Intramolecular Vibrations Research Articles

Intramolecular Vibrations and Structural Nonrigidity of Different Type Hydrogen-Bonded Complexes

Intramolecular Vibrations and Structural Nonrigidity of Different Type Hydrogen-Bonded Complexes

Molecular Orbital Delocalization/Localization-Induced Crystal-to-Crystal Photochromism of Schiff Bases without ortho-Hydroxyl Groups

Solid-state photochromic compounds can be used in molecular switch and memory, smart window, and so forth. However, a new photochromic mechanism was rarely reported. Photochromic Schiff bases without ortho-hydroxyl groups (thioamide hydrazones) have been prepared, which are drastically different from the traditional photochromic Schiff bases (e.g., salicylal anils and pyrazolone thiosemicarbazones). Systematic experimental and theoretical studies of thioamide hydrazone confirm the crystal-to-crystal photochromism and thermo-enhanced photochromism. The original faint yellow form changes to yellow after UV irradiation and can further be bleached by visible light irradiation. Besides, the decolored form can automatically change to yellow in dark at room temperature or by heating. The structures of the three forms (the original form, the colored form, and the decolored form) show that the intramolecular torsion and vibration lead to the increase/decrease of the donor (nitrogen atom)–acceptor (sulfur atom) dis...

Predicted infrared spectra in the HF stretching band of the H2-HF complex.

The infrared spectra with hydrogen fluoride (HF) and deuterium fluoride (DF) (v2 = 1 ← 0) for eight isotropic species of H2-HF complex are predicted, based on our newly constructed high-accuracy ab initio potential energy surface [D. Yang et al., J. Chem. Phys. 148, 184301 (2018)]. The radial discrete variable representation/angular finite basis representation method and Lanczos algorithm were used to determine the ro-vibrational energy levels and wave functions for eight species of H2-HF complex (para-H2-HF, ortho-H2-HF, para-D2-HF, ortho-D2-HF, para-H2-DF, ortho-H2-DF, para-D2-DF, and ortho-D2-DF) with separating the inter- and intra-molecular vibrations. Bound states properties including their dissociation energies and rotational constants were presented. The calculated band origins are all red shifted to the isolated HF molecule and in good agreement with available experimental values. The frequencies and line intensities of ro-vibrational transitions in the HF stretching band were further calculated, and the predicted infrared spectra are consistent with available observed spectra. Among them, the spectra for three isotopic species of H2-HF (para-H2-DF, para-D2-DF, and ortho-D2-DF) were predicted for the first time.

Design of a Pyrene Scaffold Multifunctional Material: Real-Time Turn-On Chemosensor for Nitric Oxide, AIEE Behavior, and Detection of TNP Explosive.

A dual-emission pyrene-based new fluorescent probe (N-(4-nitro-phenyl)-N′-pyren-1-ylmethyl-ene-ethane-1,2-diamine (PyDA-NP)) displays green fluorescence for nitric oxide (NO) sensing, whereas it exhibits blue emission in the aggregated state. The mechanism of nitric oxide (NO/NO+) sensing is based on N-nitrosation of aromatic secondary amine, which was not interfered by reactive oxygen species and reactive nitrogen species. The aggregation-induced enhancement of emission (AIEE) behaviors of the PyDA-NP could be attributed to the restriction of intramolecular rotation and vibration, resulting in rigidity enhancement of the molecules. The AIEE behavior of the probe was well established from fluorescence, dynamic light scattering, scanning electron microscopy, transmission electron microscopy, X-ray diffraction, optical fluorescence microscopy, and time-resolved photoluminescence studies. In a H2O/CH3CN binary mixture (8:2 v/v), the probe showed maximum aggregation with extensive (833-fold) increases in fluorescence intensity and high quantum yield (0.79). The aggregated state of the probe was further applied for the detection of nitroexplosives. It displayed efficient sensing of 2,4,6-trinitrophenol (TNP), corroborating mainly the charge-transfer process from pyrene to a highly electron-deficient TNP moiety. Furthermore, for the on-site practical application of the proposed analytical system, a contact-mode analysis was performed.

Intramolecular Vibrations Complement the Robustness of Primary Charge Separation in a Dimer Model of the Photosystem II Reaction Center.

The energy conversion of oxygenic photosynthesis is triggered by primary charge separation in proteins at the photosystem II reaction center. Here, we investigate the impacts of the protein environment and intramolecular vibrations on primary charge separation at the photosystem II reaction center. This is accomplished by combining the quantum dynamic theories of condensed phase electron transfer with quantum chemical calculations to evaluate the vibrational Huang-Rhys factors of chlorophyll and pheophytin molecules. We report that individual vibrational modes play a minor role in promoting charge separation, contrary to the discussion in recent publications. Nevertheless, these small contributions accumulate to considerably influence the charge separation rate, resulting in subpicosecond charge separation almost independent of the driving force and temperature. We suggest that the intramolecular vibrations complement the robustness of the charge separation in the photosystem II reaction center against the inherently large static disorder of the involved electronic energies.

Charge migration kinetics at a nanoscale ZnO/molecule interface structure: A stochastic Schrödinger equation approach

Charge separation dynamics at a hybrid organic/inorganic interface is simulated. The intensively studied para-sexiphenyl/ZnO systems was taken as an example. By extending earlier computations, the work is focused on the hole motion in a cluster of 2553 molecules placed on a flat ZnO surface. A specific case of hole dynamics is studied where the electron injected into the ZnO lattice stays immobile close to the surface. To follow hole motion on a picosecond time-scale, relaxation processes due to intramolecular vibrations are included in the framework of a stochastic Schrödinger equation approach. Respective solutions are confronted with those of an ordinary time-dependent Schrödinger equation exclusively displaying coherent transfer. In the case of excluding dissipative effects, the created hole quickly overcomes the attractive Coulomb-interaction with respect to the immobile electron. However, the hole can escape only partly from the Coulomb well, when taking additional hole relaxation into account.

Toward a Reliable Description of the Lattice Vibrations in Organic Molecular Crystals: The Impact of van der Waals Interactions.

This work assesses the reliability of different van der Waals (vdW) methods to describe lattice vibrations of molecular crystals in the framework of density functional theory (DFT). To accomplish this task, calculated and experimental lattice phonon Raman spectra of a pool of organic molecular crystals are compared. We show that the many-body dispersion (MBD@rsSCS) van der Waals method of Ambrosetti et al. and the pairwise method of Grimme et al. (D3-BJ) outperform the other tested approaches (i.e., the D2 method of Grimme, the TS method of Tkatchenko and Scheffler, and the nonlocal functional vdW-DF-optPBE of Klimeš et al.). For the worse-performing approaches the results could not even be fixed by the introduction of scaling parameters, as commonly used for high-energy intramolecular vibrations. Interestingly, when using the experimentally determined unit cell parameters, DFT calculations using the PBE functional without corrections for long-range vdW interactions provide spectra of similar accuracy as the MBD@rsSCS and D3-BJ simulations.

Intrinsic Analysis of Radiative and Room-Temperature Nonradiative Processes Based on Triplet State Intramolecular Vibrations of Heavy Atom-Free Conjugated Molecules toward Efficient Persistent Room-Temperature Phosphorescence.

The radiative rate ( kp) of the lowest triplet excited state (T1) and the nonradiative rate based on intramolecular vibrations at room temperature [ knr(RT)] from T1 for heavy atom-free conjugated structures are determined by considering the triplet yield and quenching rate from T1. Donor substitution did not strongly influence knr(RT) but greatly enhanced kp. The knr(RT) values were comparable between donor-substituted molecules and nonsubstituted molecules, which we explain by similar vibrational spin-orbit coupling (SOC) related to the transition from T1 to the ground state (S0). We attribute the enhancement of kp induced by donor substitution to the appearance of a large SOC between high-order singlet excited states (Sm) and T1 together with the large transition dipole moments of the Sm-S0 transitions. Knowledge of this mechanism is important for developing future efficient persistent room-temperature phosphorescence from doped aromatic materials and aromatic crystals.

Directed polaron propagation in linear polypeptides induced by intramolecular vibrations and external electric pulses.

We study the propagation of α-helix polarons in a model describing the nonadiabatic interaction between an electron and a lattice of quantum mechanical oscillators at physiological temperature. We show that when excited by a subpicosecond electric pulse, as induced by experimentally observed subpicosecond charge separation, the polaron is displaced by up to hundreds of lattice sites before the electron becomes delocalised. We discuss biophysical implications of our results.

Strain relaxation and epitaxial relationship of perylene overlayer on Ag(110).

We present a room temperature STM study of perylene self-assembly on Ag(110) beyond the monolayer coverage regime. Coupling of the perylene aromatic boards yields π-π bonded stacks. The perylene stacks self-assemble into a continuous three-dimensional epitaxial overlayer of (3 × 5) symmetry. The self-assembly is driven by thermodynamic balance established under coupling of the intra- and intermolecular interactions and the molecule-substrate interaction all accommodating the short-range thermal motion of the constituent molecules. The balance bestows to the overlayer the unique ability to accommodate the underlying substrate morphology and to spread over the surface steps as a single structure preserving its lateral order and keeping epitaxial relationship with every surface terrace. The complete epitaxy is driven by (i) anchoring of half of the perylene stacks into specific adsorption sites on each terrace, (ii) interlacing of the perylene stacks across the steps within the entire H-bonded network, and (iii) relaxation of the overlayer strain via enhancement of the overlayer-specific vibrational modes and short-range thermal motion of the constituent molecules. This complete epitaxy phenomenon is described via (i) structural and statistical analysis of the molecularly resolved STM topographies, (ii) monitoring of the short-range molecular displacements under the strain relaxation, (iii) highlighting of specific intra-molecular and inter-molecular vibration modes through detailed analysis of HREELS spectra, and (iv) parametrization of the intermolecular interaction via pair potential calculation.

Spectroscopy of Proton Coordination with Ethylenediamine.

Protonated ethylenediamine monomer, dimer, and trimer were produced in the gas phase by an electrical discharge/supersonic expansion of argon seeded with ethylenediamine (C2H8N2, en) vapor. Infrared spectra of these ions were measured in the region from 1000 to 4000 cm-1 using laser photodissociation and argon tagging. Computations at the CBS-QB3 level were performed to explore possible isomers and understand the infrared spectra. The protonated monomer exhibits a gauche conformation and an intramolecular hydrogen bond. Its parallel shared proton vibration occurs as a broad band around 2785 cm-1, despite the formally equivalent proton affinities of the two amino groups involved, which usually leads to low frequency bands. The barrier to intramolecular proton transfer is 2.2 kcal mol-1 and does not vanish upon addition of the zero-point energy, unlike the related protonated ammonia dimer. The structure of the dimer is formed by chelation of the monomer's NH3+ group, thereby localizing the excess proton and increasing the frequency of the intramolecular shared proton vibration to 3157 cm-1. Other highly fluxional dimer structures with facile intermolecular proton transfer and concomitant structural reorganization were computed to lie within 2 kcal mol-1 of the experimentally observed structure. The spectrum of the trimer is rather diffuse, and a clear assignment is not possible. However, an isomer with an intramolecular proton transfer like that of the monomer is most consistent with the experimental spectrum.

Terahertz-infrared spectroscopy of Shewanella oneidensis MR-1 extracellular matrix.

Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000cm-1 in the temperature range from 5 to 300K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300cm-1 and mainly determine the terahertz absorption. When cooled down to liquid helium temperatures, the bands in Shewanella oneidensis MR-1 and cytochrome c reveal a distinct fine structure. In all three materials, we identify the presence of liquid bound water in the form of librational and translational absorption bands at ≈200 and ≈600cm-1, respectively. The sharp excitations seen above 1000cm-1 are assigned to intramolecular vibrations.

Pressure tuning of light-induced superconductivity in K3C60.

Optical excitation at terahertz frequencies has emerged as an effective means to dynamically manipulate complex materials. In the molecular solid K3C60, short mid-infrared pulses transform the high-temperature metal into a non-equilibrium state with the optical properties of a superconductor. Here we tune this effect with hydrostatic pressure and find that the superconducting-like features gradually disappear at around 0.3 GPa. Reduction with pressure underscores the similarity with the equilibrium superconducting phase of K3C60, in which a larger electronic bandwidth induced by pressure is also detrimental for pairing. Crucially, our observation excludes alternative interpretations based on a high-mobility metallic phase. The pressure dependence also suggests that transient, incipient superconductivity occurs far above the 150 K hypothesised previously, and rather extends all the way to room temperature.

Solar Selective Volumetric Receivers for Harnessing Solar Thermal Energy

Given the largely untapped solar energy resource, there has been an ongoing international effort to engineer improved solar-harvesting technologies. Toward this, the possibility of engineering a solar selective volumetric receiver (SSVR) has been explored in the present study. Common heat transfer liquids (HTLs) typically have high transmissivity in the visible-near infrared (VIS-NIR) region and high emission in the midinfrared region, due to the presence of intramolecular vibration bands. This precludes them from being solar absorbers. In fact, they have nearly the opposite properties from selective surfaces such as cermet, TiNOX, and black chrome. However, liquid receivers which approach the radiative properties of selective surfaces can be realized through a combination of anisotropic geometries of metal nanoparticles (or broad band absorption multiwalled carbon nanotubes (MWCNTs)) and transparent heat mirrors. SSVRs represent a paradigm shift in the manner in which solar thermal energy is harnessed and promise higher thermal efficiencies (and lower material requirements) than their surface absorption-based counterparts. In the present work, the “effective” solar absorption to infrared emission ratio has been evaluated for a representative SSVR employing copper nanospheroids/MWCNTs and Sn-In2O3 based heat mirrors. It has been found that a solar selectivity comparable to (or even higher than) cermet-based Schott receiver is achievable through control of the cut-off solar selective wavelength. Theoretical calculations show that the thermal efficiency of Sn-In2O3 based SSVR is 6–7% higher than the cermet-based Schott receiver. Furthermore, stagnation temperature experiments have been conducted on a laboratory-scale SSVR to validate the theoretical results. It has been found that higher stagnation temperatures (and hence higher thermal efficiencies) compared to conventional surface absorption-based collectors are achievable through proper control of nanoparticle concentration.

Quantum chemical approach for condensed-phase thermochemistry (V): Development of rigid-body type harmonic solvation model

This letter proposes an approximate treatment of the harmonic solvation model (HSM) assuming the solute to be a rigid body (RB-HSM). The HSM method can appropriately estimate the Gibbs free energy for condensed phases even where an ideal gas model used by standard quantum chemical programs fails. The RB-HSM method eliminates calculations for intra-molecular vibrations in order to reduce the computational costs. Numerical assessments indicated that the RB-HSM method can evaluate entropies and internal energies with the same accuracy as the HSM method but with lower calculation costs.

Impact of undamped and damped intramolecular vibrations on the efficiency of photosynthetic exciton energy transfer

In recent years, the role of molecular vibrations in exciton energy transfer taking place during the first stage of photosynthesis attracted increasing interest. Here, we present a model formulated as a Lindblad-type master equation that enables us to investigate the impact of undamped and especially damped intramolecular vibrational modes on the exciton energy transfer, particularly its efficiency. Our simulations confirm the already reported effects that the presence of an intramolecular vibrational mode can compensate the energy detuning of electronic states, thus promoting the energy transfer; and, moreover, that the damping of such a vibrational mode (in other words, vibrational relaxation) can further enhance the efficiency of the process by generating directionality in the energy flow. As a novel result, we show that this enhancement surpasses the one caused by pure dephasing, and we present its dependence on various system parameters (time constants of the environment-induced relaxation and excitation processes, detuning of the electronic energy levels, frequency of the intramolecular vibrational modes, Huang–Rhys factors, temperature) in dimer model systems. We demonstrate that vibrational-relaxation-enhanced exciton energy transfer (VREEET) is robust against the change of these characteristics of the system and occurs in wide ranges of the investigated parameters. With simulations performed on a heptamer model inspired by the Fenna–Matthews–Olson (FMO) complex, we show that this mechanism can be even more significant in larger systems at T = 300 K. Our results suggests that VREEET might be prevalent in light-harvesting complexes.

Vibrational and Thermal Properties of Oxyanionic Crystals

The vibrational and thermal properties of dolomite and alkali chlorates and perchlorates were studied in the gradient approximation of density functional theory using the method of a linear combination of atomic orbitals (LCAO). Long-wave vibration frequencies, IR and Raman spectra, and mode Gruneisen parameters were calculated. Equation-of-state parameters, thermodynamic potentials, entropy, heat capacity, and thermal expansion coefficient were also determined. The thermal expansion coefficient of dolomite was established to be much lower than for chlorates and perchlorates. The temperature dependence of the heat capacity at T > 200 K was shown to be generally governed by intramolecular vibrations.

Terahertz spectroscopy of 2,4,6-trinitrotoluene molecular solids from first principles.

We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional theory that includes Tkatchenko–Scheffler pair-wise dispersion interactions. Furthermore, we show that for these polymorphs the theoretical results are only weakly affected by many-body dispersion contributions. The absence of dispersion interactions, however, causes sizable shifts in vibrational frequencies and directly affects the spatial character of the vibrational modes. Mode assignment allows for a distinction between the contributions of the monoclinic and orthorhombic polymorphs and shows that modes in the range from 0 to ca. 3.3 THz comprise both inter- and intramolecular vibrations, with the former dominating below ca. 1.5 THz. We also find that intramolecular contributions primarily involve the nitro and methyl groups. Finally, we present a prediction for the terahertz spectrum of 1,3,5-trinitrobenzene, showing that a modest chemical change leads to a markedly different terahertz spectrum.

Increase in Dynamical Collectivity and Directionality of Orange Carotenoid Protein in the Photo-Protective State

Photo-protection is crucial for photosynthesis efficiency. Cyanobacteria have evolved a unique photo-protection mechanism mediated by Orange Carotenoid Protein (OCP). OCP binds a single ketocarotenoid as the chromophore, essential to its photo-protective function. Under strong green-blue (or white) illumination or high chaotrope concentration, OCP converts from the orange state OCPO to the activated or photo-protective red state OCPR. The OCPR facilitates dissipation of excess energy via direct interaction with allophycocyanin (APC) cores of the light-harvesting antenna Phycobilisome (PB). Picosecond intramolecular dynamics are critical to the photo-protective conformational switching, energy transfer between the APC and OCP, and energy dissipation. In particular intramolecular vibrations at THz frequencies can both provide efficient access to intermediate state conformations and couple to embedded chromophore vibrations for energy dissipation. Here we characterize global picosecond flexibility using temperature dependent terahertz spectroscopy on OCP solutions. The THz absorbance decreases and structural resilience increases in the photoactive state. The dynamical turn on temperature for picosecond dynamics shifts from 200K in OCPO to 250K in OCPR, signifying a substantial increase in vibrational collectivity and structural stability. To characterize the nature of the intramolecular vibrations in more detail, we employ our recently developed technique Polarization-Varying Anisotropic Terahertz Microscopy (PV-ATM). The technique isolates specific vibrational bands associated with long range collective motions of the protein structure. For the first time we demonstrate intramolecular vibrational changes with photoexcitation. In particular we find an increase in vibrational directionality in the photo-activated OCP in the 60-72 cm−1 and 85-100 cm−1 bands. In addition, the orientation of the vibrational motions switches for the 38-48 cm−1 band. We suggest that the increased dynamical collectivity and directionality changes with photo-state contribute to OCP efficiently binding and interacting with the APC complex to optimize photo-protective function.

Excited State Properties of a Thermally Activated Delayed Fluorescence Molecule in Solid Phase Studied by Quantum Mechanics/Molecular Mechanics Method

Excited state properties of a thermally activated delayed fluorescence molecule (4-(10H-phenoxazin-10-yl)phenyl)(dibenzo[b,d]thiophen-2-yl)methanone (DBT-BZ-PXZ) are theoretically studied in liquid (tetrahydrofuran (THF)) and solid phases, respectively. Solvent environment in THF is considered by polarizable continuum model (PCM) and the molecule in solid phase is investigated by a combined quantum mechanics and molecular mechanics (QM/MM) method. Results show that the geometrical changes between ground state (S0) and lowest singlet excited state (S1) are hindered in solid phase by the restricted intramolecular rotation (RIR) and restricted intramolecular vibration (RIV) effects, which brings smaller values of Huang–Rhys (HR) factors and reorganization energies compared to those in liquid phase. Thus, nonradiative energy consumptions are suppressed and enhanced fluorescent efficiency is found in solid phase. The calculated prompt fluorescence efficiency (ΦPrompt) and delayed fluorescence efficiency (ΦTADF...