Contributions beyond direct random-phase approximation in the binding energy of solid ethane, ethylene, and acetylene.

The random-phase approximation (RPA) includes a subset of higher than second-order correlation-energy contributions, but stays in the same complexity class as the second-order Møller-Plesset perturbation theory (MP2) in both Gaussian-orbital and plane-wave codes. This makes RPA a promising ab initio electronic structure approach for the binding energies of molecular crystals. Still, some issues stand out in practical applications of RPA. Notably, compact clusters of nonpolar molecules are poorly described, and the interaction energies strongly depend on the reference single-determinant state. Using the many-body expansion of the binding energy of a crystal, we investigate those issues and the effect of beyond-RPA corrections. We find the beneficial effect of quartic-scaling exchange and non-ring coupled-cluster doubles corrections. The nonadditive interactions in compact trimers of molecules are improved by using the self-consistent Hartree-Fock orbitals instead of the usual Kohn-Sham states, but this kind of orbital input also leads to underestimated dimer energies. Overall, a substantial improvement over the RPA with a renormalized singles approach is possible at a modest quartic-scaling cost, which encourages further research into additional RPA corrections.

Magnetically Induced Binary Ferrocene with Oxidized Iron.

Ferrocene is perhaps the most popular and well-studied organometallic molecule, but our understanding of its structure and electronic properties has not changed for more than 70 years. In particular, all previous attempts of chemically oxidizing pure ferrocene by binding directly to the iron center have been unsuccessful, and no significant change in structure or magnetism has been reported. Using a metal organic framework host material, we were able to fundamentally change the electronic and magnetic structure of ferrocene to take on a never-before observed physically stretched/bent high-spin Fe(II) state, which readily accepts O2 from air, chemically oxidizing the iron from Fe(II) to Fe(III). We also show that the binding of oxygen is reversible through temperature swing experiments. Our analysis is based on combining Mößbauer spectroscopy, extended X-ray absorption fine structure, in situ infrared, SQUID, thermal gravimetric analysis, and energy dispersive X-ray fluorescence spectroscopy measurements with ab initio modeling.

Assessment of random phase approximation and second-order Møller-Plesset perturbation theory for many-body interactions in solid ethane, ethylene, and acetylene.

The relative energies of different phases or polymorphs of molecular solids can be small, less than a kilojoule/mol. A reliable description of such energy differences requires high-quality treatment of electron correlations, typically beyond that achievable by routinely applicable density functional theory (DFT) approximations. At the same time, high-level wave function theory is currently too computationally expensive. Methods employing an intermediate level of approximations, such as Møller-Plesset (MP) perturbation theory and the random phase approximation (RPA), are potentially useful. However, their development and application for molecular solids has been impeded by the scarcity of necessary benchmark data for these systems. In this work, we employ the coupled-cluster method with singles, doubles, and perturbative triples to obtain a reference-quality many-body expansion of the binding energy of four crystalline hydrocarbons with a varying π-electron character: ethane, ethene, and cubic and orthorhombic forms of acetylene. The binding energy is resolved into explicit dimer, trimer, and tetramer contributions, which facilitates the analysis of errors in the approximate approaches. With the newly generated benchmark data, we test the accuracy of MP2 and non-self-consistent RPA. We find that both of the methods poorly describe the non-additive many-body interactions in closely packed clusters. Using different DFT input states for RPA leads to similar total binding energies, but the many-body components strongly depend on the choice of the exchange-correlation functional.

Fast and accurate quantum Monte Carlo for molecular crystals.

Computer simulation plays a central role in modern-day materials science. The utility of a given computational approach depends largely on the balance it provides between accuracy and computational cost. Molecular crystals are a class of materials of great technological importance which are challenging for even the most sophisticated ab initio electronic structure theories to accurately describe. This is partly because they are held together by a balance of weak intermolecular forces but also because the primitive cells of molecular crystals are often substantially larger than those of atomic solids. Here, we demonstrate that diffusion quantum Monte Carlo (DMC) delivers subchemical accuracy for a diverse set of molecular crystals at a surprisingly moderate computational cost. As such, we anticipate that DMC can play an important role in understanding and predicting the properties of a large number of molecular crystals, including those built from relatively large molecules which are far beyond reach of other high-accuracy methods.

Efficient and accurate description of adsorption in zeolites.

Accurate theoretical methods are needed to correctly describe adsorption on solid surfaces or in porous materials. The random phase approximation (RPA) with singles corrections scheme and the second order Møller-Plesset perturbation theory (MP2) are two schemes, which offer high accuracy at affordable computational cost. However, there is little knowledge about their applicability and reliability for different adsorbates and surfaces. Here, we calculate adsorption energies of seven different molecules in zeolite chabazite to show that RPA with singles corrections is superior to MP2, not only in terms of accuracy but also in terms of computer time. Therefore, RPA with singles is a suitable scheme for obtaining highly accurate adsorption energies in porous materials and similar systems.

Lattice energies of molecular solids from the random phase approximation with singles corrections.

We use the random phase approximation (RPA) method with the singles correlation energy contributions to calculate lattice energies of ten molecular solids. While RPA gives too weak binding, underestimating the reference data by 13.7% on average, much improved results are obtained when the singles are included at the GW singles excitations (GWSE) level, with average absolute difference to the reference data of only 3.7%. Consistently with previous results, we find a very good agreement with the reference data for hydrogen bonded systems, while the binding is too weak for systems where dispersion forces dominate. In fact, the overall accuracy of the RPA+GWSE method is similar to an estimated accuracy of the reference data.

Placental passage of olomoucine II, but not purvalanol A, is affected by p-glycoprotein (ABCB1), breast cancer resistance protein (ABCG2) and multidrug resistance-associated proteins (ABCCs).

1. Purine cyclin-dependent kinase inhibitors have recently been recognised as promising candidates for the treatment of various cancers. While pharmacodynamic properties of these compounds are relatively well understood, their pharmacokinetics including possible interactions with placental transport systems have not been characterised to date. 2. In this study, we investigated transplacental passage of olomoucine II and purvalanol A in rat focusing on possible role of p-glycoprotein (ABCB1), breast cancer resistance protein (ABCG2) and/or multidrug resistance-associated proteins (ABCCs). Employing the in situ method of dually perfused rat term placenta, we demonstrate transplacental passage of both olomoucine II and purvalanol A against the concentration gradient in foetus-to-mother direction. Using several ATP-binding cassette (ABC) drug transporter inhibitors, we confirm the participation of ABCB1, ABCG2 and ABCCs transporters in the placental passage of olomoucine II, but not purvalanol A. 3. Transplacental passage of olomoucine II and purvalanol A from mother to foetus is significantly reduced by active transporters, restricting thereby foetal exposure and providing protection against harmful effects of these xenobiotics. Importantly, we demonstrate that in spite of their considerable structural similarity, the two molecules utilise distinct placental transport systems. These facts should be kept in mind when introducing these prospective anticancer candidates and/or their analogues into the clinical area.

The accurate calculation of the band gap of liquid water by means of GW corrections applied to plane-wave density functional theory molecular dynamics simulations.

Knowledge about the intrinsic electronic properties of water is imperative for understanding the behaviour of aqueous solutions that are used throughout biology, chemistry, physics, and industry. The calculation of the electronic band gap of liquids is challenging, because the most accurate ab initio approaches can be applied only to small numbers of atoms, while large numbers of atoms are required for having configurations that are representative of a liquid. Here we show that a high-accuracy value for the electronic band gap of water can be obtained by combining beyond-DFT methods and statistical time-averaging. Liquid water is simulated at 300 K using a plane-wave density functional theory molecular dynamics (PW-DFT-MD) simulation and a van der Waals density functional (optB88-vdW). After applying a self-consistent GW correction the band gap of liquid water at 300 K is calculated as 7.3 eV, in good agreement with recent experimental observations in the literature (6.9 eV). For simulations of phase transformations and chemical reactions in water or aqueous solutions whereby an accurate description of the electronic structure is required, we suggest to use these advanced GW corrections in combination with the statistical analysis of quantum mechanical MD simulations.

Singles correlation energy contributions in solids.

The random phase approximation to the correlation energy often yields highly accurate results for condensed matter systems. However, ways how to improve its accuracy are being sought and here we explore the relevance of singles contributions for prototypical solid state systems. We set out with a derivation of the random phase approximation using the adiabatic connection and fluctuation dissipation theorem, but contrary to the most commonly used derivation, the density is allowed to vary along the coupling constant integral. This yields results closely paralleling standard perturbation theory. We re-derive the standard singles of Görling-Levy perturbation theory [A. Görling and M. Levy, Phys. Rev. A 50, 196 (1994)], highlight the analogy of our expression to the renormalized singles introduced by Ren and coworkers [Phys. Rev. Lett. 106, 153003 (2011)], and introduce a new approximation for the singles using the density matrix in the random phase approximation. We discuss the physical relevance and importance of singles alongside illustrative examples of simple weakly bonded systems, including rare gas solids (Ne, Ar, Xe), ice, adsorption of water on NaCl, and solid benzene. The effect of singles on covalently and metallically bonded systems is also discussed.

The nature of bonding and electronic properties of graphene and benzene with iridium adatoms.

Recent theoretical simulations predicted that graphene decorated with Ir adatoms could realize a two-dimensional topological insulator with a substantial band gap. Our understanding of how the electronic properties of graphene change in the presence of metal adatoms is however still limited, as the binding is quite complex involving static and dynamic correlation effects together with relativistic contributions, which makes the theoretical description of such systems quite challenging. We applied the quantum chemical complete active space second order perturbation theory (CASPT2) method and density functional theory beyond the standard local density functional approach including relativistic spin-orbit coupling (SOC) effects on Ir-benzene and Ir-graphene complexes. The CASPT2-SOC method revealed a strong binding affinity of Ir for benzene (33.1 kcal mol(-1)) at a 1.81 Å distance, which was of a single reference character, and a weaker binding affinity (6.3 kcal mol(-1)) at 3.00 Å of a multireference character. In the Ir-graphene complex, the quartet ground-state of the Ir atom changed to the doublet state upon adsorption, and the binding energy predicted by optB86b-vdW-SOC functional remained high (33.8 kcal mol(-1)). In all cases the dynamic correlation effects significantly contributed to the binding. The density of states calculated with the hybrid functional HSE06 showed that the gap of 0.3 eV was induced in graphene by the adsorbed Ir atom even in scalar relativistic calculation, in contrast to metallic behaviour predicted by local density approximation. The results suggest that the strong correlation effects contribute to the opening of the band gap in graphene covered with the Ir adatoms. The value of the magnetic anisotropy energy of 0.1 kcal mol(-1) predicted by HSE06 is lower than those calculated using local functionals.

Kohn-Sham band gaps and potentials of solids from the optimised effective potential method within the random phase approximation.

We present an implementation of the optimised effective potential (OEP) scheme for the exact-exchange (EXX) and random phase approximation (RPA) energy functionals and apply these methods to a range of bulk materials. We calculate the Kohn-Sham (KS) potentials and the corresponding band gaps and compare them to the potentials obtained by standard local density approximation (LDA) calculations. The KS gaps increase upon going from the LDA to the OEP in the RPA and finally to the OEP for EXX. This can be explained by the different depth of the potentials in the bonding and interstitial regions. To obtain the true quasi-particle gaps the derivative discontinuities or G0W0 corrections need to be added to the RPA-OEP KS gaps. The predicted G0W0@RPA-OEP quasi-particle gaps are about 5% too large compared to the experimental values. However, compared to G0W0 calculations based on local or semi-local functionals, where the errors vary between different materials, we obtain a rather consistent description among all the materials.

Zirconia--a stationary phase capable of the separation of polar markers of myocardial metabolism in hydrophilic interaction chromatography.

Creatine, phosphocreatine, and adenine nucleotides are highly polar markers of myocardial metabolism that are poorly retained on RP silica sorbents. Zirconia represents an alternative material to silica with high promise to be used in hydrophilic interaction chromatography (HILIC). This study describes a first systematic investigation of the ability of ZrO2 to separate creatine, phosphocreatine, adenosine 5'-monophosphate, adenosine 5'-diphosphate, and adenosine 5'-triphosphate and compares the results with those obtained on TiO2 . All analytes showed a HILIC-like retention pattern when mobile phases of different strengths were tested. Stronger retention and better column performance were achieved in organic-rich mobile phases as compared to aqueous conditions, where poor retention and insufficient column performance were observed. The effect of mobile phase pH and ionic strength was evaluated as well. The analysis of myocardial tissue demonstrated that all compounds were separated in a relevant biological material and thus proved ZrO2 as a promising phase for HILIC of biological samples that deserves further investigation.

Simultaneous determination of the novel thiosemicarbazone anti-cancer agent, Bp4eT, and its main phase I metabolites in plasma: application to a pilot pharmacokinetic study in rats.

Novel thiosemicarbazone metal chelators are extensively studied anti-cancer agents with marked and selective activity against a wide variety of cancer cells, as well as human tumor xenografts in mice. This study describes the first validated LC-MS/MS method for the simultaneous quantification of 2-benzoylpyridine 4-ethyl-3-thiosemicarbazone (Bp4eT) and its main metabolites (E/Z isomers of the semicarbazone structure, M1-E and M1-Z, and the amidrazone metabolite, M2) in plasma. Separation was achieved using a C18 column with ammonium formate/acetonitrile mixture as the mobile phase. Plasma samples were treated using solid-phase extraction on 96-well plates. This method was validated over the concentration range of 0.18-2.80 µM for Bp4eT, 0.02-0.37 µM for both M1-E and M1-Z, and 0.10-1.60 µM for M2. This methodology was applied to the analysis of samples from in vivo experiments, allowing for the concentration-time profile to be simultaneously assessed for the parent drug and its metabolites. The current study addresses the lack of knowledge regarding the quantitative analysis of thiosemicarbazone anti-cancer drugs and their metabolites in plasma and provides the first pharmacokinetic data on a lead compound of this class.

Identification of in vitro metabolites of the novel anti-tumor thiosemicarbazone, DpC, using ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry.

Di-2-pyridylketone-4-cyclohexyl-4-methyl-3-thiosemicarbazone (DpC) is a promising analogue of the dipyridyl thiosemicarbazone class currently under development as a potential anti-cancer drug. In fact, this class of agents shows markedly greater anti-tumor activity and selectivity than the clinically investigated thiosemicarbazone, Triapine®. However, further development of DpC requires detailed data concerning its metabolism. Therefore, we focused on the identification of principal phase I and II metabolites of DpC in vitro. DpC was incubated with human liver microsomes/S9 fractions and the samples were analyzed using ultra-performance liquid chromatography (UPLC(TM)) with electrospray ionization quadrupole-time-of-flight (Q-TOF) mass spectrometry. An Acquity UPLC BEH C(18) column was implemented with 2 mM ammonium acetate and acetonitrile in gradient mode as the mobile phase. The chemical structures of metabolites were proposed based on the accurate mass measurement of the protonated molecules as well as their main product ions. Ten phase I and two phase II metabolites were detected and structurally described. The metabolism of DpC occurred via oxidation of the thiocarbonyl group, hydroxylation and N-demethylation, as well as the combination of these reactions. Conjugates of DpC and the metabolite, M10, with glucuronic acid were also observed as phase II metabolites. Neither sulfate nor glutathione conjugates were detected. This study provides the first information about the chemical structure of the principal metabolites of DpC, which supports the development of this promising anti-cancer drug and provides vital data for further pharmacokinetic and in vivo metabolism studies.

The role of van der Waals forces in water adsorption on metals.

The interaction of water molecules with metal surfaces is typically weak and as a result van der Waals (vdW) forces can be expected to be of importance. Here we account for the systematic poor treatment of vdW forces in most popular density functional theory exchange-correlation functionals by applying accurate non-local vdW density functionals. We have computed the adsorption of a variety of exemplar systems including water monomer adsorption on Al(111), Cu(111), Cu(110), Ru(0001), Rh(111), Pd(111), Ag(111), Pt(111), and unreconstructed Au(111), and small clusters (up to 6 waters) on Cu(110). We show that non-local correlations contribute substantially to the water-metal bond in all systems, whilst water-water bonding is much less affected by non-local correlations. Interestingly non-local correlations contribute more to the adsorption of water on the reactive transition metal substrates than they do on the noble metals. The relative stability, adsorption sites, and adsorption geometries of competing water adstructures rarely differ when comparing results obtained with semi-local functionals and the non-local vdW density functionals, which explains the previous success of semi-local functionals in characterizing adsorbed water structures on a number of metal surfaces.

Understanding the role of ions and water molecules in the NaCl dissolution process.

The dissolution of NaCl in water is one of the most common everyday processes, yet it remains poorly understood at the molecular level. Here we report the results of an extensive density functional theory study in which the initial stages of NaCl dissolution have been examined at low water coverages. Our specific approach is to study how the energetic cost of moving an ion or a pair of ions to a less coordinated site at the surface of various NaCl crystals varies with the number of water molecules adsorbed on the surface. This "microsolvation" approach allows us to study the dependence of the defect energies on the number of water molecules in the cluster and thus to establish when and where dissolution becomes favorable. Moreover, this approach allows us to understand the roles of the individual ions and water molecules in the dissolution process. Consistent with previous work we identify a clear preference for dissolution of Cl ions over Na ions. However, the detailed information obtained here leads to the conclusion that the process is governed by the higher affinity of the water molecules to Na ions than to Cl ions. The Cl ions are released first as this exposes more Na ions at the surface creating favorable adsorption sites for water. We discuss how this mechanism is likely to be effective for other alkali halides.

On the accuracy of van der Waals inclusive density-functional theory exchange-correlation functionals for ice at ambient and high pressures.

Density-functional theory (DFT) has been widely used to study water and ice for at least 20 years. However, the reliability of different DFT exchange-correlation (xc) functionals for water remains a matter of considerable debate. This is particularly true in light of the recent development of DFT based methods that account for van der Waals (vdW) dispersion forces. Here, we report a detailed study with several xc functionals (semi-local, hybrid, and vdW inclusive approaches) on ice Ih and six proton ordered phases of ice. Consistent with our previous study [B. Santra, J. Klimes, D. Alfè, A. Tkatchenko, B. Slater, A. Michaelides, R. Car, and M. Scheffler, Phys. Rev. Lett. 107, 185701 (2011)] which showed that vdW forces become increasingly important at high pressures, we find here that all vdW inclusive methods considered improve the relative energies and transition pressures of the high-pressure ice phases compared to those obtained with semi-local or hybrid xc functionals. However, we also find that significant discrepancies between experiment and the vdW inclusive approaches remain in the cohesive properties of the various phases, causing certain phases to be absent from the phase diagram. Therefore, room for improvement in the description of water at ambient and high pressures remains and we suggest that because of the stern test the high pressure ice phases pose they should be used in future benchmark studies of simulation methods for water.

The economic burden of the ankylosing spondylitis in the Czech Republic: comparison between 2005 and 2008.

To investigate the burden of ankylosing spondylitis in the Czech Republic as a baseline for future health economic evaluations. Data were obtained from two cross-sectional studies Beda I (2005) and Beda II (2008), performed in 1,008 and 509 patients, respectively. Methodology used was Cost-of-Illness prevalence-based analysis bottom-up approach. Analysis was performed from payer (health insurance companies) and societal perspective (including productivity costs using friction cost approach). Mean age of sample in Beda I and Beda II was 50.2 and 52.5 years, male were present by 61.0 and 62.7 %; average disease duration was 23.0 and 26.4 years, respectively. Mean total annual costs per patient in the sample were €4,782 in Beda I and €5806 in Beda II. Average direct costs per patient in the sample per year are estimated at €1,812 (Beda I) and €2,588 (Beda II) with the average productivity costs €2,970 (Beda I) and €3,218 (Beda II). We observed a small decrement in percentage (6.7 %) of productivity costs for Beda II as an influence of higher consumption of biologic drugs, hence higher direct costs and possible productivity preservation. The largest direct cost burdens were spa procedures (45.3 %, Beda I) and biological drugs (52.8 %, Beda II). Unique analysis of the burden of the AS in the Central-Eastern Europe presents health care resource and cost consumption by comparing two cross-sectional prevalence-based studies. Further analysis should be carried to obtain data connecting health status with costs consumption in order to analyse the AS from this perspective.

Escherichia coli-producing extended-spectrum beta-lactamase CTX-M-15 in a captive South American tapir (Tapirus terrestris).

Only a few reports exist on the occurrence of resistant bacteria in zoo animals. Therefore, an isolation of multiresistant Escherichia coli from the lungs of a captive South American tapir (Tapirus terrestris) lead to its characterization and further investigation of samples from animals inhabiting the same paddock and from the shared environment. The tapir suffered from an intermandibular abscess and pneumonia and was euthanatized after unsuccessful therapy, including administration of antibiotics. The authors performed selective isolation of extended-spectrum beta-lactamase (ESBL)-positive E. coli strains and identification of resistance genes using polymerase chain reaction. Seven multiresistant, ESBL-producing E. coli isolates were obtained, all belonging to the B2 phylogenetic group and showing identical profile on pulsed-field gel electrophoresis. These isolates carried several resistance genes, including the gene bla(CTX-M-15). This case demonstrates the transmission of related epidemiologically important E. coli isolates whose potential transmission to other animals and zoo staff can be assumed.

Using Noncovalent Interactions to Test the Precision of Projector-Augmented Wave Data Sets.

The projector-augmented wave (PAW) method is one of the approaches that are widely used to approximately treat core electrons and thus to speed up plane-wave basis set electronic structure calculations. However, PAW involves approximations, and it is thus important to understand how they affect the results. Tests of the precision of PAW data sets often use the properties of isolated atoms or atomic solids. While this is sufficient to identify problematic PAW data sets, little information has been gained to understand the origins of the errors and suggest ways to correct them. Here, we show that the interaction energies of molecular dimers are very useful not only to identify problematic PAW data sets but also to uncover the origin of the errors. Using dimers from the S22 and S66 test sets and other dimers, we find that the error in the interaction energy is composed of a short-range component with an exponential decay and a long-range electrostatic part caused by an error in the total charge density. We propose and evaluate a simple improvable scheme to correct the long-range error and find that even in its simple and readily usable form, it is able to reduce the interaction energy errors to less than half on average for hydrogen-bonded dimers.