Interpretation of molecular electron transport in ab initio many-electron framework incorporating zero-point nuclear motion effects

A computational methodology, founded on chemical concepts, is presented for interpreting the role of nuclear motion in the electron transport through single-molecule junctions (SMJ) using many-electron ab initio quantum chemical calculations. Within this approach the many-electron states of the system, computed at the SOS-ADC(2) level, are followed along the individual normal modes of the encapsulated molecules. The inspection of the changes in the partial charge distribution of the many-electron states allows the quantification of the electron transport and the estimation of transmission probabilities. This analysis improves the understanding of the relationship between internal motions and electron transport. Two SMJ model systems are studied for validation purposes, constructed from a conductor (BDA, benzene-1,4-diamine) and an insulator molecule (DABCO, 1,4-diazabicyclo[2.2.2]octane). The trends of the resulting transmission probabilities are in agreement with the experimental observations, demonstrating the capability of the approach to distinguish between conductor and insulator type systems, thereby offering a straightforward and cost-effective tool for such classifications via quantum chemical calculations.

Determining Structures of Layer-by-Layer Spin-Coated Zinc Dicarboxylate-Based Metal-Organic Thin Films

Thin films of crystalline solids with substantial free volume from organic chromophores and metal secondary building units (SBUs) are promising for engineering new optoelectronic properties through control of interchromophore coupling. Zn-based SBUs are especially relevant in this case because they avoid quenching the chromophore's luminescence. We find that layer-by-layer spin-coating using Zn acetate dihydrate and benzene-1,4-dicarboxylic acid (H2BDC) and biphenyl-4,4'-dicarboxylic acid (H2BPDC) linkers easily produces crystalline thin films. However, analysis of the grazing-incidence wide-angle X-ray scattering (GIWAXS) data reveals the structures of these films vary significantly with the linker, and metal-to-linker molar ratio used for fabrication. Under equimolar conditions, H2BPDC creates a type of structure like that proposed for SURMOF-2, whereas H2BDC generates a different metal-hydroxide-organic framework. Large excess of Zn2+ ions causes the growth of layered zinc hydroxides, irrespective of the linker used. Density functional theory (DFT) calculations provide structural models with minimum total energy that are consistent with the experimentally observed diffractograms. In the broader sense, this work illustrates the importance in this field of careful structural determination, e.g., by utilizing GIWAXS and DFT simulations to determine the structure of the obtained crystalline metal-organic thin films, so properties can be rationally engineered and explained.

Improved Approach for ab Initio Calculations of Rate Coefficients for Secondary Reactions in Acrylate Free-Radical Polymerization

Secondary reactions in radical polymerization pose a challenge when creating kinetic models for predicting polymer structures. Despite the high impact of these reactions in the polymer structure, their effects are difficult to isolate and measure to produce kinetic data. To this end, we used solvation-corrected M06-2X/6-311+G(d,p) ab initio calculations to predict a complete and consistent data set of intrinsic rate coefficients of the secondary reactions in acrylate radical polymerization, including backbiting, β-scission, radical migration, macromonomer propagation, mid-chain radical propagation, chain transfer to monomer and chain transfer to polymer. Two new approaches towards computationally predicting rate coefficients for secondary reactions are proposed: (i) explicit accounting for all possible enantiomers for reactions involving optically active centers; (ii) imposing reduced flexibility if the reaction center is in the middle of the polymer chain. The accuracy and reliability of the ab initio predictions were benchmarked against experimental data via kinetic Monte Carlo simulations under three sufficiently different experimental conditions: a high-frequency modulated polymerization process in the transient regime, a low-frequency modulated process in the sliding regime at both low and high temperatures and a degradation process in the absence of free monomers. The complete and consistent ab initio data set compiled in this work predicts a good agreement when benchmarked via kMC simulations against experimental data, which is a technique never used before for computational chemistry. The simulation results show that these two newly proposed approaches are promising for bridging the gap between experimental and computational chemistry methods in polymer reaction engineering.

Extracting the electronic structure signal from X-ray and electron scattering in the gas phase

X-ray and electron scattering from free gas-phase molecules is examined using the independent atom model (IAM) and ab initio electronic structure calculations. The IAM describes the effect of the molecular geometry on the scattering, but does not account for the redistribution of valence electrons due to, for instance, chemical bonding. By examining the total, i.e. energy-integrated, scattering from three molecules, fluoroform (CHF3), 1,3-cyclohexadiene (C6H8) and naphthalene (C10H8), the effect of electron redistribution is found to predominantly reside at small-to-medium values of the momentum transfer (q ≤ 8 Å-1) in the scattering signal, with a maximum percent difference contribution at 2 ≤ q ≤ 3 Å-1. A procedure to determine the molecular geometry from the large-q scattering is demonstrated, making it possible to more clearly identify the deviation of the scattering from the IAM approximation at small and intermediate q and to provide a measure of the effect of valence electronic structure on the scattering signal.

Serine protease inhibitor 3 (Serpin3) from Penaeus vannamei selectively interacts with Vibrio parahaemolyticus PirAvp

Acute Hepatopancreatic Necrosis Disease (AHPND) represents a significant challenge in the field of shrimp aquaculture. This disease is primarily caused by Vibrio parahaemolyticus strains harbouring the pVA1 plasmid encoding the PirAvp and PirBvp toxins. To combat this epidemic and mitigate its devastating consequences, it is crucial to identify and characterize the receptors responsible for the binding of these pathogenic toxins. Our studied discovered that Penaeus vannamei's Serine protease inhibitor 3 (PvSerpin3) derived from shrimp hepatopancreatic tissues could bind to recombinant PirAvp , confirming its role as a novel PirAvp -binding protein (PA BP). Through comprehensive computational methods, we revealed two truncated PirAvp -binding proteins derived from PvSerpin3 called Serpin3(13) and Serpin3(22), which had higher affinity to PirAvp than the full-length PvSerpin3. The PA BP genes were amplified from a cDNA library that was reversed from total RNA extracted from shrimp, cloned and expressed in Escherichia coli. Three PA BP inclusion bodies were refolded to obtain the soluble form, and the recovery efficacy was found to be 100% for Serpin3 and Serpin3(13), while Serpin3(22) had a recovery efficacy of roundly 50%. Co-Immunoprecipitation (co-IP) and dot blot assays substantiated the interaction of these recombinant PA BPs with both recombinant PirAvp and VPAHPND (XN89)-producing natural toxins.

Ab Initio Density Functional Theory Calculation: Americium Hydrolysis Mechanism

The hydrolysis mechanism of americium was calculated using density functional theory, and the detailed microscopic reaction mechanism was obtained. The results show that americium reacts with water along the octet state to produce oxides and H2, and that this reaction is exothermic. The interaction between Am and O atoms gradually changes from initially electrostatic interaction to covalent interaction, and continues to strengthen. During the reaction process, Am atoms always lose electrons, the 5f orbital is obviously involved, and there is df orbital hybridization. This study provides the necessary theoretical data support for the theoretical and experimental study of the actinide system.

Accurate ab initio potential energy surface, rovibrational energy levels and resonance interactions of triplet ( X ~ 3 B1 ) methylene

In this work, we report rovibrational energy levels for four isotopologues of methylene (CH2 , CHD, CD2 , and 13 CH2 ) in their ground triplet electronic state (X ~ 3 B1 ) from variational calculation up to ~10,000 cm-1 and using a new accurate ab initio potential energy surface (PES). Triplet methylene exhibits a large-amplitude bending vibration and can reach a quasilinear configuration due to its low barrier (~2000 cm-1 ). To construct the ab initio PES, the Dunning's augmented correlation-consistent core-valence orbital basis sets were employed up to the sextuple-ζ quality [aug-cc-pCVXZ, X = T, Q, 5, and 6] combined with the single- and double-excitation unrestricted coupled cluster approach with a perturbative treatment of triple excitations [RHF-UCCSD(T)]. We have shown that the accuracy of the ab initio energies is further improved by including the corrections due to the scalar relativistic effects, DBOC and high-order electronic correlations. For the first time, all the available experimental rovibrational transitions were reproduced with errors less than 0.12 cm-1 , without any empirical corrections. Unlike more "traditional" nonlinear triatomic molecules, we have shown that even the energies of the ground vibrational state (000) with rather small rotational quantum numbers are strongly affected by the very pronounced rovibrational resonance interactions. Accordingly, the polyad structure of the vibrational levels of CH2 and CD2 was analyzed and discussed. The comparison between the energy levels obtained from the effective Watson A-reduced Hamiltonian, from the generating-function approach and from a variational calculation was given.

Transforming Cl-Containing Waste Plastics into Carbon Resource for Steelmaking: Theoretical Insight

The accumulation of waste plastics poses a significant environmental challenge, leading to persistent pollution in terrestrial and aquatic ecosystems. A practical approach to address this issue involves the transformation of postconsumer waste plastics into industrially valuable products. This study focuses on an example of harnessing the carbon content in these polymers for carbon-demanding industrial processes, thereby reducing waste plastics from the environment and alleviating the demand for mined carbon resources. Employing quantum simulations, we examine the viability of polychloroprene as a carburizing agent in the steelmaking process. Our simulations reveal that polychloroprene exhibits excellent carbon diffusivity in molten iron, with a theoretical diffusion coefficient of 8.983 × 10-5cm2 s-1. This value competes favorably with that of metallurgical coke and surpasses the carbon diffusivity of other polymers, such as polycarbonate, polyurethane, and polysulfide. Additionally, our findings demonstrate that the chlorine content in polychloroprene does not permeate into molten iron but instead remains confined to the molten iron and slag interface.

Can Dative Bond Between Two Anions Possible?

Formation of a genuine chemical bond between two similarly charged fragments is beyond expectation. Any such interaction generally lies in the realm of non-covalent interaction. Herein, formation of a strong dative covalent bond between two anionic fragments is reported for the first time. Calculation using ab initio coupled cluster theory reveals the formation of an unprecedented strong H3 Be- ←X- (X- =CH3 - , CN- , OH- , F- ) dative covalent bond. The calculated bond dissociation energies in polar solvents are significant, which indicates the possibility of their experimental realization.

Energy Landscape of Relaxation and Interaction of an Amino Acid, Glutamine (L), on Pristine and Au/Ag/Cu-Doped TiO2 Surfaces

Studying the interaction of inorganic systems with organic ones is a highly important avenue for finding new drugs and treatment methods. Tumor cells show an increased demand for amino acids due to their rapid proliferation; thus, targeting their metabolism is becoming a potential oncological therapeutic strategy. One of the inorganic materials that show antitumor properties is titanium dioxide, while its doping was found to enhance interactions with biological systems. Thus, in this study, we investigated the energy landscape of glutamine (L), an amino acid, on pristine and doped TiO2 surfaces. We first locally optimized 2D-slab structures of pristine and Au/Ag/Cu-doped anatase (001 and 101 surfaces) and similarly optimized a single molecule of glutamine in vacuum. Next, we placed the pre-optimized glutamine molecule in various orientations and on a variety of locations onto the relaxed substrate surfaces (in vacuum) and performed ab initio relaxations of the molecule on the substrate slabs. We employed the DFT method with a GGA-PBE functional implemented in the Quantum Espresso code. Comparisons of the optimized conformations and electronic structures of the amino acid in vacuum and on the surfaces yield useful insights into various biological processes.

Hierarchical Self-Assembly and Conformation of Tb Double-Decker Molecular Magnets: Experiment and Molecular Dynamics

Nanostructures, fabricated by locating molecular building blocks in well-defined positions, for example, on a lattice, are ideal platforms for studying atomic-scale quantum effects. In this context, STM data obtained from self-assembled Bis(phthalocyaninato) Terbium (III) (TbPc2) single-molecule magnets on various substrates have raised questions about the conformation of the TbPc2 molecules within the lattice. In order to address this issue, molecular dynamics simulations were carried out on a 2D assembly of TbPc2 molecules. The calculations are in excellent agreement with the experiment, and thus improve our understanding of the self-assembly process. In particular, the calculated electron density of the molecular assembly compares well with STM contrast of self-assembled TbPc2 on Au(111), simultaneously providing the conformation of the two Pc ligands of the individual double-decker molecule. This approach proves valuable in the identification of the STM contrast of LnPc2 layers and could be used in similar cases where it is difficult to interpret the STM images of an assembly of molecular complexes.

Emerging Trends of Computational Chemistry and Molecular Modeling in Froth Flotation: A Review

Froth flotation is the most versatile process in mineral beneficiation, extensively used to concentrate a wide range of minerals. This process comprises mixtures of more or less liberated minerals, water, air, and various chemical reagents, involving a series of intermingled multiphase physical and chemical phenomena in the aqueous environment. Today's main challenge facing the froth flotation process is to gain atomic-level insights into the properties of its inherent phenomena governing the process performance. While it is often challenging to determine these phenomena via trial-and-error experimentations, molecular modeling approaches not only elicit a deeper understanding of froth flotation but can also assist experimental studies in saving time and budget. Thanks to the rapid development of computer science and advances in high-performance computing (HPC) infrastructures, theoretical/computational chemistry has now matured enough to successfully and gainfully apply to tackle the challenges of complex systems. In mineral processing, however, advanced applications of computational chemistry are increasingly gaining ground and demonstrating merit in addressing these challenges. Accordingly, this contribution aims to encourage mineral scientists, especially those interested in rational reagent design, to become familiarized with the necessary concepts of molecular modeling and to apply similar strategies when studying and tailoring properties at the molecular level. This review also strives to deliver the state-of-the-art integration and application of molecular modeling in froth flotation studies to assist either active researchers in this field to disclose new directions for future research or newcomers to the field to initiate innovative works.

Ab Initio Calculations on the Ground and Excited Electronic States of Thorium-Ammonia, Thorium-Aza-Crown, and Thorium-Crown Ether Complexes

Positively charged metal-ammonia complexes are known to host peripheral, diffuse electrons around their molecular skeleton. The resulting neutral species form materials known as expanded or liquid metals. Alkali, alkaline earth, and transition metals have been investigated previously in experimental and theoretical studies of both the gas and condensed phase. This work is the first ab initio exploration of an f-block metal-ammonia complex. The ground and excited states are calculated for Th^0-3+ complexes with ammonia, crown ethers, and aza-crown ethers. For Th³⁺ complexes, the one valence electron Th populates the metal's 6d or 7f orbitals. For Th^0-2+, the additional electrons prefer occupation of the outer s- and p-type orbitals of the complex, except Th(NH₃)₁₀, which uniquely places all four electrons in outer orbitals of the complex. Although thorium coordinates up to ten ammonia ligands, octa-coordinated complexes are more stable. Crown ether complexes have a similar electronic spectrum to ammonia complexes, but excitations of electrons in the outer orbitals of the complex are higher in energy. Aza-crown ethers disfavor the orbitals perpendicular to the crowns, attributed to the N-H bonds pointing along the plane of the crowns.

Performance and Mechanism of Chlorine Dioxide on BTEX Removal in Liquid and Indoor Air

With the development of the chemical industry, benzene, toluene, ethylbenzene, and xylene (BTEX) have gradually become the major indoor air pollutants. Various gas treatment techniques are widely used to prevent the physical and mental health hazards of BTEX in semi-enclosed spaces. Chlorine dioxide (ClO₂) is an alternative to chlorine as a secondary disinfectant with a strong oxidation ability, a wide range of action, and no carcinogenic effects. In addition, ClO₂ has a unique permeability which allows it to eliminate volatile contaminants from the source. However, little attention has been paid to the removal of BTEX by ClO₂, due to the difficulty of removing BTEX in semi-enclosed areas and the lack of testing methods for the reaction intermediates. Therefore, this study explored the performance of ClO₂ advanced oxidation technology on both liquid and gaseous benzene, toluene, o-xylene, and m-xylene. The results showed that ClO₂ was efficient in the removal of BTEX. The byproducts were detected by gas chromatography-mass spectrometry (GC-MS) and the reaction mechanism was speculated using the ab initio molecular orbital calculations method. The results demonstrated that ClO₂ could remove the BTEX from the water and the air without causing secondary pollution.

Ab initio calculations of the interaction potentials and thermodynamic functions for ArN and ArN. J Comput Chem 2023;44:1189-1198. [PMID: 36708239 DOI: 10.1002/jcc.27078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Argon compounds play an important role in the mass spectrometry with inductively coupled plasma and other applications. At the same time, there is a little knowledge of their electronic terms and thermodynamic functions due to the complexity of experimental observations. In this work, the ab initio simulations are performed to obtain the interatomic interaction potentials for the ground and excited states of ArN and ArN⁺ . Using these potentials, the vibrational-rotational partition functions and thermodynamic properties in the gas phase are calculated for these molecules at the temperature range of 298.15-10,000 K. The errors of the thermodynamic functions associated with the approximation of interatomic interaction potentials are estimated.

COSMO Models for the Pharmaceutical Development of Parenteral Drug Formulations

The aqueous solubility of active pharmaceutical ingredients is one of the most important features to be considered during the development of parenteral formulations in the pharmaceutical industry. Computational modelling has become in the last years an integral part of pharmaceutical development. In this context, ab initio computational models, such as COnductor-like Screening MOdel (COSMO), have been proposed as promising tools for the prediction of results without the effective use of resources. Nevertheless, despite the clear evaluation of computational resources, some authors had not achieved satisfying results and new calculations and algorithms have been proposed over the years to improve the outcomes. In the development and production of aqueous parenteral formulations, the solubility of Active Pharmaceutical Ingredients (APIs) in an aqueous and biocompatible vehicle is a decisive step. This work aims to study the hypothesis that COSMO models could be useful in the development of new parenteral formulations, mainly aqueous ones.

Minimal Molecular Building Blocks for Screening in Quasi-Two-Dimensional Organic-Inorganic Lead Halide Perovskites

Layered hybrid organic-inorganic lead halide perovskites have intriguing optoelectronic properties, but some of the most interesting perovskite systems, such as defective, disordered, or mixed perovskites, require multiple unit cells to describe and are not accessible within state-of-the-art ab initio theoretical approaches for computing excited states. The principal bottleneck is the calculation of the dielectric matrix, which scales formally as O(N⁴). We develop here a fully ab initio approximation for the dielectric matrix, known as IPSA-2C, in which we separate the polarizability of the organic/inorganic layers into minimal building blocks, thus circumventing the undesirable power-law scaling. The IPSA-2C method reproduces the quasi-particle band structures and absorption spectra for a series of Ruddlesden-Popper perovskites to high accuracy, by including critical nonlocal effects neglected in simpler models, and sheds light on the complicated interplay of screening between the organic and inorganic sublattices.

Two-Dimensional Films Based on Graphene/Li4Ti5O12 and Carbon Nanotube/Li4Ti5O12 Nanocomposites as a Prospective Material for Lithium-Ion Batteries: Insight from Ab Initio Modeling

The combination of spinel Li₄Ti₅O₁₂ (LTO) with carbon nanostructures, such as graphene (G) and carbon nanotubes (CNTs), provides all of the required properties for modern chemical power sources such as Li-ion batteries (LIBs) and supercapacitors (SCs). G/LTO and CNT/LTO composites demonstrate a superior reversible capacity, cycling stability, and good rate performances. In this paper, an ab initio attempt to estimate the electronic and capacitive properties of such composites was made for the first time. It was found that the interaction between LTO particles and CNTs was higher than that with graphene due to the larger amount of transfer charge. Increasing the graphene concentration raised the Fermi level and enhanced the conductive properties of G/LTO composites. For CNT/LTO samples, the radius of CNT did not affect the Fermi level. For both G/LTO and CNT/LTO composites, an increase in the carbon ratio resulted in a similar reduction in quantum capacitance (QC). It was observed that during the charge cycle in the real experiment, the non-Faradaic process prevailed during the charge cycle, while the Faradaic process prevailed during the discharge cycle. The obtained results confirm and explain the experimental data and improve the understanding of the processes occurring in G/LTO and CNT/LTO composites for their usages in LIBs and SCs.

IBIL Measurement and Optical Simulation of the DI Center in 4H-SiC

In this paper, D_I defects are studied via experiments and calculations. The 2 MeV H⁺ is used to carry on an ion-beam-induced luminescence (IBIL) experiment to measure the in-situ luminescence of untreated and annealed 4H-SiC at 100 K. The results show that the luminescence intensity decreases rapidly with increasing H⁺ fluence, which means the losses of optical defect centers. In addition, the evident peak at 597 nm (2.07 eV) is the characteristic peak of 4H-SiC, and the weak peak between 400 nm and 450 nm is attributed to the D_I optical center. Moreover, the first-principles calculation of 4H-SiC is adopted to discuss the origin of D_I defects. The optical transition of the defect Si_C(C_Si)₂ from q = 0 to q = 1 is considered the experimental value of the D_I defect center.

Understanding the Exchange Interaction between Paramagnetic Metal Ions and Radical Ligands: DFT and Ab Initio Study on Semiquinonato Cu(II) Complexes

The exchange coupling, represented by the J parameter, is of tremendous importance in understanding the reactivity and magnetic behavior of open-shell molecular systems. In the past, it was the subject of theoretical investigations, but these studies are mostly limited to the interaction between metallic centers. The exchange coupling between paramagnetic metal ions and radical ligands has hitherto received scant attention in theoretical studies, and thus the understanding of the factors governing this interaction is lacking. In this paper, we use DFT, CASSCF, CASSCF/NEVPT2, and DDCI3 methods to provide insight into exchange interaction in semiquinonato copper(II) complexes. Our primary objective is to identify structural features that affect this magnetic interaction. We demonstrate that the magnetic character of Cu(II)-semiquinone complexes are mainly determined by the relative position of the semiquinone ligand to the Cu(II) ion. The results can support the experimental interpretation of magnetic data for similar systems and can be used for the in-silico design of magnetic complexes with radical ligands.

Fanpy: A python library for prototyping multideterminant methods in ab initio quantum chemistry

Fanpy is a free and open-source Python library for developing and testing multideterminant wavefunctions and related ab initio methods in electronic structure theory. The main use of Fanpy is to quickly prototype new methods by making it easier to convert the mathematical formulation of a new wavefunction ansätze to a working implementation. Fanpy is designed based on our recently introduced Flexible Ansatz for N-electron Configuration Interaction (FANCI) framework, where multideterminant wavefunctions are represented by their overlaps with Slater determinants of orthonormal spin-orbitals. In the simplest case, a new wavefunction ansatz can be implemented by simply writing a function for evaluating its overlap with an arbitrary Slater determinant. Fanpy is modular in both implementation and theory: the wavefunction model, the system's Hamiltonian, and the choice of objective function are all independent modules. This modular structure makes it easy for users to mix and match different methods and for developers to quickly explore new ideas. Fanpy is written purely in Python with standard dependencies, making it accessible for various operating systems. In addition, it adheres to principles of modern software development, including comprehensive documentation, extensive testing, quality assurance, and continuous integration and delivery protocols. This article is considered to be the official release notes for the Fanpy library.

Dynamics of Correlated Double-Ionization of Two-Electron Quantum Dots in Laser Fields

Using an ab initio, time-dependent calculational method, we study the non-linear dynamics of a two-electron quantum dot in the presence of ultrashort Thz laser pulses. The analysis of the contribution of the various partial waves to two-electron joint radial and energy distribution patterns revealed strongly correlated electron ejection channels. In the double-ionization process, regardless of the photon energy, the two-electron wave packets are born and remain concentrated until the pulse's peak; at later times, and depending on the photon energy of the field, distinctly different patterns emerge. Our calculations also showed the gradual transition of the radial and energy patterns from a single-peak to a doubly peaked structure, associated with the direct and the sequential double-ionization mechanisms, respectively.

Density functional theory and CCSD(T) evaluation of ionization potentials, redox potentials, and bond energies related to zirconocene polymerization catalysts

Quantum-mechanical-based computational design of molecular catalysts requires accurate and fast electronic structure calculations to determine and predict properties of transition-metal complexes. For Zr-based molecular complexes related to polyethylene catalysis, previous evaluation of density functional theory (DFT) and wavefunction methods only examined oxides and halides or select reaction barrier heights. In this work, we evaluate the performance of DFT against experimental redox potentials and bond dissociation enthalpies (BDEs) for zirconocene complexes directly relevant to ethylene polymerization catalysis. We also examined the ability of DFT to compute the fourth atomic ionization potential of zirconium and the effect the basis set selection has on the ionization potential computed with CCSD(T). Generally, the atomic ionization potential and redox potentials are very well reproduced by DFT, but we discovered relatively large deviations of DFT-calculated BDEs compared to experiment. However, evaluation of BDEs with CCSD(T) suggests that experimental values should be revisited, and our CCSD(T) values should be taken as most accurate.

The Prominence of Facilitator π-Holes: The Classic N←N Pnictogen Bonding in Nitrobenzene-Ammonia Dimer with its Structural Elucidation and Experimental Characterization at Low Temperatures

The nitrogen of nitro group is a paradigmatic pnictogen due the presence of a π-hole and a number of studies have been performed recently on prototypical nitromethane (NM). Homodimers and heterodimers of NM are sustained by π-hole driven pnictogen bonds hosted by nitrogen. To understand the effect of substitution on this π-hole and thus the pnictogen bond, heterodimers of nitrobenzene (NB; phenyl substitution in place of methyl) with ammonia (AM) have been probed, as a test case, using matrix isolation infrared spectroscopy and ab initio computations. Of the four structures optimized on the potential energy surface the energetically dominant global minimum, stabilized by π-hole driven O=N←N pnictogen bonding with co-operative N-H←O hydrogen bonding, was experimentally identified at low temperatures. A comparison of the pnictogen bonding of NB-AM dimers with NM counterpart (NM-AM dimers) divulged the dominance of electrostatic origin of pnictogen bonding in both the class of dimers. The reduced strength of pnictogen bonding in NB-AM dimers in comparison to NM-AM dimers was discerned, which has been established to be a consequence of the reduced electrostatic potential at the π-hole of NB relative to that in NM. The strength of π-hole driven pnictogen bond was directly correlated with the binding energy and the infrared shifts in the signature vibrational bands of the NB, NM and AM submolecules due to dimerization under matrix isolated conditions at low temperatures.

Quasi-2D SnO2 Thin Films for Gas Sensors: Chemoresistive Response and Temperature Effect on Adsorption of Analytes

We performed in silico calculations of electrical conductivity of quasi-2D SnO₂ thin films with a (110) surface-prospect material for sensitive element of gas sensors. Electronic structure, charge transfer and chemoresistive response of quasi-2D SnO₂ thin films during adsorption of alcohol molecules (ethanol, methanol, isopropanol and butanol) and ketones (acetone, cyclopentanone and cyclohexanone) were calculated. It was found that the electrical conductivity of quasi-2D SnO₂ thin films decreases within 4-15% during adsorption of analytes. The influence of temperature on the concentration of analytes on the surface of quasi-2D SnO₂ thin films was explored in dependence analyte's type.

Synthesis, Characterization, and Electronic Properties of ZnO/ZnS Core/Shell Nanostructures Investigated Using a Multidisciplinary Approach

ZnO/ZnS core/shell nanostructures, which are studied for diverse possible applications, ranging from semiconductors, photovoltaics, and light-emitting diodes (LED), to solar cells, infrared detectors, and thermoelectrics, were synthesized and characterized by XRD, HR-(S)TEM, and analytical TEM (EDX and EELS). Moreover, band-gap measurements of the ZnO/ZnS core/shell nanostructures have been performed using UV/Vis DRS. The experimental results were combined with theoretical modeling of ZnO/ZnS (hetero)structures and band structure calculations for ZnO/ZnS systems, yielding more insights into the properties of the nanoparticles. The ab initio calculations were performed using hybrid PBE0 and HSE06 functionals. The synthesized and characterized ZnO/ZnS core/shell materials show a unique three-phase composition, where the ZnO phase is dominant in the core region and, interestingly, the auxiliary ZnS compound occurs in two phases as wurtzite and sphalerite in the shell region. Moreover, theoretical ab initio calculations show advanced semiconducting properties and possible band-gap tuning in such ZnO/ZnS structures.

Quasiparticle Self-Consistent GW Study of Simple Metals

The GW method is a standard method to calculate the electronic band structure from first principles. It has been applied to a large variety of semiconductors and insulators but less often to metallic systems, in particular, with respect to a self-consistent employment of the method. In this work, we take a look at all-electron quasiparticle self-consistent GW (QSGW) calculations for simple metals (alkali and alkaline earth metals) based on the full-potential linearized augmented-plane-wave approach and compare the results to single-shot (i.e., non-selfconsistent) G0W0 calculations, density-functional theory (DFT) calculations in the local-density approximation, and experimental measurements. We show that, while DFT overestimates the bandwidth of most of the materials, the GW quasiparticle renormalization corrects the bandwidths in the right direction, but a full self-consistent calculation is needed to consistently achieve good agreement with photoemission data. The results mainly confirm the common belief that simple metals can be regarded as nearly free electron gases with weak electronic correlation. The finding is particularly important in light of a recent debate in which this seemingly established view has been contested.

TiO2 Gas Sensors Combining Experimental and DFT Calculations: A Review

Gas sensors play an irreplaceable role in industry and life. Different types of gas sensors, including metal-oxide sensors, are developed for different scenarios. Titanium dioxide is widely used in dyes, photocatalysis, and other fields by virtue of its nontoxic and nonhazardous properties, and excellent performance. Additionally, researchers are continuously exploring applications in other fields, such as gas sensors and batteries. The preparation methods include deposition, magnetron sputtering, and electrostatic spinning. As researchers continue to study sensors with the help of modern computers, microcosm simulations have been implemented, opening up new possibilities for research. The combination of simulation and calculation will help us to better grasp the reaction mechanisms, improve the design of gas sensor materials, and better respond to different gas environments. In this paper, the experimental and computational aspects of TiO2 are reviewed, and the future research directions are described.

Incommensurate magnetic ordering in CrB2

Incommensurate magnetism in CrB₂is studied in terms of a spin model based on density functional theory calculations. Heisenberg exchange interactions derived from the paramagnetic phase using the disordered local moment (DLM) theory show significant differences compared with those resulting from the treatment of the material as a ferromagnet; of these two methods, the DLM theory is found to give a significantly more realistic description. We calculate strongly ferromagnetic interactions between Cr planes but largely frustrated interactions within Cr planes. Although we find that the ground state ordering vector is sensitive to exchange interactions over a large number of neighbour shells, theq-vector of the incommensurate spin spiral state is satisfactorily reproduced by the theory (0.213 compared with the known ordering vector0.285×(2π)/(a/2)along Γ-K). The strong geometric frustration of the exchange interactions causes a rather low Néel temperature (about 97 K), also in good agreement with experiment.

Frenkel pair formation energy for cubic Fe3O4in DFT + U calculations

The cubic phase of magnetite is stabilized above the Verwey transition temperature of about 120 K via a complex electron-phonon interaction that is still not very well understood. In this work using the DFT + U method we describe our attempt to calculate point defect formation energies for this cubic phase in the static approximation. The electronic structure calculations and atomic relaxation peculiarities are discussed in this context. Only the cubic phase model with a small band gap and charge disproportionation (Fe²⁺/Fe³⁺) gives an adequate point defect formation energies, not the semi-metallic model. The relaxation of the local defect atomic structure and the relaxation of the surrounding crystal matrix are analyzed. Point defects cause only local perturbations of atomic positions and charge-orbital order. After analysis of the supercell size effects for up to 448 atoms, we justify the use of small supercells with 56 atoms to make calculations for the cubic phase. The extensive experimental results of Dieckmannet alon defects in magnetite at high temperature are deployed for comparison of our DFT + U results on Frenkel pair formation energies.

Atomic and Electronic Structure of the Al2O3/Al Interface during Oxide Propagation Probed by Ab Initio Grand Canonical Monte Carlo

Identifying the structure of the Al₂O₃/Al interface is important for advancing its performance in a wide range of applications, including microelectronics, corrosion barriers, and superconducting qubits. However, beyond the study of a few select terminations of the interface using computational methods, and top-down, laterally averaged spectroscopic and microscopic analyses, the explicit structure of the interface and the initial stages of propagation of the interface into the metal are largely unresolved. In this study, we utilize ab initio grand canonical Monte Carlo to perform a physically motivated, unbiased exploration of the interfacial composition and configuration space. We find that at equilibrium, the interface is atomically sharp with aluminum vacancies and propagates in a layer-by-layer fashion, with aluminum excess in the oxide layer at the interfacial plane. Oxygen incorporation, aluminum vacancy formation, and aluminum vacancy annihilation are the building blocks of Al₂O₃ formation at the interface. The localized interfacial mid-gap states from under-coordinated aluminum atoms from the oxide and the immediate depletion of aluminum states near the Fermi level upon oxygen incorporation prevent oxygen dissolution ahead of the interface front and result in the layer-by-layer propagation of the interface. This is in sharp contrast to the ZrO₂/Zr system, which forms interfacial sub-oxides, and also explains the favorable self-healing nature of the Al₂O₃/Al system. The occupied interfacial mid-gap states also increase the calculated n-type Schottky barrier heights. Additionally, we identify that interfacial aluminum core-level shifts linearly depend on the aluminum coordination number, whereas interfacial oxygen core-level shifts depend on long-range ordering at the interface. The detailed geometric and electronic insights into the interface structure and evolution expand our understanding of this fundamental interface and have important implications for the engineering and design of Al₂O₃/Al-based corrosion coatings with enhanced barrier properties, controllable transistor technologies, and noise-free superconducting qubits.

Structural Significance of His73 in F-Actin Dynamics: Insights from Ab Initio Study

F-actin dynamics (polymerization and depolymerization) are associated with nucleotide exchange, providing the driving forces for dynamic cellular activities. As an important residue in the nucleotide state-sensing region in actin, His73 is often found to be methylated in natural actin and directly participates in F-actin dynamics by regulating nucleotide exchange. The interaction between His73 and its neighboring residue, Gly158, has significance for F-actin dynamics. However, this weak chemical interaction is difficult to characterize using classic molecular modeling methods. In this study, ab initio modeling was employed to explore the binding energy between His73 and Gly158. The results confirm that the methyl group on the His73 side chain contributes to the structural stability of atomistic networks in the nucleotide state-sensing region of actin monomers and confines the material exchange (Pi release) pathway within F-actin dynamics. Further binding energy analyses of actin structures under different nucleotide states showed that the potential model of His73/Gly158 hydrogen bond breaking in the material exchange mechanism is not obligatory within F-actin dynamics.

Designing boron-cluster-centered zwitterionic Y-shaped clocked QCA molecules

Quantum-dot cellular automata (QCA) is a nanoscale, transistor-less device technology. A single molecule may provide an elementary QCA device known as a cell. Molecular redox centers function as quantum dots, and the configuration of mobile charge on the dots encodes device states useful for classical computing. Molecular QCA may support ultra-high device densities and THz-scale switching speeds at room temperature. An applied electric field may be used to clock molecular QCA, providing power gain to boost weakened signals, as well as quasi-adiabatic device operation for minimal power dissipation in QCA devices and circuits. A zwitterionic, Y-shaped, three-dot molecule may function as a field-clocked QCA cell. We focus on the design of a counterion built into the center of the cell.Ab initiocomputations demonstrate that choice of counterion determines the number of mobile charges for encoding the device state on the three quantum dots. We useB5H52-orB4CH5-as the central counterionic linker for two different Y-shaped, three-dot QCA molecules. While both molecules support the desired device states, the number of trapped charges in the counterion determines the number of mobile holes on the molecular quantum dots. This, in turn, determines whether the device state is encoded by a hole or an electron. This choice of encoding determines how the molecular QCA cell responds to a clocking field. The two counterions studied here lead to two QCA molecules with opposite responses to the clock, similar to the complementary responses of PMOS and NMOS transistors to gated voltage control.

Magnetic ground state of supported monatomic Fe chains from first principles

A new computational scheme is presented based on a combination of the conjugate gradient and the Newton-Raphson method to self-consistently minimize the energy within local spin-density functional theory, thus to identify the ground state magnetic order of a finite cluster of atoms. The applicability of the newab initiooptimization method is demonstrated for Fe chains deposited on different metallic substrates. The optimized magnetic ground states of the Fe chains on Rh(111) are analyzed in details and a good comparison is found with those obtained from an extended Heisenberg model containing first principles based interaction parameters. Moreover, the effect of the different bilinear spin-spin interactions in the formation of the magnetic ground states is monitored. In case of Fe chains on Nb(110) spin-spiral configurations with opposite rotational sense are found as compared to previous spin-model results which hints on the importance of higher order chiral interactions. The wavelength of the spin-spiral states of Fe chains on Re(0001) was obtained in good agreement with scanning tunneling microscopy experiments.

Unveiling the structural, dynamical, elastic, and electronic properties of cuboid silver tetrathiotungstate by means ofab initiocalculations

We present for the first time a theoretical study of the structural stability and physical properties of the newly synthesized Ag₂WS₄. The study contributes to a better understanding of its electronic and vibrational properties, which is fundamental for the optimization of the technological applications of Ag₂WS₄. Calculations have been carried out by means of density-functional theory. The obtained results support that Ag₂WS₄is thermodynamically, mechanically, and dynamically stable in a tetragonal layered structure, in good agreement with experiments. Calculations have also been used to obtain phonon frequencies, their assignments, and the Raman scattering spectrum. Furthermore, we show that Ag₂WS₄has a brittle structure, that is governed by van der Waals interactions, which favors its exfoliation as a low-dimensional structure. Additionally, the results show that Ag₂WS₄has a band gap of 2.02 eV with a favorable band-edge diagram for water splitting as well as for optoelectronic applications.

Heterometallic Hexanuclear [Cu2 Ln4 ] Complexes Showing Zero-field SMM Behaviour and Magnetocaloric Effect

Three heterometallic hexanuclear 3d-4f complexes bearing the formula [Cu₂ (L)₂ Ln₄ (L)₄ (o-van)₂ ] [L=2-((E)-((2-hydroxyphenyl)imino]methyl)phenol; o-van=ortho-vanillin] (Ln^III =Gd^III (1), Dy^III (2), and Tb^III (3)) have been synthesized and characterized. DC magnetic susceptibility measurements reveal overall antiferromagnetic interactions in 1 and 3, whereas co-existence of ferro- as well as antiferromagnetic interactions were observed in 2. The magnetocaloric effect has been observed for 1 with an entropy change (-ΔS_m ) of 22.3 J kg^-1  K^-1 at 3 K and 7 T. Zero-field single molecule magnet (SMM) behaviour has been observed for 2, where Raman relaxation and quantum tunneling of magnetization (QTM) played a role in magnetization relaxation. The Cu-O-Ln angle well explains the magnetic exchange coupling occurring in the complexes. BS-DFT calculation for the complexes provides an estimate of the exchange interactions between the paramagnetic centres. Ab initio calculations performed for complex 2 established a good correlation to the experimental relaxation dynamics.

Ab initioscreening of two-dimensional CuQxand AgQxchalcogenides

Two-dimensional (2D) chalcogenides have attracted great interest from the scientific community due to their intrinsic physical-chemical properties, which are suitable for several technological applications. However, most of the reported studies focused on particular compounds and composition, e.g., MoS₂, MoSe₂, WS₂, and WSe₂. Thus, there is an increased interest to extend our knowledge on 2D chalcogenides. Here, we report a density functional theory (DFT) screening of 2D coinage-metal chalcogenides (MQ_x), whereM= Cu, Ag,Q= S, Se, Te,x= 0.5, 1.0, 1.5, 2.0, with the aim to improve our atomistic understanding of the physical-chemical properties as a function of cation (M), anion (Q), and composition (x). Based on 258 DFT calculations, we selected a set of 22 stableMQ_xmonolayers based on phonons analyses, where we identified 9 semiconductors (7 AgQ_xand 2 CuQ_x), with band gaps from 0.07 eV up to 1.67 eV, while the remaining systems have a metallic character. Using all 258 systems, we found a logarithmic correlation between the average weighted bond lengths and effective coordination number of cations and anions. As expected, the monolayer cohesive energies increase with the radius of theQspecies (i.e., from S to Te). Furthermore, an increase in the anion size diminishes the work function for nearly allMQ_xmonolayers, which can be explained by the nature of the electronic states at the valence band maximum.

Connection between water's dynamical and structural properties: Insights from ab initio simulations

SignificanceFirst-principles calculations, which explicitly account for the electronic structure of matter, can shed light on the molecular structure and dynamics of water in its supercooled state. In this work, we use density functional theory, which relies on a functional to describe electronic exchange and correlations, to evaluate which functional best describes the temperature evolution of bulk water transport coefficients. We also assess the validity of the Stokes-Einstein relation for all the functionals in the temperature range studied, and explore the link between structure and dynamics. Based on these results, we show how transport coefficients can be computed from structural descriptors, which require shorter simulation times to converge, and we point toward strategies to develop better functionals.

Probing the charge transfer and electron-hole asymmetry in graphene-graphene quantum dot heterostructure

In recent years, graphene-based van der Waals (vdW) heterostructures have come into prominence showcasing interesting charge transfer dynamics which is significant for optoelectronic applications. These novel structures are highly tunable depending on several factors such as the combination of the two-dimensional materials, the number of layers and band alignment exhibiting interfacial charge transfer dynamics. Here, we report on a novel graphene based 0D-2D vdW heterostructure between graphene and amine-functionalized graphene quantum dots (GQD) to investigate the interfacial charge transfer and doping possibilities. Using a combination ofab initiosimulations and Kelvin probe force microscopy (KPFM) measurements, we confirm that the incorporation of functional GQDs leads to a charge transfer induced p-type doping in graphene. A shift of the Dirac point by 0.05 eV with respect to the Fermi level (E_F) in the graphene from the heterostructure was deduced from the calculated density of states. KPFM measurements revealed an increment in the surface potential of the GQD in the 0D-2D heterostructure by 29 mV with respect to graphene. Furthermore, we conducted power dependent Raman spectroscopy for both graphene and the heterostructure samples. An optical doping-induced gating effect resulted in a stiffening of theGband for electrons and holes in both samples (graphene and the heterostructure), suggesting a breakdown of the adiabatic Born-Oppenheimer approximation. Moreover, charge imbalance and renormalization of the electron-hole dispersion under the additional influence of the doped functional GQDs is pointing to an asymmetry in conduction and carrier mobility.

Linker Functionalization Strategy for Water Adsorption in Metal-Organic Frameworks

Water adsorption in metal-organic frameworks has gained a lot of scientific attention recently due to the potential to be used in adsorption-based water capture. Functionalization of their organic linkers can tune water adsorption properties by increasing the hydrophilicity, thus altering the shape of the water adsorption isotherms and the overall water uptake. In this work, a large set of functional groups is screened for their interaction with water using ab initio calculations. The functional groups with the highest water affinities form two hydrogen bonds with the water molecule, acting as H-bond donor and H-bond acceptor simultaneously. Notably, the highest binding energy was calculated to be -12.7 Kcal/mol for the -OSO₃H group at the RI-MP2/def2-TZVPP-level of theory, which is three times larger than the reference value. Subsequently, the effect of the functionalization strategy on the water uptake is examined on a selected set of functionalized MOF-74-III by performing Monte Carlo simulations. It was found that the specific groups can increase the hydrophilicity of the MOF and enhance the water uptake with respect to the parent MOF-74-III for relative humidity (RH) values up to 30%. The saturation water uptake exceeded 800 cm³/cm³ for all candidates, classifying them among the top performing materials for water harvesting.

Unraveling Heat Transport and Dissipation in Suspended MoSe2 from Bulk to Monolayer

Understanding heat flow in layered transition metal dichalcogenide (TMD) crystals is crucial for applications exploiting these materials. Despite significant efforts, several basic thermal transport properties of TMDs are currently not well understood, in particular how transport is affected by material thickness and the material's environment. This combined experimental-theoretical study establishes a unifying physical picture of the intrinsic lattice thermal conductivity of the representative TMD MoSe₂ . Thermal conductivity measurements using Raman thermometry on a large set of clean, crystalline, suspended crystals with systematically varied thickness are combined with ab initio simulations with phonons at finite temperature. The results show that phonon dispersions and lifetimes change strongly with thickness, yet the thinnest TMD films exhibit an in-plane thermal conductivity that is only marginally smaller than that of bulk crystals. This is the result of compensating phonon contributions, in particular heat-carrying modes around ≈0.1 THz in (sub)nanometer thin films, with a surprisingly long mean free path of several micrometers. This behavior arises directly from the layered nature of the material. Furthermore, out-of-plane heat dissipation to air molecules is remarkably efficient, in particular for the thinnest crystals, increasing the apparent thermal conductivity of monolayer MoSe₂ by an order of magnitude. These results are crucial for the design of (flexible) TMD-based (opto-)electronic applications.

High-Throughput Design of Interfacial Perpendicular Magnetic Anisotropy at Heusler/MgO Heterostructures

The perpendicular magnetic anisotropy (PMA) at ferromagnet/insulator interfaces has important technological applications, such as in the fields of magnetic recording and sensing devices. The perpendicular magnetic tunnel junctions (p-MTJs) with strong PMA have recently attracted increasing interest because they offer high stability and device performance toward low energy consumption. Heusler alloys are a large family of compounds that offer promising magnetic properties for developing p-MTJs. However, it is challenging to select appropriate combinations of Heusler ferromagnets and insulators with the desired interfacial properties. Here, we report a systematic high-throughput screening approach to search for candidate Heusler/MgO material interfaces with strong PMA and other desired material properties for spintronic technologies. On the basis of the open quantum material repositories, we developed a series of material descriptors, including formation energy, convex hull distance, magnetic ordering, lattice misfit, magnetic anisotropy constant, cleavage energy, and tunnel magnetoresistance, to filter candidate Heusler/MgO interfaces among the possible 40 000 ternary Heusler compounds. After a comprehensive screening, five full-Heusler compounds, including Co₂CrAl, Co₂FeAl, Co₂HfSn, Fe₂IrGa, and Mn₂IrGe, and two half-Heusler compounds, PtCrSb and PtMnAs, were found to be promising for designing p-MTJs. This work demonstrates a new way for the high-throughput design of functional material interfaces for spintronic applications via exploiting the open quantum material repositories and developing effective material descriptors along with the large-scale ab initio calculations for material interfaces.

Substituent effects in π-hole regium bonding interactions between Au(p-X-Py)2 complexes and Lewis bases: an ab initio study

For the first time, long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated. The Au(I) atom is coordinated to two para -substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide some experimental support to the existence of regium π-hole bonding in [Au(Py) 2 ] + derivatives.

The influence of tetrel bonds on the acidities of group 14 tetrafluoride - inorganic acid complexes

Ab initio methods were used to determine the influence of tetrel bond formation on the acidity. The systems composed of inorganic acids and tetrafluorides of 14 group elements have been tested - HA/EF₄ , where HA = H₂ O, NH₃ , HF, HCN, HNC, HCNO, HOCN and E = C, Si, Ge, Sn or Pb. It turns out that the electron density flow involved with formation of tetrel bond to carbon-based systems leads to negligible increase in acidity. In the case of the acceptor compounds based on the remaining 14 group elements however, the effect is much more apparent, as most of those compounds may be considered a Brønsted superacids. The electronic stability of anions formed after the deprotonation of aforementioned complexes has been investigated. Vast majority of the anions were found to exhibit significant electron binding energies.

Influence of the hBN Dielectric Layers on the Quantum Transport Properties of MoS2 Transistors

The encapsulation of single-layer 2D materials within hBN has been shown to improve the mobility of these compounds. Nevertheless, the interplay between the semiconductor channel and the surrounding dielectrics is not yet fully understood, especially their electron-phonon interactions. Therefore, here, we present an ab initio study of the coupled electrons and phonon transport properties of MoS2-hBN devices. The characteristics of two transistor configurations are compared to each other: one where hBN is treated as a perfectly insulating, non-vibrating layer and one where it is included in the ab initio domain as MoS2. In both cases, a reduction of the ON-state current by about 50% is observed as compared to the quasi-ballistic limit. Despite the similarity in the current magnitude, explicitly accounting for hBN leads to additional electron-phonon interactions at frequencies corresponding to the breathing mode of the MoS2-hBN system. Moreover, the presence of an hBN layer around the 2D semiconductor affects the Joule-induced temperature distribution within the transistor.

Prediction of the RNA Tertiary Structure Based on a Random Sampling Strategy and Parallel Mechanism

Background: Macromolecule structure prediction remains a fundamental challenge of bioinformatics. Over the past several decades, the Rosetta framework has provided solutions to diverse challenges in computational biology. However, it is challenging to model RNA tertiary structures effectively when the de novo modeling of RNA involves solving a well-defined small puzzle. Methods: In this study, we introduce a stepwise Monte Carlo parallelization (SMCP) algorithm for RNA tertiary structure prediction. Millions of conformations were randomly searched using the Monte Carlo algorithm and stepwise ansatz hypothesis, and SMCP uses a parallel mechanism for efficient sampling. Moreover, to achieve better prediction accuracy and completeness, we judged and processed the modeling results. Results: A benchmark of nine single-stranded RNA loops drawn from riboswitches establishes the general ability of the algorithm to model RNA with high accuracy and integrity, including six motifs that cannot be solved by knowledge mining-based modeling algorithms. Experimental results show that the modeling accuracy of the SMCP algorithm is up to 0.14 Å, and the modeling integrity on this benchmark is extremely high. Conclusion: SMCP is an ab initio modeling algorithm that substantially outperforms previous algorithms in the Rosetta framework, especially in improving the accuracy and completeness of the model. It is expected that the work will provide new research ideas for macromolecular structure prediction in the future. In addition, this work will provide theoretical basis for the development of the biomedical field.

Excellent Ultracold Molecular Candidates From Group VA Hydrides: Whether Do Nearby Electronic States Interfere?

By means of highly accurate ab initio calculations, we identify two excellent ultracold molecular candidates from group VA hydrides. We find that NH and PH are suitable for the production of ultracold molecules, and the feasibility and advantage of two laser cooling schemes are demonstrated, which involve different spin-orbit states (A 3 Π 2 andX 3 Σ 1 - ). The internally contracted multireference configuration interaction method is applied in calculations of the six low-lying Λ-S states of NH and PH with the spin-orbit coupling effects included, and excellent agreement is achieved between the computed and experimental spectroscopic data. We find that the locations of crossing point between theA 3 Π andΣ - 5 states of NH and PH are higher than the corresponding v' = 2 vibrational levels of theA 3 Π state indicating that the crossings with higher electronic states would not affect laser cooling. Meanwhile, the extremely small vibrational branching loss ratios of theA 3 Π 2 →a 1 Δ 2 transition for NH and PH (NH: 1.81 × 10-8; PH: 1.08 × 10-6) indicate that thea 1 Δ 2 intermediate electronic state will not interfere with the laser cooling. Consequently, we construct feasible laser-cooling schemes for NH and PH using three lasers based on theA 3 Π 2 →X 3 Σ 1 - transition, which feature highly diagonal vibrational branching ratioR 00 (NH: 0.9952; PH: 0.9977), the large number of scattered photons (NH: 1.04×105; PH: 8.32×106) and very short radiative lifetimes (NH: 474 ns; PH: 526 ns). Our work suggests that feasible laser-cooling schemes could be established for a molecular system with extra electronic states close to those chosen for laser-cooling.

Benchmarking Density Functional Approximations for Excited-State Properties of Fluorescent Dyes

This study presents an extensive analysis of the predictive power of time-dependent density functional theory in determining the excited-state properties of two groups of important fluorescent dyes, difluoroboranes and hydroxyphenylimidazo[1,2-a]pyridine derivatives. To ensure statistically meaningful results, the data set is comprised of 85 molecules manifesting diverse photophysical properties. The vertical excitation energies and dipole moments (in the electronic ground and excited states) of the aforementioned dyes were determined using the RI-CC2 method (reference) and with 18 density functional approximations (DFA). The set encompasses DFAs with varying amounts of exact exchange energy (EEX): from 0% (e.g., SVWN, BLYP), through a medium (e.g., TPSSh, B3LYP), up to a major contribution of EEX (e.g., BMK, MN15). It also includes range-separated hybrids (CAM-B3LYP, LC-BLYP). Similar error profiles of vertical energy were obtained for both dye groups, although the errors related to hydroxyphenylimidazopiridines are significantly larger. Overall, functionals including 40-55% of EEX (SOGGA11-X, BMK, M06-2X) ensure satisfactory agreement with the reference vertical excitation energies obtained using the RI-CC2 method; however, MN15 significantly outperforms them, providing a mean absolute error of merely 0.04 eV together with a very high correlation coefficient (R2 = 0.98). Within the investigated set of functionals, there is no single functional that would equally accurately determine ground- and excited-state dipole moments of difluoroboranes and hydroxyphenylimidazopiridine derivatives. Depending on the chosen set of dyes, the most accurate μGS predictions were delivered by MN15 incorporating a major EEX contribution (difluoroboranes) and by PBE0 containing a minor EEX fraction (hydroxyphenylimidazopiridines). Reverse trends are observed for μES, i.e., for difluoroboranes the best results were obtained with functionals including a minor fraction of EEX, specifically PBE0, while in the case of hydroxyphenylimidazopiridines, much more accurate predictions were provided by functionals incorporating a major EEX contribution (BMK, MN15).

Connecting Gas-Phase Computational Chemistry to Condensed Phase Kinetic Modeling: The State-of-the-Art

In recent decades, quantum chemical calculations (QCC) have increased in accuracy, not only providing the ranking of chemical reactivities and energy barriers (e.g., for optimal selectivities) but also delivering more reliable equilibrium and (intrinsic/chemical) rate coefficients. This increased reliability of kinetic parameters is relevant to support the predictive character of kinetic modeling studies that are addressing actual concentration changes during chemical processes, taking into account competitive reactions and mixing heterogeneities. In the present contribution, guidelines are formulated on how to bridge the fields of computational chemistry and chemical kinetics. It is explained how condensed phase systems can be described based on conventional gas phase computational chemistry calculations. Case studies are included on polymerization kinetics, considering free and controlled radical polymerization, ionic polymerization, and polymer degradation. It is also illustrated how QCC can be directly linked to material properties.

Phase transition mechanism of hexagonal graphite to hexagonal and cubic diamond:ab initiosimulation

Ab initiomolecular dynamics simulations are used to elucidate the mechanism of the phase transition in shock experiments from hexagonal graphite (HG) to hexagonal diamond (HD) or to cubic diamond (CD). The transition from HG to HD is found to occur swiftly in very small time of 0.2 ps, with large cooperative displacements of all the atoms. We observe that alternate layers of atoms in HG slide in opposite directions by 1/6 along the ±[2, 1, 0], which is about 0.7 Å, while simultaneously puckering by about ±0.25 Å perpendicular to thea-bplane. The transition from HG to CD occurred with more complex cooperative displacements. In this case, six successive HG layers slide in pairs by 1/3 along [0, 1, 0], [-1, -1, 0] and [1, 0, 0], respectively along with the puckering as above. We have also performed calculations of the phonon spectrum in HG at high pressure, which reveal soft phonon modes that may facilitate the phase transition involving the sliding and puckering of the HG layers. We have further calculated the Gibbs free energy, including the vibrational energy and entropy, and derived the phase diagram between HG and CD phases.