Outer-Sphere Contributions to the Electronic Structure of Type Zero Copper Proteins

Bioinorganic canon states that active-site thiolate coordination promotes rapid electron transfer (ET) to and from type 1 copper proteins. In recent work, we have found that copper ET sites in proteins also can be constructed without thiolate ligation (called “type zero” sites). Here we report multifrequency electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and nuclear magnetic resonance (NMR) spectroscopic data together with density functional theory (DFT) and spectroscopy-oriented configuration interaction (SORCI) calculations for type zero Pseudomonas aeruginosa azurin variants. Wild-type (type 1) and type zero copper centers experience virtually identical ligand fields. Moreover, O-donor covalency is enhanced in type zero centers relative that in the C112D (type 2) protein. At the same time, N-donor covalency is reduced in a similar fashion to type 1 centers. QM/MM and SORCI calculations show that the electronic structures of type zero and type 2 are intimately linked to the orientation and coordination mode of the carboxylate ligand, which in turn is influenced by outer-sphere hydrogen bonding

Hybrid functional calculations of the Al impurity in silica: Hole localization and electron paramagnetic resonance parameters

We performed first-principle calculations based on the supercell and cluster approaches to investigate the neutral Al impurity in smoky quartz. Electron paramagnetic resonance measurements suggest that the oxygens around the Al center undergo a polaronic distortion which localizes the hole being on one of the four oxygen atoms. We find that the screened exchange hybrid functional successfully describes this localization and improves on standard local density approaches or on hybrid functionals that do not include enough exact exchange such as B3LYP. We find a defect level at about 2.5 eV above the valence band maximum, corresponding to a localized hole in a O 2p orbital. The calculated values of the g tensor and the hyperfine splittings are in excellent agreement with experiment.Comment: 5 pages, 2 figures, 1 tabl

Di- and Trinuclear Mixed-Valence Copper Amidinate Complexes from Reduction of Iodine

Molecular examples of mixed-valence copper complexes through chemical oxidation are rare but invoked in the mechanism of substrate activation, especially oxygen, in copper-containing enzymes. To examine the cooperative chemistry between two metals in close proximity to each other we began studying the reactivity of a dinuclear Cu(I) amidinate complex. The reaction of [(2,6-Me2C6H3N)2C(H)]2Cu2, 1, with I2 in tetrahydrofuran (THF), CH3CN, and toluene affords three new mixed-valence copper complexes [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I3)(THF)2, 2, [(2,6-Me2C6H3N)2C(H)]2Cu2(μ2-I) (NCMe)2, 3, and [(2,6-Me2C6H3N)2C(H)]3Cu3(μ3-I)2, 4, respectively. The first two compounds were characterized by UV-vis and electron paramagnetic resonance spectroscopies, and their molecular structure was determined by X-ray crystallography. Both di- and trinuclear mixed-valence intermediates were characterized for the reaction of compound 1 to compound 4, and the molecular structure of 4 was determined by X-ray crystallography. The electronic structure of each of these complexes was also investigated using density functional theory

Laboratory Characterization and Astrophysical Detection of Vibrationally Excited States of Vinyl Cyanide in Orion-KL

New laboratory data of CH$_2$CHCN (vinyl cyanide) in its ground and vibrationally excited states at the microwave to THz domain allow searching for these excited state transitions in the Orion-KL line survey. Frequency-modulated spectrometers combined into a single broadband 50-1900 GHz spectrum provided measurements of CH$_2$CHCN covering a spectral range of 18-1893 GHz, whose assignments was confirmed by Stark modulation spectra in the 18-40 GHz region and by ab-initio anharmonic force field calculations. For analyzing the emission lines of CH$_2$CHCN species detected in Orion-KL we used the excitation and radiative transfer code (MADEX) at LTE conditions. The rotational transitions of the ground state of this molecule emerge from four cloud components of hot core nature which trace the physical and chemical conditions of high mass star forming regions in the Orion-KL Nebula. The total column density of CH$_2$CHCN in the ground state is (3.0$\pm$0.9)x10$^{15}$ cm$^{-2}$. We report on the first interstellar detection of transitions in the v10=1/(v11=1,v15=1) dyad in space, and in the v11=2 and v11=3 states in Orion-KL. The lowest energy vibrationally excited states of vinyl cyanide such as v11=1 (at 328.5 K), v15=1 (at 478.6 K), v11=2 (at 657.8 K), the v10=1/(v11=1,v15=1) dyad (at 806.4/809.9 K), and v11=3 (at 987.9 K) are populated under warm and dense conditions, so they probe the hottest parts of the Orion-KL source. Column density and rotational and vibrational temperatures for CH$_2$CHCN in their ground and excited states, as well as for the isotopologues, have been constrained by means of a sample of more than 1000 lines in this survey. Moreover, we present the detection of methyl isocyanide (CH$_3$NC) for the first time in Orion-KL and a tentative detection of vinyl isocyanide (CH$_2$CHNC) and give column density ratios between the cyanide and isocyanide isomers.Comment: 46 pages, 22 figures, 14 tables, 9 online table

Search for LBV Candidates in the M33 Galaxy

A total of 185 luminous blue variable (LBV) candidates with V < 18.5 and B-V < 0.35 are selected based on the photometrical Survey of Local Group Galaxies made by P. Massey et al. 2006. The candidates were selected using aperture photometry of H-alpha images. The primary selection criterion is that the prospective candidate should be a blue star with H-aplha emission. In order not to miss appreciably reddened LBV candidates, we compose an additional list of 25 presumably reddened (0.35 < B-V < 1.2, V < 18.5) emission star candidates. A comparison with the list of known variables in the M33 galaxy showed 29% of our selected candidates to be photometrically variable. We also find our list to agree well with the lists of emission-line objects obtained in earlier papers using different methods.Comment: 6 figure

Unraveling the performance of dispersion-corrected functionals for the accurate description of weakly bound natural polyphenols

Long-range non-covalent interactions play a key role in the chemistry of natural polyphenols. We have previously proposed a description of supramolecular polyphenol complexes by the B3P86 density functional coupled with some corrections for dispersion. We couple here the B3P86 functional with the D3 correction for dispersion, assessing systematically the accuracy of the new B3P86-D3 model using for that the well-known S66, HB23, NCCE31, and S12L datasets for non-covalent interactions. Furthermore, the association energies of these complexes were carefully compared to those obtained by other dispersion-corrected functionals, such as B(3)LYP-D3, BP86-D3 or B3P86-NL. Finally, this set of models were also applied to a database composed of seven non-covalent polyphenol complexes of the most interest.FDM acknowledges financial support from the Swedish Research Council (Grant No. 621-2014-4646) and SNIC (Swedish National Infrastructure for Computing) for providing computer resources. The work in Limoges (IB and PT) is supported by the “Conseil Régional du Limousin”. PT gratefully acknowledges the support by the Operational Program Research and Development Fund (project CZ.1.05/2.1.00/03.0058 of the Ministry of Education, Youth and Sports of the Czech Republic). IB gratefully acknowledges financial support from “Association Djerbienne en France”

Improved catalytic activity of ruthenium–arene complexes in the reduction of NAD+

A series of neutral Ru-II half-sandwich complexes of the type [(eta(6)-arene)Ru(N,N')Cl] where the arene is para-cymene (p-cym), hexamethylbenzene (hmb), biphenyl (bip), or benzene (bn) and N,N' is N-(2-aminoethyl) -4-(trifluoromethyl)benzenesulfonamide (TfEn), N-(2-aminoethyl)-4-toluenesulfonamide (TsEn), or N-(2-aminoethyl)-methylenesulfonamide (MsEn) were synthesized and characterized. X-ray crystal structures of [(p-cym)Ru(MsEn)Cl] (1), [(hmb)Ru(TsEn)Cl] (5), [(hmb)Ru(TfEn)Cl] (6), [(bip)Ru(MsEn)Cl] (7), and [(bip)Ru(TsEn)Cl] (8) have been determined. The complexes can regioselectively catalyze the transfer hydrogenation of NAD(+) to give 1,4-NADH in the presence of formate. The turnover frequencies (TOF) when the arene is varied decrease in the order bn > bip > p-cym > hmb for complexes with the same N,N' chelating ligand. The TOF decreased with variation in the N,N' chelating ligand in the order TfEn > TsEn > MsEn for a given arene. [(bn)Ru(TfEn)Cl] (12) was the most active, with a TOP of 10.4 h(-1). The effects of NAD(+) and formate concentration on the reaction rates were determined for [(p-cym)Ru(TsEn)Cl] (2). Isotope studies implicated the formation of [(arene)Ru(N,N')(H)] as the rate-limiting step. The coordination of formate and subsequent CO2 elimination to generate the hydride were modeled computationally by density functional theory (DFT). CO2 elimination occurs via a two-step process with the coordinated formate first twisting to present its hydrogen toward the metal center. The computed barriers for CO2 release for arene = benzene follow the order MsEn > TsEn > TfEn, and for the Ms En system the barrier followed bn < hmb, both consistent with the observed rates. The effect of methanol on transfer hydrogenation rates in aqueous solution was investigated. A study of pH dependence of the reaction in D2O gave the optimum pH* as 7.2 with a TOF of 1.58 h(-1) for 2. The series of compounds reported here show an improvement in the catalytic activity by an order of magnitude compared to the ethylenediamine analogues

Comparison of Many-Particle Representations for Selected Configuration Interaction: II. Numerical Benchmark Calculations

The present work is the second part in our three-part series on the comparison of many-particle representations for the selected configuration interaction (CI) method. In this work, we present benchmark calculations based on our selected CI program called the iterative configuration expansion (ICE) that is inspired by the CIPSI method of Malrieu and co-workers (Malrieu J. Chem. Phys. 1973, 58, (12), 5745−5759). We describe the main parameters that enter in this algorithm and perform benchmark calculations on a set of 21 small molecules and compare ground state energies with full configuration interaction (FCI) results (FCI21 test set). The focus is the comparison of the performance of three different types of many-particle basis functions (MPBFs): (1) individual Slater determinants (DETS), (2) individual spin-adapted configuration state functions (CSFs), and (3) all CSFs of a given total spin that can be generated from spatial configurations (CFGs). An analysis of the cost of the calculation in terms of the number of wavefunction parameters and the energy error is evaluated for the DET-, CFG-, and CSF-based ICE. The main differences for the three many-particle basis representations show up in the number of wavefunction parameters and the rate of convergence toward the FCI limit with the thresholds of the ICE. Next, we analyze the best way to extrapolate the ICE energies toward the FCI results as a function of the thresholds. The efficiency of the extrapolation is investigated relative to the FCI21 test set as well as near FCI calculations on three moderately sized hydrocarbon molecules CH4, C2H4, and C4H6. Finally, we comment on the size-inconsistency error for the three many-particle representations and compare it with the error in the total energy. The implication for selected CI implementations with any of the three many-particle representations is discussed

Development of NOTCH, an all-electron, beyond-NDDO semiempirical method: Application to diatomic molecules

In this work, we develop a new semiempirical method, dubbed NOTCH (Natural Orbital Tied Constructed Hamiltonian). Compared to existing semiempirical methods, NOTCH is less empirical in its functional form as well as parameterization. Specifically, in NOTCH, (1) the core electrons are treated explicitly; (2) the nuclear–nuclear repulsion term is calculated analytically, without any empirical parameterization; (3) the contraction coefficients of the atomic orbital (AO) basis depend on the coordinates of the neighboring atoms, which allows the size of AOs to depend on the molecular environment, despite the fact that a minimal basis set is used; (4) the one-center integrals of free atoms are derived from scalar relativistic multireference equation-of-motion coupled cluster calculations instead of empirical fitting, drastically reducing the number of necessary empirical parameters; (5) the (AA|AB) and (AB|AB)-type two-center integrals are explicitly included, going beyond the neglect of differential diatomic overlap approximation; and (6) the integrals depend on the atomic charges, effectively mimicking the “breathing” of AOs when the atomic charge varies. For this preliminary report, the model has been parameterized for the elements H–Ne, giving only 8 empirical global parameters. Preliminary results on the ionization potentials, electron affinities, and excitation energies of atoms and diatomic molecules, as well as the equilibrium geometries, vibrational frequencies dipole moments, and bond dissociation energies of diatomic molecules, show that the accuracy of NOTCH rivals or exceeds those of popular semiempirical methods (including PM3, PM7, OM2, OM3, GFN-xTB, and GFN2-xTB) as well as the cost-effective ab initio method Hartree–Fock-3c