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In this paper, we investigate the secondary structure of the Piv-Pro-d-Ser-NHMe peptide by means of nuclear magnetic resonance (NMR) and electronic circular dichroism (ECD) experiments, in conjunction with theoretical simulations based on molecular dynamics and time-dependent density functional theory calculations including polarizable embedding to account for solvent effects. The various experimental and theoretical protocols are assessed and validated, and are shown to provide a consistent description of the turn structure adopted by this peptide in solution. In addition, a simple fitting procedure is proposed to make the simulated and experimental ECD almost perfectly match. This full methodology is finally tested on another small peptide, enlightening its efficiency and robustness.

In this paper, we employed a multidisciplinary approach, combining experimental techniques and density functional theory (DFT) calculations to elucidate key features of the copper coordination environment of the bacterial lytic polysaccharide monooxygenase (LPMO) from Serratia marcescens ( Sm AA10). The structure of the holo -enzyme was successfully obtained by X-ray crystallography. We then determined the copper(II) binding affinity using competing ligands and observed that the affinity of the histidine brace ligands for copper is significantly higher than previously described. UV-vis, advanced electron paramagnetic resonance (EPR), and X-ray absorption spectroscopy (XAS) techniques, including high-energy resolution fluorescence detected (HERFD) XAS, were further used to gain insight into the copper environment in both the Cu(II) and Cu(I) redox states. The experimental data were successfully rationalized by DFT models, offering valuable information on the electronic structure and coordination geometry of the copper center. Finally, the Cu(II)/Cu(I) redox potential was determined using two different methods at ca . 350 mV vs NHE and rationalized by DFT calculations. This integrated approach not only advances our knowledge of the active site properties of Sm AA10 but also establishes a robust framework for future studies of similar enzymatic systems.

Kohn-Sham density functional theory is the most widely used method for electronic structure calculations of solid-state systems. The screened-exchange functionals developed following the influential work of Scuseria and co-workers in 2003-2006 have significantly improved the accuracy of the predictions of solid-state properties. This work assesses six screened-exchange density functionals for the prediction of 60 band gaps (database BG60) and 68 lattice constants (database LC68). The band gaps are calculated with both consistently calculated lattice constants and experimental lattice constants. Results for the nonlocal screened-exchange functionals are compared with those for six widely used or recently developed local functionals. The results show that all the screened-exchange functionals have smaller mean absolute errors (MAEs) than any of the local functionals. All the functionals except HLE17 overestimate (on average) the lattice constants, and M06-SX gives the best performance among the compared functionals, with a MAE of 0.051 Å. All the functionals underestimate (on average) the band gaps, and M06-SX outperforms all other functionals, with a MAE of 0.47 eV. M06-SX also has the lowest root-mean-squared error for both LC68 and BG60. For the subdatabases of BG60, M06-SX shows better performance for ionic crystals and systems with large band gaps, while HSE12s gives better results for semiconductors and systems with small band gaps. Overall, M06-SX shows the best performance for solid-state systems, followed by N12-SX and HSE12s. The best-performing local functionals are M06-L, revM06-L, and HLE17 for band gaps and M06-L and revM06-L for lattice constants. We found that M06-SX, revM06-L, and N12-SX not only are well optimized for a broad array of chemical properties but also have very good performance for the databases in this paper, making them well-suited for applications involving heterogeneous chemistry.

The carbon starvation-induced protein D (CsiD) is a recently characterized iron(II)/α-ketoglutarate-dependent oxygenase that activates a glutarate molecule as substrate at the C 2 position to exclusively produce ( S )-2-hydroxyglutarate products. This selective hydroxylation reaction by CsiD is an important component of the lysine biodegradation pathway in Escherichia coli ; however, little is known on the details and the origin of the selectivity of the reaction. So far, experimental studies failed to trap and characterize any short-lived catalytic cycle intermediates. As no computational studies have been reported on this enzyme either, we decided to investigate the chemical reaction mechanism of glutarate activation by an iron(IV)-oxo model of the CsiD enzyme. In this work, we present a density functional theory study on a large active site cluster model of CsiD and investigate the glutarate hydroxylation pathways by a high-valent iron(IV)-oxo species leading to ( S )-2-hydroxyglutarate, ( R )-2-hydroxyglutarate, and 3-hydroxyglutarate. In agreement with experimental observation, the favorable product channel leads to pro- S C 2 -H hydrogen atom abstraction to form ( S )-2-hydroxyglutarate. The reaction is stepwise with a hydrogen atom abstraction by an iron(IV)-oxo species followed by OH rebound from a radical intermediate. The work presented in this paper shows that despite the fact that the C-H bond strengths at the C 2 and C 3 positions of glutarate are similar in the gas phase, substrate binding and positioning guide the reaction to an enantioselective reaction process by destabilizing the hydrogen atom abstraction pathways for the pro- R C 2 -H and C 3 -H positions. Our studies predict the chemical properties of the iron(IV)-oxo species and its rate constants with glutarate and deuterated-glutarate. Moreover, the work shows little protein motions during the catalytic process, while the substrate entrance into the substrate binding pocket appears to be guided by three active site arginine residues that position the substrate for pro- S C 2 -H hydrogen atom abstraction. Finally, the calculations show that irrespective of the position of the substrate and what C-H bond is closest to the metal center, the lowest energy pathway is for a selective pro- S C 2 -H hydrogen atom abstraction.

The prediction of protein-ligand binding affinities using free energy perturbation (FEP) is becoming increasingly routine in structure-based drug discovery. Most FEP packages use molecular dynamics (MD) to sample the configurations of proteins and ligands, as MD is well-suited to capturing coupled motion. However, MD can be prohibitively inefficient at sampling water molecules that are buried within binding sites, which has severely limited the domain of applicability of FEP and its prospective usage in drug discovery. In this paper, we present an advancement of FEP that augments MD with grand canonical Monte Carlo (GCMC), an enhanced sampling method, to overcome the problem of sampling water. We accomplished this without degrading computational performance. On both old and newly assembled data sets of protein-ligand complexes, we show that the use of GCMC in FEP is essential for accurate and robust predictions for ligand perturbations that disrupt buried water.

Geopolymer nanocomposites incorporating carbon nanotube (CNT)/graphene-based nanomaterials have become an exciting area of research because of their exceptional interface compatibility, providing improved mechanical, electrical, and thermal properties for next-generation construction materials. Accordingly, geopolymers are superior candidates for the implementation of graphene-based nanocomposites. In this paper, a comprehensive examination through equilibrium density functional theory (DFT) with and without the contribution of van der Waals (vdW) dispersion interaction, along with ReaxFF molecular dynamics (ReaxFF-MD) computational modeling approaches, was carried out to comprehend the interaction mechanisms and adsorption energies between graphene-based nanosheets and primary aqueous species of geopolymer structure. Results showed that the interaction of Si-(OH)4 aqueous species with the pristine graphene substrate has the weakest physical binding adsorption. The adsorption energy of silicate species on the pristine graphene substrate increased when involving interactions with sodium or potassium cations. Graphene-based nanomaterial surface functionalization with hydroxyl or carboxyl groups led to the higher adsorption energies of silicate and aluminate species due to the stronger electrostatic interaction. Computations also revealed that Na+, compared to K+, mostly increased the interfacial binding between the geopolymer and CNT/graphene-based nanomaterials. The computed MD results exhibited some qualitative agreement with ab initio calculations (at 0 K), with an overestimation tendency as expected due to the contribution of kinetic energy at 300 K. DFT results refute literature assumptions of a covalent oxo-bridging bond between silicon and carbon atoms, confirming electrostatic interactions (Coulomb interaction), with van der Waals (vdW) dispersion forces also playing a significant role in adsorption energy. Our study provides a systematic quantification of missing binding energy parameters and their implications for upscaling interface effects to the nanocomposite level. [ABSTRACT FROM AUTHOR]

In the present paper, the mechanisms of N 2 O reduction by H 2 were systemically examined over various polyoxometalate-supported single-atom catalysts (SACs) M 1 /PTA (M = Fe, Co, Mn, Ru, Rh, Os, Ir, and Pt; PTA = [PW 12 O 40 ] 3- ) by means of density functional theory calculations. Among these M 1 /PTA SACs, Os 1 /PTA SAC possesses high activity for N 2 O reduction by H 2 with a relatively low rate-determining barrier. The favorable catalytic pathway involves the first and second N 2 O decomposition over the Os 1 /PTA SAC and hydrogenation of the key species after the second N 2 O decomposition. Molecular geometry and electronic structure analyses along the favorable reaction pathway indicate that a strong charge-transfer cooperative effect of metal and support effectively improves the catalytic activity of Os 1 /PTA SAC. The isolated Os atom not only plays the role of adsorption and activation of the N 2 O molecule but also works as an electron transfer medium in the whole reaction process. Meanwhile, the PTA support with very high redox stability has also been proven to be capable of transporting the electron to promote the whole reaction. We expect that our computation results can provide ideas for designing new SACs for N 2 O reduction by using H 2 selective catalytic reduction technology.

Dye-sensitized solar cells based on boron dipyrromethene (BODIPY) have gained widespread attention in recent years because of their easy structural modification, strong light absorption, and photostability. In this paper, a series of dyes with single or double acceptors based on the BODIPY framework have been designed and compared by density functional theory calculation. Results show that the dyes with double acceptors exhibit smaller band gap and broader red-shift absorption peaks than their counterparts with single acceptors. To further improve the dye performance, polythiophenes and electron donating groups are successively introduced into BODIPY and donor moieties of double-acceptor dyes. The introduction of polythiophene effectively improved the light harvesting efficiency (LHE) from 0.79 to 0.96. And, the stronger electron donating groups create a narrow band gap, resulting in a broad absorption band in the range of 400-1600 nm. These modifications not only broaden the absorption range but also facilitate electron injection, thereby improving the photoelectric conversion efficiency, which is beneficial for the potential application of BODIPY sensitizers in the field of photovoltaics.

Graphene-based single-atom catalysts have attracted increasing interest due to their potential to catalyze the direct conversion of CH4 to CH3OH. In particular, the porphyrin-like FeN4 complex has recently been reported to convert CH4 to CH3OH at low temperatures with high selectivity. However, only N2O and H2O2, which are high-cost and scarce compared to O2, can be used as the oxidant of the reaction. In this paper, we perform density functional theory calculations on graphitic MN4G-BN (M = Fe, Co, Cu) and CuN4G-PN systems to evaluate the CH4 oxidation to CH3OH using O2. We found that the addition of B doping adjacent to the Fe and Co centers as well as P doing adjacent to the Cu center facilitates a facile OO bond dissociation with an activation barrier of less than 0.4 eV, resulting in active M–O and inactive B/P–O sites. This low barrier is due to the early OO bond elongation at the O2 adsorption step and the stability of the atomically adsorbed O atoms. In the subsequent CH4 oxidation, the resultant OCuN4G-OPN is found to be significantly more CH4-reactive than the OFeN4G-OBN and OCoN4G-OBN with a H–CH3 activation barrier of only 0.66 eV. Such high reactivity is due to the proximity of the electron-acceptor orbital (i.e., the Cu–O lowest unoccupied molecular orbital) toward the Fermi level. Moreover, the CH4 oxidation on CuN4G-PN is predicted to form CH3OH with high exothermicity and high resistance to overoxidation. This study suggests a high possibility for CuN4G-PN as a potential catalyst for the stepwise conversion of CH4 to CH3OH using O2 at low temperatures. [ABSTRACT FROM AUTHOR]

Dissolved gas detection is very important for an oil-immersed transformer fault. We examined the adsorption characteristics and sensitivity processes of monolayer NbSe2 doped with Ag, Pd, and Pt on five typical gases (H2, CO, CO2, CH4, and C2H2) in oil-immersed transformer using first-principles calculations. While the Pd–NbSe2 system only has great desorption properties for H2 at high temperature, the Ag/Pt–NbSe2 system has outstanding adsorption and desorption possessions for H2 at ambient and high temperature. Therefore, micro-nanomaterials prepared by Ag/Pd/Pt–NbSe2 are expected to be used as sensors for detecting H2. The micro-nanomaterials prepared by NbSe2 and Ag/Pd/Pt–NbSe2 systems can be used for C2H2 desorption at ambient temperature and high temperatures, but the desorption effect is not excellent. Micro-nanomaterials prepared by NbSe2 and Pd/Pt–NbSe2 have excellent adsorption and desorption performance for CH4 and CO2 desorption at ambient temperature and are candidates for CH4 and CO2 sensors. This paper systematically studies the potential application of a metal-doped monolayer NbSe2 system in transformer oil gas dissolution and provides theoretical guidance for metal-doped NbSe2 micro-nanomaterials for transformer oil gas detection. It is theoretically proven that the metal-doped monolayer NbSe2 micro-nanomaterials provides an excellent scheme for detecting dissolved gas in transformer oil. [ABSTRACT FROM AUTHOR]

[NiFe] hydrogenases catalyze the reversible conversion of molecular hydrogen to protons and electrons. This seemingly simple reaction has attracted much attention because of the prospective use of H 2 as a clean fuel. In this paper, we have studied the full reaction mechanism of this enzyme with various computational methods. Geometries were obtained with combined quantum mechanical and molecular mechanics (QM/MM) calculations. To get more accurate energies and obtain a detailed account of the surroundings, we performed big-QM calculations with 819 atoms in the QM region. Moreover, QM/MM thermodynamic cycle perturbation calculations were performed to obtain free energies. Finally, density matrix renormalisation group complete active space self-consistent field calculations were carried out to study the electronic structures of the various states in the reaction mechanism. Our calculations indicate that the Ni-L state is not involved in the reaction mechanism. Instead, the Ni-C state is reduced by one electron and then the bridging hydride ion is transferred to the sulfur atom of Cys546 as a proton and the two electrons transfer to the Ni ion. This step turned out to be rate-determining with an energy barrier of 58 kJ/mol, which is consistent with the experimental rate of 750 ± 90 s -1 (corresponding to ∼52 kJ/mol). The cleavage of the H-H bond is facile with an energy barrier of 33 kJ/mol, according to our calculations. We also find that the reaction energies are sensitive to the size of the QM system, the basis set, and the density functional theory method, in agreement with previous studies.

As a low-cost support, MXenes have attracted more and more attention in developing nanoenzymes with enhanced peroxidase- or oxidase-like activity. In this paper, we report a simple way to synthesize a N-doped Ti3C2Tx MXene, which provides a support platform for developing MXene-based nanozymes with an attractive structure and performance. By anchoring copper nanoparticles on N-doped Ti3C2Tx Cu nanoparticles, Cu nanoparticles (NPs)/N-doped Ti3C2Tx with satisfactory structural stability was prepared, displaying a synergistic effect and enhanced peroxidase-like activity. The superior peroxidase-like activity was confirmed by the oxidation kinetics of 3,3′,5,5′-tetramethylbenzidine (TMB) and density functional theory calculations. The characteristics of peroxidase-like nanozymes have promoted the development of colorimetric biosensors to evaluate the performance of Cu NPs/N-doped Ti3C2Tx. As expected, the nanozyme exhibits gratifying sensitivity, high selectivity, a low detection limit of 5 μM, and practicability in the detection of serum samples. Remarkably, the Cu NPs/N-doped Ti3C2Tx has remarkable stability and maintains its peroxidase-like activity after 1 month of storage. This work has laid a solid foundation for guiding the design of metal NPs/nonmetal-doped MXenes with outstanding peroxidase-like activity and expanding their application in biosensors. [ABSTRACT FROM AUTHOR]

Two recent papers in this journal called into question the suitability of the correlation consistent basis sets for density functional theory (DFT) calculations, because the sets were designed for correlated methods such as configuration interaction, perturbation theory, and coupled cluster theory. These papers focused on the ability of the correlation consistent and other basis sets to reproduce total energies, atomization energies, and dipole moments obtained from "quasi-exact" multiwavelet results. Undesirably large errors were observed for the correlation consistent basis sets. One of the papers argued that basis sets specifically optimized for DFT methods were "essential" for obtaining high accuracy. In this work we re-examined the performance of the correlation consistent basis sets by resolving problems with the previous calculations and by making more appropriate basis set choices for the alkali and alkaline-earth metals and second-row elements. When this is done, the statistical errors with respect to the benchmark values and with respect to DFT optimized basis sets are greatly reduced, especially in light of the relatively large intrinsic error of the underlying DFT method. When judged with respect to high-quality Feller-Peterson-Dixon coupled cluster theory atomization energies, the PBE0 DFT method used in the previous studies exhibits a mean absolute deviation more than a factor of 50 larger than the quintuple zeta basis set truncation error. [ABSTRACT FROM AUTHOR]

The compound 3,3′-diindolylmethane (DIM) is a major in vivo product of digestion of indole-3-carbinol (I3C) (phytochemical from Brassicaceae family plants) and a main mediator of its chemopreventive and chemotherapeutic effects. In our previous paper, we have reported the impact of structural differences between DIM and I3C on their biological activity. In this paper, the coinfluence of two factors: polymorphism and temperature, on the topology, nature (Coulombic/polarization/dispersion/repulsion), and strength of interaction pattern in DIM are in our area of interest. Upon polymorph screening it has been found that DIM crystallizes in two polymorphic forms, form I (already known) and form II (newly obtained). differential scanning calorimetry indicated a slightly lower melting point for form I than for form II (436 versus 440 K) and the lack of phase transitions in both polymorphs. The crystal and molecular structures of both polymorphs have been determined as a function of temperature by single-crystal X-ray diffraction. The structure of polymorph I is monoclinic, space group C2/c, while polymorph II is orthorhombic, space group P212121. The DIM molecule adopts a twisted (both 1H-indole rings are aligned along the same direction, but they are twisted by about 61.5°) and a half-chair (the molecule is bent, and both 1H-indole rings make an angle of 68.9°) conformation, respectively, in forms I and II, which remain almost unaffected by temperature changes. Despite different relative orientations of both 1H-indole moieties in forms I and II, the differences in the interaction patterns revealed by quantum theory of atoms in molecules (QTAIM), reduced density gradient (RDS), Hirshfeld surfaces (3D HS), and two-dimensional molecular fingerprints (2D MF) are relatively small. The distribution of intermolecular interactions in the crystal of form II is by 5% less balanced than in that of form I. The Manhattan and Euclidean distances between the interactions do not exceed 3.76% and 2.21%, respectively, while the Bhattacharaya coefficient does not exceed 0.35. Solid state PDB/DPN calculations have revealed that in solid the twisted conformation of the molecule is less stable by 118.7 kJ/mol than that of the half-hair one, but despite this, polymorph I is more stable due to a greater number of weak intermolecular interactions stabilizing the crystalline packing. (In the gas phase the half-hair conformation of the molecule is less stable by 0.788 kJ/mol than the twisted one, which may be attributed to the existence of many weak interactions and crystal packing effects in the solid state, which are absent in the gas phase.) The key interaction stabilizing the twisted versus chair conformation and determining crystalline packing in both polymorphs of DIM is the NH···π one. The factor responsible for the locked conformation of DIM in both forms is the electrostatic potential complementarity of the regions of N-H···π, linking neighboring molecules, which permits easy overcoming of any repulsive interactions that may force rotation of the molecule. The commercial sample of DIM was found to contain approximately 50% of form I and 50% of form II. [ABSTRACT FROM AUTHOR]

Beyond carbon allotropes, other nanostructuressuch as fullereneB80are attracting a growing interest due to their potentialapplications. The use of new materials based on fullerene B80is still in a premature stage; however many of these applicationswould require the use of B80in solution. This paper reportsan unprecedented density functional theory (DFT) analysis on the interactionmechanism between B80and two choline-based ionic liquidsas a first insight for the fullerene B80solvation by ionicliquids. The analysis of properties such as binding energies, chargedistributions or intermolecular interactions shed light on the mainfeatures, which should govern interaction between ionic liquids andfullerene B80. In addition, the optimization of systemscomposed by six ionic pairs around a fullerene B80hassupplied some information about the first solvation shell at the molecularlevel. As a summary, this paper provides the first insights in therational design of ionic liquids with suitable properties for thesolvation of B80. [ABSTRACT FROM AUTHOR]

In nature, the protonation of oxo bridges is a commonly encountered mechanism for fine-tuning chemical properties and reaction pathways. Often, however, the protonation states are difficult to establish experimentally. This is of particular importance in the oxygen evolving complex of photosystem II, where identification of the bridging oxo protonation states is one of the essential requirements toward unraveling the mechanism. In order to establish a combined experimental and theoretical protocol for the determination of protonation states, we have systematically investigated a series of Mn model complexes by Mn K pre-edge X-ray absorption spectroscopy. An ideal test case for selective bis-μ-oxo-bridge protonation in a Mn dimer is represented by the system [MnIV2(salpn)2(μ-OHn)2]n+. Although the three species [MnIV2(salpn)2(μ-O)2], [MnIV2(salpn)2(μ-O)(μ-OH)]+ and [MnIV2(salpn)2(μ-OH)2]2+ differ only in the protonation of the oxo bridges, they exhibit distinct differences in the pre-edge region while maintaining the same edge energy. The experimental spectra are correlated in detail to theoretically calculated spectra. A time-dependent density functional theory approach for calculating the pre-edge spectra of molecules with multiple metal centers is presented, using both high spin (HS) and broken symmetry (BS) electronic structure solutions. The most intense pre-edge transitions correspond to an excitation of the Mn 1s core electrons into the unoccupied orbitals of local eg character (dz² and dxy based in the chosen coordinate system). The lowest energy experimental feature is dominated by excitations of 1s-α electrons, and the second observed feature is primarily attributed to 1s-β electron excitations. The observed energetic separation is due to spin polarization effects in spin-unrestricted density functional theory and models final state multiplet effects. The effects of spin polarization on the calculated Mn K pre-edge spectra, in both the HS and BS solutions, are discussed in terms of the strength of the antiferromagnetic coupling and associated changes in the covalency of Mn-O bonds. The information presented in this paper is complemented with the X-ray emission spectra of the same compounds published in an accompanying paper. Taken together, the two studies provide the foundation for a better understanding of the X-ray spectroscopic data of the oxygen evolving complex (OEC) in photosystem II. [ABSTRACT FROM AUTHOR]

Predicting crystal structure has always been a challenging problem for physical sciences. Recently, computational methods have been built to predict crystal structure with success but have been limited in scope and computational time. In this paper, we review computational methods such as density functional theory and machine learning methods used to predict crystal structure. We also explored the breadth versus accuracy of building a model to predict across any crystal structure using machine learning. We extracted 24 913 unique chemical formulas existing between 290 and 310 K from the Pearson Crystal Database. Of these 24 913 formulas, there exists 10 711 unique crystal structures referred to as entry prototypes. Common entries might have hundreds of chemical compositions, while the vast majority of entry prototypes is represented by fewer than ten unique compositions. To include all data in our predictions, entry prototypes that lacked a minimum number of representatives were relabeled as “Other”. By selecting the minimum numbers to be 150, 100, 70, 40, 20, and 10, we explored how limiting class sizes affected performance. Using each minimum number to reorganize the data, we looked at the classification performance metrics: accuracy, precision, and recall. Accuracy ranged from 97 ± 2 to 85 ± 2%; average precision ranged from 86 ± 2 to 79 ± 2%, while average recall ranged from 73 ± 2 to 54 ± 2% for minimum-class representatives from 150 to 10, respectively. [ABSTRACT FROM AUTHOR]

The exfoliation energy, the energy required to peel off an atomic layer from the surface of a bulk material, is of fundamental importance in the science and engineering of two-dimensional materials. Traditionally, the exfoliation energy of a material has been obtained from first-principles by calculating the difference in the ground-state energy between (i) a slab of N atomic layers (N ≫ 1) and (ii) a slab of N – 1 atomic layers plus an atomic layer separated from the slab. In this paper, we prove that the exfoliation energy can be obtained exactly as the difference in the ground-state energy between a bulk material (per atomic layer) and a single isolated layer. The proposed method is (i) tremendously lower in computational cost than the traditional approach because it does not require calculations on thick slabs, (ii) still valid even if there is a surface reconstruction of any kind, (iii) capable of taking into account the relaxation of the single exfoliated layer (both in-plane lattice parameters and atomic positions), and (iv) easily combined with all kinds of many-body computational methods. As a proof of principles, we calculated exfoliation energies of graphene, hexagonal boron nitride, MoS2, and phosphorene using density-functional theory. In addition, we found that the in-plane relaxation of an exfoliated layer accounts for 5% of one-layer exfoliation energy of phosphorene while it is negligible (<0.4%) in the other cases. [ABSTRACT FROM AUTHOR]

This paper identified a new excited-state proton transfer (ESPT) mechanism for 2,6-diazaindoles (2,6-DAI) in aqueous (H2O) solution based on time-dependent density functional theory. The calculated results show that the excited-state three proton transfer reaction cannot occur because the 2,6-DAI with two water molecules do not form hydrogen bond wires; this finding was different from those reported in previous experiments (Chung et al. J. Am. Chem. Soc. 2017, 139, 6396-6402). 2,6-DAI with three water molecules form 2,6-DAI·(H2O)3 clusters, whereas 2,6-DAI with four water molecules form 2,6-DAI·(H2O)4 cluster. These clusters participate in the ESPT reaction. To determine the ESPT mechanism of 2,6-DAI·(H2O)3 and 2,6-DAI·(H2O)4 clusters, we constructed the potential energy curves of S1 and S0 states. The results confirmed the simultaneous presence of both 2,6-DAI·(H2O)3 and 2,6-DAI·(H2O)4 clusters and only one proton transfer pathway. By calculating the transition states of 2,6-DAI·(H2O)3 and 2,6-DAI·(H2O)4 clusters, we found that the ESPT reaction is a consistent mechanism. Our work investigated the number of water molecules involved in the ESPT and paved the way to further study the intermolecular hydrogen bonding interactions in the biological field. [ABSTRACT FROM AUTHOR]

Nitrogen-containing anthraquinone derivatives are widely applied in vegetable fiber dyes. In this paper, the fluorescence quenching mechanism by an acylamino group twist in the excited state for the 1-(acylamino)anthraquinones (AYAAQs) derivatives in acetonitrile is investigated by density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methods. The calculated Stokes shift is in good agreement with the experimental data. The energy profiles show that each AYAAQs derivative reveals a barrierless twist process, indicating that the involvement of acylamino group rotation in addition to proton transfer becomes as another important coordinate in the excited state relaxation pathway. The effects of electron-substituted group promote twist process compared with 1-aminoanthraquinone (AAQ). Then, the cross points are searched by the constructed linearly interpolated internal coordinate (LIIC) pathways for AYAAQs, demonstrating that the potential energy curves of the S1 and T2 states intersect each other and are in accord with the El-Sayed rules. So one can conclude that the acylamino group twist and following intersystem crossing (ISC) processes are important nonradiative inactivation channel for the S1 state of the AYAAQs derivatives, which is more prone to proton transfer process and can explain the low fluorescence efficiency. In addition, we have measured the phosphorescence spectra of AAQ, and on this basis, it can be predicted that the phosphorescence may occur for the AYAAQs derivatives. [ABSTRACT FROM AUTHOR]

This paper reports on UV-stimulated synthesis of methylcyanotriacetylene carried out in cryogenic rare gas matrixes via coupling of smaller precursors: propyne and cyanodiacetylene. The detection was possible due to the strong visible ã ³A' → X ¹A1 phosphorescence of CH3C7N, discovered in the course of this work. The ensuing measurements of electronic spectroscopy revealed the formally forbidden B ¹E-X ¹A1 system, as well as the allowed one E ¹A1-X ¹A1, with origins at approximately 3.32 and 5.4 eV, respectively. It was also possible to revisit the spectroscopic characterization of cyanotriacetylene, HC7N, formed in parallel to the title photoproduct. Spectral assignments were assisted with a density functional theory study. [ABSTRACT FROM AUTHOR]

Among the 20 directly encoded proteinogenic amino acids, arginine is one of five remaining cases for which the crystal structure of a racemic crystalline phase has not yet been reported. In this paper, the crystal structure of DL-arginine is determined by exploiting modern methods for analysis of powder X-ray diffraction data, in conjunction with periodic DFT-D calculations. The crystal structure of dl-arginine provides interesting contrasts and comparisons to that of the enantiomerically pure crystalline phase (L-arginine), which was also determined recently from powder X-ray diffraction data. [ABSTRACT FROM AUTHOR]

Formate, as an excellent hydrogen-storage material, has recently become increasingly important because formate has low toxicity, is easy to store and transport, and contains relatively high energy density. In this paper, we give an overview of the recent strategies in the conversion of bicarbonate into formate by water splitting with a general metallic Zn powder, which mainly includes: (1) hydrogen production from water with Zn; (2) formate syntheses from bicarbonate with water-derived hydrogen; (3) catalytic role of ZnO and Zn/ZnO interface and reducing role of active intermediate of Zn hydride species (Zn-H); (4) density function theory calculation for formate synthesis from bicarbonate and water with Zn; (5) solar-to-chemical energy conversion efficiency estimation. The novel options of this proposed strategy are mainly the hydrogen being in situ formed from water with metal Zn as a reductant, and the plausible autocatalytic reaction mechanism. When coupled with reducing ZnO into Zn by solar energy, a highly efficient solar-fuel process can be expected. [ABSTRACT FROM AUTHOR]

An investigation of the optical and excitonic properties of photocatalytic compounds based on both experimental and theoretical approaches is proposed. More specifically, this paper reports, for the first time, the local-field, optical anisotropy, and excitonic effects in BiVO4, an active photocatalytic material in the visible range. The analyses are based on electron energy-loss spectroscopy measurements, ground-state density functional theory calculations, including crystal local-field effects, and many-body corrections using the Bethe-Salpeter equation. These results are supported by a comparison with two materials, namely, TiO2 anatase and rutile, which are well-known to differ in their photocatalytic properties, those being important and negligible, respectively. The analogies found for these two categories of compounds allow the proposal of criteria that appear to be essential for producing an optimal photocatalytic material. [ABSTRACT FROM AUTHOR]

Hydrogenolysis is an important approach for depolymerization of lignin, which provides attractive new sustainable platforms of fuels, chemicals, and materials. The theory of lignin hydrogenolysis is, however, still unsound, which limits the development of this approach and causes inconsistencies among experimental studies. In this paper, density functional theory is employed to investigate the initial hydrogenolytic cleavages of recognized five different types of interaromatic unit linkages of lignin, assuming the presence of hydrogen free radicals. The relative free energies of reactant complexes, reaction free energy changes, and rate constants for candidate reactions are calculated comprehensively at 298-538 K. On the basis of the results of calculation and a rapid equilibrium hypothesis, the major reaction channel is decided for each linkage, and its kinetics is assessed. It is concluded that the hydrogenolysis occurs at β-O-4 ether, diphenyl ether 4-O-5', and β-1' diphenylmethane linkages instantaneously if these are accessible to hydrogen free radicals, while β-5 phenylcoumaran and β-β' pinoresinol linkages are virtually inert to hydrogenolysis. [ABSTRACT FROM AUTHOR]

Recent advances in nano/molecular electronics and electrochemistry made it possible to continuously tune the fractional charge q of single molecules and to use vibrational spectroscopic methods to monitor such changes. Approaches to compute vibrational frequencies ω(q) of fractionally charged species based on the density functional theory (DFT) are faced with an important issue: the basic quantity used in these calculations, the total energy, should exhibit piecewise linearity with respect to the fractional charge, but approximate, commonly utilized exchange correlation functionals do not obey this condition. In this paper, with the aid of a simple and representative example, we benchmark results for ω(q) obtained within the DFT against ab initio methods, namely, coupled cluster singles and doubles and also second- and third-order Møller-Plesset perturbation) expansions. These results indicate that, in spite of missing the aforementioned piecewise linearity, DFT-based values ω(q) can reasonably be trusted. [ABSTRACT FROM AUTHOR]

Gold plays a major role in nanochemistry, catalysis, and electrochemistry. Accordingly, hundreds of studies apply density functionals to study chemical bonding with gold, yet there is no systematic attempt to assess the accuracy of these methods applied to gold. This paper reports a benchmark against 51 experimental bond enthalpies of AuX systems and seven additional polyatomic and cationic molecules. Twelve density functionals were tested, covering meta functionals, hybrids with variable HF exchange, double-hybrid, dispersion-corrected, and nonhybrid GGA functionals. The defined benchmark data set probes all types of bonding to gold from very electronegative halides that force Au+ electronic structure, via covalently bonded systems, hard and soft Lewis acids and bases that either work against or complement the softness of gold, the Au2 molecule probing gold's bond with itself, and weak bonds between gold and noble gases. Zero-point vibrational corrections are relatively small for Au-X bonds, ~ 11-12 kJ/mol except for Au-H bonds. Dispersion typically provides ~5 kJ/mol of the total bond enthalpy but grows with system size and is 10 kJ/mol for AuXe and AuKr. HF exchange and LYP correlation produce weaker bonds to gold. Most functionals provide similar trend accuracy, though somewhat lower for M06 and M06L, but very different numerical accuracy. Notably, PBE and TPSS functionals with dispersion display the smallest numerical errors and very small mean signed errors (0-6 kJ/mol), i.e. no bias toward over- or under-binding. Errors are evenly distributed versus atomic number, suggesting that relativistic effects are treated fairly; the mean absolute error is almost halved from B3LYP (45 kJ/mol) to TPSS and PBE (23 kJ/mol, including difficult cases); 23 kJ/mol is quite respectable considering the diverse bonds to gold and the complication of relativistic effects. Thus, studies that use DFT with effective core potentials for gold chemistry, with no alternative due to computational cost, are on solid ground using TPSS-D3 or PBE-D3. [ABSTRACT FROM AUTHOR]

The presence of the fluorocarbon group in fluorinated alcohols makes them an important class of molecules that have diverse applications in the field of separation techniques, synthetic chemistry, polymer industry, and biology. In this paper, we have performed the density function theory calculation along with atom in molecule analysis, molecular dynamics simulation, and IR measurements of bulk monofluoroethanol (MFE) and compared them with the data for bulk ethanol (ETH) to understand the effect of the fluorocarbon group in the structure and the hydrogen bond network of bulk MFE. It has been found that the intramolecular O-H···F hydrogen bond is almost absent in bulk MFE. Molecular dynamics simulation and density function theory calculation along with atom in molecule analysis clearly depict that in the case of bulk MFE, a significant amount of intermolecular O-H···F and C-H···F hydrogen bonds are present along with the intermolecular O-H···O hydrogen bond. The presence of intermolecular O-H···F and C-H···F hydrogen bonds causes the difference in the IR spectrum of bulk MFE as compared to bulk ETH. This study clearly depicts that the organic fluorine (fluorocarbon) of MFE acts as a hydrogen bond acceptor and plays a significant role in the structure and hydrogen bond network of bulk MFE through the formation of weak O-H···F as well C-H···F hydrogen bonds, which may be one of the important reasons behind the unique behavior of the fluoroethanols. [ABSTRACT FROM AUTHOR]

Silver carboxylate salts are widely used as additives in palladium-catalyzed C-H functionalization reactions. However, the role of these silver additives is often not fully understood. This paper describes an investigation of the role of AgOPiv in the stoichiometric activation of C6F5H at a well-defined PdII complex as well as in the PdII-catalyzed oxidative dimerization of 2-alkylthiophenes. Both in situ NMR spectroscopy and H/D exchange studies of the reactions of C6F5H implicate a role for AgOPiv in the C-H cleavage event, generating Ag-C6F5 as an intermediate. The catalytic studies show similar trends despite the different conditions and substrates, suggesting that AgOPiv promotes a similar metalation of the thiophene in the catalytic transformations. This proposal is supported by DFT calculations, which show energetically feasible pathways for concerted metalation-deprotonation of both 2-methylthiophene and pentafluorobenzene at [Ag(OPiv)]2. These studies suggest that initial metalation of C-H substrates at AgI carboxylates should be considered as a plausible pathway in C-H functionalization reactions involving mixtures of Ag and Pd salts. [ABSTRACT FROM AUTHOR]

Matter is nearsighted, that is, for a fixed chemical potential, the charge density is only sensitive to perturbations within a radius R. While it is known that the resultant change in the density at point r0 from some perturbation at some other point R (Δn(r0,R)) is a monotonically decreasing function, a plausible range of a chemically significant Δn(r0,R) and the value of R needed to cause these perturbations has not been well studied. Using the functional group, which upon satisfying the necessary atoms/bonds specific to that functional group retains a characteristic chemistry, this paper provides an initial study into the magnitude of both Δn and R, the radius beyond which to affect a given property. Values for Δn are shown to be robust across a variety of DFT functionals and provide a framework for the transfer of the functional group concept to other disciplines, such as metallurgy. [ABSTRACT FROM AUTHOR]

To support the development and characterization of chromophores with targeted photophysical properties, excited-state electronic structure calculations should rapidly and accurately predict how derivatization of a chromophore will affect its excitation and emission energies. This paper examines whether a time-independent excited-state density functional theory (DFT) approach meets this need through a case study of BODIPY chromophore photophysics. A restricted open-shell Kohn-Sham (ROKS) treatment of the S1 excited state of BODIPY dyes is contrasted with linear-response time-dependent density functional theory (TDDFT). Vertical excitation energies predicted by the two approaches are remarkably different due to overestimation by TDDFT and underestimation by ROKS relative to experiment. Overall, ROKS with a standard hybrid functional provides the more accurate description of the S1 excited state of BODIPY dyes, but excitation energies computed by the two methods are strongly correlated. The two approaches also make similar predictions of shifts in the excitation energy upon functionalization of the chromophore. TDDFT and ROKS models of the S1 potential energy surface are then examined in detail for a representative BODIPY dye through molecular dynamics sampling on both model surfaces. We identify the most significant differences in the sampled surfaces and analyze these differences along selected normal modes. Differences between ROKS and TDDFT descriptions of the S1 potential energy surface for this BODIPY derivative highlight the continuing need for validation of widely used approximations in excited state DFT through experimental benchmarking and comparison to ab initio reference data. [ABSTRACT FROM AUTHOR]

Vanadium-catalyzed deoxydehydration (DODH) reactions provide a cost-effective approach for the conversion of vicinal diols to olefin and polycyclic aromatic hydrocarbons. In this paper, density functional theory (DFT) calculations employing M06 and M06-L methods were conducted to clarify the mechanism of V-catalyzed DODH. Three types of mechanisms generally proposed for transition-metal-catalyzed DODH, associated with the previously omitted spin crossover processes, were considered herein. As a result, a different catalytic cycle including a new olefin-formation mechanism was located, which is in contrast to the findings of a recent study. We found that the favorable mechanism involves the condensation of diols to form vanadium(V) diolate, reduction of the vanadium(V) diolate by PPh3, and spin-crossover steps to form a triplet vanadium(III) diolate. Thereafter, single C–O bond cleavage occurs followed by another spin crossover to form a singlet alkylvanadium(V) intermediate. The final concerted V–O/C–O bond cleavage generates an olefin and finishes the catalytic cycle. The reduction of vanadium(V) diolate by PPh3 and the extrusion of olefin have close overall free energy barriers of 34.3 and 33.7 kcal/mol, respectively. These results suggest that both steps influence the reaction rate. On the other hand, the two mechanisms starting by the reduction of the oxovanadium(V) catalyst with either PPh3 or a secondary alcohol were excluded due to their higher energy demands in the reduction and the olefin-formation stages. The good consistency between the experimental observations and the calculation results verified the proposed mechanism and also enabled us to clarify the reason for the efficiency of different reductants. [ABSTRACT FROM AUTHOR]

Merocyanine dyes, owing to their unique photochemical properties, are widely used to fabricate probes for the detection of biologically active small molecules and bioimaging. In this paper, merocyanine-based probes were proved of undergoing unwanted hydrolysis. To explore the strategies toward avoiding the hydrolysis, the detailed hydrolysis mechanism was first investigated, which was also confirmed by density functional theory (DFT) calculation. Then a series of merocyanine dyes were rationally designed. Influences of molecular structures of the probes, the analytical media such as pH and components of the solution on the hydrolysis were systematically studied. The experimental results suggest that merocyanine based probes with low electron density are more likely to suffer the hydrolysis, which could be exacerbated by the well-accepted strategy for constructing type-II probes. It is worth noting that chemical surroundings could also exert distinctive influence on the hydrolysis. The hydrolysis could be obviously aggravated when fetal calf serum or DMSO was deployed. Our findings will definitely provide an effective and reliable approach for guiding the rational design of highly robust merocyanine-based probes and the optimization of the analytical media, which is helpful in terms of avoiding the hydrolysis of the probes and hydrolysis caused analytical errors. [ABSTRACT FROM AUTHOR]

Atomic layer deposition (ALD) has been recognized as a promising method to deposit conformal and uniform thin film of copper for future electronic devices. However, many aspects of the reaction mechanism and the surface chemistry of copper ALD remain unclear. In this paper, we employ plane wave density functional theory (DFT) to study the transmetalation ALD reaction of copper dimethylamino-2-propoxide [Cu(dmap)2] and diethylzinc [Et2Zn] that was realized experimentally by Lee et al. We find that the Cu(dmap)2 molecule adsorbs and dissociates through the scission of one or two Cu-O bonds into surface-bound dmap and Cu(dmap) fragments during the copper pulse. As Et2Zn adsorbs on the surface covered with Cu(dmap) and dmap fragments, butane formation and desorption was found to be facilitated by the surrounding ligands, which leads to one reaction mechanism, while the migration of ethyl groups to the surface leads to another reaction mechanism. During both reaction mechanisms, ligand diffusion and reordering are generally endothermic processes, which may result in residual ligands blocking the surface sites at the end of the Et2Zn pulse, and in residual Zn being reduced and incorporated as an impurity. We also find that the nearby ligands play a cooperative role in lowering the activation energy for formation and desorption of byproducts, which explains the advantage of using organometallic precursors and reducing agents in Cu ALD. The ALD growth rate estimated for the mechanism is consistent with the experimental value of 0.2 Å/cycle. The proposed reaction mechanisms provide insight into ALD processes for copper and other transition metals. [ABSTRACT FROM AUTHOR]

One of the most significant aspects in the development of dye-sensitized solar cells is the exploration and design of high-efficiency and low-cost dyes. This paper reports the theoretical design of various triphenylamine analogues, wherein the central nitrogen moiety establishes an sp2-hybridization, which endows a significant participation in the charge-transfer properties. Density functional theory (DFT) and time-dependent DFT methodologies were utilized to investigate the geometry, electronic structure, photochemical properties, and electrochemical properties of these dyes. Different exchange-correlation functionals were initially evaluated to establish a proper methodology for calculating the excited-state energy of the reference dye, known as DIA3. Consequently, TD-LC-ωPBE with a damping parameter of 0.175 Bohr-1 best correlates with the experimental value. Four new dyes, namely, Dhk1, Dhk2, Dhk3, and Dhk4, were designed by modifying the rigidity of the donor moiety. According to the results, altering the type and position of binding in the donor group leads to distinct planarity of the dyes, which significantly affects their properties. The designed Dhk4 dye showed more red-shifted and broadened absorption spectra owing to the enhanced coplanarity between its donor and π-bridge moiety, which brings an advantage for its potential use as sensitizer for photovoltaic applications. [ABSTRACT FROM AUTHOR]

A new strategy for the catalytic synthesis of substituted 1H-indenes via metalloradical activation of o-cinnamyl N-tosyl hydrazones is presented, taking advantage of the intrinsic reactivity of a CoIII carbene radical intermediate. The reaction uses readily available starting materials and is operationally simple, thus representing a practical method for the construction of functionalized 1H-indene derivatives. The cheap and easy to prepare low spin cobalt(II) complex [CoII(MeTAA)] (MeTAA = tetramethyltetraaza[14]annulene) proved to be the most active catalyst among those investigated, which demonstrates catalytic carbene radical reactivity for a nonporphyrin cobalt(II) complex, and for the first time catalytic activity of [CoII(MeTAA)] in general. The methodology has been successfully applied to a broad range of substrates, producing 1H-indenes in good to excellent yields. The metallo-radical catalyzed indene synthesis in this paper represents a unique example of a net (formal) intramolecular carbene insertion reaction into a vinylic C(sp2)-H bond, made possible by a controlled radical ring-closure process of the carbene radical intermediate involved. The mechanism was investigated computationally, and the results were confirmed by a series of supporting experimental reactions. Density functional theory calculations reveal a stepwise process involving activation of the diazo compound leading to formation of a CoIII-carbene radical, followed by radical ring-closure to produce an indanyl/benzyl radical intermediate. Subsequent indene product elimination involving a 1,2-hydrogen transfer step regenerates the catalyst. Trapping experiments using 2,2,6,6-tetra-methylpiperidine-1-oxyl (TEMPO) radical or dibenzoylperoxide (DBPO) confirm the involvement of cobalt(III) carbene radical intermediates. Electron paramagnetic resonance spectroscopic spin-trapping experiments using phenyl N-tert-butylnitrone (PBN) reveal the radical nature of the reaction. [ABSTRACT FROM AUTHOR]

A systematic theoretical study on conformational transformations of monosubstituted (ortho- and para-) aromatic nitroso oxides R-C6H4NOO was performed. The existence of two rotation axes enables two types of conformational transitions in substituted arylnitroso oxides: trans/cis (rotation around the N-O bond) and syn/anti (rotation around the C-N bond, which is important in ortho isomers). The complete set of conformers was localized for R-C6H4NOO using four selected density functional (M06-L, mPWPW91, OLYP, and HCTH) and augmented polarization basis set of triple splitting. It was found that the activation enthalpy of the trans-cis conformational transition is nearly insensitive to the nature of R and ranges within 58-60 kJ/mol for para isomers. The ortho substituent has an insignificant effect on ΔH≠trans→cis: it increases this value by ∼5 kJ/mol in syn isomers and decreases it by ∼3 kJ/mol in anti isomers. On the contrary, the syn-anti conformational barrier is considerably affected by the substituent R; an increase in the electron-withdrawing properties of R decreases ΔH≠syn→anti. The activation enthalpies grow with increasing polarity of the solvent, as it was found using IEFPCM calculation. The values of relaxation time for all conformational equilibria were calculated and compared with known lifetimes of aromatic nitroso oxides. Our results suggest that syn/anti transitions occur fast enough in the scale of the experimental lifetime. However, trans/cis transformations proceed more slowly. And under certain conditions discussed in the paper, the rate of this conformational transition limits that of irreversible decay of nitroso oxide. [ABSTRACT FROM AUTHOR]

The interaction of molecules with titanium oxide substrates may lead to substantial modifications of their optical properties, in particular a red shift of the absorption spectrum compared to that of bare titania. In the present paper we discuss the role of the interface between two molecules, catechol and dopamine, with gas-phase (TiO2)N clusters (N = 2, 4, 6). We studied, for the interface, the bidentate modes (the molecule bonded to two Ti sites via its two oxygen sites), which was the most energetically favorable, followed by the chelated modes (the molecule bonded to one Ti site via its two oxygen sites), and the monodentate mode (the molecule bonded to one Ti site via one oxygen site). The absorption spectra were calculated with time-dependent functional-theory with CAM-B3LYP for the description of charge-transfer excitations. We observe a red shift of the molecule/cluster systems with respect to the molecules and clusters alone. Moreover, the chelated mode was found to present bands at lower energies than the other modes, making it the most interesting mode to tune the absorption edge of these systems. [ABSTRACT FROM AUTHOR]

A new phosphorescent iridium(III) complex, bis[2′,6′-difluorophenyl-4-formylpyridinato-N,C4′]iridium(III) (picolinate) (IrC), was synthesized, fully characterized by various spectroscopic techniques, and utilized for the detection of CN- on the basis of the widely known hypothesis of the formation of cyanohydrins. The solid-state structure of the developed IrC was authenticated by single-crystal X-ray diffraction. Notably, the iridium(III) complex exhibits intense red phosphorescence in the solid state at 298 K (ΦPL = 0.16) and faint emission in acetonitrile solution (ΦPL = 0.02). The cyanide anion binding properties with IrC in pure and aqueous acetonitrile solutions were systematically investigated using two different channels: i.e., by means of UV-vis absorption and photoluminescence. The addition of 2.0 equiv of cyanide to a solution of the iridium(III) complex in acetonitrile (c = 20 μM) visibly changes the color from orange to yellow. On the other hand, the PL intensity of IrC at 480 nm was dramatically enhanced ∼5.36 × 10²-fold within 100 s along with a strong signature of a blue shift of the emission by ∼155 nm with a detection limit of 2.16 × 10-8 M. The cyanohydrin formation mechanism is further supported by results of a ¹H NMR titration of IrC with CN-. As an integral part of this work, phosphorescent test strips have been constructed by impregnating Whatman filter paper with IrC for the trace detection of CN- in the contact mode, exhibiting a detection limit at the nanogram level (∼265 ng/mL). Finally, density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were performed to understand the electronic structure and the corresponding transitions involved in the designed phosphorescent iridium(III) complex probe and its cyanide adduct. [ABSTRACT FROM AUTHOR]

A new lanthanum oxide, KLa5O5(VO4)2, was synthesized using a flux growth technique that involved solid-state reaction under an air atmosphere at 900 °C. The crystal structure was solved and refined using an innovative approach recently established and based on three-dimensional (3D) electron diffraction data, using precession of the electron beam and then validated against Rietveld refinement and denisty functional theory (DFT) calculations. It crystallizes in a monoclinic unit cell with space group C2/m and has unit cell parameters of a = 20.2282(14) Å, b = 5.8639(4) Å, c = 12.6060(9) Å, and β = 117.64(1)°. Its structure is built on Cresnel-like two-dimensional (2D) units (La5O5) of 4*3 (OLa4) tetrahedra, which run parallel to (001) plane, being surrounded by isolated VO4 tetrahedra. Four isolated vanadate groups create channels that host K+ ions. Substitution of K+ cations by another alkali metal is possible, going from lithium to rubidium. Li substitution led to a similar phase with a primitive monoclinic unit cell. A complementary selected area electron diffraction (SAED) study highlighted diffuse streaks associated with stacking faults observed on high-resolution electron microscopy (HREM) images of the lithium compound. Finally, preliminary catalytic tests for ethanol oxidation are reported, as well as luminescence evidence. This paper also describes how solid-state chemists can take advantages of recent progresses in electron crystallography, assisted by DFT calculations and powder X-ray diffraction (PXRD) refinements, to propose new structural types with potential applications to the physicist community. [ABSTRACT FROM AUTHOR]

Two-dimensional (2D) π-conjugated microporous polymers recently attracted tremendous interest due to their unique structural and electronic properties compared with 1D polymers and also graphene. In this paper, we present a comprehensive electronic structure investigation of several representative 2D conjugated polymers by virtue of first-principles density functional theory (DFT) calculations. A comparison of how spatial distribution of frontier molecular orbitals and charge carriers evolves in 1D and 2D conjugated oligomers as a function of system size is given. We also report the relationships between HOMO-LUMO gaps/ionization potential (IP)/electron affinity (EA)/structural reorganization energy upon charge doping and the oligomer size. These findings are insightful for understanding the electronic structure difference between 1D and 2D π-conjugated polymers and informative for designing new functional materials. [ABSTRACT FROM AUTHOR]

This paper provides spectral characterizations of the two isomers of the 1-methylenepyrene cation, namely, the 1-pyrenemethylium and a pyrene-like isomer owing a tropylium cycle. Both are possible photodissociation products of the 1-methylpyrene cation and were proposed as potential contributors to the diffuse interstellar bands. In that respect, vibrational and electronic spectra are computed for the optimized structures at the density functional theory (DFT) and time-dependent (TD-)DFT levels. Finite temperature effects on these spectra are estimated from molecular dynamics simulations within the density functional-based tight-binding (DFTB) and TD-DFTB frameworks, these methods being first benchmarked against DFT and TD-DFT calculations. The computed spectra allow discrimination of the two isomers. When the temperature increases, bands are observed to redshift and merge. The isomerization mechanism is investigated with the metadynamics technique, a biased dynamics scheme allowing to probe reaction mechanisms with high energy barriers by investigating the free energy surface at various temperatures. Four pathways with similar barrier heights (3.5-4 eV) are found, showing that the interconversion process would only occur in interstellar clouds under photoactivation. The present study opens the way to simulations on larger methyl- and methylenePAHs of astrophysical interest and their experimental investigation. [ABSTRACT FROM AUTHOR]

Solid-oxide fuel cells are promising devices for sustainable power generation. Electrolyte materials play an important role in connecting the anode and cathode, and they influence the performance of the device. In this context, gadolinium-doped ceria (GDC) has proven to be an efficient electrolyte material, although the presence of dopant clusters can lower its efficiency. After usage, dopant clusters start appearing at dislocations, translocations, grain boundaries, or surfaces. Hence, the study of dopant clustering at the atomic level near these regions becomes of vital importance, as it allows us to understand the reasons for the occurrence of this phenomenon and its impact on the oxygen conduction. In this context, the present paper studies the impact of dopant clustering near the (111) GDC surface. We have studied two different gadolinium concentrations in the material, of approximately 7% and 14%, which are close to the optimum concentration of 10%. Our results indicate that surface relaxation is a key factor in determining the preference of defect clusters to be found in the surface. We have also calculated the relative abundance of different defect clusters at different temperatures, including the configurational entropy term. It was revealed that working temperatures (650-1100 K) show the relative abundance of different cluster structures, displaying that, at high concentrations, preferred dopant clusters resemble the structure of Gd2O3, showing the formation of gadolinia domains. Finally, we show that oxygen diffusion will be affected by the formation of these domains. After evaluating the oxygen mobility, we conclude that oxygen vacancies will be trapped by the gadolinium clusters at the surface. These vacancy traps prevent oxygen diffusion, thereby affecting negatively the performance of the material and the fuel cell in general. [ABSTRACT FROM AUTHOR]

Although tautomerization may directly affect the chemical or biological properties of molecules, real-space investigation on the tautomeric behaviors of organic molecules in a larger area of molecular networks has been scarcely reported. In this paper, we choose guanine (G) molecule as a model system. From the interplay of high-resolution scanning tunneling microscopy (STM) imaging and density functional theory (DFT) calculations, we have successfully achieved the tautomeric recognition, separation, and interconversion of G molecular networks (formed by two tautomeric forms G/9H and G/7H) with the aid of NaCl on the Au(111) surface in ultrahigh vacuum (UHV) conditions. Our results may serve as a prototypical system to provide important insights into tautomerization related issues, which should be intriguing to biochemistry, pharmaceutics, and other related fields. [ABSTRACT FROM AUTHOR]

The interface of biological moleculeswith inorganic surfaces hasbeen the subject of several recent studies. Experimentally some aminoacids are evidenced to play a critical role in the adhesion and selectivityon oxide surfaces; however, detailed information on how the watermolecules on the hydrated surface are able to mediate the adsorptionis still missing. Accurate total energy ab initiocalculations based on dispersion-corrected density functional theoryhave been performed to investigate the adsorption of selected aminoacids on the hydrated ZnO(101̅0) surface, and the results arepresented and discussed in this paper. We have also investigated therole played by water in the determination of the most energeticallyfavorable adsorption configurations of the selected amino acids. Wehave found that for some amino acids the most energetically favorableconfigurations involve the deprotonation of the molecule if the waterscreening is not effective. [ABSTRACT FROM AUTHOR]

As a continuation of our previous work (J. Phys. Chem. B, 2014, 118, 11330) on the solvation of C60 by ionic liquids (ILs) using Molecular Dynamic simulations, this paper reports a systematic density functional theory (DFT) analysis on the interaction mechanism between C60 and 24 different ionic liquids (belonging to the imidazolium, piperazinium, and cholinium groups). Properties such as binding energies, charge distributions, intermolecular interactions, or electronic structure were analyzed as a function of the selected ILs. The stronger IL-C60 interactions would be related with p-p stacking between the C60 surface and anions such as salycilate ([SA]). Likewise, the electronic structure analysis pointed to a well-defined relationship between the energetics of IL-C60 systems and IL features. Therefore, ILs with deep HOMO energies as well as weak interaction between both ions would be a priori good candidates for C60 solvation. Although only short-range interactions are studied in the framework of DFT, this work provides useful information for the rational design of ILs that could exhibit suitable features as C60 solvents. [ABSTRACT FROM AUTHOR]

The Bürgi-Dunitz trajectory traces points along the pathway of bond formation between a nucleophile and electrophile. Previous X-ray crystallographic studies of some molecules containing a nucleophilic nitrogen atom and electrophilic carbonyl group provided some initial evidence for various degrees of bond formation via initial n→π* interactions. Observation of a complete set of points along the trajectory, however, has not yet been attained. In this paper, we present a DFT computational study investigating substituted 2-(dimethylamino)biphenyl-2'-carboxaldehydes as substrates for further examination of n→π* interactions and as a potential framework for more complete tracing of the Bürgi-Dunitz trajectory. These compounds are particulary suitable for study because of the rotational freedom granted by the C-C bond connecting the two aromatic rings allowing the molecule to choose the degree of interaction between the two complementary groups. The extent of interaction is measured by interatomic distance, NBO second-order perturbative analysis energies, volume of transferred electron density as provided by ETS-NOCV analysis, and differences in energies between models that allow for n→π* interactions and those that do not. A series of substituted biphenyls are ultimately identified as future synthetic targets that have maximum potential for providing improved tracing of the Bürgi-Dunitz trajectory. [ABSTRACT FROM AUTHOR]

The reaction mechanism of Rh(III)-catalyzedcross-dehydrogenativearyl–aryl coupling between benzamides and haloarenes was investigatedthrough detailed density functional theoretical (DFT) studies in termsof regioselectivity and deuterium kinetic isotope effects (KIEs).Three possible routes including one PivO–-assistedreaction route and two non-PivO–-assisted reactionroutes have been studied. The calculated results refute the proposedmechanism (without PivO–-assisted process) in theexperimental paper and demonstrate that the PivO–-assisted reaction mechanism is the most favored. Meanwhile, thecalculation revealed that the PivO–anion playsa crucial role as a proton acceptor in the C–H bond activation,especially when the second C–H activation of haloareneareneproceeds via a SE3 mechanism. The SE3 mechanismis presented for the Rh(III)-catalyzed aryl–aryl reaction forthe first time. Our mechanism is evaluated by the calculations ofthe para-/meta-regioselectivityand KIEs. And it is found that the second activation process is therate-determining step of the whole catalytic cycle. All these calculatedproperties agree well with the experiment and Glorius’s proposalthat the Rh(III)-catalyzed cross-dehydrogenative C–C couplingreaction proceeds by dual C–H activations. Our theoreticalstudies suggest that the Rh(III) complex catalyst strongly affectsthe mechanisms of the second C–H activation step and thus thiswork might provide insight into the design of new catalytic systems. [ABSTRACT FROM AUTHOR]

Optically active polycarbonates (PCs) are considered as candidates for new and valuable materials because of their well-defined chemical structures and special physical properties. Previous studies on asymmetric alternating copolymerization of cyclopentene oxide (CPO) and CO2 regarding chiral zinc catalysts provided poly(cyclopentene carbonate) (PCPC) with moderate enantioselectivity, and thus, the development of highly efficient catalysts for this enantioselective polymerization is highly desirable. This research work is enlightened by the DFT calculations. In this paper, we clearly describe the use of intramolecular dinuclear zinc-AzePhenol complex as a high performance catalyst for the asymmetric copolymerization of CPO and CO2, affording completely alternating PCPC under very mild conditions (1 atm CO2, 30 °C) in 98% yield with <99% enantioselectivity for (S,S)-configuration. The dinuclear catalyst is prepared in situ from the reaction of multidentate semiazecrown ether ligand and ZnEt2, followed by treatment with an alcohol additive. In addition, our previous studies indicated that this catalyst also showed excellent enantioselectivity in the asymmetric copolymerization of cyclohexene oxide (CHO) and CO2. In order to obtain more information on the mechanism of the catalytic copolymerization, the chemical structures of PCPC are characterized by ¹H NMR and 13C NMR spectroscopy, and the nonlinear effect is also investigated in this copolymerization. A plausible catalytic cycle for the present reaction system is outlined. The reaction of chiral ligand with ZnEt2, followed by the ethyl group exchange with EtOH, affords the ethoxy-bridged dinuclear zinc complex. The copolymerization reaction is initiated by the insertion of CO2 into the Zn-OEt bond to give a carbonate-ester-bridged complex. The two zinc centers are situated sufficiently close to each other to allow a synergistic effect in the copolymerization, meaning that one zinc atom acts as Lewis acid to activate the epoxide, the other is responsible for carbonate propagation through the nucleophilic attack of carbonate ester at the back side of the cis-epoxide by a six-membered transition state. Furthermore, the dinuclear zinc structure of the catalyst remains intact throughout the catalytic copolymerization. The proposed mechanism implies that the intramolecular dinuclear zinc catalyst is very important for future research into the copolymerization of other epoxides with CO2. [ABSTRACT FROM AUTHOR]