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Environmental effects in excitation energy transfer have mostly been modeled by baths of harmonic oscillators, but to what extent such modeling provides a reliable description of actual interactions between molecular systems and environments remains an open issue. We address this issue by investigating fluctuations in the excitation energies of the light harvesting 2 complex using a realistic all-atomistic simulation of the potential energy surface. Our analyses reveal that molecular motions exhibit significant anharmonic features, even for underdamped intramolecular vibrations. In particular, we find that the anharmonicity contributes to the broadening of spectral densities and substantial overlaps between neighboring peaks, which complicates the meaning of mode frequencies constituting a bath model. Thus, we develop a strategy to construct a minimally underdamped harmonic bath that has a clear connection to all-atomistic dynamics by utilizing actual normal modes of molecules but optimizing their frequencies such that the resulting bath model can best reproduce the all-atomistic simulation results. By subtracting the underdamped contribution from the entire fluctuations, we also show that identifying a residual spectral density representing all other contributions with overdamped behavior is possible. We find that this can be fitted well with a well-established analytic form of a spectral density function or, alternatively, modeled as explicit time dependent fluctuations with muti-exponential or power law type correlation functions. We provide an assessment and the implications of these possibilities. The approach presented here can also serve as a general strategy to construct a simplified bath model that can effectively represent the underlying all-atomistic bath dynamics. [ABSTRACT FROM AUTHOR]

This document is an erratum for a previous paper titled "Modified Fermi's golden rule rate expressions." The erratum corrects an error in equation (41) by adding a missing factor of 1/2. The correction does not change any major conclusions or implications of the paper, but it does require the correction of figures 1-4, which show results of model calculations. The corrected figures and their captions are provided in the erratum. [Extracted from the article]

Fermi's golden rule (FGR) serves as the basis for many expressions of spectroscopic observables and quantum transition rates. The utility of FGR has been demonstrated through decades of experimental confirmation. However, there still remain important cases where the evaluation of a FGR rate is ambiguous or ill-defined. Examples are cases where the rate has divergent terms due to the sparsity in the density of final states or time dependent fluctuations of system Hamiltonians. Strictly speaking, assumptions of FGR are no longer valid for such cases. However, it is still possible to define modified FGR rate expressions that are useful as effective rates. The resulting modified FGR rate expressions resolve a long standing ambiguity often encountered in using FGR and offer more reliable ways to model general rate processes. Simple model calculations illustrate the utility and implications of new rate expressions. [ABSTRACT FROM AUTHOR]

Peptides are promising therapeutic agents for various biological targets due to their high efficacy and low toxicity, and the design of peptide ligands with high binding affinity to the target of interest is of utmost importance in peptide‐based drug design. Introducing a conformational constraint to a flexible peptide ligand using a side‐chain lactam‐bridge is a convenient and efficient method to improve its binding affinity to the target. However, in general, such a small structural modification to a flexible ligand made with the intent of lowering the configurational entropic penalty for binding may have unintended consequences in different components of the binding enthalpy and entropy, including the configurational entropy component, which are still not clearly understood. Toward probing this, we examine different components of the binding enthalpy and entropy as well as the underlying structure and dynamics, for a side‐chain lactam‐bridged peptide inhibitor and its flexible analog forming complexes with vascular endothelial growth factor (VEGF), using all‐atom molecular dynamics simulations. It is found that introducing a side‐chain lactam‐bridge constraint into the flexible peptide analog led to a gain in configurational entropy change but losses in solvation entropy, solute internal energy, and solvation energy changes upon binding, pinpointing the opportunities and challenges in drug design. The present study features an interplay between configurational and solvation entropy changes, as well as the one between binding enthalpy and entropy, in ligand‐target binding upon imposing a conformational constraint into a flexible ligand. [ABSTRACT FROM AUTHOR]

Vascular endothelial growth factor 165 (VEGF165) is a prominent isoform of the VEGF-A protein that plays a crucial role in various angiogenesis-related diseases. It is homodimeric, and each of its monomers is composed of two domains connected by a flexible linker. DNA aptamers, which have emerged as potent therapeutic molecules for many proteins with high specificity and affinity, can also work for VEGF165. A DNA aptamer heterodimer composed of monomers of V7t1 and del5-1 connected by a flexible linker (V7t1:del5-1) exhibits a greater binding affinity with VEGF165 compared to either of the two monomers alone. Although the structure of the complex formed between the aptamer heterodimer and VEGF165 is unknown due to the highly flexible linkers, gaining structural information will still be valuable for future developments. Toward this end of accessing structural information, we adopt an ensemble docking approach here. We first obtain an ensemble of structures for both VEGF165 and the aptamer heterodimer by considering both small- and large-scale motions. We then proceed through an extraction process based on ensemble docking, molecular dynamics simulations, and binding free energy calculations to predict the structures of the VEGF165/V7t1:del5-1 complex. Through the same procedures, we reach a new aptamer heterodimer that bears a locked nucleic acid-modified counterpart of V7t1, namely RNV66:del5-1, which also binds well with VEGF165. We apply the same protocol to the monomeric units V7t1, RNV66, and del5-1 to target VEGF165. We observe that V7t1:del5-1 and RNV66:del5-1 show higher binding affinities with VEGF165 than any of the monomers, consistent with experiments that support the notion that aptamer heterodimers are more effective anti-VEGF165 aptamers than monomeric aptamers. Among the five different aptamers studied here, the newly designed RNV66:del5-1 shows the highest binding affinity with VEGF165. We expect that our ensemble docking approach can help in de novo designs of homo/heterodimeric anti-angiogenic drugs to target the homodimeric VEGF165. [ABSTRACT FROM AUTHOR]

The realization of quantum advantage with noisy-intermediate-scale quantum (NISQ) machines has become one of the major challenges in computational sciences. Maintaining coherence of a physical system with more than ten qubits is a critical challenge that motivates research on compact system representations to reduce algorithm complexity. Toward this end, the variational quantum eigensolver (VQE) used to perform quantum simulations is considered to be one of the most promising algorithms for quantum chemistry in the NISQ era. We investigate reduced mapping of one spatial orbital to a single qubit to analyze the ground state energy in a way that the Pauli operators of qubits are mapped to the creation/annihilation of singlet pairs of electrons. To include the effect of non-bosonic (or non-paired) excitations, we introduce a simple correction scheme in the electron correlation model approximated by the geometrical mean of the bosonic (or paired) terms. Employing it in a VQE algorithm, we assess ground state energies of H2O, N2, and Li2O in good agreement with full configuration interaction (FCI) models respectively, using only 6, 8, and 12 qubits with quantum gate depths proportional to the squares of the qubit counts. With the adopted seniority-zero approximation that uses only one half of the qubit counts of a conventional VQE algorithm, we find that our non-bosonic correction method reaches reliable quantum chemistry simulations at least for the tested systems. [ABSTRACT FROM AUTHOR]

Expressions for analytical molecular gradients of core-excited states have been derived and implemented for the hierarchy of algebraic diagrammatic construction (ADC) methods up to extended second-order within the core–valence separation (CVS) approximation. We illustrate the use of CVS-ADC gradients by determining relaxed core-excited state potential energy surfaces and optimized geometries for water, formic acid, and benzene. For water, our results show that in the dissociative lowest core-excited state, a linear configuration is preferred. For formic acid, we find that the O K-edge lowest core-excited state is non-planar, a fact that is not captured by the equivalent core approximation where the core-excited atom with its hole is replaced by the "Z + 1" neighboring atom in the periodic table. For benzene, the core-excited state gradients are presented along the Jahn–Teller distorted geometry of the 1s → π* excited state. Our development may pave a new path to studying the dynamics of molecules in their core-excited states. [ABSTRACT FROM AUTHOR]

Understanding nonradiative transition mechanisms is important in various situations. However, compared with radiative processes where temporal profiles of photon emission can be monitored in a straightforward manner, experimentally accessing the rate information may not be an easy task with nonradiative transitions. Hence, applying theoretical tools toward predicting the rates can be a useful tactic. Such predictions become very useful in designing optoelectronic materials as in the molecules adopted for constructing organic light‐emitting diodes (OLEDs). The correlation function formalism is a method that can fulfill the purpose of designing OLED materials. The formalism requires information regarding the vibrational normal modes of the two electronic states before and after the transition. Because the method is also based on harmonic oscillator approximation, it can actually fail to provide high reliability when there is a large geometric distortion between the initial and the final states. In fact, the harmonic normal mode picture is more prone to lose reliability in the Cartesian coordinates than in the internal ones even at a small distortion, and hence adopting internal coordinates may be more preferable for practical calculations. This is because normal mode mixing becomes less severe when molecular coordinates are described with internal degrees of freedom such as bond stretching, bending, and torsion. In this regard, how much more reliable the nonradiative rate predictions in OLED materials become with the use of internal coordinate system deserves a close inspection. In this account, we review on the derivation of the correlation function formalism and provide how it can be adapted toward the use of the internal coordinates. As a demonstration, we evaluate the intersystem crossing and the internal conversion rates of a series of thermally activated delayed fluorescence (TADF) molecules with both Cartesian and internal coordinate systems. Overall, handling transitions involving substantial structural changes is improved indeed with the internal coordinates. However, limitations are still apparent for the TADF systems with a flexible donor–acceptor type construct especially when the inevitable inter‐domain twisting takes place with the electronic transition. Future prospect for handling the issue is commented as a concluding remark. [ABSTRACT FROM AUTHOR]

Mapping basis solutions provide efficient ways for simulating mixed quantum–classical (MQC) dynamics in complex systems by matching multiple quantum states of interest to some fictitious physical states. Recently, various MQC methods were devised such that two harmonic oscillators are employed to represent each electronic state, showing improvements over one-oscillator-based methods. Here, we introduce and analyze newly modified mapping approximations of the quantum–classical Liouville equation (QCLE) using two oscillators for each electronic state. We design two separate mapping relations that we can adopt toward simulating dynamics and computing expectation values. Through the process, two MQC methods can be constructed, one of which actually reproduces the population dynamics of the forward and backward trajectory solution of QCLE. By applying the methods to spin–boson systems with a range of parameters, we find out that the choice of mapping relations greatly affects the simulation results. We also show that further improvement is possible through using modified identity operator formulations. Our findings may be helpful in constructing improved MQC methods in the future. [ABSTRACT FROM AUTHOR]

In open quantum system dynamics, rich information about the major energy relaxation channels and corresponding relaxation rates can be elucidated by monitoring the vibrational energy flow among individual bath modes. However, such calculations often become tremendously difficult as the complexity of the subsystem–bath coupling increases. In this paper, we attempt to make this task feasible by using a mixed quantum–classical method, the Poisson-bracket mapping equation with non-Hamiltonian modification (PBME-nH) [H. W. Kim and Y. M. Rhee, J. Chem. Phys. 140, 184106 (2014)]. For a quantum subsystem bilinearly coupled to harmonic bath modes, we derive an expression for the mode energy in terms of the classical positions and momenta of the nuclei, while keeping consistency with the energy of the quantum subsystem. The accuracy of the resulting expression is then benchmarked against a numerically exact method by using relatively simple models. Although our expression predicts a qualitatively correct dissipation rate for a range of situations, cases involving a strong vibronic resonance are quite challenging. This is attributed to the inherent lack of quantum back reaction in PBME-nH, which becomes significant when the subsystem strongly interacts with a small number of bath modes. A rigorous treatment of such an effect will be crucial for developing quantitative simulation methods that can handle generic subsystem–bath coupling. [ABSTRACT FROM AUTHOR]

Triplet harvesting processes are essential for enhancing efficiencies of fluorescent organic light-emitting diodes. Besides more conventional thermally activated delayed fluorescence and triplet-triplet annihilation, the hot exciton mechanism has been recently noticed because it helps reduce the efficiency roll-off and improve device stability. Hot exciton materials enable the conversion of triplet excitons to singlet ones via reverse inter-system crossing from high-lying triplet states and thereby the depopulation of long-lived triplet excitons that are prone to chemical and/or efficiency degradation. Although their anti-Kasha characteristics have not been clearly explained, numerous molecules with behaviors assigned to the hot exciton mechanism have been reported. Indeed, the related developments appear to have just passed the stage of infancy now, and there will likely be more roles that computational elucidations can play. With this perspective in mind, we review some selected experimental studies on the mechanism and the related designs and then on computational studies. On the computational side, we examine what has been found and what is still missing with regard to properly understanding this interesting mechanism. We further discuss potential future points of computational interests toward aiming for eventually presenting in silico design guides. [ABSTRACT FROM AUTHOR]

Macugen is a therapeutic RNA aptamer against vascular endothelial growth factor (VEGF)‐165, the VEGF isoform primarily responsible for angiogenesis. It has been reported that Macugen inhibits angiogenesis by specifically binding to the heparin binding domain (HBD) of VEGF165. The mechanism of the molecular recognition between HBD and Macugen is investigated here using all‐atom molecular dynamics simulations. We find that Macugen recognizes HBD by an induced‐fit mechanism with major conformational changes in Macugen and almost no changes in the structure of HBD, whereas HBD recognizes Macugen by a conformational selection mechanism. [ABSTRACT FROM AUTHOR]

The vascular endothelial growth factor receptor 2 (VEGFR-2) is a member of receptor tyrosine kinases (RTKs) and is a dimeric membrane protein that functions as a primary regulator of angiogenesis. As is usual with RTKs, spatial alignment of its transmembrane domain (TMD) is essential toward VEGFR-2 activation. Experimentally, the helix rotations within TMD around their own helical axes are known to participate importantly toward the activation process in VEGFR-2, but the detailed dynamics of the interconversion between the active and inactive TMD forms have not been clearly elucidated at the molecular level. Here, we attempt to elucidate the process by using coarse grained (CG) molecular dynamics (MD) simulations. We observe that inactive dimeric TMD in separation is structurally stable over tens of microseconds, suggesting that TMD itself is passive and does not allow spontaneous signaling of VEGFR-2. By starting from the active conformation, we reveal the mechanism of TMD inactivation through analyzing the CG MD trajectories. We observe that interconversions between a left-handed overlay and a right-handed one are essential for the process of going from an active TMD structure to the inactive form. In addition, our simulations find that the helices can rotate properly when the overlaying structure of the helices interconverts and when the crossing angle of the two helices changes by larger than ~40 degrees. As the activation right after the ligand attachment on VEGFR-2 will take place in the reverse manner of this inactivation process, these structural aspects will also appear importantly for the activation process. The rather large change in helix configuration for activation also explains why VEGFR-2 rarely self-activate and how the activating ligand structurally drive the whole VEGFR-2. This mechanism of TMD activation / inactivation within VEGFR-2 may help in further understanding the overall activation processes of other RTKs. [ABSTRACT FROM AUTHOR]

A highly efficient anthracene‐based 5‐(4‐(10‐phenylanthracen‐9‐yl)phenyl)‐5H‐benzofuro[3,2‐c]carbazole (ATDBF) with nearly 100% exciton utilization efficiency is developed for highly efficient nondoped blue organic light‐emitting diodes (OLEDs) through inter‐ and intramolecular triplet exciton up‐converting mechanisms. The ATDBF emitter opens hybridized hot excitons, triplet–triplet fusion (TTF), and mixed TTF/hot exciton channels for triplet exciton to singlet exciton conversion. The molecular design adopting a benzofuro[3,2‐c]carbazole (BFCz) donor manages the singlet and triplet excited states for hybridized triplet exciton up‐conversion mechanisms, which enable a high external quantum efficiency (EQE) of 7.93% in the ATDBF blue device with color coordinates of (0.15, 0.06). This is one of the best efficiencies of the nondoped blue OLEDs with a y color coordinate below 0.06. [ABSTRACT FROM AUTHOR]

Cohosts based on hole transporting and electron transporting materials often act as exciplexes in the form of intermolecular charge transfer complexes. Indeed, exciplex-forming cohosts have been widely developed as the host materials for efficient phosphorescent organic light-emitting diodes (OLEDs). In host–guest systems of OLEDs, the guest can be excited by two competing mechanisms, namely, excitation energy transfer (EET) and charge transfer (CT). Experimentally, it has been reported that the EET mechanism is dominant and the excitons are primarily formed in the host first and then transferred to the guest in phosphorescent OLEDs based on exciplex-forming cohosts. With this, exciplex-forming cohosts are widely employed for avoiding the formation of trapped charge carriers in the phosphorescent guest. However, theoretical studies are still lacking toward elucidating the relative importance between EET and CT processes in exciting the guest molecules in such systems. Here, we obtain the kinetics of guest excitation processes in a few trimer model systems consisting of an exciplex-forming cohost pair and a phosphorescent guest. We adopt the Förster resonance energy transfer (FRET) rate constants for the electronic transitions between excited states toward solving kinetic master equations. The input parameters for calculating the FRET rate constants are obtained from density functional theory (DFT) and time-dependent DFT. The results show that while the EET mechanism is important, the CT mechanism may still play a significant role in guest excitations. In fact, the relative importance of CT over EET depends strongly on the location of the guest molecule relative to the cohost pair. This is understandable as both the coupling for EET and the interaction energy for CT are strongly influenced by the geometric constraints. Understanding the energy transfer pathways from the exciplex state of cohost to the emissive state of guest may provide insights for improving exciplex-forming materials adopted in OLEDs. [ABSTRACT FROM AUTHOR]

As understanding experimentally observed two‐dimensional electronic spectroscopy (2DES) signals usually requires theoretical modeling, various approaches have been applied to simulating the spectra. It will be desirable to develop a method that is free from parameters that are adjusted based on spectroscopic outcomes. Often, such parameters without any a priori known information come from quantum chemical calculations that can only be achieved at the atomistic resolution, and a necessity arises for designing a scheme that can be readily used for generating 2DES spectra even for atomistic models of complex systems. Here, we present such an approach based on mixed quantum‐classical Poisson bracket mapping equation formalism, which can be extended to all‐atom simulations. We check its performance by adopting a two‐state toy model and show that we can efficiently construct 2D spectra. We show that our scheme can yield reasonable 2D spectra even when high‐frequency vibrations modulate the population dynamics. [ABSTRACT FROM AUTHOR]

Coupling between pigment excitations and nuclear movements in photosynthetic complexes is known to modulate the excitation energy transfer (EET) efficiencies. Toward providing microscopic information, researchers often apply simulation techniques and investigate how vibrations are involved in EET processes. Here, reports on such roles of nuclear movements are discussed from a theory perspective. While vibrations naturally present random thermal fluctuations that can affect energy transferring characteristics, they can also be intertwined with exciton structures and create more specific non-adiabatic energy transfer pathways. For reliable simulations, a bath model that accurately mimics a given molecular system is required. Methods for obtaining such a model in combination with quantum chemical electronic structure calculations and molecular dynamics trajectory simulations are discussed. Various quantum dynamics simulation tools that can handle pigment-to-pigment energy transfers together with their vibrational characters are also touched on. Behaviors of molecular vibrations often deviate from ideality, especially when all-atom details are included, which practically forces us to treat them classically. We conclude this perspective by considering some recent reports that suggest that classical descriptions of bath effects with all-atom details may still produce valuable information for analyzing sophisticated contributions by vibrations to EET processes. [ABSTRACT FROM AUTHOR]

Quinone cyanine 9 (QCy9) is one of the strongest photoacids known to date. The origin of "super"‐photoacidity was investigated via time‐resolved fluorescence (TF) with high time resolution to accurately resolve the ultrafast dynamics of the excited‐state proton transfer (ESPT) to solvent. The ESPT of QCy9 in water is found to proceed fully by two ultrafast time constants of 40 fs (65 %) and 200 fs (35 %). More importantly, the initially created base form of QCy9 in the excited state undergoes a significant dynamic red shift of over 2700 cm−1 by solvation. We suggest that the entirely ultrafast reaction rate and the massive solvation of the conjugate base could make QCy9 a particularly strong photoacid. Quantum chemical calculations show that structural diversity leads to the nonexponential behavior of the ESPT dynamics. [ABSTRACT FROM AUTHOR]

Multichromophore systems (MCSs) are envisioned as building blocks of molecular optoelectronic devices. While it is important to understand the characteristics of energy transfer in MCSs, the effect of multiple donors on energy transfer has not been understood completely, mainly due to the lack of a platform to investigate such an effect systematically. Here, a systematic study on how the number of donors (nD) and interchromophore distances affect the efficiency of energy transfer (ηFRET) is presented. Specifically, ηFRET is calculated for a series of model MCSs using simulations, a series of multiporphyrin dendrimers with systematic variation of nD and interdonor distances is synthesized, and ηFRETs of those dendrimers using transient absorption spectroscopy are measured. The simulations predict ηFRET in the multiporphyrin dendrimers well. In particular, it is found that ηFRET is enhanced by donor‐to‐donor energy transfer only when structural heterogeneity exists in an MCS, and the relationships between the ηFRET enhancement and the structural parameters of the MCS are revealed. [ABSTRACT FROM AUTHOR]

Free energy calculations may provide vital information for studying various chemical and biological processes. Quantum mechanical methods are required to accurately describe interaction energies, but their computations are often too demanding for conformational sampling. As a remedy, level correction schemes that allow calculating high level free energies based on conformations from lower level simulations have been developed. Here, we present a variation of a Monte Carlo (MC) resampling approach in relation to the weighted histogram analysis method (WHAM). We show that our scheme can generate free energy surfaces that can practically converge to the exact one with sufficient sampling, and that it treats cases with insufficient sampling in a more stable manner than the conventional WHAM-based level correction scheme. It can also provide a guide for checking the uncertainty of the level-corrected surface and a well-defined criterion for deciding the extent of smoothing on the free energy surface for its visual improvement. We demonstrate these aspects by obtaining the free energy maps associated with the alanine dipeptide and proton transfer network of the KillerRed protein in explicit water, and exemplify that the MC resampled WHAM scheme can be a practical tool for producing free energy surfaces of realistic systems. [ABSTRACT FROM AUTHOR]

Interpolated potential energy surfaces (PESs) have been used for performing reliable molecular dynamics (MD) simulations of small molecular reactions. In this article, we extend this method to MD simulations in condensed phase and show that the same scheme can also be feasibly used when it is supplemented with additional terms for describing intermolecular interactions. We then apply the approach for studying the resolvation process of coumarin 153 in a number of polar solvents. We find that the interpolated surface actually reproduces experimentally found features much better than the conventional force field based potential especially in terms of both dynamics Stokes shift in the short time limit and solute vibrational decoherence. This shows that the solute vibrational effect is important to some degree along the resolvation and should be modeled properly for accurate description of the related dynamics. The stability issue of trajectories on the interpolated PESs is also discussed, in regard to the goal of reliably performing long time simulations. Operational limitations of the present scheme are also discussed. [ABSTRACT FROM AUTHOR]

Firefly bioluminescence has been widely studied due to its high quantum yield and its broad range of color modulation, but debates on the origin of its color modulation and the exact chemical form of the emitter are still ongoing. Herein, the keto‐enolate transformation of the oxyluciferin–luciferase complex is investigated using quantum mechanics/molecular mechanics (QM/MM) free energy simulations. We find that the free energy profile of this transformation largely depends on the protonation state of the phenoxy oxygen in oxyluciferin. Although the keto‐enolate transformation can be facilitated by protonation of this oxygen atom, the overall transformation is still unlikely and only the keto form will predominantly exist along our hypothesized reaction path. Nevertheless, we show with additional calculations with a modestly modified protein electric field that the energetics of the transformation can be heavily modulated with the protein electrostatics. This suggests that carefully modeling the protein–ligand interaction is key to understanding the reaction mechanism of the firefly bioluminescence and that it is not yet appropriate to completely rule out the possibility of having enolate participation. [ABSTRACT FROM AUTHOR]

KillerRed is the first genetically encoded photosensitizer that can induce cytotoxicity upon light exposure. Nevertheless, its phototoxicity is still lower than that of chemical photosensitizers, and the efforts to further develop KillerRed variants with enhanced phototoxicity have been impeded because the mechanism by which it generates cytotoxic reactive oxygen species (ROS) has remained elusive. To shed light on this issue, we employ quantum mechanics/molecular mechanics (QM/MM) modeling with statistical free energy analysis to examine the photo-induced electron transfer reaction occurring in KillerRed. We identify a deprotonated tyrosine residue (Tyr110) as an electron donor and further show that adjacent glutamate and serine residues play essential roles in deprotonating Tyr110. We also show that water mediation is important in the proton transfer and that protein fluctuations importantly govern the fate of the excited system. We provide clues about why KillerRed can only exhibit a low ROS yield and suggest future directions of mutagenesis toward an enhanced phototoxicity. [ABSTRACT FROM AUTHOR]

DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge–dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n+ (n = 1–4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA·K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge–dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA·Mn+ complexes, as the charge n increases, the charge–dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge–dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions. [ABSTRACT FROM AUTHOR]

We analyze the environment-induced fluctuation of pigment excitation energies in the Fenna–Matthews–Olson (FMO) complex from various perspectives, by employing an interpolation-based all-atom potential energy model for describing realistic pigment vibrations. We conduct molecular dynamics simulations on a 100 ns timescale, which is an extent that can enclose the effect of static disorder, and demonstrate its timescale separation from fast dynamic disorder. We extract the spectral densities of the complex by considering both the site and the exciton bases. We show that exciton delocalization reduces the effective environmental fluctuation and rationalize this aspect based on a model of fluctuating molecular aggregates. We also obtained the spectral density of the lowest exciton state under low temperature conditions and show that it reasonably well reproduces the experimental result. Finally, by additionally performing non-equilibrium excited state trajectory simulations, we show that the system lies well within the linear response regime after photo-absorption and that the pigments do not visit anharmonic regions of the potential surface to a significant extent. This indicates that methodologies based on harmonic bath models are indeed reasonable approaches for describing the excited state dynamics of the FMO complex. [ABSTRACT FROM AUTHOR]

Detailed molecular dynamics simulations of an acid–base reaction have been the subject of extensive investigations. Here we report the excited state proton transfer dynamics of pyranine (8-hydroxypyrene-1,3,6-trisulfonic acid, HPTS) in acetate buffer by time-resolved fluorescence (TF) and quantum mechanical/effective fragment potential molecular dynamics (QM/EFP-MD) simulations. High time resolution in TF and TF spectra measurements allows the acquisition of accurate reaction kinetics. Upon the photoexcitation of HPTS, the proton (deuterium) is transferred coherently to acetate in 60 fs (80 fs) for a contact pair of HPTS (DPTS) and acetate by a hydrogen bond, which comprises approximately 28% of the population. ESPT proceeds slowly on a picosecond time scale for the remaining HPTS as reported previously. Coherent wave packet motions of the reactant (acid) and the product (conjugate base) enable the acquisition of the vibrational spectra of excited states via TF (VETF). A comparison of the VETFs of the reactant and the product and the calculation of the Huang–Rhys factors (vibrational reorganization energies) identify the vibrational modes that actively participate in the coherent proton transfer. In particular, the 246 cm−1 vibrational mode, which consists of in-plane skeletal stretching motion, promotes the ESPT by transferring the donor oxygen towards the acceptor oxygen in acetate. QM/EFP MD simulations corroborate the experiment and provide molecular details of the ESPT. [ABSTRACT FROM AUTHOR]