Structured States of Disordered Proteins from Genomic Sequences.

Protein flexibility ranges from simple hinge movements to functional disorder. Around half of all human proteins contain apparently disordered regions with little 3D or functional information, and many of these proteins are associated with disease. Building on the evolutionary couplings approach previously successful in predicting 3D states of ordered proteins and RNA, we developed a method to predict the potential for ordered states for all apparently disordered proteins with sufficiently rich evolutionary information. The approach is highly accurate (79%) for residue interactions as tested in more than 60 known disordered regions captured in a bound or specific condition. Assessing the potential for structure of more than 1,000 apparently disordered regions of human proteins reveals a continuum of structural order with at least 50% with clear propensity for three- or two-dimensional states. Co-evolutionary constraints reveal hitherto unseen structures of functional importance in apparently disordered proteins.

Ultrafast Coherent Exciton Couplings and Many-Body Interactions in Monolayer WS2.

Transition metal dichalcogenides (TMDs) are quantum confined systems with interesting optoelectronic properties, governed by Coulomb interactions in the monolayer (1L) limit, where strongly bound excitons provide a sensitive probe for many-body interactions. Here, we use two-dimensional electronic spectroscopy (2DES) to investigate many-body interactions and their dynamics in 1L-WS2 at room temperature and with sub-10 fs time resolution. Our data reveal coherent interactions between the strongly detuned A and B exciton states in 1L-WS2. Pronounced ultrafast oscillations of the transient optical response of the B exciton are the signature of a coherent 50 meV coupling and coherent population oscillations between the two exciton states. Supported by microscopic semiconductor Bloch equation simulations, these coherent dynamics are rationalized in terms of Dexter-like interactions. Our work sheds light on the role of coherent exciton couplings and many-body interactions in the ultrafast temporal evolution of spin and valley states in TMDs.

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.

Subthalamic and pallidal oscillations and their couplings reflect dystonia severity and improvements by deep brain stimulation.

BACKGROUND: Deep brain stimulation (DBS) targeting the globus pallidus internus (GPi) and subthalamic nucleus (STN) is employed for the treatment of dystonia. Pallidal low-frequency oscillations have been proposed as a pathophysiological marker for dystonia. However, the role of subthalamic oscillations and STN-GPi coupling in relation to dystonia remains unclear. OBJECTIVE: We aimed to explore oscillatory activities within the STN-GPi circuit and their correlation with the severity of dystonia and efficacy achieved by DBS treatment. METHODS: Local field potentials were recorded simultaneously from the STN and GPi from 13 dystonia patients. Spectral power analysis was conducted for selected frequency bands from both nuclei, while power correlation and the weighted phase lag index were used to evaluate power and phase couplings between these two nuclei, respectively. These features were incorporated into generalized linear models to assess their associations with dystonia severity and DBS efficacy. RESULTS: The results revealed that pallidal theta power, subthalamic beta power and subthalamic-pallidal theta phase coupling and beta power coupling all correlated with clinical severity. The model incorporating all selected features predicts empirical clinical scores and DBS-induced improvements, whereas the model relying solely on pallidal theta power failed to demonstrate significant correlations. CONCLUSIONS: Beyond pallidal theta power, subthalamic beta power, STN-GPi couplings in theta and beta bands, play a crucial role in understanding the pathophysiological mechanism of dystonia and developing optimal strategies for DBS.

Spin-Vibronic Coupling Controls the Intersystem Crossing of Iodine-Substituted BODIPY Triplet Chromophores.

4,4-Difluoro-4-borata-3a-azonia-4a-aza-s-indacene (BODIPY) dyes are extensively used in various applications of their triplet states, ranging from photoredox catalysis, through triplet sensitization to photodynamic therapy. However, the rational design of BODIPY triplet chromophores by ab initio modelling is limited by their strong interactions of spin, electronic and vibrational dynamics. In particular, spin-vibronic coupling is often overlooked when estimating intersystem crossing (ISC) rates. In this study, a combined experimental and theoretical approach using spin-vibronic coupling to correctly describe ISC in BODIPY dyes was developed. For this purpose, seven π-extended BODIPY derivatives with iodine atoms in different positions were examined. It was found that the heavy-atom effect of iodine atoms is site specific, causing high triplet yields in only some positions. This site-specific ISC was explained by El-Sayed rules, so both the contribution and character of the molecular orbitals involved in the excitation must be considered when predicting the ISC rates. Overall, the rational design of BODIPY triplet chromophores requires using (i) the high-quality electronic structure theory, including both static and dynamical correlations; and (ii) the two-component wave function Hamiltonian, and rationalizing; and (iii) ISC based on the character of the molecular orbitals of heavy atoms involved in the excitation, expanding El-Sayed rules beyond their traditional applications.

13C CSA Tensors and Orientational Order of Model and Dimer Mesogens Comprising of Phenyl Benzoate.

A Model mesogen and its symmetrical Dimer made up of phenyl benzoate core unit are investigated by 13C NMR spectroscopy. The existence of layer order in smectic A and smectic C phases of Dimer mesogen is established by powder X-ray diffraction. The chemical shift anisotropy (CSA) tensors of Model mesogen are determined by 2D separation of undistorted powder patterns by effortless recoupling (SUPER) experiment and are utilized for calculating the order parameters employing the alignment-induced chemical shifts (AIS). Additionally, 2D separated local field (SLF) NMR is availed for extracting 13C-1H dipolar couplings for both mesogens and used for computing the order parameters. A good agreement in the order parameters calculated from 13C-1H dipolar couplings and AIS is observed. Accordingly, the main order parameter (Szz) for the phenyl rings of the Model mesogen is found to be in the range 0.54-0.82, and for the Dimer mesogen, the values span 0.64-0.82 across mesophases. Since the phenyl benzoate core unit is frequently employed structural moiety for constructing the main chain as well as side chain liquid crystalline polymers and liquid crystalline elastomers, the CSA tensors reported here will be of immense utility for the structural characterization of these materials.

Steady as they hover: kinematics of kestrel wing and tail morphing during hovering flights.

Wind-hovering birds exhibit remarkable steadiness in flight, achieved through the morphing of their wings and tail. We analysed the kinematics of two nankeen kestrels (Falco cenchroides) engaged in steady wind-hovering flights in a smooth flow wind tunnel. Motion-tracking cameras were used to capture the movements of the birds as they maintained their position. The motion of the birds' head and body, and the morphing motions of their wings and tail were tracked and analysed using correlation methods. The results revealed that wing sweep, representing the flexion/extension movement of the wing, played a significant role in wing motion. Additionally, correlations between different independent degrees of freedom (DoF), including wing and tail coupling, were observed. These kinematic couplings indicate balancing of forces and moments necessary for steady wind hovering. Variation in flight behaviour between the two birds highlighted the redundancy of DoF and the versatility of wing morphing in achieving control. This study provides insights into fixed-wing craft flight control from the avian world and may inspire novel flight control strategies for future fixed-wing aircraft.

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.

Extracting Scalar Couplings From Complex 1H NMR Spectra Using a Simple 2D J-Resolved Sequence.

Measurement of scalar couplings between protons is a very challenging task because of complex multiplet patterns and severe overlapping of these multiplets in congested 1D spectra. Numerous 2D J-resolved sequences now exist that utilize either the Zangger-Sterk or PSYCHE or z-filter elements along with selective refocusing and pure-shift schemes to generate high-resolution phase-sensitive spectra with simple doublets in F 1 $$ {F}_1 $$ dimension. Herein, we present a 2D J-resolved sequence that employs a simple element consisting of hard pulses and inter-pulse delays to generate phase-sensitive spectra. This simple element in combination with selective refocusing eliminates all the undesired components including the intense axial peaks, thus provides clean 2D J-resolved spectra with signals of only two targeted protons with simple doublets in F 1 $$ {F}_1 $$ dimension and full multiplets of target protons in F 2 $$ {F}_2 $$ dimension. This high selectivity thus obviates the need for extra filtering elements and pure-shift acquisition schemes that are integrated into existing sequences to facilitate coupling measurements in overcrowded signals. It is therefore anticipated that this sequence, with the ease of implementation and ability to extract coupling values from highly congested spectra, should turn out an important tool for structural and conformational analyses in chemical and biological studies.

Full configurational and conformational analysis of artemisinin by one-bond carbon-carbon residual dipolar couplings at natural abundance.

Configurational and conformational analysis of the biologically relevant natural product artemisinin was conducted using carbon-carbon residual dipolar couplings (1DCC RDCs) at natural abundance. These RDCs were measured through the 2D-INADEQUATE NMR experiment using a sample aligned in a compressed poly (methyl methacrylate) (PMMA) gel swollen in CDCl3. Singular value decomposition (SVD) fitting analysis of all carbon-carbon bonds, 1DCC RDCs, in relation to the full configuration/conformational space (32 diastereoisomers) of artemisinin, unambiguously identified the correct configuration of artemisinin.

Hydrogen bond formation may enhance RDC-based discrimination of enantiomers.

The distinction of enantiomers based on residual anisotropic parameters obtained by alignment in chiral poly-γ-benzyl-L-glutamate (PBLG) is among the strongest in high-resolution NMR spectroscopy. However, large variations in enantiodifferentiation among different solutes are frequently observed. One hypothesis is that the formation of hydrogen bonds between solute and PBLG is important for the distinction of enantiomers. With a small set of three almost spherical enantiomeric pairs, for which 1DCH residual dipolar couplings are measured, we address this issue in a systematic way: borneol contains a single functional group that can act as a hydrogen bond donor, camphor has a single group that may act as a hydrogen bond acceptor, and quinuclidinol can act as both hydrogen bond donor and acceptor. The results are unambiguous: although camphor shows low enantiodifferentiation with PBLG and alignment that can be predicted well by the purely steric TRAMITE approach, the distinction of enantiomers for the other enantiomeric pairs is significantly higher with alignment properties that must involve a specific interaction in addition to steric alignment.

DFT investigation of coupling constant anomalies in substituted ß-lactams.

ß-lactams are a chemically diverse group of molecules with a wide range of biological activities. Having recently observed curious trends in 2JHH coupling values in studies on this structural class, we sought to obtain a more comprehensive understanding of these diagnostic NMR parameters, specifically interrogating 1JCH, 2JCH, and 2JHH, to differentiate 3- and 4-monosubstituted ß-lactams. Further investigation using computational chemistry methods was employed to explore the geometric and electronic origins for the observed and calculated differences between the two substitution patterns.

Revealing elusive conformations of sucrose from hydrogen bond J-coupling in H2O: A combined NMR and quantum mechanics study.

Hydrogen bonding is a crucial feature of biomolecules, but its characterization in glycans dissolved in aqueous solutions is challenging due to rapid hydrogen exchange between hydroxyl groups and H2O. In principle, the scalar (J) coupling constant can reveal the relative orientation of the atoms in the molecule. In contrast to J-coupling through H-bonds reported in proteins and nucleic acids, research on J-coupling through H-bonds in glycans dissolved in water is lacking. Here, we use sucrose as a model system for H-bonding studies; its structure, which consists of glucose (Glc) and fructose (Frc), is well-studied, and it is readily available. We apply the in-phase, antiphase-HSQC-TOCSY and quantify previously unreported through H-bond J-values for Frc-OH1-Glc-OH2 in H2O. While earlier reports of Brown and Levy indicate this H-bond as having only a single direction, our reported findings indicate the potential presence of two involving these same atoms, namely, G2OH âž” F1O and F1OH âž” G2O (where F and G stand for Frc and Glc, respectively). The calculated density functional theory J-values for the G2OH âž” F1O agree with the experimental values. Additionally, we detected four other possible H-bonds in sucrose, which require different phi, psi (ϕ, ψ) torsion angles. The ϕ, ψ values are consistent with previous predictions of du Penhoat et al. and Venable et al. Our results will provide new insights into the molecular structure of sucrose and its interactions with proteins.

Simulation of oriented NMR spectra: Combining molecular dynamics and chemical shift tensor calculations.

Solid state NMR is widely used to study the orientation and other structural features of proteins and peptides in lipid bilayers. Using data obtained by PISEMA (Polarization Inversion Spin Exchange at Magic Angle) experiments, periodic spectral patterns arise from well-aligned α-helical molecules. Significant problems in the interpretation of PISEMA spectra may arise for systems that do not form perfectly defined secondary structures, like α-helices, or the signal pattern is disturbed by molecular motion. Here, we present a new method that combines molecular dynamics simulation with tensorial orientational constraints (MDOC) and chemical shift tensor calculations for the simulation and interpretation of PISEMA-like spectra. The calculations include the spectra arising from non α-helical molecules and molecules with non-uniform intrinsic mobility. In a first step, dipolar or quadrupolar interaction tensors drive molecular rotations and reorientations to obtain the proper mean values as observed in corresponding NMR experiments. In a second step, the coordinate snapshots of the MDOC simulations are geometry optimized with the isotropic 15 N chemical shifts as constraints using Bond Polarization Theory (BPT) to provide reliable 15 N CS tensor data. The averaged dipolar 1 H-15 N couplings and the δzz tensor components can then be combined to simulate PISEMA patterns. We apply this method to the ß-helical peptide gramicidin A (gA) and demonstrate that this method enables the assignment of most PISEMA resonances. In addition, MDOC simulations provide local order parameters for the calculated sites. These local order parameters reveal large differences in backbone mobility between L- and D-amino acids of gA.

A Simple Expression for the Screening of Excitonic Couplings between Chlorophylls as Inferred for Photosystem I Trimers.

The Coulomb coupling between transition densities of the pigments in photosynthetic pigment-protein complexes, termed excitonic coupling, is a key factor for the description of optical spectra and energy transfer. A challenging question is the quantification of the screening of the excitonic coupling by the optical polarizability of the environment. We use the equivalence between the sophisticated quantum chemical polarizable continuum (PCM) model and the simple electrostatic Poisson-TrEsp approach to analyze the distance and orientation dependence of the dielectric screening between chlorophylls in photosystem I trimers. On the basis of these calculations we find that the vacuum couplings Vmn(0) and the couplings in the dielectric medium Vmn=fmnVmn(0) are related by the empirical screening factor fmn=0.60+39.6θ(|κmn|-1.17)exp(-0.56Rmn/Å), where κmn is the usual orientational factor of the dipole-dipole coupling between the pigments, Rmn is the center-to-center distance, and the Heaviside-function θ(|κmn|-1.17) ensures that the exponential distance dependence only contributes for in-line type dipole geometries. We are confident that the present expression can be applied also to other pigment-protein complexes with chlorophyll or related pigments of similar shape. The variance between the Poisson-TrEsp and the approximate coupling values is found to decrease by a factor of 8 and 3-4 using the present expression, instead of an exponential distance dependent or constant screening factor, respectively, assumed previously in the literature.

Bond Formation at C8 in the Nucleoside and Nucleotide Purine Scaffold: An Informative Selection.

This paper presents methods for the introduction and exchange of substituents in a nucleobase and its nucleosides and nucleotides with emphasis on the C8-position in the purine skeleton. The nucleobase is open for electrophilic and nucleophilic chemistry. The nucleophilic chemistry consists mainly of displacement reactions when the C8-substituent is a good leaving group such as a halogen atom. The heteroatom in amines, sulfides, or oxides is a good nucleophile. Halides are good reaction partners. Metal-promoted cross-coupling reactions are important for carbylations. Direct oxidative metalation reactions using sterically hindered metal amides offer chemo- and regio-selectivity besides functional tolerance and simplicity. The carbon site is highly nucleophilic after metalation and adds electrophiles resulting in chemical bond formation. Conditions for metal-assisted reactions are described for nucleobases and their glycosides.

Organotransition Metal Chemistry of Terpenes: Syntheses, Structures, Reactivity and Molecular Rearrangements.

The impact of organometallic chemistry on the terpene field only really blossomed in the 1960s and 1970s with the realisation that carbon-carbon bond formation under mild conditions could be achieved by using nickel or iron carbonyls as synthetic reagents. Concomitantly, the development of palladium derivatives capable of the controlled coupling of isoprene units attracted the attention of numerous highly talented researchers, including future Nobel laureates. We discuss briefly how early work on the syntheses of simple monoterpenes soon progressed to sesquiterpenes and diterpenes of increasing complexity, such as humulene, flexibilene, vitamin A, or pheromones of commercial value, in particular those used in perfumery (muscone, lavandulol), or grandisol and red scale pheromone as replacements for harmful pesticides. As the field progressed, there has been more emphasis on developing organometallic routes to enantiopure rather than racemic products, as well as gaining precise mechanistic data on the transformations, notably the course of metal-promoted molecular rearrangements that have long been a feature of terpene chemistry. We note the impact of the enormously enhanced analytical techniques, high-field NMR spectroscopy and X-ray crystallography, and their use to re-examine the originally proposed structures of terpenes and their organometallic derivatives. Finally, we highlight the very recent ground-breaking use of the crystalline sponge method to acquire structural data on low-melting or volatile terpenes. The literature cited herein covers the period 1959 to 2023.

Estimating nonlinear effects of random slopes: A comparison of multilevel structural equation modeling with a two-step, a single-indicator, and a plausible values approach.

Multilevel structural equation modeling (MSEM) is a statistical framework of major relevance for research concerned with people's intrapersonal dynamics. An application domain that is rapidly gaining relevance is the study of individual differences in the within-person association (WPA) of variables that fluctuate over time. For instance, an individual's social reactivity - their emotional response to social situations - can be represented as the association between repeated measurements of the individual's social interaction quantity and momentary well-being. MSEM allows researchers to investigate the associations between WPAs and person-level outcome variables (e.g., life satisfaction) by specifying the WPAs as random slopes in the structural equation on level 1 and using the latent representations of the slopes to predict outcomes on level 2. Here, we are concerned with the case in which a researcher is interested in nonlinear effects of WPAs on person-level outcomes - a U-shaped effect of a WPA, a moderation effect of two WPAs, or an effect of congruence between two WPAs - such that the corresponding MSEM includes latent interactions between random slopes. We evaluate the nonlinear MSEM approach for the three classes of nonlinear effects (U-shaped, moderation, congruence) and compare it with three simpler approaches: a simple two-step approach, a single-indicator approach, and a plausible values approach. We use a simulation study to compare the approaches on accuracy of parameter estimates and inference. We derive recommendations for practice and provide code templates and an illustrative example to help researchers implement the approaches.

Photoexcitation of Distinct Divalent Palladium Complexes in Cross-Coupling Amination Under Air.

The development of metal complexes that function as both photocatalyst and cross-coupling catalyst remains a challenging research topic. So far, progress has been shown in palladium(0) excited-state transition metal catalysis for the construction of carbon-carbon bonds where the oxidative addition of alkyl/aryl halides to zero-valent palladium (Pd0 ) is achievable at room temperature. In contrast, the analogous process with divalent palladium (PdII ) is uphill and endothermic. For the first time, we report that divalent palladium can act as a light-absorbing species that undergoes double excitation to realize carbon-nitrogen (C-N) cross-couplings under air. Differently substituted aryl halides can be applied in the mild, and selective cross-coupling amination using palladium acetate as both photocatalyst and cross-coupling catalyst at room temperature. Density functional theory studies supported by mechanistic investigations provide insight into the reaction mechanism.

Mechanisms for radical reactions initiating from N-hydroxyphthalimide esters.

Due to their ease of preparation, stability, and diverse reactivity, N-hydroxyphthalimide (NHPI) esters have found many applications as radical precursors. Mechanistically, NHPI esters undergo a reductive decarboxylative fragmentation to provide a substrate radical capable of engaging in diverse transformations. Their reduction via single-electron transfer (SET) can occur under thermal, photochemical, or electrochemical conditions and can be influenced by a number of factors, including the nature of the electron donor, the use of Brønsted and Lewis acids, and the possibility of forming charge-transfer complexes. Such versatility creates many opportunities to influence the reaction conditions, providing a number of parameters with which to control reactivity. In this perspective, we provide an overview of the different mechanisms for radical reactions involving NHPI esters, with an emphasis on recent applications in radical additions, cyclizations and decarboxylative cross-coupling reactions. Within these reaction classes, we discuss the utility of the NHPI esters, with an eye towards their continued development in complexity-generating transformations.