Impact of DNA on interactions between core proteins of Hepatitis B virus-like particles comprising different C-terminals.

Hepatitis B virus (HBV) virus-like particles (VLPs) are promising therapeutic agents derived from HBV core proteins (Cp). This study investigates the assembly dynamics of HBV VLPs, which is crucial for their potential as drug carriers or gene delivery systems. Coarse-grained molecular dynamics simulations explore the impact of C-terminal domain length (in the Cp ranging from Cp149 to wild-type Cp183) on Cp assembly and stability, particularly in the presence of DNA. Our findings reveal that the C-terminal nucleic acid binding region significantly influences Cp assembly and stability of trimers comprising Cp dimers. Shorter C-terminal domains (Cp164, Cp167) enhance stability and protein-protein interactions, while interactions between naturally occurring Cp183 are destabilized in the absence of DNA. Interestingly, DNA addition further stabilizes Cp assemblies, and this effect is influenced by the length of the nucleic acid binding region. Shorter C-terminal domains show less dependency on DNA content. This stabilization is attributed to electrostatic forces between positively charged C-terminal chains and negatively charged nucleic acids. Our study sheds light on the molecular mechanisms governing protein-protein and protein-DNA interactions in HBV VLP assembly, providing insights into Cp processability and informing the development of efficient gene therapy carriers using VLP technology.

On-off conduction photoswitching in modelled spiropyran-based metal-organic frameworks.

Materials with photoswitchable electronic properties and conductance values that can be reversibly changed over many orders of magnitude are highly desirable. Metal-organic framework (MOF) films functionalized with photoresponsive spiropyran molecules demonstrated the general possibility to switch the conduction by light with potentially large on-off-ratios. However, the fabrication of MOF materials in a trial-and-error approach is cumbersome and would benefit significantly from in silico molecular design. Based on the previous proof-of-principle investigation, here, we design photoswitchable MOFs which incorporate spiropyran photoswitches at controlled positions with defined intermolecular distances and orientations. Using multiscale modelling and automated workflow protocols, four MOF candidates are characterized and their potential for photoswitching the conductivity is explored. Using ab initio calculations of the electronic coupling between the molecules in the MOF, we show that lattice distances and vibrational flexibility tremendously modulate the possible conduction photoswitching between spiropyran- and merocyanine-based MOFs upon light absorption, resulting in average on-off ratios higher than 530 and 4200 for p- and n-conduction switching, respectively. Further functionalization of the photoswitches with electron-donating/-withdrawing groups is demonstrated to shift the energy levels of the frontier orbitals, permitting a guided design of new spiropyran-based photoswitches towards controlled modification between electron and hole conduction in a MOF.

Multiscale Model of CVD Growth of Graphene on Cu(111) Surface.

Due to its outstanding properties, graphene has emerged as one of the most promising 2D materials in a large variety of research fields. Among the available fabrication protocols, chemical vapor deposition (CVD) enables the production of high quality single-layered large area graphene. To better understand the kinetics of CVD graphene growth, multiscale modeling approaches are sought after. Although a variety of models have been developed to study the growth mechanism, prior studies are either limited to very small systems, are forced to simplify the model to eliminate the fast process, or they simplify reactions. While it is possible to rationalize these approximations, it is important to note that they have non-trivial consequences on the overall growth of graphene. Therefore, a comprehensive understanding of the kinetics of graphene growth in CVD remains a challenge. Here, we introduce a kinetic Monte Carlo protocol that permits, for the first time, the representation of relevant reactions on the atomic scale, without additional approximations, while still reaching very long time and length scales of the simulation of graphene growth. The quantum-mechanics-based multiscale model, which links kinetic Monte Carlo growth processes with the rates of occurring chemical reactions, calculated from first principles makes it possible to investigate the contributions of the most important species in graphene growth. It permits the proper investigation of the role of carbon and its dimer in the growth process, thus indicating the carbon dimer to be the dominant species. The consideration of hydrogenation and dehydrogenation reactions enables us to correlate the quality of the material grown within the CVD control parameters and to demonstrate an important role of these reactions in the quality of the grown graphene in terms of its surface roughness, hydrogenation sites, and vacancy defects. The model developed is capable of providing additional insights to control the graphene growth mechanism on Cu(111), which may guide further experimental and theoretical developments.

Twisting of Porphyrin by Assembly in a Metal-Organic Framework yielding Chiral Photoconducting Films for Circularly-Polarized-Light Detection.

While materials based on organic molecules usually have either superior optoelectronic or superior chiral properties, the combination of both is scarce. Here, a crystalline chiroptical film based on porphyrin with homochiral side groups is presented. While the dissolved molecule has a planar, thus, achiral porphyrin core, upon assembly in a metal-organic framework (MOF) film, the porphyrin core is twisted and chiral. The close packing and the crystalline order of the porphyrin cores in the MOF film also results in excellent optoelectronic properties. By exciting the Soret band of porphyrin, efficient photoconduction with a high On-Off-ratio is realized. More important, handedness-dependent circularly-polarized-light photoconduction with a dissymmetry factor g of 4.3×10-4 is obtained. We foresee the combination of such assembly-induced chirality with the rich porphyrin chemistry will enable a plethora of organic materials with exceptional chiral and optoelectronic properties.

Hierarchical Coarse-Grained Strategy for Macromolecular Self-Assembly: Application to Hepatitis B Virus-Like Particles.

Macromolecular self-assembly is at the basis of many phenomena in material and life sciences that find diverse applications in technology. One example is the formation of virus-like particles (VLPs) that act as stable empty capsids used for drug delivery or vaccine fabrication. Similarly to the capsid of a virus, VLPs are protein assemblies, but their structural formation, stability, and properties are not fully understood, especially as a function of the protein modifications. In this work, we present a data-driven modeling approach for capturing macromolecular self-assembly on scales beyond traditional molecular dynamics (MD), while preserving the chemical specificity. Each macromolecule is abstracted as an anisotropic object and high-dimensional models are formulated to describe interactions between molecules and with the solvent. For this, data-driven protein-protein interaction potentials are derived using a Kriging-based strategy, built on high-throughput MD simulations. Semi-automatic supervised learning is employed in a high performance computing environment and the resulting specialized force-fields enable a significant speed-up to the micrometer and millisecond scale, while maintaining high intermolecular detail. The reported generic framework is applied for the first time to capture the formation of hepatitis B VLPs from the smallest building unit, i.e., the dimer of the core protein HBcAg. Assembly pathways and kinetics are analyzed and compared to the available experimental observations. We demonstrate that VLP self-assembly phenomena and dependencies are now possible to be simulated. The method developed can be used for the parameterization of other macromolecules, enabling a molecular understanding of processes impossible to be attained with other theoretical models.

Analytical Model of CVD Growth of Graphene on Cu(111) Surface.

Although the CVD synthesis of graphene on Cu(111) is an industrial process of outstanding importance, its theoretical description and modeling are hampered by its multiscale nature and the large number of elementary reactions involved. In this work, we propose an analytical model of graphene nucleation and growth on Cu(111) surfaces based on the combination of kinetic nucleation theory and the DFT simulations of elementary steps. In the framework of the proposed model, the mechanism of graphene nucleation is analyzed with particular emphasis on the roles played by the two main feeding species, C and C2. Our analysis reveals unexpected patterns of graphene growth, not typical for classical nucleation theories. In addition, we show that the proposed theory allows for the reproduction of the experimentally observed characteristics of polycrystalline graphene samples in the most computationally efficient way.

Interplay of structural dynamics and electronic effects in an engineered assembly of pentacene in a metal-organic framework.

Charge carrier mobility is an important figure of merit to evaluate organic semiconductor (OSC) materials. In aggregated OSCs, this quantity is determined by inter-chromophoric electronic and vibrational coupling. These key parameters sensitively depend on structural properties, including the density of defects. We have employed a new type of crystalline assembly strategy to engineer the arrangement of the OSC pentacene in a structure not realized as crystals to date. Our approach is based on metal-organic frameworks (MOFs), in which suitably substituted pentacenes act as ditopic linkers and assemble into highly ordered π-stacks with long-range order. Layer-by-layer fabrication of the MOF yields arrays of electronically coupled pentacene chains, running parallel to the substrate surface. Detailed photophysical studies reveal strong, anisotropic inter-pentacene electronic coupling, leading to efficient charge delocalization. Despite a high degree of structural order and pronounced dispersion of the 1D-bands for the static arrangement, our experimental results demonstrate hopping-like charge transport with an activation energy of 64 meV dominating the band transport over a wide range of temperatures. A thorough combined quantum mechanical and molecular dynamics investigation identifies frustrated localized rotations of the pentacene cores as the reason for the breakdown of band transport and paves the way for a crystal engineering strategy of molecular OSCs that independently varies the arrangement of the molecular cores and their vibrational degrees of freedom.

A coarse-grained xDLVO model for colloidal protein-protein interactions.

Colloidal protein-protein interactions (PPIs) of attractive and repulsive nature modulate the solubility of proteins, their aggregation, precipitation and crystallization. Such interactions are very important for many biotechnological processes, but are complex and hard to control, therefore, difficult to be understood in terms of measurements alone. In diluted protein solutions, PPIs can be estimated from the osmotic second virial coefficient, B22, which has been calculated using different methods and levels of theory. The most popular approach is based on the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory and its extended versions, i.e. xDLVO. Despite much efforts, these models are not fully quantitative and must be fitted to experiments, which limits their predictive value. Here, we report an extended xDLVO-CG model, which extends existing models by a coarse-grained representation of proteins and the inclusion of an additional ion-protein dispersion interaction term. We demonstrate for four proteins, i.e. lysozyme (LYZ), subtilisin (Subs), bovine serum albumin (BSA) and immunoglobulin (IgG1), that semi-quantitative agreement with experimental values without the need to fit to experimental B22 values. While most likely not the final step in the nearly hundred years of research in PPIs, xDLVO-CG is a step towards predictive PPIs calculations that are transferable to different proteins.

Adsorption of sulfur mustard on clean and water-saturated ZnO(101¯0): Structural diversity from first-principles calculations.

We investigate the adsorption of a chemical warfare agent, namely sulfur mustard (SM), on clean and water-saturated ZnO(101¯0) surfaces using density functional theory calculations to understand the first step of its efficient neutralization to less toxic chemical compounds. We determine the relative stability of various SM conformers adsorbed at different sites on both ZnO surfaces. The unique hydrogen bonding patterns obtained for the idealized clean and the more realistic water-saturated ZnO surface are analyzed and their influence on the stability of the SM@ZnO structures is demonstrated. We find that absolute values of the calculated binding and interaction energies are significantly higher for the clean than for the water-saturated ZnO surface due to the formation of Cl⋯Zn and S⋯Zn contacts. The high adsorptive reactivity of the clean ZnO surface is also evident from the strong structural changes of the initial local energy minimum gas-phase conformations of the SM molecules upon adsorption. This phenomenon is not observed for the water-saturated ZnO surface, which has almost no impact on the SM conformation after adsorption, leaving it as it exists in the gas phase. The insights from the results obtained provide a missing piece toward the understanding of the complex mechanism of SM neutralization on ZnO surfaces.

Sampling of the conformational landscape of small proteins with Monte Carlo methods.

Computer simulation provides an increasingly realistic picture of large-scale conformational change of proteins, but investigations remain fundamentally constrained by the femtosecond timestep of molecular dynamics simulations. For this reason, many biologically interesting questions cannot be addressed using accessible state-of-the-art computational resources. Here, we report the development of an all-atom Monte Carlo approach that permits the modelling of the large-scale conformational change of proteins using standard off-the-shelf computational hardware and standard all-atom force fields. We demonstrate extensive thermodynamic characterization of the folding process of the α-helical Trp-cage, the Villin headpiece and the ß-sheet WW-domain. We fully characterize the free energy landscape, transition states, energy barriers between different states, and the per-residue stability of individual amino acids over a wide temperature range. We demonstrate that a state-of-the-art intramolecular force field can be combined with an implicit solvent model to obtain a high quality of the folded structures and also discuss limitations that still remain.

Tuning Optical Properties by Controlled Aggregation: Electroluminescence Assisted by Thermally-Activated Delayed Fluorescence from Thin Films of Crystalline Chromophores.

Several photophysical properties of chromophores depend crucially on intermolecular interactions. Thermally-activated delayed fluorescence (TADF) is often influenced by close packing of the chromophore assembly. In this context, the metal-organic framework (MOF) approach has several advantages: it can be used to steer aggregation such that the orientation within aggregated structures can be predicted using rational approaches. We demonstrate this design concept for a DPA-TPE (diphenylamine-tetraphenylethylene) chromophore, which is non-emissive in its solvated state due to vibrational quenching. Turning this DPA-TPE into a ditopic linker makes it possible to grow oriented MOF thin films exhibiting pronounced green electroluminescence with low onset voltages. Measurements at different temperatures clearly demonstrate the presence of TADF. Finally, this work reports that the layer-by-layer process used for MOF thin film deposition allows the integration of the TADF-DPA-TPE in a functioning LED device.

Crystalline assembly of perylene in metal-organic framework thin film: J-aggregate or excimer? Insight into the electronic structure.

The spatial orientation of chromophores defines the photophysical and optoelectronic properties of a material and serves as the main tunable parameter for tailoring functionality. Controlled assembly for achieving a predefined spatial orientation of chromophores is rather challenging. Metal-organic frameworks (MOFs) are an attractive platform for exploring the virtually unlimited chemical space of organic components and their self-assembly for device optimization. Here, we demonstrate the impact of interchromophore interactions on the photophysical properties of a surface-anchored MOF (SURMOF) based on 3,9-perylenedicarboxylicacid linkers. We predict the structural assembly of the perylene molecules in the MOF via robust periodic density functional theory calculations and discuss the impact of unit topology and π-π interaction patterns on spectroscopic and semiconducting properties of the MOF films. We explain the dual nature of excited states in the perylene MOF, where strong temperature-modulated excimer emission, enhanced by the formation of perylene J-aggregates, and low stable monomer emission are observed. We use band-like and hopping transport mechanisms to predict semiconducting properties of perylene SURMOF-2 films as a function of inter-linker interactions, demonstrating both p-type and n-type conduction mechanisms. Hole carrier mobility up to 7.34 cm2Vs-1is predicted for the perylene SURMOF-2. The results show a promising pathway towards controlling excimer photophysics in a MOF while controlling charge carrier mobility on the basis of a predictive model.

Single-walled carbon nanotubes in tetrahydrofuran solution: microsolvation from first-principles calculations.

The molecular interactions between the commonly used solvent tetrahydrofuran (THF) and single-walled carbon nanotubes (SWCNT) are studied using density functional theory calculations and Car-Parrinello molecular dynamics simulations. The competitive interplay between THF-THF and THF-SWCNT interactions via C-H⋯O and C-H⋯π hydrogen bonds is analyzed in detail. The binding energies for different global and local energy minima configurations of THF monomers, dimers, trimers, and tetramers on SWCNT(10,0) were determined. The adsorbed species are analyzed in terms of their coordination to the surface via weak hydrogen bonds of the C-H⋯π type and in terms of their ability to form intermolecular C-H⋯O hydrogen bonds, which are responsible for the self-aggregation of THF molecules and a possible dimerization or tetramerization process. A special focus is put on the pseudorotation of the THF molecules at finite temperatures and on the formation of blue-shifting hydrogen bonds.

Stabilization of Pancake Bonding in (TCNQ)2 .- Dimers in the Radical-Anionic Salt (N-CH3-2-NH2-5Cl-Py)(TCNQ)(CH3CN) Solvate and Antiferromagnetism Induction.

We report a new antiferromagnetic radical-anion salt (RAS) formed from 7,7,8,8-tetracyanquinonedimethane (TCNQ) anion and 2-amino-5-chloro-pyridine cation with the composition of (N-CH3-2-NH2-5Cl-Py)(TCNQ)(CH3CN). The crystallographic data indicates the formation of (TCNQ)2 .- radical-anion π-dimers in the synthesized RAS. Unrestricted density functional theory calculations show that the formed π-dimers characterize with strong π-stacking "pancake" interactions, resulting in high electronic coupling, enabling efficient charge transfer properties, but π-dimers cannot be stable in the isolated conditions as a result of strong Coulomb repulsions. In a crystal, where (TCNQ)2 .- π-dimers bound in the endless chainlets via supramolecular bonds with (N-CH3-2-NH2-5-Cl-Py)+ cations, the repulsion forces are screened, allowing for specific parallel π-stacking interactions and stable radical-anion dimers formation. Measurements of magnetic susceptibility and magnetization confirm antiferromagnetic properties of RAS, what is in line with the higher stability of ground singlet state of the radical-anion pair, calculated by means of the DFT. Therefore, the reported radical-anion (N-CH3-2-NH2-5Cl-Py)(TCNQ)(CH3CN) solvate has promising applications in novel magnetics with supramolecular structures.

Effect of Geometrical Structure, Drying, and Synthetic Method on Aminated Chitosan-Coated Magnetic Nanoparticles Utility for HSA Effective Immobilization.

Human serum albumin (HSA) is one of the most frequently immobilized proteins on the surface of carriers, including magnetic nanoparticles. This is because the drug-HSA interaction study is one of the basic pharmacokinetic parameters determined for drugs. In spite of many works describing the immobilization of HSA and the binding of active substances, research describing the influence of the used support on the effectiveness of immobilization is missing. There are also no reports about the effect of the support drying method on the effectiveness of protein immobilization. This paper examines the effect of both the method of functionalizing the polymer coating covering magnetic nanoparticles (MNPs), and the drying methods for the immobilization of HSA. Albumin was immobilized on three types of aminated chitosan-coated nanoparticles with a different content of amino groups long distanced from the surface Fe3O4-CS-Et(NH2)1-3. The obtained results showed that both the synthesis method and the method of drying nanoparticles have a large impact on the effectiveness of immobilization. Due to the fact that the results obtained for Fe3O4-CS-Et(NH2)2 significantly differ from those obtained for the others, the influence of the geometry of the shell structure on the ability to bind HSA was also explained by molecular dynamics.

Photoconductivity in Metal-Organic Framework (MOF) Thin Films.

Photoconductivity is a characteristic property of semi-conductors. Herein, we present a photo-conducting crystalline metal-organic framework (MOF) thin film with an on-off photocurrent ratio of two orders of magnitude. These oriented, surface-mounted MOF thin films (SURMOFs), contain porphyrin in the framework backbone and C60 guests, loaded in the pores using a layer-by-layer process. By comparison with results obtained for reference MOF structures and based on DFT calculations, we conclude that donor-acceptor interactions between the porphyrin of the host MOF and the C60 guests give rise to a rapid charge separation. Subsequently, holes and electrons are transported through separate channels formed by porphyrin and by C60 , respectively. The ability to tune the properties and energy levels of the porphyrin and fullerene, along with the controlled organization of donor-acceptor pairs in this regular framework offers potential to increase the photoconduction on-off ratio.

Highly Efficient One-Dimensional Triplet Exciton Transport in a Palladium-Porphyrin-Based Surface-Anchored Metal-Organic Framework.

Efficient photon-harvesting materials require easy-to-deposit materials exhibiting good absorption and excited-state transport properties. We demonstrate an organic thin-film material system, a palladium-porphyrin-based surface-anchored metal-organic framework (SURMOF) thin film that meets these requirements. Systematic investigations using transient absorption spectroscopy confirm that triplets are very mobile within single crystalline domains; a detailed analysis reveals a triplet transfer rate on the order of 1010 s-1. The crystalline nature of the SURMOFs also allows a thorough theoretical analysis using the density functional theory. The theoretical results reveal that the intermolecular exciton transfer can be described by a Dexter electron exchange mechanism that is considerably enhanced by virtual charge-transfer exciton intermediates. On the basis of the photophysical results, we predict exciton diffusion lengths on the order of several micrometers in perfectly ordered, single-crystalline SURMOFs. In the presently available samples, strong interactions of excitons with domain boundaries present in these metal-organic thin films limit the diffusion length to the diameter of these two-dimensional grains, which amount to about 100 nm. Our results demonstrate high potential of SURMOFs for light-harvesting applications.

Conductance Photoswitching of Metal-Organic Frameworks with Embedded Spiropyran.

Conductive metal-organic frameworks (MOFs) as well as smart, stimuli-responsive MOF materials have attracted considerable attention with respect to advanced applications in energy harvesting and storage as well as in signal processing. Here, the conductance of MOF films of type UiO-67 with embedded photoswitchable nitro-substituted spiropyrans was investigated. Under UV irradiation, the spiropyran (SP) reversibly isomerizes to the open merocyanine (MC) form, a zwitterionic molecule with an extended conjugated π-system. The light-induced SP-MC isomerization allows for remote control over the conductance of the SP@UiO-67 MOF film, and the conductance can be increased by one order of magnitude. This research has the potential to contribute to the development of a new generation of photoelectronic devices based on smart hybrid materials.

Solvation of diclofenac in water from atomistic molecular dynamics simulations - interplay between solute-solute and solute-solvent interactions.

The solubility-permeability relationship of active pharmaceutical ingredients determines the efficacy of their usage. Diclofenac (DCL), which is a widely used nonsteroidal anti-inflammatory drug, is characterized by extremely good membrane permeability, but low water solubility limiting drug effectiveness. The present research focuses on the fundamental explanation of this limitation using the combination of ab initio and classical molecular dynamics simulations of different ionic forms of DCL in water, namely, ionized, un-ionized and the mixture of them both. The analysis of diclofenac solvation in an aqueous environment is used to understand the origin of drug precipitation, especially in gastric pH. The used computational approach reveals the formation of micelle-like self-associated aggregates of diclofenac in water as the result of intermolecular π-π interactions and C-Hπ hydrogen bonds. The DCL aggregation in water is shown to depend mostly on drug concentration, protonation and temperature of the aqueous environment. The detected self-association properties of the drug in water are likely to be of great importance during the development of new drug formulations and fabrication of drug adsorbents for wastewater.

New indenylidene-type metathesis catalysts bearing unsymmetrical N-heterocyclic ligands with mesityl and nitrobenzyl substituents.

ABSTRACT: New indenylidene-type second generation catalysts bearing modified unsymmetrically substituted N-heterocyclic carbene ligands were synthesized. The complexes contain an N-mesityl and N'-nitrobenzyl substituted NHC ligand. The precursors of free carbenes-imidazolinium salts-were obtained in an easy and environment-friendly way (under aqueous or neat conditions). The new catalysts were prepared by reaction of in situ generated carbenes with a 1st generation indenylidene catalyst, containing pyridine ligands instead of tricyclohexylphosphine. The complexes were tested in RCM, CM, and ene-yne metathesis model reactions in commercial-grade solvents in air. Their activities were compared with that of commercially available indenylidene catalyst. The structures of complexes and their stability were investigated using static DFT calculations with mixed basis set.