Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation.

Low-complexity nucleotide repeat sequences, which are implicated in several neurological disorders, undergo liquid-liquid phase separation (LLPS) provided the number of repeat units, n, exceeds a critical value. Here, we establish a link between the folding landscapes of the monomers of trinucleotide repeats and their propensity to self-associate. Simulations using a coarse-grained Self-Organized Polymer (SOP) model for (CAG)n repeats in monovalent salt solutions reproduce experimentally measured melting temperatures, which are available only for small n. By extending the simulations to large n, we show that the free-energy gap, ΔGS, between the ground state (GS) and slipped hairpin (SH) states is a predictor of aggregation propensity. The GS for even n is a perfect hairpin (PH), whereas it is a SH when n is odd. The value of ΔGS (zero for odd n) is larger for even n than for odd n. As a result, the rate of dimer formation is slower in (CAG)30 relative to (CAG)31, thus linking ΔGS to RNA-RNA association. The yield of the dimer decreases dramatically, compared to the wild type, in mutant sequences in which the population of the SH decreases substantially. Association between RNA chains is preceded by a transition to the SH even if the GS is a PH. The finding that the excitation spectrum-which depends on the exact sequence, n, and ionic conditions-is a predictor of self-association should also hold for other RNAs (mRNA for example) that undergo LLPS.

Quantitative NMR analysis of the kinetics of prenucleation oligomerization and aggregation of pathogenic huntingtin exon-1 protein.

The N-terminal region of the huntingtin protein, encoded by exon-1 (httex1) and containing an expanded polyglutamine tract, forms fibrils that accumulate in neuronal inclusion bodies, resulting in Huntington's disease. We previously showed that reversible formation of a sparsely populated tetramer of the N-terminal amphiphilic domain, comprising a dimer of dimers in a four-helix bundle configuration, occurs on the microsecond timescale and is an essential prerequisite for subsequent nucleation and fibril formation that takes place orders of magnitude slower on a timescale of hours. For pathogenic httex1, such as httex1Q35 with 35 glutamines, NMR signals decay too rapidly to permit measurement of time-intensive exchange-based experiments. Here, we show that quantitative analysis of both the kinetics and mechanism of prenucleation tetramerization and aggregation can be obtained simultaneously from a series of 1H-15N band-selective optimized flip-angle short-transient heteronuclear multiple quantum coherence (SOFAST-HMQC) correlation spectra. The equilibria and kinetics of tetramerization are derived from the time dependence of the 15N chemical shifts and 1H-15N cross-peak volume/intensity ratios, while the kinetics of irreversible fibril formation are afforded by the decay curves of 1H-15N cross-peak intensities and volumes. Analysis of data on httex1Q35 over a series of concentrations ranging from 200 to 750 µM and containing variable (7 to 20%) amounts of the Met7O sulfoxide species, which does not tetramerize, shows that aggregation of native httex1Q35 proceeds via fourth-order primary nucleation, consistent with the critical role of prenucleation tetramerization, coupled with first-order secondary nucleation. The Met7O sulfoxide species does not nucleate but is still incorporated into fibrils by elongation.

Interaction of the bacterial division regulator MinE with lipid bicelles studied by NMR spectroscopy.

The bacterial MinE and MinD division regulatory proteins form a standing wave enabling MinC, which binds MinD, to inhibit FtsZ polymerization everywhere except at the midcell, thereby assuring correct positioning of the cytokinetic septum and even distribution of contents to daughter cells. The MinE dimer undergoes major structural rearrangements between a resting six-stranded state present in the cytoplasm, a membrane-bound state, and a four-stranded active state bound to MinD on the membrane, but it is unclear which MinE motifs interact with the membrane in these different states. Using NMR, we probe the structure and global dynamics of MinE bound to disc-shaped lipid bicelles. In the bicelle-bound state, helix α1 no longer sits on top of the six-stranded ß-sheet, losing any contact with the protein core, but interacts directly with the bicelle surface; the structure of the protein core remains unperturbed and also interacts with the bicelle surface via helix α2. Binding may involve a previously identified excited state of free MinE in which helix α1 is disordered, thereby allowing it to target the membrane surface. Helix α1 and the protein core undergo nanosecond rigid body motions of differing amplitudes in the plane of the bicelle surface. Global dynamics on the sub-millisecond time scale between a ground state and a sparsely populated excited state are also observed and may represent a very early intermediate on the transition path between the resting six-stranded and active four-stranded conformations. In summary, our results provide insights into MinE structural rearrangements important during bacterial cell division.

Transient excited states of the metamorphic protein Mad2 and their implications for function.

The spindle checkpoint complex is a key surveillance mechanism in cell division that prevents premature separation of sister chromatids. Mad2 is an integral component of this spindle checkpoint complex that recognizes cognate substrates such as Mad1 and Cdc20 in its closed (C-Mad2) conformation by fastening a "seatbelt" around short peptide regions that bind to the substrate recognition site. Mad2 is also a metamorphic protein that adopts not only the fold found in C-Mad2, but also a structurally distinct open conformation (O-Mad2) which is incapable of binding substrates. Here, we show using chemical exchange saturation transfer (CEST) and relaxation dispersion (CPMG) NMR experiments that Mad2 transiently populates three other higher free energy states with millisecond lifetimes, two in equilibrium with C-Mad2 (E1 and E2) and one with O-Mad2 (E3). E1 is a mimic of substrate-bound C-Mad2 in which the N-terminus of one C-Mad2 molecule inserts into the seatbelt region of a second molecule of C-Mad2, providing a potential pathway for autoinhibition of C-Mad2. E2 is the "unbuckled" conformation of C-Mad2 that facilitates the triage of molecules along competing fold-switching and substrate binding pathways. The E3 conformation that coexists with O-Mad2 shows fluctuations at a hydrophobic lock that is required for stabilizing the O-Mad2 fold and we hypothesize that E3 represents an early intermediate on-pathway towards conversion to C-Mad2. Collectively, the NMR data highlight the rugged free energy landscape of Mad2 with multiple low-lying intermediates that interlink substrate-binding and fold-switching, and also emphasize the role of molecular dynamics in its function.

NMR spectroscopy, excited states and relevance to problems in cell biology - transient pre-nucleation tetramerization of huntingtin and insights into Huntington's disease.

Solution nuclear magnetic resonance (NMR) spectroscopy is a powerful technique for analyzing three-dimensional structure and dynamics of macromolecules at atomic resolution. Recent advances have exploited the unique properties of NMR in exchanging systems to detect, characterize and visualize excited sparsely populated states of biological macromolecules and their complexes, which are only transient. These states are invisible to conventional biophysical techniques, and play a key role in many processes, including molecular recognition, protein folding, enzyme catalysis, assembly and fibril formation. All the NMR techniques make use of exchange between sparsely populated NMR-invisible and highly populated NMR-visible states to transfer a magnetization property from the invisible state to the visible one where it can be easily detected and quantified. There are three classes of NMR experiments that rely on differences in distance, chemical shift or transverse relaxation (molecular mass) between the NMR-visible and -invisible species. Here, I illustrate the application of these methods to unravel the complex mechanism of sub-millisecond pre-nucleation oligomerization of the N-terminal region of huntingtin, encoded by exon-1 of the huntingtin gene, where CAG expansion leads to Huntington's disease, a fatal autosomal-dominant neurodegenerative condition. I also discuss how inhibition of tetramerization blocks the much slower (by many orders of magnitude) process of fibril formation.

A mountaineering strategy to excited states: Accurate vertical transition energies and benchmarks for substituted benzenes.

In an effort to expand the existing QUEST database of accurate vertical transition energies [Véril et al. WIREs Comput. Mol. Sci. 2021, 11, e1517], we have modeled more than 100 electronic excited states of different natures (local, charge-transfer, Rydberg, singlet, and triplet) in a dozen of mono- and di-substituted benzenes, including aniline, benzonitrile, chlorobenzene, fluorobenzene, nitrobenzene, among others. To establish theoretical best estimates for these vertical excitation energies, we have employed advanced coupled-cluster methods including iterative triples (CC3 and CCSDT) and, when technically possible, iterative quadruples (CC4). These high-level computational approaches provide a robust foundation for benchmarking a series of popular wave function methods. The evaluated methods all include contributions from double excitations (ADC(2), CC2, CCSD, CIS(D), EOM-MP2, STEOM-CCSD), along with schemes that also incorporate perturbative or iterative triples (ADC(3), CCSDR(3), CCSD(T)(a) ⋆ , and CCSDT-3). This systematic exploration not only broadens the scope of the QUEST database but also facilitates a rigorous assessment of different theoretical approaches in the framework of a homologous chemical series, offering valuable insights into the accuracy and reliability of these methods in such cases. We found that both ADC(2.5) and CCSDT-3 can provide very consistent estimates, whereas among less expensive methods SCS-CC2 is likely the most effective approach. Importantly, we show that some lower order methods may offer reasonable trends in the homologous series while providing quite large average errors, and vice versa. Consequently, benchmarking the accuracy of a model based solely on absolute transition energies may not be meaningful for applications involving a series of similar compounds.

Modeling the effect of substituents on the electronically excited states of indole derivatives.

A proper understanding of excited state properties of indole derivatives can lead to rational design of efficient fluorescent probes. The optically active L a $$ {L}_a $$ and L b $$ {L}_b $$ excited states of a series of substituted indoles, where a substituent was placed on position four, were calculated using equation of motion coupled cluster and time dependent density functional theory. The results indicate that most substituted indoles have a brighter second excited state corresponding to experimental absorption maxima, but a few with electron withdrawing substituents absorb more on the first excited state. Absorption on the first excited state may increase their fluorescence quantum yield, making them better probes. Electronic structure methods were found to predict the energies of the systems with electron withdrawing substituents more accurately than those with electron donating substituents. The excited states of both states correlated well with electrophilicity, similar to the experimental trends for the absorption maxima. Overall, these computational studies indicate that theory can be used to predict excited state properties of substituted indoles, when the substituent is an electron withdrawing group.

Ground and excited state charge transfer at aqueous nanodiamonds.

Nanodiamonds (NDs) are unique carbonaceous materials with exceptionally high stability, hardness, and notable electronic properties. Their applications in photocatalysis, biomedicine, and energy materials are usually carried out in aqueous environments, where they interact with aqueous adsorbates. Especially, electron density may rearrange from the diamond material toward oxidative adsorbates such as oxygen, which is known as charge transfer doping. In this article, we quantify the charge transfer doping for NDs with inhomogeneous surface coverings (hydroxyl, fluorine, and amorphous carbon), as well as NDs doped with heteroatoms (B, Si, N) using hybrid density functional theory (DFT) calculations. The transfer doping magnitude is largely determined by the NDs' highest occupied molecular orbital energies, which can in turn be modified by the surface covering and doping. However, local modifications of the ND structures do not have any local effects on the magnitude of the charge transfer. We furthermore analyze the impact of aqueous adsorbates on the excited states of an aqueous ND in the context of photocatalysis via time-dependent DFT. Here, we find that the excited electrons are biased to move in the direction of the respective oxidative adsorbate. Surprisingly, we find that also unreactive species such as nitrous oxide may attract the excited electrons, which is probably due to the positive partial charge that is induced by the local N 2 O solvation geometry.

Ab initio investigation of excited state charge transfer pathways in differently capped bithiophene cages.

The electronic excitations of conformationally constrained bithiophene cage systems as previously investigated by Lewis et al. (J. Am. Chem. Soc. 143, 18548 (2021)) are revisited, employing the correlated ab initio Scaled Opposite-Spin Algebraic Diagrammatic Construction Second Order electronic structure method. Quantitative descriptors are determined to assess the extent of charge transfer between the bithiophene moieties and the capping domains, represented by either phenyl or triazine groups. The investigation substantiates intrinsic differences in the photophysical behavior of these two structural variants and reveals the presence of lower-energy excited states characterized by noteworthy charge transfer contributions in the triazine cage system. The manifestation of this charge transfer character is discernible even at the Franck-Condon geometry, persisting throughout the relaxation of the excited state. By examining isolated monomer building blocks, we confirm the existence of analogous charge transfer contributions in their excitations. Employing this methodological approach facilitates the prospective identification of potential wall/cap chromophore pairs, wherein charge transfer pathways can be accessed within the energetically favorable regime.

How do spin-scaled double hybrids designed for excitation energies perform for noncovalent excited-state interactions? An investigation on aromatic excimer models.

Time-dependent double hybrids with spin-component or spin-opposite scaling to their second-order perturbative correlation correction have demonstrated competitive robustness in the computation of electronic excitation energies. Some of the most robust are those recently published by our group (M. Casanova-Páez, L. Goerigk, J. Chem. Theory Comput. 2021, 20, 5165). So far, the implementation of these functionals has not allowed correctly calculating their ground-state total energies. Herein, we define their correct spin-scaled ground-state energy expressions which enables us to test our methods on the noncovalent excited-state interaction energies of four aromatic excimers. A range of 22 double hybrids with and without spin scaling are compared to the reasonably accurate wavefunction reference from our previous work (A. C. Hancock, L. Goerigk, RSC Adv. 2023, 13, 35964). The impact of spin scaling is highly dependent on the underlying functional expression, however, the smallest overall errors belong to spin-scaled functionals with range separation: SCS- and SOS- ω PBEPP86, and SCS-RSX-QIDH. We additionally determine parameters for DFT-D3(BJ)/D4 ground-state dispersion corrections of these functionals, which reduce errors in most cases. We highlight the necessity of dispersion corrections for even the most robust TD-DFT methods but also point out that ground-state based corrections are insufficient to completely capture dispersion effects for excited-state interaction energies.

Effect of Benzo-Annelation on Triplet State Energies in Polycyclic Conjugated Hydrocarbons.

In a series of earlier studies, the effect of benzo-annelation was found to be a useful tool for tuning the aromaticity in polycyclic conjugated compounds to desired level. In this work we studied the (anti)aromaticity of benzo-annelated derivatives of three conjugated hydrocarbons (anthracene, fluoranthene and biphenylene) in their lowest lying singlet (S0) and triplet (T1) states by means of the energy effect (ef), harmonic oscillator model of aromaticity (HOMA), multicentre delocalization indices (MCI), magnetically induced current densities (MICDs) and nucleus independent chemical shifts (NICS). We showed that benzo-annelation is a topology-based effect which can be used to modify the T1 state excitation energies (E(T1)). A quantitative model was established being able to accurately predict the E(T1) based only on the numbers of angularly, linearly and geminally annelated benzene rings. In addition, it was demonstrated that the E(T1) can be directly related to the (anti)aromatic character of the central ring in the studied molecules in their S0 state.

The Excited-State N-H Tautomerization Rate in Free-Base Corroles.

Corrole is a tetrapyrrolic dye with a structure that resembles porphyrin, apart from a single missing carbon. The absence of this carbon results in the re-arrangement of the double bonds within the macrocycle, and the presence of three pyrrolic protons in the central cavity in its free-base form. These protons lead to the existence of two distinct tautomeric structures that exist in a dynamic equilibrium. Although the ground-state energies of the tautomers are similar, the excited states show a significant difference in energy which unbalances the equilibrium between the tautomers and results in rapid excited-state tautomerization, favouring one tautomeric species over the other. Although the excited-state tautomerization process has been known for a long time, very few studies have been performed on it, leaving many key aspects of the process poorly understood. Herein we show how ultrafast photoluminescence can be used to experimentally determine the rates of excited-state tautomerization and activation energies of three free-base corrole derivatives thus allowing us to completely describe the excited-state dynamics of the unusual excited state of free-base corrole and opening the door to the development of new materials that can exploit its unique characteristics.

The Origin of Dual-Emission in PLICT Compounds - an Empirical Approach.

Fluorescence spectroscopy proves to be a powerful and versatile tool in scientific research, demanding ongoing advancements of fluorescence probes to cater to a broad range of applications. The particular interest lies in the development of fluorophores with multiplexing capability, emitting from more than one excited state depending on the polarity and viscosity of the surrounding medium. Here, we present a variety of novel dual planarized intramolecular charge transfer (PLICT) emitters based on cyano-1-aminoindole structures. We have chosen a combination of experimental studies, theoretical calculations and the creation of a unique fluorophore cataloging map. This map serves as a useful tool for empirically determining the origin of both fluorescence bands.

Modeling Excited States of Molecular Organic Aggregates for Optoelectronics.

Light-driven phenomena in organic molecular aggregates underpin several mechanisms relevant to optoelectronic applications. Modeling these processes is essential for aiding the design of new materials and optimizing optoelectronic devices. In this review, we cover the use of different atomistic models, excited-state dynamics, and transport approaches for understanding light-activated phenomena in molecular aggregates, including radiative and nonradiative decay pathways. We consider both intra- and intermolecular mechanisms and focus on the role of conical intersections as facilitators of internal conversion. We explore the use of the exciton models for Frenkel and charge transfer states and the electronic structure methods and algorithms commonly applied for excited-state dynamics. Throughout the review, we analyze the approximations employed for the simulation of internal conversion, intersystem crossing, and reverse intersystem crossing rates and analyze the molecular processes behind single fission, triplet-triplet annihilation, Dexter energy transfer, and Förster energy transfer.

Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain.

The well-known phenomenon of phase separation in synthetic polymers and proteins has become a major topic in biophysics because it has been invoked as a mechanism of compartment formation in cells, without the need for membranes. Most of the coacervates (or condensates) are composed of Intrinsically Disordered Proteins (IDPs) or regions that are structureless, often in interaction with RNA and DNA. One of the more intriguing IDPs is the 526-residue RNA-binding protein, Fused in Sarcoma (FUS), whose monomer conformations and condensates exhibit unusual behavior that are sensitive to solution conditions. By focussing principally on the N-terminus low-complexity domain (FUS-LC comprising residues 1-214) and other truncations, we rationalize the findings of solid-state NMR experiments, which show that FUS-LC adopts a non-polymorphic fibril structure (core-1) involving residues 39-95, flanked by fuzzy coats on both the N- and C-terminal ends. An alternate structure (core-2), whose free energy is comparable to core-1, emerges only in the truncated construct (residues 110-214). Both core-1 and core-2 fibrils are stabilized by a Tyrosine ladder as well as hydrophilic interactions. The morphologies (gels, fibrils, and glass-like) adopted by FUS seem to vary greatly, depending on the experimental conditions. The effect of phosphorylation is site-specific. Simulations show that phosphorylation of residues within the fibril has a greater destabilization effect than residues that are outside the fibril region, which accords well with experiments. Many of the peculiarities associated with FUS may also be shared by other IDPs, such as TDP43 and hnRNPA2. We outline a number of problems for which there is no clear molecular explanation.

Role of Dark States and Stokes Shift Simulations for Tetraphenylpyrazine Compared to Other Donor-Acceptor Photosensitizers.

An excellent agreement for simulated and measured absorption and emission spectra is found for four donor-acceptor aromatic molecules (tetraphenylpyrazine, tetraphenylethene, distirylanthracene and hexaphenylsilole) whose derivatives serve as solid state photosensitizers. After comparing several hybrid TDDFT functionals, EOM-CCSD, and experiments, the best agreement was found with TD-B3LYP and double zeta basis sets (6-31G** and def2-SVP) for one molecule in gas phase. A full characterisation of twelve to twenty electronic excited states was performed in every system. Symmetry-forbidden bands are found in the absorption spectra by sampling fifty to hundred geometries from a Wigner distribution. The density of states in the region 2-6 eV was also analysed, showing a very packed region of excited states and suggesting that dark electronic states may play a role in the dynamics of some of the photoexcited systems. Further calculations were done with QM/xTB at geometries extracted from previously published X-ray data to evaluate the influence of the environment on the excitations of the four aggregated molecular crystals.

N-Aromatic Complexation in Tetraphenyl Porphyrin Iron (III)-Pyridine: Evidence of Spin-Flip via Gas-Phase Electronic Spectroscopy.

There is growing interest in the electronic properties of metalloporphyrins especially in relation to their interactions with other molecular species in their local environment. Here, UV-VIS laser photodissociation spectroscopy in vacuo has been applied to an iron-centred metalloporphyrin (FeTPP+) and its N-aromatic adduct with pyridine (py) to determine the electronic effect of complexation. Both the metalloporphyrin (FeTPP+) and pyridine adduct (FeTPP+⋅py) absorb strongly across the spectral region studied (652-302 nm: 1.91-4.10 eV). Notably, a large blue shift was observed for the dominant Soret band (41 nm) upon complexation (0.47 ± 0.02 eV), indicative of strong pyridine binding. Significant differences in the profiles (i.e. number and position of bands) of the electronic spectra are evident comparing FeTPP+ and FeTPP+⋅py. Time-dependent density functional theory calculations were used to assign the spectra, revealing that the FeIII spin-state flips from S = 3/2 to S = 5/2 upon complexation with pyridine. For FeTPP+, all bright spectral transitions are found to be π-π* in character, with electron density variously distributed across the porphyrin and/or its phenyl substituents. Similar electronic excitations are observed for FeTPP+⋅py, with an additional bright transition which involves charge transfer from the porphyrin to the pyridine moiety.

Reactive Oxygen Species Generated in Situ During Carbamazepine Photodegradation at 222 nm Far-UVC: Unexpected Role of H2O Molecules.

When 222 nm far-UVC is used to drive AOPs, photolysis emerges as a critical pathway for the degradation of numerous organic micropollutants (OMPs). However, the photodegradation mechanisms of the asymmetrically polarized OMPs at 222 nm remain unclear, potentially posing a knowledge barrier to the applications of far-UVC. This study selected carbamazepine (CBZ), a prevalent aquatic antiepileptic drug that degrades negligibly at 254 nm, to investigate its photodegradation mechanisms at 222 nm. Accelerated CBZ treatment by 222 nm far-UVC was mainly attributed to in situ ROS generation via self-sensitized photodegradation of CBZ. By quenching experiments and EPR tests, •OH radicals were identified as the major contributor to the CBZ photodegradation, whereas O2•- played a minor role. By deoxygenation and solvent exchange experiments, the H2O molecules were demonstrated to play a crucial role in deactivating the excited singlet state of CBZ (1CBZ*) at 222 nm: generating •OH radicals via electron transfer interactions with 1CBZ*. In addition, 1CBZ* could also undergo a photoionization process. The transformation products and pathways of CBZ at 222 nm were proposed, and the toxicities of CBZ's products were predicted. These findings provide valuable insights into OMPs' photolysis with 222 nm far-UVC, revealing more mechanistic details for far-UVC-driven systems.

Two-dimensional electronic-vibrational sum frequency spectroscopy for interactions of electronic and nuclear motions at interfaces.

Interactions of electronic and vibrational degrees of freedom are essential for understanding excited-states relaxation pathways of molecular systems at interfaces and surfaces. Here, we present the development of interface-specific two-dimensional electronic-vibrational sum frequency generation (2D-EVSFG) spectroscopy for electronic-vibrational couplings for excited states at interfaces and surfaces. We demonstrate this 2D-EVSFG technique by investigating photoexcited interface-active (E)-4-((4-(dihexylamino) phenyl)diazinyl)-1-methylpyridin-1- lum (AP3) molecules at the air-water interface as an example. Our 2D-EVSFG experiments show strong vibronic couplings of interfacial AP3 molecules upon photoexcitation and subsequent relaxation of a locally excited (LE) state. Time-dependent 2D-EVSFG experiments indicate that the relaxation of the LE state, S2, is strongly coupled with two high-frequency modes of 1,529.1 and 1,568.1 cm-1 Quantum chemistry calculations further verify that the strong vibronic couplings of the two vibrations promote the transition from the S2 state to the lower excited state S1 We believe that this development of 2D-EVSFG opens up an avenue of understanding excited-state dynamics related to interfaces and surfaces.

Minimal Molecular Building Blocks for Screening in Quasi-Two-Dimensional Organic-Inorganic Lead Halide Perovskites.

Layered hybrid organic-inorganic lead halide perovskites have intriguing optoelectronic properties, but some of the most interesting perovskite systems, such as defective, disordered, or mixed perovskites, require multiple unit cells to describe and are not accessible within state-of-the-art ab initio theoretical approaches for computing excited states. The principal bottleneck is the calculation of the dielectric matrix, which scales formally as O(N4). We develop here a fully ab initio approximation for the dielectric matrix, known as IPSA-2C, in which we separate the polarizability of the organic/inorganic layers into minimal building blocks, thus circumventing the undesirable power-law scaling. The IPSA-2C method reproduces the quasi-particle band structures and absorption spectra for a series of Ruddlesden-Popper perovskites to high accuracy, by including critical nonlocal effects neglected in simpler models, and sheds light on the complicated interplay of screening between the organic and inorganic sublattices.