Intramolecular Modes Research Articles

Vanillin Benzothiazole Derivative Reduces Cellular Reactive Oxygen Species and Detects Amyloid Fibrillar Aggregates in Alzheimer's Disease Brain.

The misfolding of amyloid beta (Aβ) peptides into Aβ fibrillary aggregates is a major hallmark of Alzheimer's disease (AD), which responsible for the excess production of hydrogen peroxide (H2O2), a prominent reactive oxygen species (ROS) from the molecular oxygen (O2) by the reduction of the Aβ-Cu(I) complex. The excessive production of H2O2 causes oxidative stress and inflammation in the AD brain. Here, we have designed and developed a dual functionalized molecule VBD by using π-conjugation (C═C) in the backbone structure. In the presence of H2O2, the VBD can turn into fluorescent probe VBD-1 by cleaving of the selective boronate ester group. The fluorescent probe VBD-1 can undergo intramolecular charge transfer transition (ICT) by a π-conjugative system, and as a result, its emission increases from the yellow (532 nm) to red (590 nm) region. The fluorescence intensity of VBD-1 increases by 3.5-fold upon binding with Aβ fibrillary aggregates with a high affinity (Kd = 143 ± 12 nM). Finally, the VBD reduces the cellular toxic H2O2 as proven by the CCA assay and DCFDA assay and the binding affinity of VBD-1 was confirmed by using in vitro histological staining in 8- and 18-month-old triple transgenic AD (3xTg-AD) mice brain slices.

Reaction kinetics and implications of the decomposition and formation of C2H4O isomers

Acetaldehyde, ethylene oxide, and vinyl alcohol are three C2H4O isomers that are ubiquitous in combustion over a wide temperature range. A comprehensive reaction kinetics study has been performed for reactions that occur on the same C2H4O potential energy surface, mainly including the unimolecular reactions of three C2H4O isomers and the recombination reaction of CH3 with HCO. Temperature- and pressure-dependent rate coefficients were updated or newly predicted by performing quantum chemical calculations coupled with RRKM/master equation simulations. The dominance of CC bond fission is reconfirmed for acetaldehyde decomposition at higher temperatures. The negligible contribution of CH4 + CO channel from usual tight intramolecular H-shift transition state provides indirect evidence for previously reported roaming mechanism that was proposed to explain the observation of CH4 + CO in acetaldehyde pyrolysis. For ethylene oxide pyrolysis, current experiment and kinetic prediction have a good consistency in branching ratios between the formation of acetaldehyde and vinyl alcohol products. The radicals of CH3 + HCO can also be directly generated from ethylene oxide through a well-skipping reaction mechanism especially at higher temperatures. For CH3 + HCO recombination, we highlight the importance of CH3CO + H channel that was often overlooked previously. Kinetic simulations show that the incorporation of updated rate coefficients and newly identified channels results in a measurable influence on C2 chemistry, indicating the possibility and necessity of further improvement of core mechanism in combustion kinetic models.

Broadband terahertz spectroscopy of enantiomeric polylactide

In this study, poly (L-lactide) (PLLA), poly (D-lactide) (PDLA), and their blend (stereocomplex; SC) were investigated by terahertz spectroscopy. Absorption spectra were obtained for PLLA isothermally crystallized in a temperature range of 80 °C–140 °C, and eight characteristic peaks were observed in the frequency range of 1–15 THz. No obvious spectral difference between PLLA and PDLA was observed, indicating that chirality did not affect their spectra. Conversely, the SC sample exhibited a complex peak shift behavior that was different from those of the homo-crystals. To elucidate the origins of the vibration modes, the spectral measurement of the lactide was conducted and compared with the results of PLLA. Four absorption peaks that appeared below 8 THz disappeared in the experimental of the lactide. This suggests that the vibration modes in the polylactide differ around 8 THz, and low and higher frequencies are attributed to the inter- and intramolecular vibration modes, respectively.

Discretized hierarchical equations of motion in mixed Liouville-Wigner space for two-dimensional vibrational spectroscopies of liquid water.

A model of a bulk water system describing the vibrational motion of intramolecular and intermolecular modes is constructed, enabling analysis of its linear and nonlinear vibrational spectra as well as the energy transfer processes between the vibrational modes. The model is described as a system of four interacting anharmonic oscillators nonlinearly coupled to their respective heat baths. To perform a rigorous numerical investigation of the non-Markovian and nonperturbative quantum dissipative dynamics of the model, we derive discretized hierarchical equations of motion in mixed Liouville-Wigner space, with Lagrange-Hermite mesh discretization being employed in the Liouville space of the intramolecular modes and Lagrange-Hermite mesh discretization and Hermite discretization in the Wigner space of the intermolecular modes. One-dimensional infrared and Raman spectra and two-dimensional terahertz-infrared-visible and infrared-infrared-Raman spectra are computed as demonstrations of the quantum dissipative description provided by our model.

Investigation on the Structure, Formation Mechanism, and Surface Morphology of CP–CH4 Binary Hydrate

Cyclopentane (CP) is often used as a hydrate former, which shows an excellent promotion effect in hydrate-based desalination. To elucidate the guest molecule distribution and microcosmic mechanism during hydrate formation, the in situ Raman spectroscopy of CP–methane binary hydrates is performed. The Raman spectra for the intramolecular vibration mode of host and guest molecules reveal that sII CP–methane hydrate formed with CP and CH4 encaged in large and small cages, respectively. But the small cages were not completely filling in. Because of the structure of CP with a five-membered ring, hydrogen-bonded water molecules arranged around CP forming a metastable structure, which accelerates the nucleation rate of hydrate. The peak O–H stretching vibration (ROH–H = I3170/I3400) in hydrate phase is an indication of hydrogen-bond ordering. At 3.5 MPa, the CH4 occupancy in the small cages was 0.9978 and the CP occupancy in the small cages was 0.1751. According to cage occupancies and the thermodynamic model based on van der Waals–Platteeuw, the calculated hydration number was 12.6. Cryo-scanning electron microscopy was applied to observe the surface morphology of hydrate. Energy-dispersive spectroscopy was used to distinguish hydrate from ice by identifying element C.

Sensing Bisphenol A by Means of Surface-Enhanced Raman Spectroscopy and DFT Calculations to Elucidate the Enhancement Mechanism That Dominates the Spectrum

Surface-Enhanced Raman Spectroscopy (SERS) was employed as a spectroscopic tool to detect Bisphenol A (BPA), a building block in polycarbonate and epoxy resins or an additive in other polymer plastics like PVC, which has an endocrine disruptor effect. Silver nanoparticles (AgNPs) synthesized by using different reducing agents such as hydroxylamine (Ag@HX), citrate (Ag@Cit), borohydride (Ag@BH), and β-cyclodextrin (Ag@βCD) were employed, aiming to select the best standard SERS substrate. The lowest limit of quantification was reached at a concentration of 0.01 mM (2.3 μg/mL) of a sonicated aqueous solution by using Ag@Cit NPs and identifying two enhanced bands recorded at about 350 and 460 cm−1. In order to gain insight into the nature of the enhanced bands, and therefore into which mechanism governs the SERS signal, electrochemical spectra recorded at different electrode potentials were acquired and TD-DFT calculations were applied to a neutral silver complex of BPA, Ag2-BPA, and to its monohydroxylated chemical specie, Ag2-BPA(OH), which is present in sonicated solution. The calculated electronic structure and the resonance Raman spectra point out that a surface plasmon-like resonance inside the silver cluster dominates the SERS spectrum corresponding to the physisorbed BPA(OH) species, a charge transfer enhancement mechanism or an intramolecular resonance transition localized in the phenolic framework was then discarded.

Mechanochromic Materials Based on Tetraphenylethylene-Substituted Phenothiazines: Substituent-Dependent Hypsochromic and Bathochromic Switching of Emission

Phenothiazine- and tetraphenylethylene (TPE)-based mechanochromic materials (PTZTPE-1CHO, PTZTPE-4CHO, and PTZTPE-4CN) with different electron-withdrawing substituents (−CHO and −CN) were designed and synthesized by the Suzuki cross-coupling reaction of bromo-TPEs with the corresponding boronate esters of phenothiazine. The photophysical, aggregation-induced emission, mechanochromic, thermal, and electroluminescence properties of the synthesized compounds were investigated. The cyano group-bearing derivative PTZTPE-4CN exhibited reversible mechanochromism, and its emission maximum shifted bathochromically when mechanically ground, whereas the formyl group-containing derivatives PTZTPE-1CHO and PTZTPE-4CHO exhibited hypsochromically shifted mechanochromism. The solution of PTZTPE-4CN was weakly emissive, and PTZTPE-1CHO and PTZTPE-4CHO exhibit strong fluorescence in the solution state due to the intramolecular charge transfer transitions. The electroluminescence properties of the synthesized compounds as non-annealed and annealed non-doped prompt fluorescent emitters were studied in organic light-emitting diodes, which showed a maximum external quantum efficiency of 1.2% and a luminance of 8762 cd·m–2.

Low-frequency anharmonic couplings in crystalline bromoform: Theory.

Theoretical calculations of the low-frequency anharmonic couplings of the β-phase of crystalline bromoform are presented based on density functional theory quantum chemistry calculations. The electrical and mechanical anharmonicities between intra- and intermolecular modes are calculated, revealing that the electrical anharmonicity dominates the cross-peak intensities in the 2D Raman-THz response and crystalline, as well as liquid, bromoform. Furthermore, the experimentally observed difference in relative cross-peak intensities between the two intramolecular modes of bromoform and the intermolecular modes can be explained by the C3v-symmetry of bromoform in combination with orientational averaging. The good agreement with the experimental results provides further evidence for our interpretation that the 2D Raman-THz response of bromoform is, indeed, related to the anharmonic coupling between the intra- and intermolecular modes.

New polymorphic phase of arachidic acid crystal: structure, intermolecular interactions, low-temperature stability and Raman spectroscopy combined with DFT calculations.

Saturated monocarboxylic fatty acids with long carbon chains are organic compounds widely used in several applied fields, such as energy production, thermal energy storage, antibactericidal, antimicrobial, among others. In this research, a new polymorphic phase of arachidic acid (AA) crystal was synthesized and its structural and vibrational properties were studied by single-crystal X-ray diffraction (XRD) and polarized Raman scattering. The new structure of AA was solved at two different temperature conditions (100 and 300 K). XRD analysis indicated that this polymorph belongs to the monoclinic space group P21/c (C2h5), with four molecules per unit cell (Z = 4). All molecules in the crystal lattice adopt a gauche configuration, exhibiting a R22(8) hydrogen bond pattern. Consequently, this new polymorphic phase, labeled as B form, is a polytype belonging to the monoclinic symmetry, i.e., Bm form. Complementarily, Hirshfeld's surfaces were employed to analyze the intermolecular interactions within the crystal lattice of this polymorph at temperatures of 100 and 300 K. Additionally, density functional theory (DFT) calculations were performed to assign all intramolecular vibration modes related to experimental Raman-active bands, which were properly calculated using a dimer model, considering a pair of AA molecules in the gauche configuration, according to the solved-crystal structure.

Influence of plasmons on the luminescence properties of solvatochromic merocyanine dyes with different solvatochromism.

The effect of localized surface plasmon resonance (LSPR) of a system consisting of a highly dipolar merocyanine dye and a silver nanoparticle (NP) was studied experimentally and theoretically. A theoretical model for estimating the fluorescence quantum yield (φfl) using quantum chemical calculations of intramolecular and intermolecular electronic transition rate constants was developed. Calculations show that the main deactivation channels of the lowest excited singlet state of the studied merocyanines are internal conversion (kIC(S1 → S0)) and fluorescence (kr(S1 → S0)). The intersystem-crossing transition has a low probability due to the large energy difference between the singlet and triplet levels. In the presence of plasmonic NPs, the fluorescence quantum yield is increased by a factor of two according to both experiment and computations. The calculated values of φfl, when considering changes in kr(S1 → S0) and the energy-transfer rate constant (ktransfer) from the dye to the NP was also twice as large at distances of 6-8 nm between the NP and the dye molecule. We also found that the LSPR effect can be increased or decreased depending on the value of the dielectric constant (εm) of the environment.

Theoretical study of the absorption and emission spectrum and non‐adiabatic excited state dynamics of gas‐phase xanthone

AbstractThe ground, singlet, and triplet excited state structures (S1, S2, T1, and T2) of xanthone have been calculated and characterized in the adiabatic representation by using time‐dependent density functional theory (TDDFT). However, the fast intramolecular transition mechanisms of xanthone are still under debate, and so we perform non‐adiabatic excited state dynamics of the photochemistry of xanthone gas phase and find that it follows El‐Sayed's rule. Electronic transition mechanism of xanthone is sequential from the S2 state: the singlet internal conversion (IC) time from S2 (1ππ*) to S1 (1nπ*) is 3.85 ps, the intersystem crossing (ISC) from S1 (1nπ*) to T2 (3ππ*) takes 4.76 ps, and the triplet internal conversion from T2 (3ππ*) to T1 (3nπ*) takes 472 fs. The displaced oscillator, Franck–Condon approximation, and one‐photon excitation equations were used to simulate the absorption spectra of S0 → S2 transition, with v55 being most crucial for S0 structure; the fluorescence spectra of S1 → S0 transition with v47 for S1; and the phosphorescence spectra of T1 → S0 transition with v4 for T1. Our method can reproduce the experimental absorption, fluorescence, and phosphorescence spectra of gas‐phase xanthone.

DFT Studies on the Molecular Structure, Regioisomerism, Ground and Excited state Charge Transfer Properties of Spiro‐heterocycles

AbstractThe electronic structure, stereochemical aspects and charge transfer properties of the spiro compound (5S,8S) spiro‐{6‐phenyl‐1‐aza‐3‐oxa‐7‐thia‐bicyclo[3,3,0]‐octene‐8,3’(2’H)‐indol}‐2’‐one (spiro bicyclo adduct) synthesized using the multi‐component reaction via 1,3‐dipolar cycloaddition of isatin and thioproline with the dipolarophile phenylacetylene have been studied. The two lowest energy regio‐isomers of the spiro heterocycle formed from the stereospecific dipolar reaction have been analysed along with the electron‐withdrawing and releasing substituents using DFT method at the CAM‐B3LYP/6‐311++G(d,p) level of theory. The atomic charges and the stabilization energy due to the intramolecular charge delocalization process calculated using the natural orbitals at the different molecular sites reveal the different donor‐acceptor interactions occurring in the system. The intramolecular electronic transitions (specifically n to π* and π to π*) is found to occur from the localized donor end component to the acceptor end components in the multi‐component system. The hole produced by the ionization of the entities is found to migrate from the thioproline component to the phenyl acetylene part in a time scale of around 4 fs. The electron‐withdrawing and donating substituents on the spirobicyclo adduct have been proven to tune the excited and ground state charge transfer properties uniquely. The results can shed light on how multi‐component reactions can be directed to produce spiro adducts with versatile applications.

Unveiling the molecular mechanism of spiropyran-based receptors toward cyanide sensing: A theoretical study

Spiropyran-based derivatives are widely used for highly selective colorimetric detection of cyanide ion. Herein, geometric structures, electronic characteristics, thermodynamics, density of states, frontier molecular orbital, and absorption properties for 2-(8-(hydroxymethyl)-3',3'-dimethyl-6-nitrospiro [chromene-2,2'-indolin]-1'-yl) ethanol ( SP ), 2-(8-(hydroxymethyl)-3',3'-dimethyl-6-nitro-7-((4-nitrophenyl) diazenyl)-4a,8a-dihydrospiro [chromene-2,2'-indolin]-1'-yl) ethanol ( SP-1 ), and the newly designed 2-(8-(hydroxymethyl)-3',3'-dimethyl-6-nitro-7-((4-nitrophenyl) diazenyl) -4a,8a-dihydrospiro [benzo[b][1,4]oxazine-2,2'-indolin]-1'-yl) ethanol ( SP-2 ) receptors are computed by density functional theory and time-dependent density functional theory, shedding light on their molecular mechanism toward cyanide sensing. The negative values of free-energy changes and the binding energies indicate that the CN - binding with the above-mentioned receptors is thermodynamically feasible. A sharp distinction in absorption wavelength is obtained after CN - binds to receptors, contributing to the sensitive detection of cyanide ion. Our results reveal that the difference in absorption wavelength is due to the configurational change and intramolecular charge transfer transition for receptor-CN - systems, in comparison with the π−π* transition for the receptors. This work could offer a clear theoretical guideline for fabricating high-performance probes (e.g., receptor SP-2/MC-2 ) toward cyanide. • Disclosing the molecular mechanism of spiropyran-based receptors toward cyanide detection via theoretical calculations. • Systematic analysis of geometric structures, electronic characteristics, thermodynamics, and adsorption properties. • A clear theoretical guideline for fabricating high-performance fluorescent cyanide probes.

Excitations follow (or lead?) density scaling in propylene carbonate.

Structural excitations that enable interbasin (IB) barrier crossings on a potential energy landscape are thought to play a facilitating role in the relaxation of liquids. Here, we show that the population of these excitations exhibits the same density scaling observed for α relaxation in propylene carbonate, even though they are heavily influenced by intramolecular modes. We also find that IB crossing modes exhibit a Grüneisen parameter (γG) that is approximately equivalent to the density scaling parameter γTS. These observations suggest that the well-documented relationship between γG and γTS may be a direct result of the pressure dependence of the frequency of unstable (relaxation) modes associated with IB motion.

Observation of a transient intermediate in the ultrafast relaxation dynamics of the excess electron in strong-field-ionized liquid water

A unified picture of the electronic relaxation dynamics of ionized liquid water has remained elusive despite decades of study. Here, we employ sub-two-cycle visible to short-wave infrared pump-probe spectroscopy and ab initio nonadiabatic molecular dynamics simulations to reveal that the excess electron injected into the conduction band (CB) of ionized liquid water undergoes sequential relaxation to the hydrated electron s ground state via an intermediate state, identified as the elusive p excited state. The measured CB and p-electron lifetimes are 0.26 ± 0.02 ps and 62 ± 10 fs, respectively. Ab initio quantum dynamics yield similar lifetimes and furthermore reveal vibrational modes that participate in the different stages of electronic relaxation, with initial relaxation within the dense CB manifold coupled to hindered translational motions whereas subsequent p-to-s relaxation facilitated by librational and even intramolecular bending modes of water. Finally, energetic considerations suggest that a hitherto unobserved trap state resides ~0.3-eV below the CB edge of liquid water. Our results provide a detailed atomistic picture of the electronic relaxation dynamics of ionized liquid water with unprecedented time resolution.

Broadband infrared absorption spectroscopy of low-frequency inter-molecular vibrations in crystalline poly(L-lactide)

The broadband vibrations of poly l-lactide (PLLA) were investigated by terahertz (THz) spectroscopy in the range of 2–16 THz, infrared (IR) spectroscopy, density functional theory (DFT), and classical molecular dynamics (MD) simulations. Characteristic functional group peaks were observed in the IR spectra, which were independent of the crystallinity. A simple model analysis utilizing DFT calculations with an isolated l-lactide monomer and MD simulations for nine polymer chains in a unit cell were performed to investigate the origin of intra-molecular vibrations between molecular chains. Experimentally observed peaks in the THz region were assigned to the inter- and intra-molecular vibration modes. Results showed that classical MD calculations are a particularly powerful tool for the vibrational-mode analysis of inter-molecular interactions.

Effects of molecular shape and flexibility on fast sound of organic liquids.

Inelastic x-ray scattering spectra of four organic liquids, n-hexane, cyclohexane, ethylene glycol dimethyl ether, and 1,4-dioxane, were measured, and the sound velocity in the nm-1 wavenumber and meV energy regimes was determined. Compared with the corresponding values in the hydrodynamic limit, the sound velocity in the nm-1 regime was faster, and the positive dispersion of the longitudinal modulus was stronger in liquids composed of ring structures (cyclohexane and 1,4-dioxane) than in those of linear chain structures (n-hexane and ethylene glycol dimethyl ether). Molecular dynamics simulation of n-hexane and cyclohexane was also performed. The difference in the positive dispersion of the longitudinal modulus was reproduced by simulation, and it was elucidated by the difference in the longitudinal modulus in the q = 0 limit and the THz frequency regime. The excess part of the longitudinal modulus from the hydrodynamic limit was further divided into various contributions, and the smaller excess modulus of n-hexane was mainly ascribed to two reasons. The first one is that the shear modulus of n-hexane is smaller in the THz regime, and the second one is that the positive dispersion of the bulk modulus due to the vibrational energy relaxation is weaker. The second mechanism was further interpreted in terms of the fast vibrational energy relaxation of intramolecular modes associated with the chain deformation of n-hexane.

Synthesis, crystal structure, Hirshfeld surface analysis, thermal, luminescent properties, and computational studies of the new triazole derivative 1-(5-methyl-1-(pyridin-2-ylmethyl)-1H-1,2,3-triazol-4-yl)ethan-1-one

The title compound, 1-(5-methyl-1-(pyridin-2-ylmethyl)-1H-1,2,3-triazol-4-yl)ethan-1-one, a new triazole derivative with formulae C11H12N4O, which has been synthesized and structurally characterized by MS, elemental analysis, FT-IR, and single-crystal X-ray diffraction. Spectroscopic results are consistent with the proposed structure and XRD experiments. Single-crystal X-ray diffraction analysis indicated that the compound crystallizes in the monoclinic space group P21/n (N°14), Z = 4, and unit cell parameters a = 12.987(2) Å, b = 4.4539(5) Å, c = 19.060(2) Å, β = 93.993(3) °, V = 1099.8(2) Å3. The molecular structure and crystal packing are stabilized by hydrogen-bond-like-interactions CH···O, and weak π ··· π interactions. Thermal studies show a stable phase at 240 °C. Luminescent properties show a benzenoid band pattern, which was assigned to π*- π transition bands and the less energetic band assigned to intramolecular CT transitions and agrees with emission experiments in solution. DFT molecular and crystal calculations show a molecular behavior in the solid state, which agrees with thermal and luminescent properties.

Evidence for Water Antibonding Orbital Mixing in the Hydrated Electron from Its Oxygen 1s X-ray Absorption Spectrum.

The X-ray absorption spectrum (XAS) of the hydrated electron (e(aq)-) has been simulated using time-dependent density functional theory with a quantum mechanics/molecular mechanics description. A unique XAS peak at 533 eV is observed with an energy and intensity in quantitative agreement with recent time-resolved experiments, allowing its assignment as arising from water O1s transitions to the singly occupied molecular orbital (SOMO) in which the excess electron resides. The transitions acquire oscillator strength due to the SOMO comprising an admixture of a cavity-localized orbital and water 4a1 and 2b2 antibonding orbitals. The mixing of antibonding orbitals has implications for the strength of couplings between e(aq)- and intramolecular modes of water.

Chemical Bonding Effects and Physical Properties of Noncentrosymmetric Hexagonal Fluorocarbonates ABCO3F (A: K, Rb, Cs; B: Mg, Ca, Sr, Zn, Cd).

The present work applied the methods of density functional theory and the van der Waals interaction PBE + D3(BJ) on the basis of localized orbitals of the CRYSTAL17 package. It featured the effect of interactions between structural elements of fluorocarbonates ABCO3F (A: K, Rb, Cs; B: Mg, Ca, Sr, Zn, Cd) on their elastic and vibrational properties. The hexagonal structures proved to consist of alternating ···B-CO3··· and ···A-F··· layers in planes ab, interconnected along axis c by infinite chains ···F-B-F···, where cations formed polyhedra AOnF3 and BOmF2. The calculations included the band energy structure, the total and partial density of electron states, the energy and band widths of the upper ns- and np-states of alkali and alkaline-earth metals, as well as nd-zinc and nd-cadmium. For hydrostatic compression, we calculated the parameters of the Birch–Murnaghan equation of state and the linear compressibility moduli along the crystal axes and bond lines. We also defined the elastic constants of single crystals to obtain the Voigt–Reuss–Hill approximations for the elastic moduli of polycrystalline materials. The study also revealed the relationship between the elastic properties and the nature of the chemical bond. Hybrid functional B3LYP made it possible to calculate the modes of normal long-wavelength oscillations, which provided the spectra of infrared absorption and Raman scattering. Intramolecular modes ν1 and ν4 with one or two maxima were found to be intense, and their relative positions depended on the lengths of nonequivalent C–O bonds.