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Surface‐mounted metal–organic frameworks (SURMOFs) are crystalline films of MOFs and have garnered a great deal of attention in the past years. So far, thin‐film MOF research has been mainly focused on the synthesis and the exploration of potential applications of these materials, while a detailed understanding of their growth is still lacking. In this report evidence is provided for the inter‐grown nature of surface‐mounted thin films of Zn‐ZIF‐8 (SURZIF‐8; ZIF=zeolitic imidazolate framework). Two distinct SURZIF‐8 thin films have been made through layer‐by‐layer (LBL) growth after applying 20 and 50 LBL cycles. They have been characterized with atomic force microscopy (AFM) and Raman micro‐spectroscopy. A detailed analysis of the Raman mapping data, inter alia using principal component analysis (PCA), revealed the existence of phase boundaries within the 20‐cycle thin film, while the 50‐cycle thin film is chemically more homogeneous. To further analyze these chemical heterogeneities, density functional theory (DFT) calculations were performed of three theoretical models providing spectroscopic fingerprints of the molecular vibrations associated with the Zn‐ZIF‐8 thin films. Based on these calculations and the experimental data distinct vibrational markers indicative for the presence of defects sites were identified.

Multipolar fluorine–amide interactions with backbone and side‐chain amides have been described as important for protein–ligand interactions and have been used to improve the potency of synthetic inhibitors. In this study, fluorine interactions within a well‐defined binding pocket on galectin‐3 were investigated systematically using phenyltriazolyl‐thiogalactosides fluorinated singly or multiply at various positions on the phenyl ring. X‐ray structures of the C‐terminal domain of galectin‐3 in complex with eight of these ligands revealed potential orthogonal fluorine–amide interactions with backbone amides and one with a side‐chain amide. The two interactions involving main‐chain amides seem to have a strong influence on affinity as determined by fluorescence anisotropy. In contrast, the interaction with the side‐chain amide did not influence affinity. Quantum mechanics calculations were used to analyze the relative contributions of these interactions to the binding energies. No clear correlation could be found between the relative energies of the fluorine–main‐chain amide interactions and the overall binding energy. Instead, dispersion and desolvation effects play a larger role. The results confirm that the contribution of fluorine–amide interactions to protein–ligand interactions cannot simply be predicted, on geometrical considerations alone, but require careful consideration of the energetic components.

For selective hydrogenation of chemicals the high selectivity is always at the expense of activity and improving both selectivity and activity is challenging. Here, by chelating with p‐fluorothiophenol (SPhF)‐arrays, both steric and electronic effects are created to boost the performance of cheap nickel‐based catalysts. Compared with dinickel phosphide, the SPhF‐chelated one exhibits nearly 12 times higher activity and especially its selectivity is increased from 38.1% and 21.3% to nearly 100% in hydrogenations of 3‐nitrostyrene and cinnamaldehyde. Commercial catalysts like Raney Ni chelating with SPhF‐array also exhibits an enhanced selectivity from 20.5% and 23.4% to ≈100% along with doubled activity. Both experimental and density functional theory (DFT) calculation prove that the superior performance is attributed to the confined flat adsorption by ordered SPhF‐arrays and downshifted d‐band center of catalysts, leading to prohibited hydrogenation of the vinyl group and accelerative H2 activation. Such a surface modification can provide an easily‐realized and low‐cost way to design catalysts for the selective hydrogenation.

Lithium–sulfur batteries are currently being explored as promising advanced energy storage systems due to the high theoretical specific capacity of sulfur. However, achieving a scalable synthesis for the sulfur electrode material whilst maintaining a high volumetric energy density remains a serious challenge. Here, a continuous ball‐milling route is devised for synthesizing multifunctional FeS2/FeS/S composites for use as high tap density electrodes. These composites demonstrate a maximum reversible capacity of 1044.7 mAh g−1 and a peak volumetric capacity of 2131.1 Ah L−1 after 30 cycles. The binding direction is also considered here for the first time between dissolved lithium polysulfides (LiPSs) and host materials (FeS2 and FeS in this work) as determined by density functional theory calculations. It is concluded that if only one lithium atom of the polysulfide bonds with the sulfur atoms of FeS2 or FeS, then any chemical interaction between these species is weak or negligible. In addition, FeS2 is shown to have a strong catalytic effect on the reduction reactions of LiPSs. This work demonstrates the limitations of a strategy based on chemical interactions to improve cycling stability and offers new insights into the development of high tap density and high‐performance sulfur‐based electrodes.

A convenient protocol for stereodivergent hydrogenation of alkynes to E- and Z-alkenes by using nickel catalysts was developed. Simple Ni(NO3)2.6 H2O as a catalyst precursor formed active nanoparticles, which were effective for the semihydrogenation of several alkynes with high selectivity for the Z-alkene (Z/E>99:1). Upon addition of specific multidentate ligands (triphos, tetraphos), the resulting molecular catalysts were highly selective for the E-alkene products (E/Z>99:1). Mechanistic studies revealed that the Z-alkene-selective catalyst was heterogeneous whereas the E-alkene-selective catalyst was homogeneous. In the latter case, the alkyne was first hydrogenated to a Z-alkene, which was subsequently isomerized to the E-alkene. This proposal was supported by density functional theory calculations. This synthetic methodology was shown to be generally applicable in >40 examples and scalable to multigram-scale experiments.

We have quantum chemically explored the Diels–Alder reactivities of a systematic series of hetero‐1,3‐butadienes with ethylene by using density functional theory at the BP86/TZ2P level. Activation strain analyses provided physical insight into the factors controlling the relative cycloaddition reactivity of aza‐ and oxa‐1,3‐butadienes. We find that dienes with a terminal heteroatom, such as 2‐propen‐1‐imine (NCCC) or acrolein (OCCC), are less reactive than the archetypal 1,3‐butadiene (CCCC), primarily owing to weaker orbital interactions between the more electronegative heteroatoms with ethylene. Thus, the addition of a second heteroatom at the other terminal position (NCCN and OCCO) further reduces the reactivity. However, the introduction of a nitrogen atom in the backbone (CNCC) leads to enhanced reactivity, owing to less Pauli repulsion resulting from polarization of the diene HOMO in CNCC towards the nitrogen atom and away from the terminal carbon atom. The Diels–Alder reactions of ethenyl‐diazene (NNCC) and 1,3‐diaza‐butadiene (NCNC), which contain heteroatoms at both the terminal and backbone positions, are much more reactive due to less activation strain compared to CCCC.

The results of theoretical simulations of reaction paths for oxaliplatin from pro-drug into its active form responsible for cytostatic effect are presented. The studies based on the quantum-chemical density functional theory approach were performed considering environmental influence resulting from the aquation or electron donation. The hybrid mechanisms: hydrolytic mixed with electron driven were found to be the energetically favourable. Electronic supplementary material The online version of this article (10.1007/s00894-020-04549-4) contains supplementary material, which is available to authorized users.

Silver nanoparticles have a great potential in a broad range of applications such as drug-delivery carriers because of their antiviral and antibacterial properties. In this study, the coating properties of silver nanoparticle (size range of 1.6 nm) with three common anti-malarial drugs, Artemisinin, Artemether, and Artesunate have been studied by using the quantum mechanical and classical atomistic molecular dynamics simulation in order to use as the drug delivery to treat malaria and COVID-19 diseases. The optimized structure, frequencies, charge distribution, and the electrostatic potential maps of the three drug molecules were simulated by using the density functional theory (DFT) at the B3LYP/6-311++g(d,p) level of theory. Then, molecular dynamics simulation was used to study the coating of AgNP with each of these drugs. The affinity of interaction was obtained as Artesunate > Artemether > Artemisinin which is in agreement with the DFT results on the adsorption of drugs on the Ag(111) slab.

The (seleno)cysteine residues in some protein families react with hydroperoxides with rate constants far beyond those of fully dissociated low molecular weight thiol or selenol compounds. In case of the glutathione peroxidases, we could demonstrate that high rate constants are achieved by a proton transfer from the chalcogenol to a residue of the active site [Orian et al. Free Radic. Biol. Med. 87 (2015)]. We extended this study to three more protein families (OxyR, GAPDH and Prx). According to DFT calculations, a proton transfer from the active site chalcogenol to a residue within the active site is a prerequisite for both, creating a chalcogenolate that attacks one oxygen of the hydroperoxide substrate and combining the delocalized proton with the remaining OH or OR, respectively, to create an ideal leaving group. The “parking postions” of the delocalized proton differ between the protein families. It is the ring nitrogen of tryptophan in GPx, a histidine in GAPDH and OxyR and a threonine in Prx. The basic principle, however, is common to all four families of proteins. We, thus, conclude that the principle outlined in this investigation offers a convincing explanation for how a cysteine residue can become peroxidatic., Graphical abstract Image 1, Highlights • In some protein families, (seleno)cysteine residues react with hydroperoxides with very high rate constants. • In GPx, DFT models of the oxidation of the catalytic site support a two-step mechanism for the H2O2 reduction. • This mechanism is here found to operate in other thiol-based enzymes, i.e. OxyR, GAPDH and Prx.

The theoretical charge density study for the gas phase of anti-leprosy drug Dapsone has been carried out in the light of the theory of atoms in molecules using density functional theory employing B3LYP(6-311G++(d, p) hybrid functional completed with dispersion corrections. The Hirshfeld surface analysis as well as fingerprint plots has been utilized to visualize and quantify the intermolecular contacts present in the molecule. The topological properties such as electron density and its Laplacian, delocalization index have been elucidated to throw light into the chemical bonding and atomic and molecular details. The electron localization function has been used to visualize and deduce information on the lone pair and the subshells of the Cl atom. The electrostatic potential visualizes the positive and negative electrostatic potential regions which are susceptible to nucleophilic and electrophilic attack. On the whole, this study provides an exact mechanism, interaction, and topological and electrostatic properties of the drug through theoretical insights which all will be a platform for our further investigation of the interaction between dapsone and dihydropteroate synthase (DHPS).

The one-pot reaction of chlorosulfonyl isocyanate (CSI) with epoxides having phenyl, benzyl and fused cyclic alkyl groups in different solvents under mild reaction conditions without additives and catalysts was studied. Oxazolidinones and five-membered cyclic carbonates were obtained in ratios close to 1:1 in the cyclization reactions. The best yields of these compounds were obtained in dichloromethane (DCM). Together with 16 known compounds, two novel oxazolidinone derivatives and two novel cyclic carbonates were synthesized with an efficient and straightforward method. Compared to the existing methods, the synthetic approach presented here provides the following distinct advantageous: being a one-pot reaction with metal-free reagent, having shorter reaction times, good yields and a very simple purification method. Moreover, using the density functional theory (DFT) method at the M06-2X/6-31+G(d,p) level of theory the mechanism of the cycloaddition reactions has been elucidated. The further investigation of the potential energy surfaces associated with two possible channels leading to oxazolidinones and five-membered cyclic carbonates disclosed that the cycloaddition reaction proceeds via an asynchronous concerted mechanism in gas phase and in DCM.

Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine-thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson-Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp (2) to sp (3), does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn-Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor-acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

Stereochemically active lone pairs are an important non-bonding effect with significant implications on crystal structure and physical properties. This work reveals the highly repulsive nature of interactions between stereochemically active lone pairs, and shows how cooperative effects lead to stronger expression of stereochemically active lone pairs, affecting their impact on thermal conductivity., In chemistry, stereochemically active lone pairs are typically described as an important non-bonding effect, and recent interest has centred on understanding the derived effect of lone pair expression on physical properties such as thermal conductivity. To manipulate such properties, it is essential to understand the conditions that lead to lone pair expression and provide a quantitative chemical description of their identity to allow comparison between systems. Here, density functional theory calculations are used first to establish the presence of stereochemically active lone pairs on antimony in the archetypical chalcogenide MnSb2O4. The lone pairs are formed through a similar mechanism to those in binary post-transition metal compounds in an oxidation state of two less than their main group number [e.g. Pb(II) and Sb(III)], where the degree of orbital interaction (covalency) determines the expression of the lone pair. In MnSb2O4 the Sb lone pairs interact through a void space in the crystal structure, and their their mutual repulsion is minimized by introducing a deflection angle. This angle increases significantly with decreasing Sb—Sb distance introduced by simulating high pressure, thus showing the highly destabilizing nature of the lone pair interactions. Analysis of the chemical bonding in MnSb2O4 shows that it is dominated by polar covalent interactions with significant contributions both from charge accumulation in the bonding regions and from charge transfer. A database search of related ternary chalcogenide structures shows that, for structures with a lone pair (SbX 3 units), the degree of lone pair expression is largely determined by whether the antimony–chalcogen units are connected or not, suggesting a cooperative effect. Isolated SbX 3 units have larger X—Sb—X bond angles and therefore weaker lone pair expression than connected units. Since increased lone pair expression is equivalent to an increased orbital interaction (covalent bonding), which typically leads to increased heat conduction, this can explain the previously established correlation between larger bond angles and lower thermal conductivity. Thus, it appears that for these chalcogenides, lone pair expression and thermal conductivity may be related through the degree of covalency of the system.

The performance of anaerobic digestion (AD) can be improved by the addition of accelerants. Three types of biomass-derived carbon-based composites (Co/C, CoO/C, and Co3O4/C) were used as accelerants to investigate the effect on AD systems in this work. These accelerants significantly improved the cumulative biogas yield (576–585 mL/g VS), and the total chemical oxygen demand degradation rate (68.48–71.11%) compared to the reference group (435.8 mL/g VS, 50.74%). The digestates with accelerants exhibited exceptional stability (59.24–63.67%) and superior fertilizer utilization (3.50–4.55%). In addition, first-principle density functional theory (DFT) calculations were conducted to provide the theoretical basis for the direct interspecies electron transfer (DIET), and a general strategy was proposed to help understand the enhanced methanogenesis pathway induced by the biomass-derived carbon-based composites. These important findings provide a novel avenue for the development of composite accelerants for AD systems.

MgO makes up about 20% of the Earth’s lower mantle; hence, its rheological behaviour is important for the dynamics and evolution of the Earth. Here, we investigate the strength of twin boundaries from 0 to 120 GPa using DFT calculations together with structure prediction methods. As expected, we find that the energy barrier and critical stress for shear-coupled migration of the 310/[001] interface vary strongly with pressure. However, what is surprising is that the twin boundary also exhibits sudden strong discontinuities in strength which can both weaken and strengthen the boundary with increasing pressure. Since twin boundary migration is a proposed mechanism for both deformation and seismic attenuation in MgO, these results may suggest that MgO can undergo sudden changes in rheology due to transitions in grain boundary structure. The multiplicity of interfaces, however, necessitates the need for further studies to examine the role that phase changes in grain boundary structure play in mediating polycrystalline plasticity in the Earth.

In this work, we demonstrate the first synthesis of vinylene‐linked 2D CPs, namely, 2D poly(phenylenequinoxalinevinylene)s 2D‐PPQV1 and 2D‐PPQV2, via the Horner–Wadsworth–Emmons (HWE) reaction of C 2‐symmetric 1,4‐bis(diethylphosphonomethyl)benzene or 4,4′‐bis(diethylphosphonomethyl)biphenyl with C 3‐symmetric 2,3,8,9,14,15‐hexa(4‐formylphenyl)diquinoxalino[2,3‐a:2′,3′‐c]phenazine as monomers. Density functional theory (DFT) simulations unveil the crucial role of the initial reversible C−C single bond formation for the synthesis of crystalline 2D CPs. Powder X‐ray diffraction (PXRD) studies and nitrogen adsorption‐desorption measurements demonstrate the formation of proclaimed crystalline, dual‐pore structures with surface areas of up to 440 m2 g−1. More importantly, the optoelectronic properties of the obtained 2D‐PPQV1 (Eg=2.2 eV) and 2D‐PPQV2 (Eg=2.2 eV) are compared with those of cyano‐vinylene‐linked 2D‐CN‐PPQV1 (Eg=2.4 eV) produced by the Knoevenagel reaction and imine‐linked 2D COF analog (2D‐C=N‐PPQV1, Eg=2.3 eV), unambiguously proving the superior conjugation of the vinylene‐linked 2D CPs using the HWE reaction., 2D CPs via the Horner–Wadsworth–Emmons Reaction: A novel methodology for the solvothermal bottom‐up synthesis of 2D vinylene‐linked conjugated polymers (2D CPs) with a nitrogen‐doped skeleton by linking hexaazatrinaphthalene (HATN) units and phenyl/biphenyl units by vinylene linkages is reported.

Cumulene compounds are notoriously difficult to prepare and study because their reactivity increases dramatically with the increasing number of consecutive double bonds. In this respect, the emerging field of on‐surface synthesis provides exceptional opportunities because it relies on reactions on clean metal substrates under well‐controlled ultrahigh‐vacuum conditions. Here we report the on‐surface synthesis of a polymer linked by cumulene‐like bonds on a Au(111) surface via sequential thermally activated dehalogenative C−C coupling of a tribenzoazulene precursor equipped with two dibromomethylene groups. The structure and electronic properties of the resulting polymer with cumulene‐like pentagon–pentagon and heptagon–heptagon connections have been investigated by means of scanning probe microscopy and spectroscopy methods and X‐ray photoelectron spectroscopy, complemented by density functional theory calculations. Our results provide perspectives for the on‐surface synthesis of cumulene‐containing compounds, as well as protocols relevant to the stepwise fabrication of carbon–carbon bonds on surfaces., Superficial interactions: On‐surface investigations of tribenzoazulene molecules functionalized with two dibromomethylene groups at the pentagon and heptagon ends reveal, after sequential annealing steps, the unambiguous formation of polymers linked by cumulene‐like bonds via selective C−C coupling induced by the sequential activation of the precursor molecules on a Au(111) surface.

Pyridine phase III, which forms at 1.69 GPa, is tetragonal and related to the previously characterized orthorhombic form II by a displacive phase transition. Phase III is similar to a high-pressure form of benzene. The soft mode governing the III→II transition has been identified using a combination of symmetry mode analysis and periodic density functional theory. A combination of single-crystal X-ray diffraction and Raman spectroscopy is used to resolve ambiguities in previous work on pyridine., Single crystals of the high-pressure phases II and III of pyridine have been obtained by in situ crystallization at 1.09 and 1.69 GPa, revealing the crystal structure of phase III for the first time using X-ray diffraction. Phase II crystallizes in P212121 with Z′ = 1 and phase III in P41212 with Z′ = ½. Neutron powder diffraction experiments using pyridine-d5 establish approximate equations of state of both phases. The space group and unit-cell dimensions of phase III are similar to the structures of other simple compounds with C 2v molecular symmetry, and the phase becomes stable at high pressure because it is topologically close-packed, resulting in a lower molar volume than the topologically body-centred cubic phase II. Phases II and III have been observed previously by Raman spectroscopy, but have been mis-identified or inconsistently named. Raman spectra collected on the same samples as used in the X-ray experiments establish the vibrational characteristics of both phases unambiguously. The pyridine molecules interact in both phases through CH⋯π and CH⋯N interactions. The nature of individual contacts is preserved through the phase transition between phases III and II, which occurs on decompression. A combination of rigid-body symmetry mode analysis and density functional theory calculations enables the soft vibrational lattice mode which governs the transformation to be identified.

We report the ability of a pyrazino[2,3-g]quinoxaline derivative substituted with eight peripheral flexible n-octyloxy chains, to sense the volatile trifluoroacetic acid in trace amounts (in parts per billion levels). The reversible detection of acid sensing behavior was visually perceivable in both solution as well as in the drop-casted film on a TLC paper based strip. Density functional theory studies were carried out to elucidate the mechanism of the sensing behavior.

Through computational calculations, CuO(001) has been identified as an active surface for methane oxidation. Experimental validation with CuO nanobelts comprised of predominantly (001) surfaces has been performed and it is confirmed that the performance of such nanobelts is much higher than normal nanoparticles and nanowires. First principle calculations further clarified that two-coordinated oxygen plays a key role for methane adsorption and oxidation.

The controlled modification of electronic and photophysical properties of polycyclic aromatic hydrocarbons by chemical functionalization, adsorption on solid supports, and supramolecular organization is the key to optimize the application of these compounds in (opto)electronic devices. Here, we present a multimethod study comprehensively characterizing a family of pyridin-4-ylethynyl-functionalized pyrene derivatives in different environments. UV–vis measurements in toluene solutions revealed absorption at wavelengths consistent with density functional theory (DFT) calculations, while emission experiments showed a high fluorescence quantum yield. Scanning tunneling microscopy (STM) and spectroscopy (STS) measurements of the pyrene derivatives adsorbed on a Cu(111)-supported hexagonal boron nitride (hBN) decoupling layer provided access to spatially and energetically resolved molecular electronic states. We demonstrate that the pyrene electronic gap is reduced with an increasing number of substituents. Furthermore, we discuss the influence of template-induced gating and supramolecular organization on the energies of distinct molecular orbitals. The selection of the number and positioning of the pyridyl termini in tetrasubstituted, trans- and cis-like-disubstituted derivatives governed the self-assembly of the pyrenyl core on the nanostructured hBN support, affording dense-packed arrays and intricate porous networks featuring a kagome lattice.

We use first-principles density functional theory to conduct an extensive structure search using the AIRSS package for elemental sulfur in the range 50–550 GPa. We then obtain the low-temperature phase diagram of sulfur in the same pressure range, including vibrational effects through the harmonic approximation. We do not find any structures lower in energy than those already reported in experiment, although the phase diagram below 100 GPa is found to be crowded with structures separated by only a few meV. We report the transition sequence I 4 1 / acd → P 1 ¯ → ICM → C 2 / m → R 3 ¯ m → I m 3 ¯ m and obtain accurate pressures for each transition, although we find the second-order C 2 / m → R 3 ¯ m transition particularly difficult to define. Contrary to previous first-principles works (Pavel et al; Rudin and Liu 1999 Phys. Rev. Lett. 83 3049–52), we do not reproduce a trigonal → simple cubic transition at either the static lattice or harmonic level. We also undertake a detailed analysis of the incommensurately modulated (ICM) phase of sulfur phase using a commensurate approximant found in the structure search. We find that the modulation amplitude is zero above 96 GPa; some 40 GPa below the experimentally reported transition to the unmodulated phase. We find that the body-centred atoms in the relaxed ICM approximant are, in addition to the dominant transverse modulation (which is a frozen-in optical phonon mode), slightly displaced longitudinally in the b-direction. We subsequently discover that this (small) longitudinal modulation is coupled to the transverse mode, and hence report previously unnoticed weak-mode coupling between transverse and longitudinal optical phonons in the ICM phase.

A novel colorimetric probe RP1 was synthesized using rhodamine derivatives and heterocyclic compounds for the purpose of detecting Cu

Exploring efficient electrocatalysts for hydrogen production with non-noble metals and earth-abundant elements is a promising pathway for achieving practical electrochemical water splitting. In this work, the electronic properties and catalytic activity of monolayer SnSe2(1−x)S2x (x = 0–1) under compressive and tensile strain were investigated using density functional theory (DFT) computations. The results showed SnSe2(1−x)S2x alloys with continuously changing bandgaps from 0.8 eV for SnSe2 to 1.59 eV for SnS2. The band structure of a SnSe2(1−x)S2x monolayer can be further tuned by applied compressive and tensile strain. Moreover, tensile strain provides a direct approach to improve the catalytic activity for the hydrogen evolution reaction (HER) on the basal plane of the SnSe2(1−x)S2x monolayer. SnSeS and SnSe0.5S1.5 monolayers showed the best catalytic activity for HER at a tensile strain of 10%. This work provides a design for improved catalytic activity of the SnSe2(1-x)S2x monolayer.

The detection of single gas molecules is a highly challenging work because it requires sensors with an ultra-high level of sensitivity. By using density functional theory, here we demonstrate that the adsorption of a paramagnetic unpaired free radical gas (NO) on a monolayer of XS2 (X = Mo, W) can trigger the transition from semiconductor to half metal. More precisely, the single-layer XS2 (X = Mo, W) with NO adsorbed on it would behave like a metal in one spin channel while acting as a semiconductor in the other spin orientation. The half-metallicity is robust and independent of the NO concentration. In contrast, no half-metallic feature can be observed after the adsorption of other free radical gases such as NO2. The unique change in electronic properties after the adsorption of NO on transition-metal sulfides highlights an effective strategy to distinguish NO from other gas species by experimentally measuring spin-resolved transmission. Our results also suggest XS2 (X = Mo, W) nanosheets can act as promising nanoscale NO sensors.

Carboxylate-assisted cobalt(III)-catalyzed C–H cyanations are highly efficient processes for the synthesis of (hetero)aromatic nitriles. We have now analyzed the cyanation of differently substituted 2-phenylpyridines in detail computationally by density functional theory and also experimentally. Based on our investigations, we propose a plausible reaction mechanism for this transformation that is in line with the experimental observations. Additional calculations, including NCIPLOT, dispersion interaction densities, and local energy decomposition analysis, for the model cyanation of 2-phenylpyridine furthermore highlight that London dispersion is an important factor that enables this challenging C–H transformation. Nonbonding interactions between the Cp* ligand and aromatic and C–H-rich fragments of other ligands at the cobalt center significantly contribute to a stabilization of cobalt intermediates and transition states.

MSOX (multiple serial structures from one crystal) serial crystallography experiments were carried out using controlled X-ray radiolysis and photon-counting detectors to determine sequences of low-dose yet high-resolution structures of copper nitrite reductase. Working at 190 K and at room temperature provides greater dynamic freedom, allowing more of the catalytic cycle to be observed than at the usual cryogenic temperature of 100 K. The approach demonstrates the potential to obtain MSOX structural movies at variable temperatures, thus providing an unparalleled level of structural information during catalysis for redox enzymes., High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate ‘structural movies’ of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a ‘top-hat’ geometry, which was rapidly transformed to a ‘side-on’ configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

The properties of bulk compounds required to be suitable for photovoltaic applications, such as excellent visible light absorption, favorable exciton formation, and charge separation are equally essential for two-dimensional (2D) materials. Here, we systematically study 2D group IV–V compounds such as SiAs2 and GeAs2 with regard to their structural, electronic and optical properties using density functional theory (DFT), hybrid functional and Bethe–Salpeter equation (BSE) approaches. We find that the exfoliation of single-layer SiAs2 and GeAs2 is highly feasible and in principle could be carried out experimentally by mechanical cleavage due to the dynamic stability of the compounds, which is inferred by analyzing their vibrational normal mode. SiAs2 and GeAs2 monolayers possess a bandgap of 1.91 and 1.64 eV, respectively, which is excellent for sunlight harvesting, while the exciton binding energy is found to be 0.25 and 0.14 eV, respectively. Furthermore, band-gap tuning is also possible by application of tensile strain. Our results highlight a new family of 2D materials with great potential for solar cell applications.

The interaction of trimethyl(methylcyclopentadienyl)platinum(IV) ((C5H4CH3)Pt(CH3)3) molecules on fully and partially hydroxylated SiO2 surfaces, as well as the dynamics of this interaction were investigated using density functional theory (DFT) and finite temperature DFT-based molecular dynamics simulations. Fully and partially hydroxylated surfaces represent substrates before and after electron beam treatment and this study examines the role of electron beam pretreatment on the substrates in the initial stages of precursor dissociation and formation of Pt deposits. Our simulations show that on fully hydroxylated surfaces or untreated surfaces, the precursor molecules remain inactivated while we observe fragmentation of (C5H4CH3)Pt(CH3)3 on partially hydroxylated surfaces. The behavior of precursor molecules on the partially hydroxylated surfaces has been found to depend on the initial orientation of the molecule and the distribution of surface active sites. Based on the observations from the simulations and available experiments, we discuss possible dissociation channels of the precursor.

Motivated by the photocatalytic reactions of small molecules on g-C3N4 by these insights, we sought to explore the adsorption of H2O and CO2 molecules on the graphene side and H2O, H2, O2, CO, NO, and CO2 molecules on the g-C3N4 side of hybrid g-C3N4/graphene nanocomposite using first-principles calculations. The atomic structure and electronic properties of hybrid g-C3N4/graphene nanocomposite is explored. The adsorption of small molecules on graphene/g-C3N4 nanocomposite is thoroughly investigated. The computational studies revels that all small molecules on graphene/g-C3N4 nanocomposite are the physisorption. The adsorption characteristics of H2O and CO2 molecules on the graphene side are similar to that on graphene. The adsorption of H2O, H2, O2, CO, NO, and CO2 molecules on the g-C3N4 side always leads to a buckle structure of graphene/g-C3N4 nanocomposite. Graphene as a substrate can significantly relax the buckle degree of g-C3N4 in g-C3N4/graphene nanocomposite.

We present a computational analysis of the terahertz spectra of the monoclinic and the orthorhombic polymorphs of 2,4,6-trinitrotoluene. Very good agreement with experimental data is found when using density functional theory that includes Tkatchenko–Scheffler pair-wise dispersion interactions. Furthermore, we show that for these polymorphs the theoretical results are only weakly affected by many-body dispersion contributions. The absence of dispersion interactions, however, causes sizable shifts in vibrational frequencies and directly affects the spatial character of the vibrational modes. Mode assignment allows for a distinction between the contributions of the monoclinic and orthorhombic polymorphs and shows that modes in the range from 0 to ca. 3.3 THz comprise both inter- and intramolecular vibrations, with the former dominating below ca. 1.5 THz. We also find that intramolecular contributions primarily involve the nitro and methyl groups. Finally, we present a prediction for the terahertz spectrum of 1,3,5-trinitrobenzene, showing that a modest chemical change leads to a markedly different terahertz spectrum.

Platinum group metals (PGMs) serve as highly active catalysts in a variety of heterogeneous chemical processes. Unfortunately, their high activity is accompanied by a high affinity for CO and thus, PGMs are susceptible to poisoning. Alloying PGMs with metals exhibiting lower affinity to CO could be an effective strategy toward preventing such poisoning. In this work, we use density functional theory to demonstrate this strategy, focusing on highly dilute alloys of PGMs (Pd, Pt, Rh, Ir and Ni) with poison resistant coinage metal hosts (Cu, Ag, Au), such that individual PGM atoms are dispersed at the atomic limit forming single atom alloys (SAAs). We show that compared to the pure metals, CO exhibits lower binding strength on the majority of SAAs studied, and we use kinetic Monte Carlo simulation to obtain relevant temperature programed desorption spectra, which are found to be in good agreement with experiments. Additionally, we consider the effects of CO adsorption on the structure of SAAs. We calculate segregation energies which are indicative of the stability of dopant atoms in the bulk compared to the surface layer, as well as aggregation energies to determine the stability of isolated surface dopant atoms compared to dimer and trimer configurations. Our calculations reveal that CO adsorption induces dopant atom segregation into the surface layer for all SAAs considered here, whereas aggregation and island formation may be promoted or inhibited depending on alloy constitution and CO coverage. This observation suggests the possibility of controlling ensemble effects in novel catalyst architectures through CO-induced aggregation and kinetic trapping. Electronic supplementary material The online version of this article (10.1007/s11244-017-0882-1) contains supplementary material, which is available to authorized users.

Structural variations of the well-known guanine quartet (G4) motif in nucleic acid structures, namely substitution of two guanine bases (G) by two adenine (A) nucleobases in mutual trans positions, are discussed and studied by density functional theory (DFT) methods. This work was initiated by three findings, namely (1) that GA mismatches are compatible with complementary pairing patterns in duplex-DNA structures and can, in principle, be extended to quartet structures, (2) that GA pairs can come in several variations, including with a N1 protonated adeninium moiety (AH), and (3) that cross-linking of the major donor sites of purine nucleobases (N1 and N7) by transition metal ions of linear coordination geometries produces planar purine quartets, as demonstrated by some of us in the past. Here, possible structures of mixed AGAG quartets both in the presence of protons and alkali metal ions are discussed, and in particular, the existence of a putative four-purine, two-metal motif. Electronic supplementary material The online version of this article (10.1007/s00775-017-1507-7) contains supplementary material, which is available to authorized users.

The adsorption properties of common gas molecules (CO, NO, and N2) on the surface of Li-decorated pristine graphene and Li-decorated boron doped graphene are investigated using density functional theory. The adsorption energy, charge transfer, and density of states of gas molecules on three surfaces have been calculated and discussed, respectively. The results show that Li-decorated pristine graphene has strong interaction with CO and N2. Compared with Li-decorated pristine graphene, Li-decorated boron doped graphene exhibit a comparable adsorption ability of CO and N2. Moreover, Li-decorated boron doped graphene have a more significant adsorption energy to NO than that of Li-decorated pristine graphene because of the chemical interaction of the NO gas molecule. The strong interaction between the NO molecule and substrate (Li-decorated boron doped graphene) induces dramatic changes to the electrical conductivity of Li-decorated boron doped graphene. The results indicate that Li-decorated boron doped graphene would be an excellent candidate for sensing NO gas.

We report the results of X-ray spectroscopy and Raman measurements of as-prepared graphene on a high quality copper surface and the same materials after 1.5 years under different conditions (ambient and low humidity). The obtained results were compared with density functional theory calculations of the formation energies and electronic structures of various structural defects in graphene/Cu interfaces. For evaluation of the stability of the carbon cover, we propose a two-step model. The first step is oxidation of the graphene, and the second is perforation of graphene with the removal of carbon atoms as part of the carbon dioxide molecule. Results of the modeling and experimental measurements provide evidence that graphene grown on high-quality copper substrate becomes robust and stable in time (1.5 years). However, the stability of this interface depends on the quality of the graphene and the number of native defects in the graphene and substrate. The effect of the presence of a metallic substrate with defects on the stability and electronic structure of graphene is also discussed., 18 pages, 6 figures, accepted to Appl. Surf. Sci

The ultra-high specific surface area of graphene endows this two-dimensional material with an excellent capacity of ion absorption. Here we show that the ion absorption properties of graphene can be tailored via mechanical deformation. By using density function theory (DFT) analysis, we found that strain could enhance the ion absorption capacity of graphene. Our results provide perspective for the development of graphene-based electrochemical devices, such as stress difference battery and mechanochemistry sensors with graphene electrodes.

The tetrazine ligation is one of the fastest bioorthogonal ligations and plays a pivotal role in time-critical in vitro and in vivo applications. However, prediction of the reactivity of tetrazines in inverse electron demand Diels–Alder-initiated ligation reactions is not straight-forward. Commonly used tools such as frontier molecular orbital theory only give qualitative and often even wrong results. Applying density functional theory, we have been able to develop a simple computational method for the prediction of the reactivity of aryl/alkyl-substituted tetrazines in inverse electron demand Diels–Alder reactions. Graphical Abstract Electronic supplementary material The online version of this article (10.1007/s00706-017-2110-x) contains supplementary material, which is available to authorized users.

DL-Norleucine (2-aminohexanoic acid, C6H13NO2) forms a double-layer structure in all known phases (α, β, γ). The crystal structure of the β-phase was redetermined at 173 K. Diffraction patterns of the α- and β-phases frequently show diffuse streaks parallel to c*, which indicates a stacking disorder of the layers. A symmetry analysis was carried out to derive possible stacking sequences. Lattice-energy minimizations by force fields and by dispersion-corrected density functional theory (DFT-D) were performed on a set of ordered model structures with Z = 4, 8 and 16 with different stacking sequences. The calculated energies depend not only on the arrangement of neighbouring double layers, but also of next-neighbouring double layers. Stacking probabilities were calculated from the DFT-D energies. According to the calculated stacking probabilities large models containing 100 double layers were constructed. Their simulated diffraction patterns show sharp reflections for h + k = 2n and diffuse streaks parallel to c* through all reflections with h + k = 2n + 1. Experimental single-crystal X-ray diffraction revealed that at 173 K norleucine exists in the β-phase with stacking disorder. After reheating to room temperature, the investigated crystal showed a diffraction pattern with strong diffuse scattering parallel to c* through all reflections with h + k = 2n + 1, which is in good agreement with the simulated disordered structure.

An efficient synthesis methodology for a series of tetrazolo[1,5-a]pyrimidines substituted at the 5- and 7-positions from the cyclocondensation reaction [CCC + NCN] was developed. The NCN corresponds to 5-aminotetrazole and CCC to β-enaminone. Two distinct products were observed in accordance with the β-enaminone substituent. When observed in solution, the compounds can be divided into two groups: (a) precursor compounds with R = CF3 or CCl3, which leads to tetrazolo[1,5-a]pyrimidines in high regioselectivity with R at the 7-position of the heterocyclic ring; and (b) precursor compounds with R = aryl or methyl, which leads to a mixture of compounds, tetrazolo[1,5-a] pyrimidines (R in the 5-position of the ring) and 2-azidopyrimidines (R in the 4-position of the ring), which was attributed to an equilibrium of azide–tetrazole. In the solid state, all compounds were found as 2-azidopyrimidines. The regiochemistry of the reaction and the stability of the products are discussed on the basis of the data obtained by density functional theory (DFT) for energetic and molecular orbital (MO) calculations.

Determining the accurate chemical structures of synthesized compounds is essential for biomedical studies and computer-assisted drug design. The unequivocal determination of N-adamantylation or N-arylation site(s) in nitrogen-rich heterocycles, characterized by a low density of hydrogen atoms, using NMR methods at natural isotopic abundance is difficult. In these compounds, the heterocyclic moiety is covalently attached to the carbon atom of the substituent group that has no bound hydrogen atoms, and the connection between the two moieties of the compound cannot always be established via conventional 1H-1H and 1H-13C NMR correlation experiments (COSY and HMBC, respectively) or nuclear Overhauser effect spectroscopy (NOESY or ROESY). The selective incorporation of 15N-labelled atoms in different positions of the heterocyclic core allowed for the use of 1H-15N (JHN) and 13C-15N (JCN) coupling constants for the structure determinations of N-alkylated nitrogen-containing heterocycles in solution. This method was tested on the N-adamantylated products in a series of azolo-1,2,4-triazines and 1,2,4-triazolo[1,5-a]pyrimidine. The syntheses of adamantylated azolo-azines were based on the interactions of azolo-azines and 1-adamatanol in TFA solution. For azolo-1,2,4-triazinones, the formation of mixtures of N-adamantyl derivatives was observed. The JHN and JCN values were measured using amplitude-modulated 1D 1H spin-echo experiments with the selective inversion of the 15N nuclei and line-shape analysis in the 1D 13С spectra acquired with selective 15N decoupling, respectively. Additional spin–spin interactions were detected in the 15N-HMBC spectra. NMR data and DFT (density functional theory) calculations permitted to suggest a possible mechanism of isomerization for the adamantylated products of the azolo-1,2,4-triazines. The combined analysis of the JHN and JCN couplings in 15N-labelled compounds provides an efficient method for the structure determination of N-alkylated azolo-azines even in the case of isomer formation. The isomerization of adamantylated tetrazolo[1,5-b][1,2,4]triazin-7-ones in acidic conditions occurs through the formation of the adamantyl cation.

Under uniform strain, there are natural physical transitions from spin-filter magnetic semiconductor (MS) to spin-gapless semiconductor (SGS) to half-metal (HM) for rare earth-based equiatomic quaternary Heusler (EQH) compounds with the formula LuCoVZ, and from HM → SGS → MS → SGS → HM for EQH compounds with the formula YCoVZ., Magnetic Heusler compounds (MHCs) have recently attracted great attention since these types of material provide novel functionalities in spintronic and magneto-electronic devices. Among the MHCs, some compounds have been predicted to be spin-filter semiconductors [also called magnetic semiconductors (MSs)], spin-gapless semiconductors (SGSs) or half-metals (HMs). In this work, by means of first-principles calculations, it is demonstrated that rare earth-based equiatomic quaternary Heusler (EQH) compounds with the formula MCoVZ (M = Lu, Y; Z = Si, Ge) are new spin-filter semiconductors with total magnetic moments of 3 µB. Furthermore, under uniform strain, there are physical transitions from spin-filter semiconductor (MS) → SGS → HM for EQH compounds with the formula LuCoVZ, and from HM → SGS → MS → SGS → HM for EQH compounds with the formula YCoVZ. Remarkably, for YCoVZ EQH compounds there are not only diverse physical transitions, but also different types of spin-gapless feature that can be observed with changing lattice constants. The structural stability of these four EQH compounds is also examined from the points of view of formation energy, cohesive energy and mechanical behaviour. This work is likely to inspire consideration of rare earth-based EQH compounds for application in future spintronic and magneto-electronic devices.

We developed an approach for determining distances between carbon nanoparticles and grafted paramagnetic ions and molecules by means of nuclear spin-lattice relaxation data. The approach was applied to copper-, cobalt- and gadolinium-grafted nanodiamonds, iron-grafted graphenes, manganese-grafted graphene oxide and activated carbon fibers that adsorb paramagnetic oxygen molecules. Our findings show that the aforementioned distances vary in the range of 2.7-5.4 Å and that the fixation of paramagnetic ions to nanoparticles is most likely implemented by means of the surface functional groups. The nuclear magnetic resonance data data are compared with the results of electron paramagnetic resonance measurements and density functional theory calculations.