, have been proposed so far, the key mechanism for its selectivity and subsequent interaction with neurotransmitters has not been established yet. We report ultraviolet (UV) and infrared (IR) spectra under ultra-cold conditions of Li+ and Na+ complexes of noradrenaline (NAd, norepinephrine), a neurotransmitter responsible for the body's response to stress or danger, in an effort to provide a molecular level understanding of the conformational changes of NAd due to its interactions with these two cations. A detailed analysis of the IR spectra, aided by quantum chemical calculations, reveals that the Li+-noradrenaline (NAd-Li+) complex forms only an extended structure, while the NAd-Na+ and protonated (NAd-H+) complexes form both folded and extended structures. This conformational preference of the NAd-Li+ complex is further explained by considering specific conformational distributions in solution. Our results clearly discern the unique structural motifs that NAd adopts when interacting with Li+ compared with other abundant cations in the human body (Na+) and can form the basis of a molecular level understanding of the selectivity of Li+ in biological systems.

Far-IR and UV spectral signatures of controlled complexation and microhydration of the polycyclic aromatic hydrocarbon acenaphthene

UV and IR spectroscopic study of the controlled complexation and microhydration of a polycyclic aromatic hydrocarbon under isolated conditions using free electron laser FELIX.

Interactions of aggregating peptides probed by IR-UV action spectroscopy

The interplay between intramolecular and formed inter-sheet hydrogen bonds and the effect of dispersion interactions on the formation of peptide dimers is studied using IR-UV action spectroscopy.

Conformational assignment of gas phase peptides and their H-bonded complexes using far-IR/THz: IR-UV ion dip experiment, DFT-MD spectroscopy, and graph theory for mode assignment

Graph theory based vibrational modes as new entities for vibrational THz spectroscopy.

THz spectroscopy of weakly bound cluster molecules in solid para-hydrogen: a sensitive probe of van der Waals interactions

The present work demonstrates that 99.9% enriched solid para-H2 below 3 K provides an excellent inert and transparent medium for the exploration of large-amplitude intermolecular vibrational motion of weakly bound van der Waals cluster molecules in the THz spectral region. THz absorption spectra have been generated for CO2/H2O and CS2/H2O mixtures embedded in enriched solid para-H2 and numerous observed transitions associated with large-amplitude librational motion of the weakly bound binary CO2H2O and CS2H2O van der Waals cluster molecules have been assigned together with tentative assignments for the ternary CS2(H2O)2 system. The interaction strength, directionality and anharmonicity of the weak van der Waals "bonds" between the molecules can be characterized via these THz spectral signatures and yield rigorous benchmarks for high-level ab initio methodologies. It is suggested that even a less stable linear conformation of the ternary CS2(H2O)2 system, where one H2O molecule is linked to each S atom of the CS2 subunit, may be formed due to the kinetics associated with the mobility of free H2O molecules in the soft para-H2 medium. In addition, the spectroscopic observations confirm a linear and planar global intermolecular potential energy minimum for the binary CS2H2O system with C2v symmetry, where the O atom on the H2O molecule is linked to one of the S atoms on the CS2 subunit. A semi-experimental value for the vibrational zero-point energy contribution of 1.93 ± 0.10 kJ mol-1 from the class of large-amplitude intermolecular vibrational modes is proposed. The combination with CCSD(T)/CBS electronic energy predictions provides a semi-experimental estimate of 5.08 ± 0.15 kJ mol-1 for the binding energy D0 of the CS2H2O van der Waals system.

Dimerization of the Benzyl Radical in a High-Temperature Pyrolysis Reactor Investigated by IR/UV Ion Dip Spectroscopy

We investigate the self-reaction of benzyl, C₇ H₇ , in a high-temperature pyrolysis reactor. The work is motivated by the observation that resonance-stabilized benzyl radicals can accumulate in reactive environments and contribute to the formation of polycyclic aromatic hydrocarbons (PAHs) and soot. Reaction products are detected by IR/UV ion dip spectroscopy, using infrared radiation from the free electron laser FELIX, and are identified by comparison with computed spectra. Among the reaction products identified by their IR absorption are several PAHs linked to toluene combustion such as bibenzyl, phenanthrene, diphenylmethane, and fluorene. The identification of 9,10-dihydrophenanthrene provides evidence for a mechanism of phenanthrene formation from bibenzyl that proceeds by initial cyclization rather than an initial hydrogen loss to stilbene.