Intramolecular Dynamics Research Articles

Theoretical Investigation on Proton Transfer Directionality and Dynamics Behavior of 3-(Benzo[d]thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde with Two Asymmetric Proton Acceptors.

A detailed theoretical investigation on the excited state intramolecular proton transfer (ESIPT) directionality and dynamics behavior of 3-(benzo[d]thiazol-2-yl)-2-hydroxy-5-methoxybenzaldehyde (BTHMB) with two unsymmetric proton acceptors (N and O2) has been performed. The hydrogen bond O1-H···N in BTHMB-a formed by the O1-H group with the N atom or O1-H···O2 in BTHMB-b formed by the O1-H group with the O2 atom is enhanced upon photoexcitation, and the strength of the O1-H···N bond is stronger, which will drive the O1-H proton to the N atom. Potential energy curves further confirm that ESIPT occurs in the N atom because of the smaller energy barrier (0.39 kcal/mol). Results of dynamics simulations manifest that no surface hopping exists between the S0 and S1 states within 300 fs, and ESIPT time constants of BTHMB-a and BTHMB-b are 48 and 151 fs, respectively. While the reverse ESIPT is observed in BTHMB-b at 294 fs, implying that the O1-H proton is transferred to the N atom instead of the O2 atom. The consistency of the calculated absorption (390 nm) and fluorescence spectra (443 and 602 nm) of BTHMB-a with the experimental values (390, 410, and 605 nm) confirms this conclusion again. The charge distribution analysis shows that the charge on the proton acceptors increases, and the O2 atom has higher electronegativity because it has more negative charges. The minimum surface electrostatic potential on the N atom in BTHMB-b correlating with the pKb value is -47.38 kcal/mol, indicating that the N atom has strong basicity. Therefore, the basicity of the N atom dominates the ESIPT process rather than the electronegativity of the O2 atom.

Rate-Engineered Plasmon-Enhanced Fluorescence for Real-Time Microsecond Dynamics of Single Biomolecules.

Single-molecule fluorescence has revealed a wealth of biochemical processes but does not give access to submillisecond dynamics involved in transient interactions and molecular dynamics. Here we overcome this bottleneck and demonstrate record-high photon count rates of >107 photons/s from single plasmon-enhanced fluorophores. This is achieved by combining two conceptual novelties: first, we balance the excitation and decay rate enhancements by the antenna's volume, resulting in maximum fluorescence intensity. Second, we enhance the triplet decay rate using a multicomponent surface chemistry that minimizes microsecond blinking. We demonstrate applications to two exemplary molecular processes: we first reveal transient encounters and hybridization of DNA with a 1 μs temporal resolution. Second, we exploit the field gradient around the nanoparticle as a molecular ruler to reveal microsecond intramolecular dynamics of multivalent complexes. Our results pave the way toward real-time microsecond studies of biochemical processes using an implementation compatible with existing single-molecule fluorescence methods.

Comparative studies on the nature and kinetics of phase transitions in plastic crystals: Hydrogen-bonded adamantane derivatives

In this paper, the results of thermal, structural, and spectroscopic studies on 3-amino-1-adamantanol (3-NH2-1-OH-ADM) were discussed with those recently published for 1-hydroxyl and 1-amine derivatives of adamantane (1-OH-ADM, 1-NH2-ADM). Calorimetric measurements showed that the examined compound, like 1-NH2-ADM, is characterized by multiple thermal events in the thermogram measured on heating and cooling. Further X-ray diffraction, Fourier-transform infrared, and Raman spectroscopy investigations suggested that two of them correspond to the transition from the ordinary crystal (OC) to the plastic crystal (PC) phase I and the transition between two PC phases (PC(I) and PC(II)), while the third subtle one is rather not related to a phase transition. Interestingly, ambient pressure dielectric studies performed during heating and cooling cycles revealed changes in the imaginary and real parts of the complex dielectric permittivity at temperatures close to the temperatures of phase transitions detected by the calorimetry. Such behavior resembled that reported for 1-NH2-ADM. Finally, isothermal time-dependent dielectric and infrared studies, supported by the analysis of asynchronous 2D-IR correlation spectra, indicated that the first endothermic peak, visible in the thermogram of 3-NH2-1-OH-ADM over an enormously large temperature interval and related to the OC-PC(I) phase transition, similarly to the one, assigned to the PC(I)-PC(II) transition in 1-NH2-ADM, has a character of the kinetic process. Importantly, during the annealing of 3-NH2-1-OH-ADM at T = 328–343 K, we observed a clear change in the dc-conductivity as well as intramolecular dynamics related to the vibrations of CH, NH2, and OH moieties that occur at different rates.

Intramolecular charge transfer dynamics of anthraquinone derivatives in the confined environments of reverse micelles

Reverse micelles (RMs) are considered important model systems for molecular dynamics and chemical reactions, where the nanopools of aqueous and nonaqueous polar cores are separated from the surrounding organic phase via a monolayer of surfactant molecules. Here, we report the intramolecular charge transfer (ICT) dynamics of anthraquinone derivatives in the methanol-in-oil RMs composed of nonionic surfactants Igepal by femtosecond transient absorption and fluorescence upconversion spectroscopy. The ICT dynamics slow down inside the RMs due to abnormally diminished solvent motions and restricted internal rotations of the (methyl)amino group during the ICT in the excited states. The micelle size-dependent dynamics of anthraquinone derivatives inside the RMs were compared with the results in bulk aliphatic alcohols and understood as the changes in the microenvironment properties such as microviscosity.

Ultrafast Excited-State Energy Transfer in Phenylene Ethynylene Dendrimer: Quantum Dynamics with the Tensor Network Method.

Photoinduced excited-state energy transfer (EET) processes play an important role in solar energy conversions. Owing to their excellent photoharvesting and exciton-transport properties, phenylene ethynylene (PE) dendrimers display great potential for improving the efficiency of solar cells. In this work, we investigated the intramolecular EET dynamics in a dendrimer composed of two linear PE units (2-ring and 3-ring) using a fully quantum description based on the tensor network method. We first constructed a diabatic model Hamiltonian based on the electronic structure calculations. Using this diabatic vibronic coupling model, we tried to obtain the main features of the EET dynamics in terms of the several diabatic models with different numbers of vibrational modes (from 4 modes to 129 modes) and to explore the corresponding vibronic coupling interactions. The results show that the EET in this PE dendrimer is ultrafast. Four modes of A' symmetry play dominant roles in the dynamics; the remaining 86 modes of A' symmetry can dampen the electronic coherence; and the modes of A″ symmetry do not exhibit significant influence on the EET process. Overall, the first-order intrastate vibronic coupling terms show the dominant role in the EET dynamics, while the second-order intrastate vibronic coupling terms cause damping of the electronic coherence and slow down the overall EET process. This work provides a microscopic understanding of the EET dynamics in PE dendrimers.

From breather soliton molecules to chaos in a laser cavity: the scenario of intermittent transitions.

Intermittency is widely observed in various nonlinear dynamical systems as an intriguing transient dynamic far from equilibrium. The internal dynamics formed by a pair of interacting optical solitons are often analogized to typical nonlinear systems. However, whether intermittency exists within the intramolecular motion remains to be investigated. Here, we study the intermittent dynamics of soliton molecules in ultrafast lasers, employing balanced optical cross-correlation techniques with sub-femtosecond temporal resolution. We demonstrate the occurrence of the bursting phase of intense variations of pulse separation within regular breather rhythms. In addition, we discover the intermittent transitions route to chaotic soliton molecules, facilitated by gain control. A series of analysis methods are used to assess the chaotic signals, providing compelling experimental evidence that soliton molecules can be analogized to their matter molecule counterparts. Our experimental findings shed light on the non-equilibrium intramolecular dynamics, providing insight into the transition of the attractors within interacting dissipative solitons in laser and fiber resonators.

Cross-hierarchical analysis of self-assembly dynamics in enzyme-treated rice gel during retrogradation

The purpose of this study was to elucidate the self-assembly dynamics of rice gel and their influence on the physical properties of enzyme-treated rice starch during storage using a cross-hierarchical analytical approach. Two enzymes, α-glucosidase (AG) and branching enzyme (BE), were used in this study. Changes in the physical properties of rice gel during storage showed that, compared to the control, the increase in G′ and G″ for AG-treated gels was lower during storage, and that the change in tanδ of AG-treated gels was lower at 0.1 Hz. Small angle X-ray scattering and ultra-small angle X-ray scattering analyses revealed that the radius of gyration of the primary aggregates was not affected by enzyme treatment, but that the rate of increase in the radius of gyration of secondary aggregates was faster in both enzyme-treated gels. Atomic force microscopy revealed that AG treatment changed the shape of the extended clusters, while BE treatment changed the connecting structure of the extended clusters. The results showed that AG and BE treatment affected the mesoscale intermolecular and intramolecular self-assembly dynamics of rice gel, causing changes in its physical properties.

Innovative lignin photocatalyst system motivated by intramolecular charge dynamics for H2O2 production

Lignin is the most abundant renewable resource with aromatic ring structures on earth, however, its intrinsic redox functional region for H2O2 production has not been fully identified due to the source diversity and structure complexity. Herein, the charge dynamics between the HOMO level with electron-donating capability and the LOMO level with electron-accepting capability are comprehensively clarified by using 14 types of customized lignin models as photocatalytic systems. The electron-transport patterns are modulated by the structure–activity relationship of effective oxygen-containing functional groups, including conjugation effects of methoxy groups, induced effects of hydroxyl or carbonyl groups, and ether bonds determining the overlap ratio of energy levels. A comprehensive evaluation and screening system is established to identify efficient lignin photocatalysts extracted from various sources and processes that are suitable for specific application scenarios, combined with theoretical calculations and molecular dynamics simulations. The fledgling H2O2 production efficiency is expected to be further improved through constructive guidance on interfering factors. The report on direct H2O2 production by O2 reduction and the action mechanism of the novel lignin photocatalyst will draw a new blueprint for the breakthrough of bio-photocatalytic functionalization.

Micro-second time-resolved X-ray single-molecule internal motions of SARS-CoV-2 spike variants

Single-molecule intramolecular dynamics were successfully measured for three variants of SARS-CoV-2 spike protein, alpha: B.1.1.7, delta: B.1.617, and omicron: B.1.1.529, with a time resolution of 100 μs using X-rays. The results were then compared with respect to the magnitude and directions of motions for the three variants. The largest 3-D intramolecular movement was observed for the omicron variant irrespective of ACE2 receptor binding. A more detailed analysis of the intramolecular motions revealed that the distribution state of intramolecular motion for the three variants was completely different with and without ACE2 receptor binding. The molecular dynamics for the trimeric spike protein of the omicron variant increased when ACE2 binding occurred. At that time, the diffusion constant increased from 71.0 [mrad2/ms] to 91.1 [mrad2/ms].

Thermodynamics of a hyperthermostable carboxylesterase from Anoxybacillus geothermalis D9

Hyperthermostable enzymes are highly desirable biocatalysts due to their exceptional stability at extreme temperatures. Recently, a hyperthermostable carboxylesterase EstD9 from Anoxybacillus geothermalis D9 was biochemically characterized. The enzyme exhibited remarkable stability at high temperature. In this study, we attempted to probe the conformational adaptability of EstD9 under extreme conditions via in silico approaches. Circular dichroism revealed that EstD9 generated new β-sheets at 80 °C, making the core of the hydrolase fold more stable. Interestingly, the profiles of molecular dynamics simulation showed the lowest scores of radius of gyration and solvent accessible surface area (SASA) at 80 °C. Three loops were responsible for protecting the catalytic site, which resided at the interface between the large and cap domains. To further investigate the structural adaptation in extreme conditions, the intramolecular interactions of the native structure were investigated. EstD9 revealed 18 hydrogen bond networks, 7 salt bridges, and 9 hydrophobic clusters, which is higher than the previously reported thermostable Est30. Collectively, the analysis indicates that intramolecular interactions and structural dynamics play distinct roles in preserving the overall EstD9 structure at elevated temperatures. This work is relevant to both fundamental and applied research involving protein engineering of industrial thermostable enzymes.

Probing H_{2} Double Ionization with Bicircular Laser Fields.

We present a kinematically complete study on strong-field double ionization of H_{2} molecules in two-color bicircular laser fields. The releasing times of electrons and protons are recorded with the double-hand attoclock. We observe the relative emission angles of two electrons oscillate with the kinetic energy release of protons, indicating the internal concerted four-body fragmentation. Using a three-dimensional molecular semiclassical ensemble model, we have disentangled the attosecond correlated electron emission in H_{2} double ionization. This work reveals the strong electron-nuclear coupling in the molecular bond breaking and may open up a new approach to experimentally accessing the intramolecular electron and bond dynamics with bicircular fields.

Synergistic Inter‐ and Intramolecular Aggregation of Dimeric Cyanine Dyes Affords Highly Efficient In Vivo Self‐Delivery and Photothermal Therapy

AbstractAdvancing photothermal therapy hinges on developing PTAs with robust in vivo delivery and therapeutic efficacy. However, effective molecular design approaches for high‐performance PTAs remain lacking. Herein a strategic design of dimeric heptamethine cyanine (Cy7) molecules is presented, covalently linked via ortho/meta/para‐phenyldithiol. These designs facilitate spontaneous nanoparticle assembly in water, attributed to efficient intermolecular aggregation, enhancing in vivo delivery. Additionally, aggregation between intramolecular Cy7 units promotes superior photothermal conversion efficiency (PCE) up to 74.1% for meta‐dimer. Remarkably, the para‐dimer variant not only achieves a high PCE of 61.1% but also exhibits the most effective pharmacokinetic profile, leading to unparalleled anticancer efficacy in vivo. This dual aggregation strategy, leveraging both inter‐ and intramolecular dynamics, equips dimeric Cy7 with superior self‐delivery and photothermal efficacy, offering a promising approach for the next generation of photothermal therapeutics.

Light-induced intramolecular domain dynamics of light-harvesting protein LH1-RC observed by the diffracted X-ray blinking method

Light-induced intramolecular domain dynamics of light-harvesting protein LH1-RC observed by the diffracted X-ray blinking method

Tuning the Softness of the Pendant Arms and the Polyazamacrocyclic Backbone to Chelate the 203Pb/212Pb Theranostic Pair.

A series of macrocyclic ligands were considered for the chelation of Pb2+: 1,4,7,10-tetrakis[2-(methylsulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (DO4S), 1,4,7-tris[2-(methylsulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane (DO3S), 1,4,7-tris[2-(methylsulfanyl)ethyl]-10-acetamido-1,4,7,10-tetraazacyclododecane (DO3SAm), 1,7-bis[2-(methylsulfanyl)ethyl]-1,4,7,10-tetraazacyclododecane-4,10-diacetic acid (DO2A2S), 1,5,9-tris[2-(methylsulfanyl)ethyl]-1,5,9-triazacyclododecane (TACD3S), 1,4,7,10-tetrakis[2-(methylsulfanyl)ethyl]-1,4,7,10-tetrazacyclotridecane (TRI4S), and 1,4,8,11-tetrakis[2-(methylsulfanyl)ethyl]-1,4,8,11-tetrazacyclotetradecane (TE4S). The equilibrium, the acid-mediated dissociation kinetics, and the structural properties of the Pb2+ complexes formed by these chelators were examined by UV-Visible and nuclear magnetic resonance (NMR) spectroscopies, combined with potentiometry and density functional theory (DFT) calculations. The obtained results indicated that DO4S, DO3S, DO3SAm, and DO2A2S were able to efficiently chelate Pb2+ and that the most suitable macrocyclic scaffold for Pb2+ is 1,4,7,10-tetrazacyclododecane. NMR spectroscopy gave insights into the solution structures of the Pb2+ complexes, and 1H-207Pb interactions confirmed the involvement of S and/or O donors in the metal coordination sphere. Highly fluxional solution behavior was discovered when Pb2+ was coordinated to symmetric ligands (i.e., DO4S and DO2A2S) while the introduction of structural asymmetry in DO3S and DO3SAm slowed down the intramolecular dynamics. The ligand ability to chelate [203Pb]Pb2+ under highly dilute reaction conditions was explored through radiolabeling experiments. While DO4S and DO3S possessed modest performance, DO3SAm and DO2A2S demonstrated high complexation efficiency under mild reaction conditions (pH = 7, 5 min reaction time). The [203Pb]Pb2+ complexes' integrity in human serum over 24 h was appreciably good for [203Pb][Pb(DO4S)]2+ (80 ± 5%) and excellent for [203Pb][Pb(DO3SAm)]2+ (93 ± 1%) and [203Pb][Pb(DO2A2S)] (94 ± 1%). These results reveal the promise of DO2A2S and DO3SAm as chelators in cutting-edge theranostic [203/212Pb]Pb2+ radiopharmaceuticals.

Carbon-sulfur bond elongation as the promoting reaction coordinate in the efficient sub-nanosecond intersystem crossing in thianaphthene derivatives.

Thiophene derivatives have become integral to OLEDs, photovoltaics, and photodynamic therapy research. A deeper understanding of their excited state dynamics and electronic relaxation mechanisms is expected to provide important physical insights of direct relevance for these applications. In this study, thianaphthene (TN), 2-methylbenzothiophene (2MBT), and 3-methylbenzothiophene (3MBT) are investigated using femtosecond broadband transient absorption and steady-state spectroscopy techniques along with time-dependent density functional calculations in cyclohexane and acetonitrile. The photophysical properties and electronic relaxation mechanisms of these derivatives are elucidated. Small fluorescence quantum yields ranging from 0.4 to 1.1% are measured. It is demonstrated that excitation of TN at 290 nm leads primarily to intersystem crossing to the triplet manifold with a lifetime of 400 ± 15 ps in either solvent, whereas four- to twofold shorter intersystem crossing lifetimes are measured for 2MBT and 3MBT depending on whether cyclohexane or acetonitrile is used. Linear interpolation of internal coordinates evidence that elongation of the S-C bonds enables ultrafast intersystem crossing in these thiophene derivatives involving singlet and triplet states with ππ* and πσ* characters. Excitation at 266 nm results in an additional 5 ± 1 ps lifetime, which is assigned to intramolecular vibrational relaxation dynamics occurring in the excited singlet state.

Mechanistic Insights into Intramolecular Energy Transfer Dynamics in Photosensitizers for Triplet-Triplet Annihilation Upconversion

Mechanistic Insights into Intramolecular Energy Transfer Dynamics in Photosensitizers for Triplet-Triplet Annihilation Upconversion

The influence of hindered rotation on electron transfer and exchange interaction in triarylamine-triptycene-perylene diimide triads.

Stretched electron-donor-bridge-acceptor triads that exhibit intramolecular twisting degrees of freedom are capable of modulating exchange interaction (J) as well as electronic couplings through variable π-overlap at the linear bond links, affecting the rate constants of photoinduced charge separation and recombination. Here we present an in-depth investigation of such effects induced by methyl substituents leading to controlled steric hindrance of intramolecular twisting around biaryl axes. Starting from the parent structure, consisting of a triphenyl amine donor, a triptycene (TTC) bridge and a phenylene-perylene diimide acceptor (Me0), one of the two phenylene linkers attached to the TTC was ortho-substituted by two methyl groups (Me2, Me3), or both such phenylene linkers by two pairs of methyl groups (Me23). Photoinduced charge separation (kCS) leading to a charge-separated (CS) state was studied by fs-laser spectroscopy, charge recombination to either singlet ground state (kS) or to the first excited local triplet state of the acceptor (kT) by ns-laser spectroscopy, whereby kinetic magnetic field effects in an external magnetic field were recorded and analysed using quantum dynamic simulations of the spin dependent kinetics of the CS state. Kinetic spectra of the initial first order rate constants of charge recombination (k(B)) exhibited characteristic J-resonances progressing to lower fields in the series Me0, Me2, Me3, Me23. From the quantum simulations, the values of the parameters J, kS, kT and kSTD, the singlet/triplet dephasing constant, were obtained. They were analysed in terms of molecular dynamics simulations of the intramolecular twisting dynamics based on potentials calculated by density functional theory. Apart from kT, all of the parameters exhibit a clear correlation with the averaged cosine square products of the biaryl angles.

Study of transient absorption spectroscopy of a D-π-A structure aggregation-induced emission luminogen and its photodynamic therapy application.

Photodynamic therapy (PDT) represents an emerging and noninvasive modality that has gained clinical approval for the treatment of cancers, leveraging photosensitizers for optimal therapeutic efficacy. In this study, we synthesized a photosensitizer (denoted as DTCSPP) exhibiting a donor-π-acceptor (D-π-A) structural motif. The DTCSPP manifests aggregation-induced emission (AIE) characteristics, along with good biocompatibility and mitochondrial targeting capabilities attributed to its intrinsic charge and D-π-A architecture. The excited-state intramolecular charge transfer of DTCSPP was systematically investigated in both solution and aggregate states using femtosecond transient absorption spectroscopy (fs-TA). The fs-TA results revealed that DTCSPP exhibited a more rapid and facile excited-state molecular motion in the solution state compared to the aggregate state, implying the predominance of nonradiative decay in its photophysical processes within the solution. Given its ability to simultaneously generate type I and type II reactive oxygen species and induce ferroptosis and autophagy in cancer cells, DTCSPP demonstrates effectiveness in PDT at both cellular and in vivo levels. This study contributes a comprehensive understanding of the excited-state intramolecular charge transfer dynamics of charged D-π-A type AIE photosensitizers, shedding light on their potential application in PDT. The multifaceted capabilities of DTCSPP underscore its promise in advancing the field of anticancer therapeutics, providing valuable insights for the identification of anticancer targets and the development of novel drugs.

Quasi-Period Dynamics of Soliton Molecules: Route to Chaos and Intrinsic Frequency Entrainment

Soliton molecules in optical resonators have attracted remarkable attention in nonlinear dynamics, driven by their compelling analogies with matter molecules. So far, while extensive research has been conducted on their generation, pulsations, and dissociation behaviors, the investigation of their quasi-periodic dynamics has been relatively limited. Here, we present a systematic exploration of the quasi-periodic dynamics of soliton molecules using advanced balanced optical cross-correlation techniques. The incommensurable quasi-period bifurcations constituted of cascaded Hopf bifurcations are found, providing an unambiguous pathway toward chaotic soliton molecules. The chaotic intramolecular dynamics are analyzed by time series, radio frequency spectra, phase portraits, and Lyapunov exponent analysis. In addition, we reveal an intrinsic frequency entrainment phenomenon experimentally. Such frequency entrainment provides a novel perspective on synchronization in optical resonators, encompassing the competition and interaction of oscillations across multiple temporal scales. Our experimental findings offer clear proof that the gain dynamics serve as the origin of the binding forces between solitons within the molecule, which are well supported by the numerical simulations. By advancing the understanding of sub-femtosecond resolved quasi-period dynamics of optical soliton molecules, this study contributes to the broader field of complex nonlinear dynamics, paving the way for future explorations into the intricate behaviors of solitons within optical resonators and relevant fields.

Facile synthesis and characterization of aza-bridged all-benzenoid quinoidal figure-eight and cage molecules.

Synthesis of conjugated compounds with unusual shape-persistent structures remains a challenge. Herein, utilizing thermodynamically reversible intermolecular Friedel-Crafts alkylation, a dynamic covalent chemistry (DCC) reaction, we facilely synthesized a figure-eight shaped macrocycle FEM and cage molecules CATPA/CACz. X-ray crystallographic analysis confirmed the chemical geometries of tetracation FEM4+(PF6 -)4 and hexacation CACz6+(SbF6 -)6. FEM and CATPA displayed higher photoluminescence quantum yield in solid states compared to that in solution, whereas CACz gave the reverse result. DFT calculations showed that fluorescence-related frontier molecular orbital profiles are mainly localized on their arms consisting of a p-quinodimethane (p-QDM) unit and two benzene rings of triphenylamine or carbazole. Owing to their space-confined structures, variable-temperature 1H NMR measurements showed that FEM, CATPA and FEM4+ have intramolecular restricted motion of phenyl rings on their chromophore arms. Accordingly, FEM and CATPA with flexible triphenylamine subunits displayed aggregation-induced emission behavior (AIE), whereas CACz with a rigid carbazole subunits structure showed no AIE behavior.