Tuning the electronic structure of gold cluster-assembled materials by altering organophosphine ligands.

Superatomic clusters can be assembled to build bulk matter, where the individual characteristics are preserved. The main benefit of these materials over conventional bulk species is the capability to tailor their features by altering the physicochemical identities of individual clusters. Electronic properties of metal clusters can be modified by a protective shell of ligands that attach to the surface and make the whole nanoparticle soluble in organic or aqueous solvents. In the present work, we demonstrate that properly chosen ligands provide not only steric protection from aggregation but also tune the redox activity of metal clusters. We investigate the role of the ligands in electronic structure tunability and ligand-field splitting. Our first-principles calculations agree with the experiments, showing that phosphine-protected gold materials are small gap semiconductors. The obtained bandgaps strongly depend on the ligand used. Hence, using phosphine and organophosphine ligands should be feasible and promising while designing the novel superatom-based materials since the desired range of the bandgap might be achieved (by the proper choice of the ligand).

Design and Investigation of Superatoms for Redox Applications: First-Principles Studies.

A superatom is a cluster of atoms that acts like a single atom. Two main groups of superatoms are superalkalis and superhalogens, which mimic the chemistry of alkali and halogen atoms, respectively. The ionization energies of superalkalis are smaller than those of alkalis (<3.89 eV for cesium atom), and the electron affinities of superhalogens are larger than that of halogens (>3.61 eV for chlorine atom). Exploring new superalkali/superhalogen aims to provide reliable data and predictions of the use of such compounds as redox agents in the reduction/oxidation of counterpart systems, as well as the role they can play more generally in materials science. The low ionization energies of superalkalis make them candidates for catalysts for CO2 conversion into renewable fuels and value-added chemicals. The large electron affinity of superhalogens makes them strong oxidizing agents for bonding and removing toxic molecules from the environment. By using the superatoms as building blocks of cluster-assembled materials, we can achieve the functional features of atom-based materials (like conductivity or catalytic potential) while having more flexibility to achieve higher performance. This feature paper covers the issues of designing such compounds and demonstrates how modifications of the superatoms (superhalogens and superalkalis) allow for the tuning of the electronic structure and might be used to create unique functional materials. The designed superatoms can form stable perovskites for solar cells, electrolytes for Li-ion batteries of electric vehicles, superatomic solids, and semiconducting materials. The designed superatoms and their redox potential evaluation could help experimentalists create new materials for use in fields such as energy storage and climate change.

Origin of Correlations between Local Conformational States of Consecutive Amino Acid Residues and Their Role in Shaping Protein Structures and in Allostery.

By analyzing the Kubo-cluster-cumulant expansion of the potential of mean force of polypeptide chains corresponding to backbone-local interactions averaged over the rotation of the peptide groups about the Cα···Cα virtual bonds, we identified two important kinds of "along-chain" correlations that pertain to extended chain segments bordered by turns (usually the ß-strands) and to the folded spring-like segments (usually α-helices), respectively, and are expressed as multitorsional potentials. These terms affect the positioning of structural elements with respect to each other and, consequently, contribute to determining their packing. Additionally, for extended chain segments, the correlation terms contribute to propagating the conformational change at one end to the other end, which is characteristic of allosteric interactions. We confirmed both findings by statistical analysis of the virtual-bond geometry of 77 950 proteins. Augmenting coarse-grained and, possibly, all-atom force fields with these correlation terms could improve their capacity to model protein structure and dynamics.

Molecular crystals vs. superatomic lattice: a case study with superalkali-superhalogen compounds.

Using a first-principles approach, we study the assembly of atomically-precise cluster solids with atomic precision. The aims are to create binary assemblies of clusters through charge transfer between neutral molecular clusters, and employing intercluster electrostatic attraction as a driving force for co-assembly. We combined pairs of complementary clusters in which one cluster is electron-donating (superalkali) and the other is electron-accepting (superhalogen). From the analysis of the binding energy between superatomic counterparts, charge transfer, and the relative size of the clusters, we analyze the resulting structures as either molecular crystals or superatomic lattices. We demonstrate that the substitution of a single atom can result in minor changes to the crystal structure of the binary solids or entirely new packing structures. The [N4Mg6Li]+[AlCl4]-, [N4Mg6Na]+[AlCl4]-, [N4Mg6K]+[AlCl4]-, [N4Mg6Li]+[AlF4]-, [N4Mg6Na]+[AlF4]-, and [N4Mg6K]+[AlF4]- compounds all form the same close-packed superatomic lattice structure through halogen bonding, with subtle differences in the orientation of the superatoms. These salts may also form molecular crystals where clusters are held to one another by electrostatic interactions. Our results emphasize how the structure of superatomic solids can be tuned upon single atom substitution.

Bimetallic superalkali substitution in the CsPbBr3 perovskite: Pseudocubic phases and tunable bandgap.

Perovskites attract attention as efficient light absorbers for solar cells due to their high-power conversion efficiency (up to 24%). The high photoelectric conversion efficiency is greatly affected by a suitable band structure. Cation substitution can be an effective approach to tune the electronic band structure of lead halide perovskites. In this work, superalkali cations were introduced to replace the Cs+ cation in the CsPbBr3 material. The bimetallic superalkalis (LiMg, NaMg, LiCa, and NaCa) were inserted since they are structurally simple systems and have a strong tendency to lose one electron to achieve a closed-shell cation. The cation substitution in the lead halide perovskite leads to changes in the shape of both valence and conduction bands compared to CsPbBr3. Introducing superalkali cations produces extra electronic states close to the Fermi level, which arise from the formation of alkali earth metal states at the top of the valence band. Our first-principles computations reveal that bimetallic superalkali substitution decreases the bandgap of the perovskite. The bandgaps of MgLi-PbBr3 (1.35 eV) and MgNa-PbBr3 (1.06 eV) are lower than the bandgap of CsPbBr3 (2.48 eV) and within the optimal bandgap (i.e., 1.1-1.4 eV) for single-junction solar cells. Thus, the MgLi-PbBr3 and MgNa-PbBr3 inorganic perovskites are promising candidates for high-efficiency solar cells.

N4Mg6M (M = Li, Na, K) superalkalis for CO2 activation.

Superatoms have exciting properties, including diverse functionalization, redox activity, and magnetic ordering, so the resulting cluster-assembled solids hold the promise of high tunability, atomic precision, and robust architectures. By utilizing adamantane-like clusters as building blocks, a new class of superatoms N4Mg6M (M = Li, Na, K) is proposed here. The studied superalkalis feature low adiabatic ionization energies, an antibonding character in the interactions between magnesium and nitrogen atoms, and highly delocalized highest occupied molecular orbital (HOMO). Consequently, the N4Mg6M superalkalis might easily lose their HOMO electrons when interacting with superhalogen electrophiles to form stable superatom [superalkali]+[superhalogen]- compounds. Moreover, the studied superalkalis interact strongly with carbon dioxide, and the resulting N4Mg6M/CO2 systems represent two strongly interacting ionic fragments (i.e., N4Mg6M+ and CO2 -). In turn, the electron affinity of the N2 molecule (of -1.8 eV) is substantially lower than that observed for carbon dioxide (EA = -0.6 eV) and consequently, the N2 was found to form the weakly bound [N4Mg6M][N2] complex rather than the desired ionic [N4Mg6M]+[N2]- product. Thus, the N4Mg6M superalkalis have high selectivity over N2 when it comes to CO2 reduction and also are themselves stable. We believe that the results described within this paper will be useful for understanding CO2 activation, which is the first step for producing fuels from CO2. Moreover, we demonstrate that designing novel superatomic systems and exploring their physicochemical features might be used to create desirable functional materials.

Modified Lennard-Jones potentials for nanoscale atoms.

A classical 6-12 Lennard-Jones (LJ) equation has been widely used to model materials and is the potential of choice in studies when the focus is on fundamental issues. Here we report a systematic study comparing the pair interaction potentials within solid-state materials (i.e., [Co6 Se8 (PEt3 )6 ][C60 ]2 , [Cr6 Te8 (PEt3 )6 ][C60 ]2 , [Ni9 Te6 (PEt3 )8 ][C60 ]) using density functional theory (DFT) calculations and LJ parametrization. Both classical (6-12 LJ) and modified LJ (mLJ) models were developed. In the mLJ approach, the exponents 6 and 12 are replaced by different integer number n and 2n, respectively, and an additional parameter (α) is introduced to describe intermolecular distance shift arising within the geometric centers' approach (instead of the shortest interatomic distance between particles). A general LJ approach reexamination reveals that in the case of nanoatoms, the attractive term decays with distance as the inverse fourth power, and the dominating at short distances repulsive term decays as the inverse eighth power. The modification of the LJ equation is even more prominent for interaction profiles, where intermolecular distance corresponds to separation between geometric centers of particles. In this approach, the attractive term decays with distance as the inverse 12th power, while the repulsive term decays rapidly (as the inverse 24th power). Thus, the mLJ models (e.g., 4-8 LJ) rather than the 6-12 classical ones seem to be a better choice for the description of binary interactions of nanoatoms. The developed mLJ models and electronic structure characteristics give an insight into the explanation of the unique physicochemical properties of superatomic-based solid-state materials.

Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.

The method for protein-structure prediction, which combines the physics-based coarse-grained UNRES force field with knowledge-based modeling, has been developed further and tested in the 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13). The method implements restraints from the consensus fragments common to server models. In this work, the server models to derive fragments have been chosen on the basis of quality assessment; a fully automatic fragment-selection procedure has been introduced, and Dynamic Fragment Assembly pseudopotentials have been fully implemented. The Global Distance Test Score (GDT_TS), averaged over our "Model 1" predictions, increased by over 10 units with respect to CASP12 for the free-modeling category to reach 40.82. Our "Model 1" predictions ranked 20 and 14 for all and free-modeling targets, respectively (upper 20.2% and 14.3% of all models submitted to CASP13 in these categories, respectively), compared to 27 (upper 21.1%) and 24 (upper 18.9%) in CASP12, respectively. For oligomeric targets, the Interface Patch Similarity (IPS) and Interface Contact Similarity (ICS) averaged over our best oligomer models increased from 0.28 to 0.36 and from 12.4 to 17.8, respectively, from CASP12 to CASP13, and top-ranking models of 2 targets (H0968 and T0997o) were obtained (none in CASP12). The improvement of our method in CASP13 over CASP12 was ascribed to the combined effect of the overall enhancement of server-model quality, our success in selecting server models and fragments to derive restraints, and improvements of the restraint and potential-energy functions.

Assessment of chemical-crosslink-assisted protein structure modeling in CASP13.

With the advance of experimental procedures obtaining chemical crosslinking information is becoming a fast and routine practice. Information on crosslinks can greatly enhance the accuracy of protein structure modeling. Here, we review the current state of the art in modeling protein structures with the assistance of experimentally determined chemical crosslinks within the framework of the 13th meeting of Critical Assessment of Structure Prediction approaches. This largest-to-date blind assessment reveals benefits of using data assistance in difficult to model protein structure prediction cases. However, in a broader context, it also suggests that with the unprecedented advance in accuracy to predict contacts in recent years, experimental crosslinks will be useful only if their specificity and accuracy further improved and they are better integrated into computational workflows.

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.

The recent NEWCT-9P version of the coarse-grained UNRES force field for proteins, with scale-consistent formulas for the local and correlation terms, has been tested in the CASP13 experiment of the blind-prediction of protein structure, in the ab initio, contact-assisted, and data-assisted modes. Significant improvement of the performance has been observed with respect to the CASP11 and CASP12 experiments (by over 10 GDT_TS units for the ab initio mode predictions and by over 15 GDT_TS units for the contact-assisted prediction, respectively), which is a result of introducing scale-consistent terms and improved handling of contact-distance restraints. As in previous CASP exercises, UNRES ranked higher in the free modeling category than in the general category that included template based modeling targets. Use of distance restraints from the predicted contacts, albeit many of them were wrong, resulted in the increase of GDT_TS by over 8 units on average and introducing sparse restraints from small-angle X-ray/neutron scattering and chemical cross-link-mass-spectrometry experiments, and ambiguous restraints from nuclear magnetic resonance experiments has also improved the predictions by 8.6, 9.7, and 10.7 GDT_TS units on average, respectively.

Magnesium-Based Clusters as Building Blocks of Electrolytes in Lithium-Ion Batteries.

Superhalogens, owing to their large electron affinity (EA, exceeding those of any halogen atom), play an essential role in physical chemistry as well as new material design. They have applications in hydrogen storage and lithium-ion batteries. Owing to the unique geometries and electronic features of magnesium-based clusters, their potential to form a new class of lithium salts has been investigated here theoretically. The idea is assessed by conducting ab initio computations on Li+ /Mgn F2n+1-2m Om- compounds (n=2, 3; m=0-3) and analyzing their performance as potential Li-ion battery electrolytes. The Mg3 F7- cluster, with large electron binding energy (EA of 7.93 eV), has been proven to serve as a building block for lithium salts. It is shown that, apart from high electronic stability, the new superhalogen-based electrolytes exhibit a set of desirable properties, including a large band gap, high electrolyte stability window, easy mobility of the Li+ , and favorable insensitivity to water.

Magnesium-Based Oxyfluoride Superatoms: Design, Structure, and Electronic Properties.

The ability of mixed ligands to form stable dinuclear and trinuclear magnesium-based superatoms has been investigated theoretically. The Mg2F5-2 mO m and Mg3F7-2 mO m systems (where m = 1-3) were found able to form stable and strongly bound anionic clusters, and those assumptions were validated by (i) the analysis of the geometrical stability; (ii) the estimated Gibbs free energies for the most probable disproportion paths these clusters might be vulnerable to (which allows examining their thermodynamic stabilities); (iii) the localization of the electron density; and (iv) the adiabatic electron affinity (AEA), vertical electron detachment energy (VDE), and adiabatic electron detachment energy (ADE) values calculated for the studied systems. It is demonstrated that the stability of the anionic daughters of these clusters increases with the number of electronegative ligands, and Mg nF2 n+1-2 mO m- ( n = 2, 3; m = 1-3) clusters are stable against electron emission. The largest electron binding energy was found for the Mg3F5O- anion (VDE = 6.826 eV). The strong VDE dependence on (i) the geometrical structure, (ii) the number of central atoms, (iii) ligand type, and (iv) bonding/antibonding character of the highest molecular orbital (HOMO) was also remarked upon and discussed.

Helical Multi-walled Carbon Nanotubes as an Efficient Material for the Dispersive Solid-Phase Extraction of Low and High Molecular Weight Polycyclic Aromatic Hydrocarbons from Water Samples: Theoretical Study.

The differences in effectiveness of multi-walled carbon nanotubes (MWCNTs) as the dispersive solid-phase extraction (dSPE) sorbent for the selective extraction of polycyclic aromatic hydrocarbons (PAHs) were explained on the basis of theoretical study. It was observed that for low molecular weight PAHs, the recoveries using non-helical and helical MWCNTs were similar. In contrary, for PAHs containing five or more aromatic rings, the extraction efficiency was higher using HMWCNTs than for non-helical ones. Principle component analysis (PCA) as well as providing structural parameters and interaction energies for adsorption processes (PAH + CNT → PAH-CNT) have been used for this purpose. All the PAH + CNT → PAH-CNT adsorption processes considered were found to be thermodynamically favorable. However, the adsorption energies (Eads) for PAHs and the helical carbon nanotube surface estimated for the B(a)P-HCNT and I(1,2,3-cd)P-HCNT are substantially less negative than those observed for PAH molecules interacting with the non-helical CNT. Namely, the Eads calculated in simulated aqueous environment for the B(a)P-MWCNT(6,2) and I(1,2,3-cd)P-MWCNT(6,2) were respectively - 43.32 and - 59.98 kcal/mol, while values of only - 7.75 kcal/mol (B(a)P-HCNT) and - 9.13 kcal/mol (I(1,2,3-cd)P-HCNT) were found for the corresponding PAH-HCNT systems. Therefore, we conclude that the replacement of MWCNTs with HCNTs leads to PAH-HCNT systems in which the interaction energies are much smaller than those estimated for the corresponding PAH-MWCNT systems. HMWCNTs are therefore recommended as the dSPE sorbent phase for the extraction of both low and high molecular weight PAHs from water samples.

Oxidizing Metal Oxides with Polynuclear Superhalogen: An ab Initio Study.

The ability of metal oxides (CoO, CuO, MgO, MnO2, NiO, SiO2, TiO2, and ZnO) to form stable systems with polynuclear superhalogen (i.e., Mg3F7) is examined on the basis of theoretical considerations supported by ab initio calculations. It is demonstrated that the MeO n ( n = 1, 2) molecules (such as CoO, CuO, MgO, MnO2, NiO, TiO2, ZnO) should form stable and strongly bound (MeO n)+(superhalogen)- salts when combined with the Mg3F7 superhalogen radical (acting as an oxidizing agent). This conclusion is supported by providing: (i) structural deformation of superhalogen upon ionization, (ii) predicted charge flow between each MeO n and superhalogen (which allows estimating the amount of electron density withdrawn from MeO n molecule during the ionization process), (iii) the localization of the spin density distribution, and (iv) the interaction energies and vertical ionization potentials (VIPs) for the compounds obtained at the CCSD(T)/6-311+G(d) level of theory. On the other hand, the Mg3F7 superhalogen was found to be incapable of ionizing molecules whose adiabatic ionization potentials (AIPs) exceed 12 eV (e.g., SiO2). I believe that the results provided in this contribution may likely be of prospective relevance in the future studies on the issue of binding and preventing metal oxide nanoparticles aggregation in the environment before they occur harmful to human health and environment.

Modeling adsorption of brominated, chlorinated and mixed bromo/chloro-dibenzo-p-dioxins on C60 fullerene using Nano-QSPR.

Many technological implementations in the field of nanotechnology have involved carbon nanomaterials, including fullerenes such as the buckminsterfullerene, C60. The unprecedented properties of such organic nanomaterials (in particular their large surface area) gained extensive attention for their potential use as organic pollutant sorbents. Sorption interactions can be very hazardous and useful at the same time. This work investigates the influence of halogenation by bromine and/or chlorine in dibenzo-p-dioxins on their sorption ability on the C60 fullerene surface. Halogenated dibenzo-p-dioxins (PXDDs, where X = Br or Cl) are ever-present in the environment and accidently produced in many technological processes in only approximately known quantities. If all combinatorial Br and/or Cl dioxin substitution possibilities are present in the environment, the experimental characterization and investigation of sorbent effectiveness is more than difficult. In this work, we have developed a quantitative structure-property relationship (QSPR) model (R2 = 0.998), predicting the adsorption energy [kcal/mol] for 1,701 PXDDs adsorbed on C60 (PXDD@C60). Based on the QSPR model reported herein, we concluded that the lowest energy PXDD@C60 complexes are those that the World Health Organization (WHO) considers to be less dangerous with respect to the aryl hydrocarbon receptor (AhR) toxicity mechanism. Therefore, the effectiveness of fullerenes as sorbent agents may be underestimated as sorption could be less effective for toxic congeners than previously believed.

Development of a novel in silico model of zeta potential for metal oxide nanoparticles: a nano-QSPR approach.

Once released into the aquatic environment, nanoparticles (NPs) are expected to interact (e.g. dissolve, agglomerate/aggregate, settle), with important consequences for NP fate and toxicity. A clear understanding of how internal and environmental factors influence the NP toxicity and fate in the environment is still in its infancy. In this study, a quantitative structure-property relationship (QSPR) approach was employed to systematically explore factors that affect surface charge (zeta potential) under environmentally realistic conditions. The nano-QSPR model developed with multiple linear regression (MLR) was characterized by high robustness [Formula: see text] and external predictivity [Formula: see text] The results clearly showed that zeta potential values varied markedly as functions of the ionic radius of the metal atom in the metal oxides, confirming that agglomeration and the extent of release of free MexOy largely depend on their intrinsic properties. A developed nano-QSPR model was successfully applied to predict zeta potential in an ionized solution of NPs for which experimentally determined values of response have been unavailable. Hence, the application of our model is possible when the values of zeta potential in the ionized solution for metal oxide nanoparticles are undetermined, without the necessity of performing more time consuming and expensive experiments. We believe that our studies will be helpful in predicting the conditions under which MexOy is likely to become problematic for the environment and human health.

When a nanoparticle meets a superhalogen: a case study with C60 fullerene.

The ability of a selected nanoparticle to form stable systems with superhalogens (i.e. AlF4, AlCl4, MgF3, MgCl3, LiF2, LiCl2, and LiI2) is examined on the basis of theoretical considerations supported by ab initio calculations. It is demonstrated that the C60 fullerene molecule should form stable and strongly bound (C60)˙(+)(superhalogen)(-) radical cation salts when combined with an appropriately chosen superhalogen radical (acting as an oxidizing agent). The conclusion is supported by providing: (i) the structural deformation of superhalogens and C60 nanoparticles upon ionization, (ii) predicted charge flow between the fullerene and each superhalogen (which allows estimating the amount of electron density withdrawn from the C60 molecule during the ionization process), (iii) the localization of the spin density distribution, and (iv) the interaction energies for the compounds obtained both at the B3LYP/6-31+G(d) level and at the B3LYP-D3/6-31+G(d) level. Solvent effects have been considered in the present study by means of the polarizable continuum model. It is found that the stability of C60/superhalogen species can be improved in solvents. We believe that the results provided in this contribution may likely be of prospective relevance in the future studies on the issue of binding and removal of this potentially risky nanoparticle.

The performance of selected semi-empirical and DFT methods in studying C60 fullerene derivatives.

The capability of reproducing the open circuit voltages (V(oc)) of 15 representative C60 fullerene derivatives was tested using the selected quantum mechanical methods (B3LYP, PM6, and PM7) together with the two one-electron basis sets. Certain theoretical treatments (e.g. PM6) were found to be satisfactory for preliminary estimates of the open circuit voltages (V(oc)), whereas the use of the B3LYP/6-31G(d) approach has been proven to assure highly accurate results. We also examined the structural similarity of 19 fullerene derivatives by employing principle component analysis (PCA). In order to express the structural features of the studied compounds we used molecular descriptors calculated with semi-empirical (PM6 and PM7) and density functional (B3LYP/6-31G(d)) methods separately. In performing PCA, we noticed that semi-empirical methods (i.e. PM6 and PM7) seem satisfactory for molecules, in which one can distinguish the aromatic and the aliphatic parts in the cyclopropane ring of PCBM (phenyl-C61-buteric acid methyl ester) and they significantly overestimate the energy of the highest occupied molecular orbital (E(HOMO)). The use of the B3LYP functional, however, is recommended for studying methanofullerenes, which closely resemble the structure of PCBM, and for their modifications.