Structure-function and engineering of plant UDP-glycosyltransferase

Natural products synthesized by plants have substantial industrial and medicinal values and are therefore attracting increasing interest in various related industries. Among the key enzyme families involved in the biosynthesis of natural products, uridine diphosphate-dependent glycosyltransferases (UGTs) play a crucial role in plants. In recent years, significant efforts have been made to elucidate the catalytic mechanisms and substrate recognition of plant UGTs and to improve them for desired functions. In this review, we presented a comprehensive overview of all currently published structures of plant UGTs, along with in-depth analyses of the corresponding catalytic and substrate recognition mechanisms. In addition, we summarized and evaluated the protein engineering strategies applied to improve the catalytic activities of plant UGTs, with a particular focus on high-throughput screening methods. The primary objective of this review is to provide readers with a comprehensive understanding of plant UGTs and to serve as a valuable reference for the latest techniques used to improve their activities.

Inverse condensation of adsorbed molecules with two conformations

Conventional gas-liquid phase transitions feature a coexistence line that has a monotonic and positive slope in line with our intuition that cooling always leads to condensation. Here, we study the inverse phenomenon, condensation of adsorbed organic molecules into dense domains upon heating. Our considerations are motivated by recent experiments [Aeschlimann et al., Angew. Chem., Int. Ed. 60, 19117-19122 (2021)], which demonstrate the partial dissolution of an ordered molecular monolayer and the mobilization of molecules upon cooling. We introduce a simple lattice model in which each site can have three states corresponding to unoccupied and two discernible molecular conformations. We investigate this model through Monte Carlo simulations, mean-field theory, and exact results based on the analytical solution of the Ising model in two dimensions. Our results should be broadly applicable to molecules with distinct conformations that have sufficiently different entropies or heat capacities.

Mobilization upon Cooling

Phase transitions between different aggregate states are omnipresent in nature and technology. Conventionally, a crystalline phase melts upon heating as we use ice to cool a drink. Already in 1903, Gustav Tammann speculated about the opposite process, namely melting upon cooling. So far, evidence for such "inverse" transitions in real materials is rare and limited to few systems or extreme conditions. Here, we demonstrate an inverse phase transition for molecules adsorbed on a surface. Molybdenum tetraacetate on copper(111) forms an ordered structure at room temperature, which dissolves upon cooling. This transition is mediated by molecules becoming mobile, i.e., by mobilization upon cooling. This unexpected phenomenon is ascribed to the larger number of internal degrees of freedom in the ordered phase compared to the mobile phase at low temperatures.

Temperature-Dependent Electronic Ground-State Charge Transfer in van der Waals Heterostructures

Electronic charge rearrangement between components of a heterostructure is the fundamental principle to reach the electronic ground state. It is acknowledged that the density of state distribution of the components governs the amount of charge transfer, but a notable dependence on temperature is not yet considered, particularly for weakly interacting systems. Here, it is experimentally observed that the amount of ground-state charge transfer in a van der Waals heterostructure formed by monolayer MoS₂ sandwiched between graphite and a molecular electron acceptor layer increases by a factor of 3 when going from 7 K to room temperature. State-of-the-art electronic structure calculations of the full heterostructure that accounts for nuclear thermal fluctuations reveal intracomponent electron-phonon coupling and intercomponent electronic coupling as the key factors determining the amount of charge transfer. This conclusion is rationalized by a model applicable to multicomponent van der Waals heterostructures.

Evolution of Electronic Structures of Polar Phthalocyanine-Substrate Interfaces

The electronic structures and core-level spectra of chlorogallium phthalocyanine (ClGaPc) molecules of different thicknesses (submonolayer to multilayer) adsorbed on a polycrystalline Au substrate and a highly oriented pyrolytic graphite (HOPG) substrate, before and after thermal annealing, were investigated using photoelectron spectroscopic techniques for better understanding the charge-transfer properties. The energy-level diagrams (ELDs) of the ClGaPc thin films are found to evolve with film thickness, substrate nature, and thermal annealing. The interfacial dipole moment in the active Au substrate and the molecular dipole moment in the inactive HOPG substrate mainly dictate the ELD. Annealed monolayer films on both the substrates seem to adopt a similar well-ordered Cl-up orientated molecular organization, which is quite interesting, as it certainly indicates a substrate-nature-independent energy minimum configuration. The strong interaction of the active Au substrate gives rise to additional charge transfer and state transfer (of Ga) as evident from the formation of a former lowest unoccupied molecular orbital (F-LUMO) level in the highest occupied molecular orbital (HOMO) region and a low binding energy peak in the Ga 2p_3/2 core level. The presence of strong F-LUMO and molecular-dipole-related HOMO_d levels in the predicted monolayer of well-ordered Cl-up oriented molecules on the Au and HOPG substrates, respectively, creates the optimum energy-level alignment (ELA) for both the systems, while the opposite shift of the vacuum levels in two different substrates makes the ionization potential (IP) for such a monolayer either minimum (on the Au substrate) or maximum (on the HOPG substrate), which is useful information for tuning the charge injection across the interface in organic semiconductor-based devices.

Binding and electronic level alignment of π-conjugated systems on metals

We review the binding and energy level alignment of π-conjugated systems on metals, a field which during the last two decades has seen tremendous progress both in terms of experimental characterization as well as in the depth of theoretical understanding. Precise measurements of vertical adsorption distances and the electronic structure together with ab initio calculations have shown that most of the molecular systems have to be considered as intermediate cases between weak physisorption and strong chemisorption. In this regime, the subtle interplay of different effects such as covalent bonding, charge transfer, electrostatic and van der Waals interactions yields a complex situation with different adsorption mechanisms. In order to establish a better understanding of the binding and the electronic level alignment of π-conjugated molecules on metals, we provide an up-to-date overview of the literature, explain the fundamental concepts as well as the experimental techniques and discuss typical case studies. Thereby, we relate the geometric with the electronic structure in a consistent picture and cover the entire range from weak to strong coupling.

Sticking with the Pointy End? Molecular Configuration of Chloro Boron-Subphthalocyanine on Cu(111)

In this combined low-temperature scanning tunneling microscopy (STM) and density functional theory (DFT) study, we investigate self-assembly of the dipolar nonplanar organic semiconductor chloro boron-subphthalocyanine (ClB-SubPc) on Cu(111). We observe multiple distinct adsorption configurations and demonstrate that these can only be understood by taking surface-catalyzed dechlorination into account. A detailed investigation of possible adsorption configurations and the comparison of experimental and computational STM images demonstrates that the configurations correspond to "Cl-up" molecules with the B-Cl moiety pointing toward the vacuum side of the interface, and dechlorinated molecules. In contrast to the standard interpretation of adsorption of nonplanar molecules in the phthalocyanine family, we find no evidence for "Cl-down" molecules where the B-Cl moiety would be pointing toward the Cu surface. We show computationally that such a configuration is unstable and thus is highly unlikely to occur for ClB-SubPc on Cu(111). Using these assignments, we discuss the different self-assembly motifs in the submonolayer coverage regime. The combination of DFT and STM is essential to gain a full atomistic understanding of the surface-molecule interactions, and our findings imply that phthalocyanines may undergo surface-catalyzed reactions hitherto not considered. Our results also indicate that care has to be taken when analyzing possible adsorption configurations of polar members of the phthalocyanine family, especially when they are adsorbed on comparably reactive surfaces like Cu(111).

Decacyclene Trianhydride at Functional Interfaces: An Ideal Electron Acceptor Material for Organic Electronics

We report the interface energetics of decacyclene trianhydride (DTA) monolayers on top of two distinct model surfaces, namely, Au(111) and Ag(111). On the latter, combined valence band photoemission and X-ray absorption measurements that access the occupied and unoccupied molecular orbitals, respectively, reveal that electron transfer from substrate to surface sets in. Density functional theory calculations confirm our experimental findings and provide an understanding not only of the photoemission and X-ray absorption spectral features of this promising organic semiconductor but also of the fingerprints associated with the interface charge transfer.

Inverse transitions in a spin-glass model on a scale-free network

In this paper, we will investigate critical phenomena by considering a model spin glass on scale-free networks. For this purpose, we consider the Ghatak-Sherrington (GS) model, a spin-1 spin-glass model with a crystal field, instead of the usual Ising-type model. Scale-free networks on which the GS model is placed are constructed from the static model, in which the number of vertices is fixed from the beginning. On the basis of the replica-symmetric solution, we obtain the analytical solutions, i.e., free energy and order parameters, and we derive the various phase diagrams consisting of the paramagnetic, ferromagnetic, and spin-glass phases as functions of temperature T, the degree exponent λ, the mean degree K, and the fraction of the ferromagnetic interactions ρ. Since the present model is based on the GS model, which considers the three states (S = 0, ± 1), the S = 0 state plays a crucial role in the λ-dependent critical behavior: glass transition temperature T(g) has a finite value, even when 2 < λ < 3. In addition, when the crystal field becomes nonzero, the present model clearly exhibits three types of inverse transitions, which occur when an ordered phase is more entropic than a disordered one.

Spin-1 Hopfield model under a random field

The goal of the present work is to investigate the role of trivial disorder and nontrivial disorder in the three-state Hopfield model under a Gaussian random field. In order to control the nontrivial disorder, the Hebb interaction is used. This provides a way to control the system frustration by means of the parameter a=p/N, varying from trivial randomness to a highly frustrated regime, in the thermodynamic limit. We performed the thermodynamic analysis using the one-step replica-symmetry-breaking mean field theory to obtain the order parameters and phase diagrams for several strengths of a, the anisotropy constant, and the random field.

Adsorption site determination of a molecular monolayer via inelastic tunneling

We have combined scanning tunneling microscopy with inelastic electron tunneling spectroscopy (IETS) and density functional theory (DFT) to study a tetracyanoethylene monolayer on Ag(100). Images show that the molecules arrange in locally ordered patterns with three nonequivalent, but undeterminable, adsorption sites. While scanning tunneling spectroscopy only shows subtle variations of the local electronic structure at the three different positions, we find that vibrational modes are very sensitive to the local atomic environment. IETS detects sizable mode frequency shifts of the molecules located at the three topographically detected sites, which permits us to determine the molecular adsorption sites through identification with DFT calculations.

Spin-glass splitting in the quantum Ghatak-Sherrington model

We propose an expanded spin-glass model, called the quantum Ghatak-Sherrington model, which considers spin-1 quantum spin operators in a crystal field and in a transverse field. The analytic solutions and phase diagrams of this model are obtained by using the one-step replica symmetry-breaking ansatz under the static approximation. Our results represent the splitting within one spin-glass (SG) phase depending on the values of crystal and transverse fields. The two separated SG phases, characterized by a density of filled states, show certain differences in their shapes and phase boundaries. Such SG splitting becomes more distinctive when the degeneracy of the empty states of spins is larger than one of their filled states.

Azimuthal reorientation of pentacene upon 2D condensation

We report a novel two-dimensional gas-solid phase transition of pentacene molecules on the Cu(110)-(2 × 1)O surface where the 2D condensation is accompanied by a reversible azimuthal rotation of the pentacene molecules. The change of the optical anisotropy associated with this reorientation allows us to explore the 2D condensation as a function of coverage and temperature by reflectance difference spectroscopy. As a result, the 2D heat of condensation of pentacene on Cu(110)-(2 × 1)O is determined to be 84 meV, which is more than one order of magnitude smaller than the respective value for 3D crystallization.

Nanoscale assembly of paramagnetic organic radicals on Au(111) single crystals

The successful thin-film deposition of a pyrene-substituted nitronyl nitroxide radical under controlled conditions has been demonstrated. The electronic properties, chemical environment at the interface, and morphology of the thin films have been investigated by a multitechnique approach. Spectroscopic and morphological analyses indicate a Stranski-Krastanov growth mode and weak physisorption of molecules onto the metallic surface. Electron spin resonance (ESR) spectroscopy shows that evaporation processes and deposition do not affect the paramagnetic character of the molecules. Useful concepts for the engineering of new, purely organic-based magnets, which may open the way to fruitful exploitation of organic molecular-beam deposition for assembly on solid surfaces in view of future technological applications, are presented.

Inverse freezing in a cluster Ising spin-glass model with antiferromagnetic interactions

Inverse freezing is analyzed in a cluster spin-glass (SG) model that considers infinite-range disordered interactions between magnetic moments of different clusters (intercluster interaction) and short-range antiferromagnetic coupling J(1) between Ising spins of the same cluster (intracluster interaction). The intercluster disorder J is treated within a mean-field theory by using a framework of one-step replica symmetry breaking. The effective model obtained by this treatment is computed by means of an exact diagonalization method. With the results we build phase diagrams of temperature T/J versus J(1)/J for several sizes of clusters n(s) (number of spins in the cluster). The phase diagrams show a second-order transition from the paramagnetic phase to the SG order at the freezing temperature T(f) when J(1)/J is small. The increase in J(1)/J can then destroy the SG phase. It decreases T(f)/J and introduces a first-order transition. In addition, inverse freezing can arise at a certain range of J(1)/J and large enough n(s). Therefore, the nontrivial frustration generated by disorder and short-range antiferromagnetic coupling can introduce inverse freezing spontaneously.

Inverse freezing in the Ghatak-Sherrington model with a random field

The present work studies the Ghatak-Sherrington (GS) model in the presence of a magnetic random field (RF). Previous results obtained from the GS model without a RF suggest that disorder and frustration are the key ingredients to produce spontaneous inverse freezing (IF). However, in this model, the effects of disorder and frustration always appear combined. In that sense, the introduction of RF allows us to study the IF under the effects of a disorder which is not a source of frustration. The problem is solved within the one step replica symmetry approximation. The results show that the first order transition between the spin glass and the paramagnetic phases, which is related to the IF for a certain range of crystal field D, is gradually suppressed when the RF is increased.