940 research outputs found
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
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
Laboratory Characterization and Astrophysical Detection of Vibrationally Excited States of Vinyl Cyanide in Orion-KL
New laboratory data of CHCHCN (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 CHCHCN 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 CHCHCN 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 CHCHCN in the ground state is (3.00.9)x10
cm. 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 CHCHCN 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
(CHNC) for the first time in Orion-KL and a tentative detection of vinyl
isocyanide (CHCHNC) and give column density ratios between the cyanide and
isocyanide isomers.Comment: 46 pages, 22 figures, 14 tables, 9 online table
Absence of Insect Juvenile Hormones in the American Dog Tick, Dermacentor veriabilis (Say) (Acari: Ixodidae), and in Ornithodoros parkeri Cooley (Acari: Argasidae)
Synganglia, salivary gland, midgut, ovary, fat body and muscle alone and in combination from the ixodid tick, Dermacentor variabilis (Say), or the argasid tick, Ornithodoros parkeri Cooley, were incubated in vitro in separate experiments with L-[methyl-3H]methionine and farnesoic acid or with [1-14C]acetate. Life stages examined in D. variabilis were 3 and 72 h old (after ecdysis) unfed nymphs, partially fed nymphs (18 and 72 h after attachment to the host), fully engorged nymphs (2 d after detachment from host), 3 and 72 h old (after eclosion) unfed females, partially fed unmated females (12–168 h after attachment to host) and mated replete females (2 d after detachment from the host). Those from O. parkeri were third and fourth stadium nymphs and female O. parkeri, 1–2 d after detachment. Corpora allata from Diploptera punctata, Periplaneta americana and Gromphadorina portentosa were used as positive controls in these experiments. No farnesol, methyl farnesoate, JH I, JH II, JH III, or JHIII bisepoxide was detected by radio HPLC from any tick analysis while JH III, methyl farnesoate, and farnesol were detected in the positive controls. To examine further for the presence of a tick, insect-juvenilizing agent, Galleria pupal–cuticle bioassays were conducted on lipid extracts from 10 and 15 d old eggs, unfed larvae (1–5 d after ecdysis), unfed nymphs (1–7 d after ecdysis), and partially fed, unmated female adults (completed slow feeding phase) of D. variabilis. Whole body extracts of fourth stadium D. punctata and JH III standard were used as positive controls. No juvenilizing activity in any of the tick extracts could be detected. Electron impact, gas chromatography–mass spectrometry of hemolymph extracts from fed, virgin (forcibly detached 7 d after attachment) and mated, replete (allowed to drop naturally) D. variabilis and fully engorged (1–2 d after detachment) O. parkeri females also failed to identify the common insect juvenile hormones. The same procedures were successful in the identification of JH III in hemolymph of fourth stadium D. punctata. Last stadium nymphal (female) O. parkeri implanted with synganglia from second nymphal instars underwent normal eclosion to the adult. The above studies in toto suggest that D. variabilis and O. parkeri do not have the ability to make the common insect juvenile hormones, and these juvenile hormones do not regulate tick metamorphosis or reproduction as hypothesized in the literature
Magnetic Properties of Monomer and Dimer Tetrahedral VOx Entities Dispersed on Amorphous Silica-based Materials: Prediction of EPR Parameters from Relativistic DFT Calculations and Broken Symmetry Approach to Exchange Couplings
Molecular structures of the isolated tetrahedral oxovanadium(IV) and bridged μ-oxo-divanadium(IV) complexes hosted by the clusters mimicking surfaces of amorphous silica-based materials were investigated using density functional theory (DFT) calculations. Principal values of the g and A tensors for the monomer vanadyl species were obtained using the coupled-perturbed DFT level of theory and the spin–orbit mean-field approximation (SOMF). Magnetic exchange interaction for the μ-oxo bridged vanadium(IV) dimer was investigated within the broken symmetry approach. An antiferromagnetic coupling of the individual magnetic moments of the vanadium(IV) centers in the [VO–O–VO]2+ bridges was revealed and discussed in detail. The coupling explains pronounced decrease of the electron paramagnetic resonance signal (EPR) intensity, observed for the reduced VOx/SiO2 samples with the increasing coverage of vanadia, in terms of transformation of the paramagnetic monomer species into the dimers with S = 0 ground state
Density functional theory
Density functional theory (DFT) finds increasing use in applications related to biological systems. Advancements in methodology and implementations have reached a point where predicted properties of reasonable to high quality can be obtained. Thus, DFT studies can complement experimental investigations, or even venture with some confidence into experimentally unexplored territory. In the present contribution, we provide an overview of the properties that can be calculated with DFT, such as geometries, energies, reaction mechanisms, and spectroscopic properties. A wide range of spectroscopic parameters is nowadays accessible with DFT, including quantities related to infrared and optical spectra, X-ray absorption and Mössbauer, as well as all of the magnetic properties connected with electron paramagnetic resonance spectroscopy except relaxation times. We highlight each of these fields of application with selected examples from the recent literature and comment on the capabilities and limitations of current methods
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
Accurate ab initio spin densities
We present an approach for the calculation of spin density distributions for
molecules that require very large active spaces for a qualitatively correct
description of their electronic structure. Our approach is based on the
density-matrix renormalization group (DMRG) algorithm to calculate the spin
density matrix elements as basic quantity for the spatially resolved spin
density distribution. The spin density matrix elements are directly determined
from the second-quantized elementary operators optimized by the DMRG algorithm.
As an analytic convergence criterion for the spin density distribution, we
employ our recently developed sampling-reconstruction scheme [J. Chem. Phys.
2011, 134, 224101] to build an accurate complete-active-space
configuration-interaction (CASCI) wave function from the optimized matrix
product states. The spin density matrix elements can then also be determined as
an expectation value employing the reconstructed wave function expansion.
Furthermore, the explicit reconstruction of a CASCI-type wave function provides
insights into chemically interesting features of the molecule under study such
as the distribution of - and -electrons in terms of Slater
determinants, CI coefficients, and natural orbitals. The methodology is applied
to an iron nitrosyl complex which we have identified as a challenging system
for standard approaches [J. Chem. Theory Comput. 2011, 7, 2740].Comment: 37 pages, 13 figure
A high‐resolution view of the coordination environment in a paramagnetic metalloprotein from its magnetic properties
Metalloproteins constitute a significant fraction of the proteome of all organisms and their characterization is critical for both basic sciences and biomedical applications. A large portion of metalloproteins bind paramagnetic metal ions, and paramagnetic NMR spectroscopy has been widely used in their structural characterization. However, the signals of nuclei in the immediate vicinity of the metal center are often broadened beyond detection. In this work, we show that it is possible to determine the coordination environment of the paramagnetic metal in the protein at a resolution inaccessible to other techniques. Taking the structure of a diamagnetic analogue as a starting point, a geometry optimization is carried out by fitting the pseudocontact shifts obtained from first principles quantum chemical calculations to the experimental ones
Geometric and Electronic Structures of the NiI and Methyl−NiIII Intermediates of Methyl-Coenzyme M Reductase†
ABSTRACT: Methyl-coenzyme M reductase (MCR) catalyzes the terminal step in the formation of biological methane from methyl-coenzyme M (Me-SCoM) and coenzyme B (CoBSH). The active site in MCR contains a Ni-F430 cofactor, which can exist in different oxidation states. The catalytic mechanism of methane formation has remained elusive despite intense spectroscopic and theoretical investigations. On the basis of spectroscopic and crystallographic data, the first step of the mechanism is proposed to involve a nucleophilic attack of the NiI active state (MCRred1) on Me-SCoM to form a NiIII-methyl intermediate, while computational studies indicate that the first step involves the attack of NiI on the sulfur of Me-SCoM, forming a CH3 radical and a NiII-thiolate species. In this study, a combination of Ni K-edge X-ray absorption spectroscopic (XAS) studies and density functional theory (DFT) calculations have been performed on the NiI (MCRred1), NiII (MCRred1-silent), and NiIII-methyl (MCRMe) states of MCR to elucidate the geometric and electronic structures of the different redox states. Ni K-edge EXAFS data are used to reveal a five-coordinate active site with an open upper axial coordination site in MCRred1. Ni K-pre-edge and EXAFS data and time-dependent DFT calculations unambiguously demonstrate the presence of a long Ni-C bond (∼2.04 Å) in the NiIII-methyl state of MCR. The formation and stability of this species support mechanism I, and the Ni-C bond length suggests a homolytic cleavage of the NiIII-methyl bon
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