Ab Initio Model Research Articles

Efficient screening of single phase forming low-activation high entropy alloys

Screening of chemical space constituting a palette of seven low-activation metallic elements (Ti, V, Cr, Mn, Fe, Ta, and W) is performed to find single-phase equiatomic/non-equiatomic body-centered cubic (BCC) quaternary/quinary high entropy alloys (HEA). A high throughput screening using ab-initio computations-assisted thermodynamic modeling strategy is implemented. Benchmarking the accuracies of the empirical models for predicting simple solid solutions HEAs is performed considering experimentally synthesized thirty-six low-activation HEAs from the literature. Based on the most efficient empirical model, compositional ranges of several new HEAs are suggested where the formation of single-phase HEA is most preferable. A thorough comparison of high-throughput screening results with CALPHAD data and experiments establishes the efficiency of the high-throughput screening strategy.

Benchmark thermodynamic analysis of methylammonium lead iodide decomposition from first principles

Hybrid organic–inorganic perovskites (HOIPs) such as methylammonium lead iodide (MAPbI3) are promising candidates for use in photovoltaic cells and other semiconductor applications, but their limited chemical stability poses obstacles to their widespread use. Ab initio modeling of finite-temperature and pressure thermodynamic equilibria of HOIPs with their decomposition products can reveal stability limits and help develop mitigation strategies. We here use a previously published experimental temperature-pressure equilibrium to benchmark and demonstrate the applicability of the harmonic and quasiharmonic approximations, combined with a simple entropy correction for the configurational freedom of methylammonium cations in solid MAPbI3 and for several density functional approximations, to the thermodynamics of MAPbI3 decomposition. We find that these approximations, together with the dispersion-corrected hybrid density functional HSE06, yield remarkably good agreement with the experimentally assessed equilibrium between T = 326 K and T = 407 K, providing a solid foundation for future broad thermodynamic assessments of HOIP stability.

Chemical reaction and strength of tricalcium phosphate nano-coating application on dental implants by atomistic calculations

The success of dental titanium implants depends on the interaction of the implant with the surrounding bone, including the type of coating that promotes osseointegration. The most popular are calcium phosphate coatings, in particular tricalcium phosphate (TCP). Since cases of delamination of coatings from titanium have been observed in practice, it is important to be able to evaluate and predict the adhesion strength of coatings of different compositions to titanium.The work involves ab initio quantum chemical modeling of the interaction of TCP with titanium oxide and calculation of their binding energy. Considering that titanium instantly oxidizes in air, calculations were carried out with titanium dioxide. The Gaussian09 DFT B3LYP package with the 6-31G basis set was used. We synthesized tricalcium phosphate stepwise by assessing the binding energies between its constituents and titanium dioxide, as well as other structural characteristics including bond lengths, bond angles, dihedral angles, and charges. A method for assessing adhesion strength at the macro level using binding energy values calculated at the nano level is proposed. The values obtained are in reasonable agreement with experimental data and other numerical calculations. Using the methods of micromechanics of inhomogeneous media for the polycrystalline/amorphous structures of hydroxyapatite (HA) and β-TCP coatings, their anisotropic elastic characteristics were averaged and the degree of their closeness to the characteristics of the Ti substrate was compared.A comparison of two CFs showed that HA has an advantage over TCP both in terms of greater chemical affinity with the titanium substrate (higher adhesive bond energy) and in terms of proximity to the substrate in terms of mechanical characteristics (lower stress concentration at the bond boundary).

(Keynote) Experimental and Computational Insights into Electronic Structure and Redox Properties of Bare and Doped Co3O4 Nanocrystals of Euhedral Morphology and Their Heterojunctions with Alien Oxides and Carbon Materials

One of the most attractive oxide materials with remarkable record of widespread applications are cobalt spinels and their derivatives obtained by doping with alien redox (3dn) and nonredox (Li) cations or via hybridization with other oxides (CeO2, TiO2, a-Al2O3) or carbon support. They have recently received a great deal of theoretical and practical attention because of an outstanding activity in many redox processes important for photo/electro/catalysis. Among many potential applications, their relevance as promising substitutes for platinum in oxygen reduction reaction (ORR) or oxygen evolution reaction (OER) can be mentioned, in particular. The properties of nanostructured cobalt spinel materials depend on their size, shape, doping and interfacing features. In this context, euhedral spinel nanocrystals that expose well defined crystallographic planes, allow for sensible investigations into establishment of the surface/bulk structure-redox reactivity relationships in real conditions.In this presentation application of S/TEM and inverse Wulff hull matching techniques supported by image simulation was discussed for elucidation the mechanism of hydrothermal synthesis of euhedral cobalt spinel nanocrystals the their shape retrieving. Periodic spin unrestricted DFT-PW91+U and hybrid DFT/HSE06 calculations were applied for modeling the morphology, structure and electronic properties (DOS structure) relevant for redox behavior of bare and doped cobalt spinel nanocrystals. The results allowed for thorough characterization of the structure and reconstruction of the exposed low index (100), (110), and (111) planes, and explain the influence of dopants. The effect of the valence state of lithium (Li+ or Li0), and its locus on the valence pining of the cobalt cations was determined. DFT calculations together with the ab initio thermodynamic modeling were used to study the electronic structure of the created defects, and stability of different terminations of cobalt spinel and Li-doped Co3O4 under various redox conditions. The associated electronic and spin relaxation processes were discussed as well. For the most stable stoichiometric (100) and (111) facets, the surface redox state diagrams in a wide stoichiometry range were constructed, and analyzed in detail. Intrinsic charge transfer processes involving electron (n-conductivity) and hole (p-conductivity) transfer between the octahedral and tetrahedral cobalt cations were modeled using a small polaron approximation (Marcus-Dupuis model). Formation of n-p junctions (Co3O4|CeO2, Li-Co3O4|CeO2) and MxCo3-xO4/carbon hybrids were analyzed by S/TEM, XPS spectroscopy (band alignment), contactless electronic conductivity and work function measurements, corroborated by DFT modeling. The redox properties of the interface and spinel faceting, and the role of electric conductivity and the nature of the carbon support functional groups were discussed in the context of the ORR, OER performance, and catalytic redox reactivity (activation of O2).AcknowledgmentsS.W. thanks for the financial support of the project “High-performance electrocatalyst for oxygen reduction reaction with low platinum content” carried on within the Program “Pearls of Science” of the Ministry of Education and Science of Poland.

Elemental partitioning and corrosion resistance of Ni–Cr alloys revealed by accurate ab-initio thermodynamic and electrochemical calculations

Elemental partitioning during thermal processing can significantly affect the corrosion resistance of bulk alloys operating in aggressive electrochemical environments, for which, despite decades of experimental and theoretical studies, the thermodynamic and electrochemical mechanisms still lack accurate quantitative descriptions. Here, we formulate an ab initio thermodynamic model to obtain the composition- and temperature-dependent free energies of formation (ΔfG) for Ni–Cr alloys, a prototypical group of corrosion-resistant metals, and discover two equilibrium states that produce the driving forces for the elemental partitioning in Ni–Cr. The results are in quantitative agreement with the experimental studies on the thermodynamic stability of Ni–Cr. We further construct electrochemical (potential–pH) diagrams by obtaining the required ΔfG values of native oxides and (oxy)hydroxides using high-fidelity ab-initio calculations that include exact electronic exchange and phononic contributions. We then analyze the passivation and electrochemical trends of Ni–Cr alloys, which closely explain various oxide-film growth and corrosion behaviors observed on alloy surfaces. We finally determine the optimal Cr content range of 14–34 at%, which provides the Ni–Cr alloys with both the preferred heat-treatment stability and superior corrosion resistance. We conclude by discussing the consequences of these findings on other Ni–Cr alloys with more complex additives, which can guide the further optimization of industrial Ni–Cr-based alloys.

Ab initio Modeling of Hydrogen Bonding of Remdesivir and Adenosine with Uridine.

Remdesivir (RDV) emerged as an effective drug against the SARS-CoV-2 virus pandemic. One of the crucial steps in the mechanism of action of RDV is its incorporation into the growing RNA strand. RDV, an adenosine analogue, forms Watson-Crick (WC) type hydrogen bonds with uridine in the complementary strand and the strength of this interaction will control efficacy of RDV. While there is a plethora of structural and energetic information available about WC H-bonds in natural base pairs, the interaction of RDV with uridine has not been studied yet at the atomic level. In this article, we aim to bridge this gap, to understand RDV and its hydrogen bonding interactions, by employing density functional theory (DFT) at the M06-2X/cc-pVDZ level. The interaction energy, QTAIM analysis, NBO and SAPT2 are performed for RDV, adenosine, and their complex with uridine to gain insights into the nature of hydrogen bonding. The computations show that RDV has similar geometry, energetic, molecular orbitals, and aromaticity as adenosine, suggesting that RDV is an effective adenosine analogue. The important geometrical parameters, such as bond distances and red-shift in the stretching vibrational modes of adenosine, RDV and uridine identify two WC-type H-bonds. The relative strength of these two H-bonds is computed using QTAIM parameters and the computed hydrogen bond energy. Finally, the SAPT2 study is performed at the minima and at non-equilibrium base pair distances to understand the dominant intermolecular physical force. This study, based on a thorough analysis of a variety of computations, suggests that both adenosine and RDV have similar structure, energetic, and hydrogen bonding behaviour.

Tailoring Se-rich glassy arsenoselenides employing the nanomilling platform

By XRPD analysis related to diffuse peak-halos in Se-rich glassy AsxSe100-x, the high-energy nanomilling driven reamorphization in these substances is recognized as molecular-to-network transformations of Se chains bridging cation polyhedrons (like AsSe3/2 pyramids) from preferential cis- to trans-configurated topology. At the medium-range structure, the process of reamorphization is revealed as enhancement in the intermediate-range ordering of these glasses due to high-angular shifted and broadened first sharp diffraction peak (FSDP) accompanied by suppression in extended-range ordering due to high-angular shifted but narrowed principal diffraction peak (PDP), so that peak-halos become more distinguishable after nanomilling. Principal trend in the XRPD patterns of glassy arsenoselenides with growing Se content is revealed as suppression in intermediate-range ordering accompanied by enhancement in extended-range ordering, resulting in more overlapped peak-halos. Irregular sequence of randomly distributed cis- and trans-configurated linkages in Se-rich g-AsxSe100-x is visualized by ab initio quantum-chemical modeling of molecular and chain-like network clusters.

Nanoscale and ultrafast in situ techniques to probe plasmon photocatalysis

Plasmonic photocatalysis uses the light-induced resonant oscillation of free electrons in a metal nanoparticle to concentrate optical energy for driving chemical reactions. By altering the joint electronic structure of the catalyst and reactants, plasmonic catalysis enables reaction pathways with improved selectivity, activity, and catalyst stability. However, designing an optimal catalyst still requires a fundamental understanding of the underlying plasmonic mechanisms at the spatial scales of single particles, at the temporal scales of electron transfer, and in conditions analogous to those under which real reactions will operate. Thus, in this review, we provide an overview of several of the available and developing nanoscale and ultrafast experimental approaches, emphasizing those that can be performed in situ. Specifically, we discuss high spatial resolution optical, tip-based, and electron microscopy techniques; high temporal resolution optical and x-ray techniques; and emerging ultrafast optical, x-ray, tip-based, and electron microscopy techniques that simultaneously achieve high spatial and temporal resolution. Ab initio and classical continuum theoretical models play an essential role in guiding and interpreting experimental exploration, and thus, these are also reviewed and several notable theoretical insights are discussed.

First-principles study of electronic properties of Zn and La doped and co-doped anatase TiO2

Ab initio computational modeling, based on Density Functional Theory, was employed to predict the influence of metal ions Zn2+ and La3+ on structural, electronic, and photocatalytic properties of anatase TiO2. Specifically, chemical modification of TiO2 was conducted by doping and co-doping the TiO2 using these ions. Properties of the chemically modified TiO2 were computationally predicted in terms of lattice parameters, electronic band structure, density of states, charge density, and absorption spectrum. It was found that co-doping TiO2 using Zn2+ and La3+ significantly reduced the bandgap and improved relative stability, and enhanced photocatalytic activity in the visible-light region was observed in comparison with pure TiO2. This research also interprets the underlying mechanism regarding why the doping and co-doping may have such influences on the properties of the chemically modified TiO2.

CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform.

Target discovery and drug evaluation for diseases with complex mechanisms call for a streamlined chemical systems analysis platform. Currently available tools lack the emphasis on reaction kinetics, access to relevant databases, and algorithms to visualize perturbations on a chemical scale providing quantitative details as well streamlined visual data analytics functionality. CytoCopasi, a Maven-based application for Cytoscape that combines the chemical systems analysis features of COPASI with the visualization and database access tools of Cytoscape and its plugin applications has been developed. The diverse functionality of CytoCopasi through ab initio model construction, model construction via pathway and parameter databases KEGG and BRENDA is presented. The comparative systems biology visualization analysis toolset is illustrated through a drug competence study on the cancerous RAF/MEK/ERK pathway. The COPASI files, simulation data, native libraries, and the manual are available on https://github.com/scientificomputing/CytoCopasi.

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.

Specific versus Nonspecific Solvent Interactions of a Biomolecule in Water.

Solvent interactions, particularly hydration, are vital in chemical and biochemical systems. Model systems reveal microscopic details of such interactions. We uncover a specific hydrogen-bonding motif of the biomolecular building block indole (C8H7N), tryptophan's chromophore, in water: a strong localized N-H···OH2 hydrogen bond, alongside unstructured solvent interactions. This insight is revealed from a combined experimental and theoretical analysis of the electronic structure of indole in aqueous solution. We recorded the complete X-ray photoemission and Auger spectrum of aqueous-phase indole, quantitatively explaining all peaks through ab initio modeling. The efficient and accurate technique for modeling valence and core photoemission spectra involves the maximum-overlap method and the nonequilibrium polarizable-continuum model. A two-hole electron-population analysis quantitatively describes the Auger spectra. Core-electron binding energies for nitrogen and carbon highlight the specific interaction with a hydrogen-bonded water molecule at the N-H group and otherwise nonspecific solvent interactions.

ExoMol line lists – LVI. The SO line list, MARVEL analysis of experimental transition data and refinement of the spectroscopic model

ABSTRACT A semi-empirical IR/Vis line list, SOLIS, for the sulphur monoxide molecule 32S16O is presented. SOLIS includes accurate empirical rovibrational energy levels, uncertainties, lifetimes, quantum number assignments, and transition probabilities in the form of Einstein A coefficients covering the $X\, {}^{3}\Sigma ^{-}$$, a\, {}^{1}\Delta , b\, {}^{1}\Sigma ^{+}, A\, {}^{3}\Pi , B\, {}^{3}\Sigma ^{-}, A^{\prime \prime }\, {}^{3}\Sigma ^{+}, A^{\prime }\, {}^{3}\Delta$, and $e\, {}^{1}\Pi$ systems and wavenumber range up to 43 303.5 cm−1 (≥230.93 nm) with J ≤ 69. SOLIS has been computed by solving the rovibronic Schrödinger equation for diatomics using the general purpose variational code Duo and starting from a published ab initio spectroscopic model of SO (including potential energy curves, coupling curves, (transition) dipole moment curves) which is refined to experimental data. To this end, a database of 50 106 experimental transitions, 48 972 being non-redundant, has been compiled through the analysis of 29 experimental sources, and a self-consistent network of 8558 rovibronic energy levels for the X, a, b, A, B, and C electronic states has been generated with the marvel algorithm covering rotational and vibrational quantum numbers J ≤ 69 and v ≤ 30 and energies up to 52 350.40 cm−1. No observed transitions connect to the $B\, {}^{3}\Sigma ^{-}$(v = 0) state which is required to model perturbations correctly, so we leave fitting the $B\, {}^3\Sigma ^-$ and $C\, {}^3\Pi$ state UV model to a future project. The SO line list is available at ExoMol from www.exomol.com.

Correlation‐Driven Magnetic Frustration and Insulating Behavior of TiF3

The halide perovskite TiF3, renowned for its intricate interplay between structure, electronic correlations, magnetism, and thermal expansion, is investigated. Despite its simple structure, understanding its low‐temperature magnetic behavior has been a challenge. Previous theories propose antiferromagnetic ordering. In contrast, experimental signatures for an ordered magnetic state are absent down to 10 K. The current study has successfully reevaluated the theoretical modeling of TiF3, unveiling the significance of strong electronic correlations as the key driver for its insulating behavior and magnetic frustration. In addition, frequency‐dependent optical reflectivity measurements exhibit clear signs of an insulating state. The analysis of the calculated magnetic data gives an antiferromagnetic exchange coupling with a net Weiss temperature of order 25 K as well as a magnetic response consistent with a S = 1/2 local moment per Ti3+. Yet, the system shows no susceptibility peak at this temperature scale and appears free of long‐range antiferromagnetic order down to 1 K. Extending ab initio modeling of the material to larger unit cells shows a tendency for relaxing into a noncollinear magnetic ordering, with a shallow energy landscape between several magnetic ground states, promoting the status of this simple, nearly cubic perovskite structured material as a candidate spin liquid.

Ab initio modelling of transport phenomena in multi-component mixtures of rarefied gases

The direct simulation Monte Carlo method based on ab initio potentials is applied to model transport phenomena in binary, ternary and quaternary mixtures of noble gases. To this end, the Couette and Fourier problems are solved over the whole range of the rarefaction parameter spanning the near free-molecular, transitional, and slip flow regimes. Moreover, analytical solutions are obtained in the limits of the free-molecular and continuous medium regimes of flow. As a result, the shear stress, heat flux through multi-component mixtures, distributions of velocity, temperature, and mole fractions of each species are calculated as a function of the gas rarefaction. An analysis of these data points out the properties which are strongly affected by the chemical composition. It is found that the largest deviations of characteristics of mixtures from those of a single gas are observed for the binary mixture of helium and krypton, while their deviations for the ternary and quaternary mixtures are smaller. A temperature variation in a mixture leads to non-uniform distributions of chemical composition due to the thermal diffusion phenomenon. Such redistributions are analyzed in both problems and their effect on the heat and momentum transfer is evaluated. The reported results can be used to evaluate the main factors determining transport phenomena in practical applications such as vacuum systems, microfluidics, gas separation technology, space research etc.

Ab-initio modeling of Sc-doped SnS2 monolayer in context of field-effect transistor based gas sensor

Scandium (Sc) doped SnS2 is proposed as a sensing material for detection of toxic gas molecules such as CO, NO, CO2, NO2, NH3, and H2S in this paper, based on first-principle study. The doping effect of scandium atom on the physicochemical parameters of pristine SnS2, as well as the adsorption mechanism, are examined first. The structural, electrical and magnetic properties are investigated by finding the density of states, charge density and band structure. A ball and stick model of adsorption systems has been developed, and the adsorption behaviour of these gases was computed using density functional theory to test the sensing capability. Due to strong covalent bonds formation the Sc-doped SnS2 monolayer displayed remarkable adsorption ability for all gas molecules, according to the findings. The charge-transfer behavior of Sc-doped SnS2 monolayer as a field-effect-transistor sensor is also investigated under applied electric fields.

Theoretical study of H-atom abstraction by CH3OȮ radicals from aldehydes and alcohols: Ab initio and comprehensive kinetic modeling

Reaction kinetics of H-atom abstraction from C1C3 alcohols, including CH3OH, C2H5OH, NC3H7OH, IC3H7OH, and C1C2 aldehydes, including CH2O, CH3CHO, by CH3OȮ radicals is investigated in this work through high-level ab initio calculations. Electronic structure optimizations are performed for all the stationary points with M06–2X/6−311++g(d,p) method. Quadratic configuration interaction method QCISD(T)/cc-pVXZ (where X = D and T) and Møller–Plesset perturbation theory MP2/cc-pVXZ (where X = D, T, and Q) are used to calculate single point energies. Subsequently, rate coefficients for all H-atom abstraction channels are determined using conventional transition state theory with unsymmetric tunneling corrections. These calculated results are updated to a recently updated model and then compared against expansive experimental datasets to investigate their influence on the model prediction performance. The updated model shows obvious discrepancies with the original model, where the updated model is less reactive for CH3CHO, C2H5OH, NC3H7OH, and IC3H7OH, while showing negligible differences for CH3OH and CH2O due to the lack of CH3OȮ radical formation. Sensitivity and flux analyses are further conducted, through which the difference between the studied species in their oxidation pathways and the relative importance of H-atom abstraction by CH3OȮ radicals is highlighted. With the updated rate parameters, the branching ratios of H-atom abstractions from CH2O and CH3CHO are significantly altered for CH3CHO, C2H5OH, NC3H7OH and IC3H7OH, with an obvious shift away from the abstraction channel by CH3OȮ. Further analyses highlight the critical roles of CH2O and CH3CHO chemistry as core chemistries for large hydrocarbons (e.g., carbon number > 1), which have been inadequately described in existing chemistry models. Systematic efforts are urgently needed to improve the existing CH2O and CH3CHO chemistries.

ComDock: A novel approach for protein-protein docking with an efficient fusing strategy

Protein-protein interaction plays an important role in studying the mechanism of protein functions from the structural perspective. Molecular docking is a powerful approach to detect protein-protein complexes using computational tools, due to the high cost and time-consuming of the traditional experimental methods. Among existing technologies, the template-based method utilizes the structural information of known homologous 3D complexes as available and reliable templates to achieve high accuracy and low computational complexity. However, the performance of the template-based method depends on the quality and quantity of templates. When insufficient or even no templates, the ab initio docking method is necessary and largely enriches the docking conformations. Therefore, it's a feasible strategy to fuse the effectivity of the template-based model and the universality of ab initio model to improve the docking performance. In this study, we construct a new, diverse, comprehensive template library derived from PDB, containing 77,685 complexes. We propose a template-based method (named TemDock), which retrieves the evolutionary relationship between the target sequence and samples in the template library and transfers similar structural information. Then, the target structure is built by superposing on the homologous template complex with TM-align. Moreover, we develop a consensus-based method (named ComDock) to integrate our TemDock and an existing ab initio method (ZDOCK). On 105 targets with templates from Benchmark 5.0, the TemDock and ComDock achieve a success rate of 68.57 % and 71.43 % in the top 10 conformations, respectively. Compared with the HDOCK, ComDock obtains better I-RMSD of hit configurations on 9 targets and more hit models in the top 100 conformations. As an efficient method for protein-protein docking, the ComDock is expected to study protein-protein recognition and reveal the various biological passways that are critical for developing drug discovery. The final results are stored at https://github.com/guofei-tju/mqz_ComDock_docking.

Comparative Structural Investigation of Histone-Like HU Proteins by Small-Angle X-ray Scattering

Nucleoid-associated proteins (NAPs) control the structure and functions of bacterial nucleoid. Histone-like HU proteins are most abundant NAPs in dividing bacterial cells. Previously, structural ensembles of conformations of HU proteins from pathogenic mycoplasmas Spiroplasma melliferum and Mycoplasma gallisepticum were obtained using NMR spectroscopy. A structural study of these mycoplasma proteins is performed by small-angle X-ray scattering (SAXS). The occurrence of individual conformations from the ensemble, obtained by NMR, is estimated from the scattering data on HU protein solutions. In particular, an approach based on characterization of equilibrium mixtures in terms of volume fractions of their components was applied. The general shape of the proteins and their oligomeric state are independently confirmed using ab initio bead modelling. The flexibility of DNA-binding protein domains is analyzed by the ensemble optimization method, which is based on comparison of the structural characteristics of conformations fitting the SAXS data to the distribution of these characteristics in a randomly generated set. The results obtained give a new insight on the variability of the structure of HU proteins, which is necessary for their functioning.

Ab Initio Shape of Supramolecular Complexes of Cucurbit[8]uril in Solution Found from Small-Angle X-ray Scattering Data

Previous studies of the spatial structure of the guest–host complexes of macrocyclic cavitands cucurbiturils with a number of nitroxyl radicals by ESR, NMR, and crystallographic methods showed that, in aqueous solutions containing a number of nitroxyl radicals as guest molecules, ordered aggregates in the form of an equilateral triangle, with three guest–host monocomplexes located in its vertices, may arise. We performed experiments on small-angle X-ray scattering of aqueous solutions of guest–host cucurbit[8]uril complexes with a stable nitroxyl radical (protonated tempoamine) and, based on the experimental results, carried out ab initio modeling of the shape of aggregates of complexes in the natural state in solution. The search for models of the shape of aggregates was performed either using no additional information about their structure or assuming the presence of a threefold axis. ESR is applied as an independent method for studying the aggregation of complexes in solution. It is shown that the shape of the particles constituting complexes at high cavitand and guest concentrations in an aqueous solution is close in its parameters to an equilateral triangle, which is in agreement with the known crystallographic and ESR data.