988 research outputs found
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
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
A Joint Venture of Ab Initio Molecular Dynamics, Coupled Cluster Electronic Structure Methods, and Liquid-State Theory to Compute Accurate Isotropic Hyperfine Constants of Nitroxide Probes in Water
The isotropic hyperfine coupling constant (HFCC, Aiso) of a pH-sensitive spin probe in a solution, HMI (2,2,3,4,5,5-hexamethylimidazolidin-1-oxyl, C9H19N2O) in water, is computed using an ensemble of state-of-the-art computational techniques and is gauged against X-band continuous wave electron paramagnetic resonance (EPR) measurement spectra at room temperature. Fundamentally, the investigation aims to delineate the cutting edge of current first-principles-based calculations of EPR parameters in aqueous solutions based on using rigorous statistical mechanics combined with correlated electronic structure techniques. In particular, the impact of solvation is described by exploiting fully atomistic, RISM integral equation, and implicit solvation approaches as offered by ab initio molecular dynamics (AIMD) of the periodic bulk solution (using the spin-polarized revPBE0-D3 hybrid functional), embedded cluster reference interaction site model integral equation theory (EC-RISM), and polarizable continuum embedding (using CPCM) of microsolvated complexes, respectively. HFCCs are obtained from efficient coupled cluster calculations (using open-shell DLPNO-CCSD theory) as well as from hybrid density functional theory (using revPBE0-D3). Re-solvation of “vertically desolvated” spin probe configuration snapshots by EC-RISM embedding is shown to provide significantly improved results compared to CPCM since only the former captures the inherent structural heterogeneity of the solvent close to the spin probe. The average values of the Aiso parameter obtained based on configurational statistics using explicit water within AIMD and from EC-RISM solvation are found to be satisfactorily close. Using either such explicit or RISM solvation in conjunction with DLPNO-CCSD calculations of the HFCCs provides an average Aiso parameter for HMI in aqueous solution at 300 K and 1 bar that is in good agreement with the experimentally determined one. The developed computational strategy is general in the sense that it can be readily applied to other spin probes of similar molecular complexity, to aqueous solutions beyond ambient conditions, as well as to other solvents in the longer run
A revised asteroid polarization-albedo relationship using WISE/NEOWISE data
We present a reanalysis of the relationship between asteroid albedo and
polarization properties using the albedos derived from the Wide-field Infrared
Survey Explorer. We find that the function that best describes this relation is
a three-dimensional linear fit in the space of log(albedo)-log(polarization
slope)-log(minimum polarization). When projected to two dimensions the
parameters of the fit are consistent with those found in previous work. We also
define p* as the quantity of maximal polarization variation when compared with
albedo and present the best fitting albedo-p* relation. Some asteroid taxonomic
types stand out in this three-dimensional space, notably the E, B, and M Tholen
types, while others cluster in clumps coincident with the S- and C-complex
bodies. We note that both low albedo and small (D<30 km) asteroids are
under-represented in the polarimetric sample, and we encourage future
polarimetric surveys to focus on these bodies.Comment: 16 pages, Accepted to Ap
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
Reduction of CO\u3csub\u3e2\u3c/sub\u3e By a Masked Two-Coordinate Cobalt(I) Complex and Characterization of a Proposed Oxodicobalt(II) Intermediate
Fixation and chemical reduction of CO2 are important for utilization of this abundant resource, and understanding the detailed mechanism of C-O cleavage is needed for rational development of CO2 reduction methods. Here, we describe a detailed analysis of the mechanism of the reaction of a masked two-coordinate cobalt(i) complex, LtBuCo (where LtBu = 2,2,6,6-tetramethyl-3,5-bis[(2,6-diisopropylphenyl)imino]hept-4-yl), with CO2, which yields two products of C-O cleavage, the cobalt(i) monocarbonyl complex LtBuCo(CO) and the dicobalt(ii) carbonate complex (LtBuCo)2(μ-CO3). Kinetic studies and computations show that the κN,η6-arene isomer of LtBuCo rearranges to the κ2N,N′ binding mode prior to binding of CO2, which contrasts with the mechanism of binding of other substrates to LtBuCo. Density functional theory (DFT) studies show that the only low-energy pathways for cleavage of CO2 proceed through bimetallic mechanisms, and DFT and highly correlated domain-based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) calculations reveal the cooperative effects of the two metal centers during facile C-O bond rupture. A plausible intermediate in the reaction of CO2 with LtBuCo is the oxodicobalt(II) complex LtBuCoOCoLtBu, which has been independently synthesized through the reaction of LtBuCo with N2O. The rapid reaction of LtBuCoOCoLtBu with CO2 to form the carbonate product indicates that the oxo species is kinetically competent to be an intermediate during CO2 cleavage by LtBuCo. LtBuCoOCoLtBu is a novel example of a thoroughly characterized molecular cobalt-oxo complex where the cobalt ions are clearly in the +2 oxidation state. Its nucleophilic reactivity is a consequence of high charge localization on the μ-oxo ligand between two antiferromagnetically coupled high-spin cobalt(ii) centers, as characterized by DFT and multireference complete active space self-consistent field (CASSCF) calculations
Photochemistry of Furyl- and Thienyldiazomethanes: Spectroscopic Characterization of Triplet 3-Thienylcarbene
Photolysis (λ \u3e 543 nm) of 3-thienyldiazomethane (1), matrix isolated in Ar or N2 at 10 K, yields triplet 3-thienylcarbene (13) and α-thial-methylenecyclopropene (9). Carbene 13 was characterized by IR, UV/vis, and EPR spectroscopy. The conformational isomers of 3-thienylcarbene (s-E and s-Z) exhibit an unusually large difference in zero-field splitting parameters in the triplet EPR spectrum (|D/hc| = 0.508 cm–1, |E/hc| = 0.0554 cm–1; |D/hc| = 0.579 cm–1, |E/hc| = 0.0315 cm–1). Natural Bond Orbital (NBO) calculations reveal substantially differing spin densities in the 3-thienyl ring at the positions adjacent to the carbene center, which is one factor contributing to the large difference in D values. NBO calculations also reveal a stabilizing interaction between the sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding σ orbital between sulfur and the neighboring carbon—an interaction that is not observed in the s-E rotamer of 13. In contrast to the EPR spectra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistinguishable under our experimental conditions. The carbene exhibits a weak electronic absorption in the visible spectrum (λmax = 467 nm) that is characteristic of triplet arylcarbenes. Although studies of 2-thienyldiazomethane (2), 3-furyldiazomethane (3), or 2-furyldiazomethane (4) provided further insight into the photochemical interconversions among C5H4S or C5H4O isomers, these studies did not lead to the spectroscopic detection of the corresponding triplet carbenes (2-thienylcarbene (11), 3-furylcarbene (23), or 2-furylcarbene (22), respectively)
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