Intramolecular Redistribution Research Articles

Electrochemical Analysis in Charge-Transfer Science: Polarity at Electrode Surfaces Affect Electrochemical Analyses for Charge-Transfer Systems

Electrochemical analysis is a vital component of the science of charge transfer (CT), and its importance cannot be overstated. Many fields, including energy science, photoredox and electrocatalysis, biomedical sensor development, environmental engineering, and electronics, rely heavily on CT and require accurate electrochemistry. [Phys. Chem. Chem. Phys. 2020, 22, 21583-21629] As a result, it is critical to pay close attention to the details of collecting, implementing, and interpreting electrochemical results to advance this broad field of science and engineering. [Current Opinion in Electrochemistry 2022, 31, 100862]The interfaces of an electrochemical cell present specific challenges for the interpretation and applicability of the analysis. The polarity of the medium on the electrode surface is not the same as the polarity of the bulk medium, and this has a significant influence on the behavior of charged and dipole species. Solvation in a condensed medium controls the dynamics of processes involving CT, including intramolecular redistribution of electron density. Polarity affects several properties of solvated species, including solubility, reactivity, electrochemical potential, and spectral transitions. [J. Phys. Chem. B 2023, 127, 6, 1443–1458]To understand changes in electrochemical potential during oxidation and reduction, it is important to analyze the relationship between the bulk electrolyte concentration and the Born microenvironmental polarity experienced by the species analyzed in the diffuse Helmholtz layer and at the surface of the working electrode during the heterogeneous steps of CT. This analysis can be used to assess the polarity experienced by redox species on the surface of polarizing working electrodes.Another critical issue in electrochemical analysis is the liquid junction that connects two different solutions, typically through a porous medium. Differences in the transport properties and activity of ions on both sides of the junction create a potential, known as the liquid potential (ELJ), which contributes to the measured voltage. To minimize ELJs, a miscible solvent solution and an electrolyte composed of ions with the same mobility throughout the transition can be used. ELJs can also be eliminated using a cell configuration with a pseudo-reference electrode that does not contain a liquid interface. However, the potential of pseudo-reference electrodes depends on the composition of the sample solution in which they are immersed, so care must be taken when interpreting the measured values.Overall, electrochemical analysis is a complex and critical part of CT science, and its accurate implementation is essential in advancing this broad field of science and engineering. Understanding the influence of the polarity of the medium, the relationship between the bulk electrolyte concentration and the Born microenvironmental polarity, and the liquid junction is crucial for interpreting electrochemical results and evaluating CT thermodynamics.

Remote regulation on the hydration sites of adenine molecules via derivatization

Hydration, as a ubiquitous and vital phenomenon in nature, has attracted great attention in the field of surface science concerning the fundamental interactions between water and organic molecules. However, the role of functional group derivatization is still elusive in terms of its potential impact on hydration. By the combination of high-resolution scanning tunneling microscopy imaging and density functional theory calculations, the hydration of 9mA molecules was realized on Au(111) in real space, forming 9mA–H2O–9mA structures. In comparison with the hydration of adenine molecules, methyl derivatization is experimentally found to remotely regulate the hydration sites from the imidazole ring to the pyrimidine ring and is further theoretically revealed to allow intramolecular electron redistribution and, therefore, steer the priority of the hydration sites. These results provide sub-molecular understandings of the relationship between derivatization and hydration, which would shed light on the regulation of hydration processes in chemically and biologically related systems.

Electronic-state chaos, intramolecular electronic energy redistribution, and chemical bonding in persisting multidimensional nonadiabatic systems.

We study the chaotic, huge fluctuation of electronic state, resultant intramolecular energy redistribution, and strong chemical bonding surviving the fluctuation with exceedingly long lifetimes of highly excited boron clusters. Those excited states constitute densely quasi-degenerate state manifolds. The huge fluctuation is induced by persisting multidimensional nonadiabatic transitions among the states in the manifold. We clarify the mechanism of their coexistence and its physical significance. In doing so, we concentrate on two theoretical aspects. One is quantum chaos and energy randomization, which are to be directly extracted from the properties of the total electronic wavefunctions. The present dynamical chaos takes place through frequent transitions from adiabatic states to others, thereby making it very rare for the system to find dissociation channels. This phenomenon leads to the concept of what we call intramolecular nonadiabatic electronic-energy redistribution, which is an electronic-state generaliztion of the notion of intramolecular vibrational energy redistribution. The other aspect is about the peculiar chemical bonding. We investigate it with the energy natural orbitals (ENOs) to see what kind of theoretical structures lie behind the huge fluctuation. The ENO energy levels representing the highly excited states under study appear to have four robust layers. We show that the energy layers responsible for chaotic dynamics and those for chemical bonding are widely separated from each other, and only when an event of what we call "inter-layer crossing" happens to burst can the destruction of these robust energy layers occur, resulting in molecular dissociation. This crossing event happens only rarely because of the large energy gaps between the ENO layers. It is shown that the layers of high energy composed of complex-valued ENOs induce the turbulent flow of electrons and electronic-energy in the cluster. In addition, the random and fast time-oscillations of those high energy ENOs serve as a random force on the nuclear dynamics, which can work to prevent a concentration of high nuclear kinetic energy in the dissociation channels.

Методика расчета синтетических спектров излучения триплетных состояний молекулярного азота в полярных сияниях

A method for calculating synthetic emission spectra of systems of triplet levels of molecular nitrogen is presented: Vegard- VK N2(A^3 Σ_u^+→X^1 Σ_g^+), the first positive system 1PG N2(〖 B〗^3 Π_g→A^3 Σ_u^+), the second positive system 2PG N2(C^3 Π_u→B^3 Π_g). The individual structures of the corresponding molecules are taken into account. The populations of the vibrational levels of the triplet states are calculated taking into account the energy transfer between triplet levels in collisional reactions and the intramolecular redistribution of energy. Examples of calculation of synthetic spectra are presented.

Bond Bundle Analysis of Ketosteroid Isomerase.

Bond bundle analysis is used to investigate enzymatic catalysis in the ketosteroid isomerase (KSI) active site. We identify the unique bonding regions in five KSI systems, including those exposed to applied oriented electric fields and those with amino acid mutations, and calculate the precise redistribution of electron density and other regional properties that accompanies either enhancement or inhibition of KSI catalytic activity. We find that catalytic enhancement results from promoting both inter- and intra-molecular electron density redistribution, between bond bundles and bond wedges within the KSI-docked substrate molecule, in the forward direction of the catalyzed reaction. Though the redistribution applies to both types of perturbed systems and is thus suggestive of a general catalytic role, we observe that bond properties (e.g., volume vs energy vs electron count) can respond independently and disproportionately depending on the type of perturbation. We conclude that the resulting catalytic enhancement/inhibition proceeds via different mechanisms, where some bond properties are utilized more by one type of perturbation than the other. Additionally, we find that the correlations between bond wedge properties and catalyzed reaction barrier energies are additive to predict those of bond bundles and atomic basins, providing a rigorous grounding for connecting changes in local charge density to resulting shifts in reaction barrier energy.

Exciton Spatial Dynamics and Self-Trapping in Carbon Nanocages.

Three-dimensional cage-shaped molecules formed from chainlike structures hold potential as unique optoelectronic materials and host compounds. Their optical, structural, and dynamical features are tunable by changes in shape and size. We perform a comparison of these properties for three sizes of strained conjugated [n.n.n]carbon nanocages composed of three paraphenylene chains (bridges) of length n = 4, 5, or 6. The exciton intramolecular redistribution occurring during nonradiative relaxation has been explored using nonadiabatic excited-state molecular dynamics. Our results provide atomistic insight into the conformational features associated with the observed red- and blue-shift trends in the absorption and fluorescence spectra, respectively, with increasing nanocage size. Their internal conversion processes involve intramolecular energy transfer that leads to exciton self-trapping on a few phenylene units at the center of a single bridge. The dependence of these dynamical features on the size of the nanocage can be used to tune their host-guest chemical properties and their use for organic electronics and catenane-like applications.

Multiorbital antiferromagnetic metal induced by intramolecular self-doping

The authors examine the spin and charge states in a multiorbital system through orbital selective NMR spectroscopy combined with fine-structure-resolvable synchrotron X-ray diffractometry. The results show an intramolecular electron redistribution leading to interorbital self-doping

Synthesis and Cyclization-Induced Charge Transfer of Rectangular Bisterthiophenesiloxanes.

Cyclization-modified terthiophene displays the change of emission behavior from locally excited (LE) to the intramolecular charge transfer (ICT) state. The rectangular bisterthiophenesiloxanes (DSiTh) was successfully prepared by π-π-stacking-aided hydrogen-bonding interactions. Cyclization-induced ICT in DSiTh could be observed, which was confirmed by absorption spectra, fluorescence spectra, and quantum chemistry analysis. The cyclization produces a strong intramolecular electron redistribution of a highly packed π-conjugated terthiophene. Thus, a distinctive variation of the dipole moment and a through-space ICT happen.

Time‐resolved Raman spectroscopy for shock‐driven intramolecular electron redistribution of cyclotrimethylene trinitramine (RDX)

AbstractShock‐driven intramolecular electron redistribution (IER) of cyclotrimethylene trinitramine (RDX) is proposed, which will be helpful for understanding the initiation and safety mechanisms of RDX materials under shock compressions. Laser‐driven shock wave was performed to generate a dynamic pressure, and time‐resolved Raman spectroscopy was used to probe the shock wave response of RDX. First‐principle calculations were utilized to identify Raman modes and determine a pressure‐dependent electron density distribution in RDX molecules. Raman peaks of RDX have blue shifts under shock loadings, which are caused by IER. According to calculations, it can be confirmed that electrons transfer from C–H and N–O bonds to N–N bonds under shock loadings in IER. We suggest that shock‐driven IER will make some chemical bonds be broken more easily under shock conditions.

Palladium‐Catalyzed Decarbonylative Trifluoromethylation of Acid Fluorides

AbstractWhile acid fluorides can readily be made from widely available or biomass‐feedstock‐derived carboxylic acids, their use as functional groups in metal‐catalyzed cross‐coupling reactions is rare. This report presents the first demonstration of Pd‐catalyzed decarbonylative functionalization of acid fluorides to yield trifluoromethyl arenes (ArCF3). The strategy relies on a Pd/Xantphos catalytic system and the supply of fluoride for transmetalation through intramolecular redistribution to the the Pd center. This strategy eliminated the need for exogenous and detrimental fluoride additives and allows Xantphos to be used in catalytic trifluoromethylations for the first time. Our experimental and computational mechanistic data support a sequence in which transmetalation by R3SiCF3 occurs prior to decarbonylation.

Palladium-Catalyzed Decarbonylative Trifluoromethylation of Acid Fluorides.

While acid fluorides can readily be made from widely available or biomass‐feedstock‐derived carboxylic acids, their use as functional groups in metal‐catalyzed cross‐coupling reactions is rare. This report presents the first demonstration of Pd‐catalyzed decarbonylative functionalization of acid fluorides to yield trifluoromethyl arenes (ArCF3). The strategy relies on a Pd/Xantphos catalytic system and the supply of fluoride for transmetalation through intramolecular redistribution to the the Pd center. This strategy eliminated the need for exogenous and detrimental fluoride additives and allows Xantphos to be used in catalytic trifluoromethylations for the first time. Our experimental and computational mechanistic data support a sequence in which transmetalation by R3SiCF3 occurs prior to decarbonylation.

Kinetic Study of Thermal Degradation of Polydimethylsiloxane: The Effect of Molecular Weight on Thermal Stability in Inert Atmosphere

Thermal degradation of polydimethylsiloxane (PDMS) of different molecular weights in inert and oxygen atmosphere is studied and discussed in detail. PDMS samples of different molecular weights were prepared by anionically initiated ring-opening polymerization of octamethylcyclotetrasiloxane in emulsion. The molecular weight of PDMS drastically affected the shape of TGA curve at higher temperatures when thermogravimetric (TGA) measurements were performed in the inert atmosphere. The thermal stability of PDMS decreased with increasing the average molecular weight of the sample, which could be explained by prevailing unzipping mechanism at lower molecular weights over intramolecular and intermolecular redistribution, which were more important at higher molecular weights. On the other hand, experiments in oxygen atmosphere showed zero effect of polydimethylsiloxane molecular weight on its thermal stability. In addition, a kinetic model describing the thermal degradation of PDMS in inert atmosphere as a function of PDMS molecular weight was proposed. The proposed kinetic model was composed of diffusion-limited kinetics step related to evaporation rates of the degradation products and of rate-determined step related to the formation of cyclic degradation products. As a result of mathematical modeling by fitting the calculated data to experimental data kinetic parameters were derived properly.

Non-radiative relaxation of photoexcited chlorophylls: theoretical and experimental study.

Nonradiative relaxation of high-energy excited states to the lowest excited state in chlorophylls marks the first step in the process of photosynthesis. We perform ultrafast transient absorption spectroscopy measurements, that reveal this internal conversion dynamics to be slightly slower in chlorophyll B than in chlorophyll A. Modeling this process with non-adiabatic excited state molecular dynamics simulations uncovers a critical role played by the different side groups in the two molecules in governing the intramolecular redistribution of excited state wavefunction, leading, in turn, to different time-scales. Even given smaller electron-vibrational couplings compared to common organic conjugated chromophores, these molecules are able to efficiently dissipate about 1 eV of electronic energy into heat on the timescale of around 200 fs. This is achieved via selective participation of specific atomic groups and complex global migration of the wavefunction from the outer to inner ring, which may have important implications for biological light-harvesting function.

Vibrationally Coherent Preparation of the Transition State for Photoisomerization of the Cyanine Dye Cy5 in Water

Femtosecond pump-continuum probe spectroscopy with impulsive excitation was employed to observe coherent wavepacket motions of the cyanine dye Cy5 in water that promote photoisomerization after optical preparation of the first excited singlet state, S1. The chief component in the excited-state vibrational coherence is a resonance Raman-inactive, 273 cm(-1) mode of mixed carbon-carbon bond length alternation and out-of-plane or twisting character. The ultrafast (30 fs) damping of these motions arises from trajectories that irreversibly cross the transition state barrier; after several recurrences to the transition state region, vibrational cooling traps a significant fraction of the excited-state molecules in the planar, Franck-Condon region of the potential energy surface. Motion in the 273 cm(-1) promoting mode is apparently launched by a change in conformation of the conjugated polyene backbone during the first few vibrations of the high-frequency C-C and C═C bond length alternation coordinates that principally contribute to the initial displacement from the Franck-Condon structure. To our knowledge, this work provides the first direct observations of the intramolecular redistribution of excited-state potential energy into reactive motions that are rapidly damped by transition state barrier-crossing events leading to photoisomerization in a conjugated polyene. These results provide insight into the vibrational dynamics that contribute to the photoisomerization of retinal protonated Schiff bases in the rhodopsins and to the formation of intramolecular charge transfer character in carotenoids in photosynthetic light-harvesting proteins.

Applicability of the protein environment equilibrium approximation for describing ultrafast biophysical processes

The theoretical description of ultrafast processes in biological systems, in particular, electron transfer in photosynthetic reaction centers, is an important problem in modern biological physics. Because these processes occur in a protein medium with which an energy exchange is possible, methods of the quantum theory of open systems must be used to describe them. But because of a high process rate and the specifics of the protein environment, basic approximations of this theory might be inapplicable. We study the applicability of the approximation of the protein environment (bath) state invariance for the dissipative dynamics of charge transfer between molecule-pigments contained in reaction centers. For this, we use model systems whose parameters are close to real ones. We conclude that this approximation can be used to describe both the monotonic and the oscillating dynamics of the reaction subsystem in large biological molecules. We consider various mechanisms for bath thermalization and show that the bath thermalization occurs not because of the intramolecular redistribution of the vibrational energy in it but because of its coupling to the reaction subsystem.

Solvation-driven charge transfer and localization in metal complexes.

ConspectusIn any physicochemical process in liquids, the dynamical response of the solvent to the solutes out of equilibrium plays a crucial role in the rates and products: the solvent molecules react to the changes in volume and electron density of the solutes to minimize the free energy of the solution, thus modulating the activation barriers and stabilizing (or destabilizing) intermediate states. In charge transfer (CT) processes in polar solvents, the response of the solvent always assists the formation of charge separation states by stabilizing the energy of the localized charges. A deep understanding of the solvation mechanisms and time scales is therefore essential for a correct description of any photochemical process in dense phase and for designing molecular devices based on photosensitizers with CT excited states.In the last two decades, with the advent of ultrafast time-resolved spectroscopies, microscopic models describing the relevant case of polar solvation (where both the solvent and the solute molecules have a permanent electric dipole and the mutual interaction is mainly dipole–dipole) have dramatically progressed. Regardless of the details of each model, they all assume that the effect of the electrostatic fields of the solvent molecules on the internal electronic dynamics of the solute are perturbative and that the solvent–solute coupling is mainly an electrostatic interaction between the constant permanent dipoles of the solute and the solvent molecules. This well-established picture has proven to quantitatively rationalize spectroscopic effects of environmental and electric dynamics (time-resolved Stokes shifts, inhomogeneous broadening, etc.). However, recent computational and experimental studies, including ours, have shown that further improvement is required.Indeed, in the last years we investigated several molecular complexes exhibiting photoexcited CT states, and we found that the current description of the formation and stabilization of CT states in an important group of molecules such as transition metal complexes is inaccurate. In particular, we proved that the solvent molecules are not just spectators of intramolecular electron density redistribution but significantly modulate it.Our results solicit further development of quantum mechanics computational methods to treat the solute and (at least) the closest solvent molecules including the nonperturbative treatment of the effects of local electrostatics and direct solvent–solute interactions to describe the dynamical changes of the solute excited states during the solvent response.

On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent.

Ribonucleic acid (RNA) modifications play an important role in the regulation of gene expression and the development of RNA-based therapeutics, but their identification, localization and relative quantitation by conventional biochemical methods can be quite challenging. As a promising alternative, mass spectrometry (MS) based approaches that involve RNA dissociation in ‘top-down’ strategies are currently being developed. For this purpose, it is essential to understand the dissociation mechanisms of unmodified and posttranscriptionally or synthetically modified RNA. Here, we have studied the effect of select nucleobase, ribose and backbone modifications on phosphodiester bond cleavage in collisionally activated dissociation (CAD) of positively and negatively charged RNA. We found that CAD of RNA is a stepwise reaction that is facilitated by, but does not require, the presence of positive charge. Preferred backbone cleavage next to adenosine and guanosine in CAD of (M+nH)n+ and (M−nH)n− ions, respectively, is based on hydrogen bonding between nucleobase and phosphodiester moieties. Moreover, CAD of RNA involves an intermediate that is sufficiently stable to survive extension of the RNA structure and intramolecular proton redistribution according to simple Coulombic repulsion prior to backbone cleavage into c and y ions from phosphodiester bond cleavage.

Dynamics of rhenium photocatalysts revealed through ultrafast multidimensional spectroscopy.

Rhenium catalysts have shown promise to promote carbon neutrality by reducing a prominent greenhouse gas, CO2, to CO and other starting materials. Much research has focused on identifying intermediates in the photocatalysis mechanism as well as time scales of relevant ultrafast processes. Recent studies have implemented multidimensional spectroscopies to characterize the catalyst's ultrafast dynamics as it undergoes the many steps of its photocycle. Two-dimensional infrared (2D-IR) spectroscopy is a powerful method to obtain molecular structure information while extracting time scales of dynamical processes with ultrafast resolution. Many observables result from 2D-IR experiments including vibrational lifetimes, intramolecular redistribution time scales, and, unique to 2D-IR, spectral diffusion, which is highly sensitive to solute-solvent interactions and motional dynamics. Spectral diffusion, a measure of how long a vibrational mode takes to sample its frequency space due to multiple solvent configurations, has various contributing factors. Properties of the solvent, the solute's structural flexibility, and electronic properties, as well as interactions between the solvent and solute, complicate identifying the origin of the spectral diffusion. With carefully chosen experiments, however, the source of the spectral diffusion can be unveiled. Within the context of a considerable body of previous work, here we discuss the spectral diffusion of several rhenium catalysts at multiple stages in the catalysis. These studies were performed in multiple polar liquids to aid in discovering the contributions of the solvent. We also performed electronic ground state 2D-IR and electronic excited state transient-2D-IR experiments to observe how spectral diffusion changes upon electronic excitation. Our results indicate that with the original Lehn catalyst in THF, relative to the ground state, the spectral diffusion slows by a factor of 3 in the equilibrated triplet metal-to-ligand charge transfer state. We attribute this slowdown to a decrease in dielectric friction as well as an increase in molecular flexibility. It is possible to partially simulate the charge transfer by altering the electron density moderately by adding electron donating or withdrawing substituents symmetrically to the bipyridine ligand. We find that unlike the significant electronic structure change induced by MLCT, such small substituent effects do not influence the spectral diffusion. A solvent study in THF, DMSO, and CH3CN found there to be an explicit solvent dependence that we can correlate to the solvent donicity, which is a measure of its nucleophilicity. Future studies focused on the solvent effects on spectral diffusion in the crucial photoinitiated state can illuminate the role the solvent plays in the catalysis.

Intramolecular Vibrational Dynamics in Free Polyatomic Molecules with C═O Chromophore Bond Excited by Resonant Femtosecond IR Laser Radiation

In nine polyatomic molecules, we have studied the intramolecular redistribution of vibrational energy from chromophore C═O group excited by a resonant femtosecond IR laser radiation at a wavelength of ∼5 μm. All experiments have been performed in the gas phase using the IR-IR pump-probe technique in combination with the spectral analysis of the probe radiation. For molecules with one C═O end group, characteristic times of intramolecular vibrational redistribution (IVR) lie in the range between 2.4 and 20 ps and correlate with the density of four-frequency Fermi resonances. The IVR times in metal carbonyl molecules are anomalously long, being ∼1.0 ns for Fe(CO)5 and ∼1.5 ns for Cr(CO)6. In the CH3(C═O)OC2H5 and H2CCH(C═O)OC2H5 molecules, it has been observed that there are two characteristic IVR times, which differ by an order of magnitude from each other; this was interpreted in terms of the developed model of "accumulating states". For the ICF2COF molecule, it has been revealed that the IVR time decreases with increasing level of the vibrational excitation of the C═O bond of the molecule.

Dynamics of radiationless transitions in large molecules: 3. Decay of vibration-phonon states

The statistical operator of the ensemble of high-frequency intramolecular vibrations associated with the phonon reservoir depends on the phonon occupation numbers under thermal equilibrium conditions. The eigenvalues of energy of statistically averaged vibration-phonon (VP) states are complex quantities. In the case of weak VP coupling, only one- and two-phonon transitions are taken into consideration for calculating the decay rate constant, in which the difference of phonon energies compensates for the difference in energy between the initial and final intramolecular states. Although the fast evolution of amplitudes of VP states is due to intramolecular redistribution of energy and is not reduced to exponential decay of the initial state, the imaginary components of the eigenvalues coincide with those predicted by Fermi’s golden rule. The relative contribution of two-phonon (combination) transitions compared with one-phonon transitions increases with an increase in the density of intramolecular states and temperature, becoming prevalent for large molecules at T ≥ D ≫ Δ0 (D = 100–200 K (70–140 cm−1) is the Debye temperature and Δ0∼10 cm−1 is the spacing between neighboring intramolecular vibration levels). When T ≥ D, the decay rate constant is K ∝ T2.