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This work aims at characterizing for the first time the 31P spin interactions determining the nuclear magnetic resonance (NMR) properties of solid black phosphorus (bP) and of its few-layer exfoliated form (fl-bP). Indeed, the knowledge of these properties is still very poor, despite the great interest received by this layered phosphorus allotrope and its exfoliated 2D form, phosphorene. By combining density functional theory (DFT) calculations and solid-state NMR experiments on suspensions of fl-bP nanoflakes and on solid bP, it has been possible to characterize the 31P homonuclear dipolar and chemical shift interactions, identifying the network of 31P nuclei more strongly dipolarly coupled and highlighting two kinds of magnetically nonequivalent 31P nuclei. These results add an important missing piece of information to the fundamental chemico-physical knowledge of bP and support future extensive applications of NMR spectroscopy to the characterization of phosphorene-based materials.

Thanks to the well-recognized role of benzaldehyde in industry, nowadays the research of new and sustainable approaches to selectively synthesize such an interesting product is receiving great attention from the chemists’ community. In this paper, a V-based catalytic biphasic system is adopted to perform toluene oxidation to benzaldehyde. Importantly, to pursue sustainability, organic solvents have been avoided, so toluene is used as substrate and co-solvent, together with water. Also, the use of hydrophobic ionic liquids has been explored. To perform oxidation, NH4VO3 catalyst, H2O2, and a safe and inexpensive co-catalyst are used. Among the tested co-catalysts, KF and O2 were found to be the best choice, to guarantee good yields, in mild reaction conditions. In fact, with such a sustainable method, up to 30% of benzaldehyde can be obtained at 60 °C and, more interestingly, the oxidative system can be recharged, raising-up the yield. The entire process results highly selective, since no traces of benzyl alcohol or benzoic acid are detected. Hence, it constitutes a very appealing synthetic route, even suitable to be easily scaled-up at an industrial level.

Dacomitinib (PF-00299804) was recently approved by the Food and Drug Administration (FDA) as a tyrosine kinase inhibitor (TKI). Unfortunately, side effects and disease resistance eventually result from its use. Off-target effects in some kinase inhibitors have arisen from drug conformational plasticity; however, the conformational states of Dacomitinib in solution are presently unknown. To fill this gap, we have used computational chemistry to explore optimized molecular geometry, properties, and ultraviolet-visible (UV-Vis) absorption spectra of Dacomitinib in dimethyl sulfoxide (DMSO) solution. Potential energy scans led to the discovery of two planar and two twisted conformers of Dacomitinib. The simulated UV-Vis spectral signatures of the planar conformers reproduced the two experimental spectral bands at 275 and 343 nm in solution. It was further discovered that Dacomitinib forms conformers through its three flexible linkers of two C-NH-C bridges, which control the orientations of the 3-chloro-4-fluoroaniline ring (Ring C) and the quinazoline ring (Rings A and B) and the 4-piperidin-1-yl-buten-2-nal side chain, and one C-O-C local bridge which controls the methoxy group locally. When in isolation, these flexible linkers form close hexagon and pentagon loops through strong intramolecular hydrogen bonding so that the "planar" conformers Daco-P1 and Daco-P2 are more stable in isolation. Such flexibility of the ligand and its ability to dock and bind with protein also depend on their interaction with the environment, in addition to their energy and spectra in isolation. However, an accurate quantum mechanical study on drug/ligand conformers in isolation provides necessary reference information for the ability to form a complex with proteins.

In the last few years, metallodrugs play a key role in the development of medicinal chemistry. The choice of metal ion, its oxidation state and stability, and the choice of inert and labile ligands are just some of the very important facts which must be considered before starting the synthesis of complexes with utilization in medicinal purpose. As a result, a lot of compounds of different transition metal ions found application for diagnostic and therapeutic purpose. Beside all, gold compounds have attracted particular attention. It is well-known that gold compounds could be used for the treatment of cancer, HIV, rheumatoid arthritis (chrysotherapy), and other diseases. This metal ion has unoccupied d-sublevels and possibility to form compounds with different oxidation states, from −1 to +5. However, gold(I) and gold(III) complexes are dominant in chemistry and medicine. Especially, gold(III) complexes are of great interest due to their structural similarity with cisplatin. Accordingly, this review summarizes the chemistry of some mononuclear and polynuclear gold(III) complexes. Special attention is given to gold(III) complexes with nitrogen-donor inert ligands (aliphatic or aromatic that have a possibility to stabilize complex) and their kinetic behavior toward different biologically relevant nucleophiles, mechanism of interaction with DNA/bovine serum albumin (BSA), cytotoxic activity, as well as computational calculations.

The molecular structures of myricetin (3,3′,4′,5,5′,7-hexahydroxyflavone; MCE) and myricitrin (myricetin 3-O-rhamnoside; MCI) are investigated by quantum chemical calculations (B3LYP/6-311G**). Two preferred molecular rotamers of MCI are predicted, corresponding to different conformations of the O-rhamnoside subunit. The rotamers are characterized by different hydrogen bonded cross-links between the hydroxy groups of the rhamnoside substituent and the parent MCE moiety. The predicted OH stretching frequencies are compared with vibrational spectra of MCE and MCI recorded for the sake of this investigation (IR and Raman). In addition, a reassignment of the C O stretching bands is suggested.

This manuscript reports the improved synthesis of the &alpha, &alpha, isomer of tetra-p-iodophenyl tetra-methyl calix[4]pyrrole and the X-ray characterization of two solvate polymorphs. In the solid state, the calix[4]pyrrole receptor adopts the cone conformation, including one acetonitrile molecule in its aromatic cavity by establishing four convergent hydrogen bonds between its nitrogen atom and the four pyrrole NHs of the former. The inclusion complexes pack into rods, displaying a unidirectional orientation. In turn, the rods form flat 2D-layers by alternating the orientation of their p-iodo substituents. The 2D layers stack on top of another, resulting in a head-to-head and tail-to-tail orientation of the complexes or their exclusive arrangement in a head-to-tail geometry. The dissimilar stacking of the layers yields two solvate polymorphs that are simultaneously present in the structures of the single crystals. The ratio of the two polymorph phases is regulated by the amount of acetonitrile added to the chloroform solutions from which the crystals grow. Halogen bonding interactions are highly relevant in the crystal lattices of the two polymorphs. We analyzed and characterized these interactions by means of density functional theory (DFT) calculations and several computational tools. Remarkably, single crystals of a solvate containing two acetonitrile molecules per calix[4]pyrrole were obtained from pure acetonitrile solution.

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.

Dyads formed by an electron donor unit (D) covalently linked to an electron acceptor (A) by an organic bridge are promising materials as molecular rectifiers. Very recently, we have reported the charge transport measurements across self-assembled monolayers (SAMs) of two D–A systems consisting of the ferrocene (Fc) electron-donor linked to a polychlorotriphenylmethane (PTM) electron-acceptor in its non-radical (SAM 1) and radical (SAM 2) forms. Interestingly, we observed that the non-radical SAM 1 showed rectification behavior of 2 orders of magnitude higher than its radical analogue dyad 2. In order to study the influence of the donor unit on the transport properties, we report herein the synthesis and characterization of two new D–A SAMs in which the electron-donor Fc unit is replaced by a tetrathiafulvalene (TTF) moiety linked to the PTM unit in its non-radical (SAM 3) and radical (SAM 4) forms. The observed decrease in the rectification ratio and increased current density for TTF-PTM based SAMs 3 and 4 in comparison to Fc-PTM based SAMs 1 and 2 are explained, supported by theoretical calculations, by significant changes in the electronic and supramolecular structures., This work was financially supported by the EC through the Marie Curie project ITN iSwitch (GA no. 642196), the projects: MOTHER (MAT2016-80826-R), granted by DGI (Spain), GenCat (2017-SGR 918), financed by DGR (Catalunya), and Severo Ochoa Program, Grant SEV-2015-0496 financed by MINECO (Spain). Computational resources were provided by the Consortium des Équipements de Calcul Intensif (CÉCI) funded by the Belgian National Fund for Scientific Research (F.R.S.-FNRS) under Grant 2.5020.11. J.C. is an FNRS research director. Authors also acknowledge the financial support from Instituto de Salud Carlos III, through “Acciones CIBER.” The Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), an initiative funded by the VI National R&D&I Plan 2008e2011, Iniciativa Ingenio 2010, Consolider Program, CIBER Actions and financed by the Instituto de Salud Carlos III with assistance from the European Regional Development Fund. We also acknowledge the Ministry of Education (MOE) of Singapore for supporting this research under award No. MOE2015-T2-2-134.

High-resolution vacuum ultraviolet photoabsorption measurements in the wavelength range of 115-320 nm (10.8-3.9 eV) have been performed together with comprehensive relativistic time-dependent density functional calculations (TDDFT) on the low-lying excited sates of tungsten hexacarbonyl, W(CO). The higher resolution obtained reveals previously unresolved spectral features of W(CO). The spectrum shows two higher-energy bands (in the energy ranges of 7.22-8.12 eV and 8.15-9.05 eV), one of them with clear vibrational structure, and a few lower-energy shoulders in addition to a couple of lower-energy metal-to-ligand charge-transfer (MLCT) bands reported in the literature before. Absolute photoabsorption cross sections are reported and, where possible, compared to previously published results. On the basis of this combined experimental/theoretical study the absorption spectrum of the complex has been totally re-assigned between 3.9 and 10.8 eV under the light of spin-orbit coupling (SOC) effects. The present comprehensive knowledge of the nature of the electronically excited states may be of relevance to estimate neutral dissociation cross sections of W(CO), a precursor molecule in focused electron beam induced deposition (FEBID) processes, from electron scattering measurements., MM and FFS acknowledge the Portuguese National Funding Agency FCT-MCTES through grants PD/BD/106038/2015 and researcher position IF-FCT IF/00380/2014, respectively, and together with PLV the research grant UID/FIS/00068/2013. KR acknowledges the Swiss National Science Foundation for an Early Postdoc Mobility fellowship. This work was also supported by Radiation Biology and Biophysics Doctoral Training Programme (RaBBiT, PD/00193/2012); UID/Multi/ 04378/ 2013 (UCIBIO). GG acknowledges partial financial support from the Spanish Ministerio de Economia, Industria y Competitividad (Project No. FIS2016-80440). CD thanks The Labex “Chimie des Systèmes Complexes” (ANR-10-LABX- 0026_CSC). The quantum chemical calculations have been performed on the computer nodes of the LCQS, Strasbourg and thanks to the computer facilities of the High Performance Computing (HPC) regional center of University of Strasbourg. The authors wish to acknowledge the beam time at the ASTRID2 synchrotron at ISA, Aarhus University, Denmark. We also acknowledge the financial support provided by the European Community's Seventh Framework Programme (FP7/ 2007-2013) CALIPSO under grant agreement number 312284. Some of this work forms part of the EU/ESF COST Action CELINA CM1301, 11 pags., 4 figs., 2 tabs. -- This article is part of the Thematic Series "Chemistry for electron-induced nanofabrication".

Through a combined scanning tunneling microscopy (STM) and density functional theory (DFT) approach, we provide a full characterization of the different chemisorbed configurations of epitaxial graphene coexisting on the Ni(111) single crystal surface. Top-fcc, top-hcp, and top-bridge are found to be stable structures with comparable adsorption energy. By comparison of experiments and simulations, we solve an existing debate, unambiguously distinguishing these configurations in high-resolution STM images and characterizing the transitions between adjacent domains. Such transitions, described in detail through atomistic models, occur not only via sharp domain boundaries, with extended defects, but predominantly via smooth in-plane distortions of the carbon network, without disruption of the hexagonal rings, which are expected not to significantly affect electron transport.

We have analyzed a set of 51 PAHs whose structures have been hypothesized from mass spectrometry data collected on samples extracted from carbon particles of combustion origin. We have obtained relationships between infrared absorption signals in the fingerprint region (mid-IR) and the chemical structures of PAHs, thus proving the potential of IR spectroscopy for the characterization of the molecular structure of aromatic combustion products. The results obtained here for the spectroscopic characterization of PAHs can be also of interest in Materials Science and Astrophysics.

Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large (34ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite (34ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved., United States. National Aeronautics and Space Administration (NASA-Exobiology), National Science Foundation (U.S.) (NSF GRFP Fellowship), National Science Foundation (U.S.) (NSF Career), National Science Foundation (U.S.) (NSF Instrument and facilities), National Science Foundation (U.S.) (NSF Low Temperature Geochemistry award)

Collagen molecules are the primary structural proteins of many biological systems. Much progress has been made in the study of the structure and function of collagen, but fundamental understanding of its electronic structures at the atomic level is still lacking. We present the results of electronic structure and bonding calculations of a specific model of type I collagen using the density functional theory-based method. Information on density of states (DOS), partial DOS, effective charges, bond order values, and intra- and inter-molecular H-bonding are obtained and discussed. We further devised an amino-acid-based potential method (AAPM) to circumvent the full self-consistent field (SCF) calculation that can be applied to large proteins. The AAPM is validated by comparing the results with the full SCF calculation of the whole type I collagen model with three strands. The calculated effective charges on each atom in the model retained at least 95% accuracy. This technique provides a viable and efficient way to study the electronic structure of large complex biomaterials at the ab initio level.

Previously we have shown that ONIOM type (QM/MM) calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and (18)O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0), 2,3,5,6-tetramethyl-1, 4-benzoquinone (duroquinone, DQ), and 2,3-dimethyl-l,4-naphthoquinone (DMNQ) incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites. The normal modes that contribute to the bands in the calculated spectra, their composition, frequency, and intensity, and how these quantities are modified upon (18)O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10-13 cm(-1) separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry in H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are "tail-less." Spectra were also calculated for reaction centers with corresponding "tail" containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated spectra.

We present the results of an experimental and theoretical investigation of monosubstituted ethyl-, vinyl-, and ethynyl-ferrocene (EtFC, VFC, and EFC) free molecules, obtained by means of synchrotron-radiation based C 1s photoabsorption (NEXAFS) and photoemission (C 1s XPS) spectroscopies, and density functional theory (DFT) calculations. Such a combined study is aimed at elucidating the role played by the C-C bond unsaturation degree of the substituent on the electronic structure of the ferrocene derivatives. Such substituents are required for molecular chemical anchoring onto relevant surfaces when ferrocenes are used for molecular electronics hybrid devices. The high resolution C 1s NEXAFS spectra exhibit distinctive features that depend on the degree of unsaturation of the hydrocarbon substituent. The theoretical approach to consider the NEXAFS spectrum made of three parts allowed to disentangle the specific contribution of the substituent group to the experimental spectrum as a function of its unsaturation degree. C 1s IEs were derived from the experimental data analysis based on the DFT calculated IE values for the different carbon atoms of the substituent and cyclopentadienyl (Cp) rings. Distinctive trends of chemical shifts were observed for the substituent carbon atoms and the substituted atom of the Cp ring along the series of ferrocenes. The calculated IE pattern was rationalized in terms of initial and final state effects influencing the IE value, with special regard to the different mechanism of electron conjugation between the Cp ring and the substituent, namely the σ/π hyperconjugation in EtFC and the π-conjugation in VFC and EFC.

Metal-stabilized phenoxyl radicals appear to be important intermediates in a variety of enzymatic oxidations. We report that transition metal coordination also supports an aminyl radical, resulting in a stable crystalline complex: [Rh(I)(trop 2 N . )(bipy)] + OTf – (where trop is 5-H-dibenzo[a,d]cycloheptene-5-yl, bipy is 2,2′-bipyridyl, OTf – is trifluorosulfonate). It is accessible under mild conditions by one-electron oxidation of the amide complex [Rh(I)(trop 2 N)(bipy)], at a potential of –0.55 volt versus ferrocene/ferrocenium. Both electron paramagnetic resonance spectroscopy and density functional theory support 57% localization of the unpaired spin at N. In reactions with H-atom donors, the Rh-coordinated aminyl behaves as a nucleophilic radical.