42 research outputs found
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
The role of dynamical polarization of the ligand to metal charge transfer excitations in {\em ab initio} determination of effective exchange parameters
The role of the bridging ligand on the effective Heisenberg coupling
parameters is analyzed in detail. This analysis strongly suggests that the
ligand-to-metal charge transfer excitations are responsible for a large part of
the final value of the magnetic coupling constant. This permits to suggest a
new variant of the Difference Dedicated Configuration Interaction (DDCI)
method, presently one of the most accurate and reliable for the evaluation of
magnetic effective interactions. This new method treats the bridging ligand
orbitals mediating the interaction at the same level than the magnetic orbitals
and preserves the high quality of the DDCI results while being much less
computationally demanding. The numerical accuracy of the new approach is
illustrated on various systems with one or two magnetic electrons per magnetic
center. The fact that accurate results can be obtained using a rather reduced
configuration interaction space opens the possibility to study more complex
systems with many magnetic centers and/or many electrons per center.Comment: 7 pages, 4 figure
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
Translation Initiation Factors eIF3 and HCR1 Control Translation Termination and Stop Codon Read-Through in Yeast Cells
Translation is divided into initiation, elongation, termination and ribosome recycling. Earlier work implicated several eukaryotic initiation factors (eIFs) in ribosomal recycling in vitro. Here, we uncover roles for HCR1 and eIF3 in translation termination in vivo. A substantial proportion of eIF3, HCR1 and eukaryotic release factor 3 (eRF3) but not eIF5 (a well-defined “initiation-specific” binding partner of eIF3) specifically co-sediments with 80S couples isolated from RNase-treated heavy polysomes in an eRF1-dependent manner, indicating the presence of eIF3 and HCR1 on terminating ribosomes. eIF3 and HCR1 also occur in ribosome- and RNA-free complexes with both eRFs and the recycling factor ABCE1/RLI1. Several eIF3 mutations reduce rates of stop codon read-through and genetically interact with mutant eRFs. In contrast, a slow growing deletion of hcr1 increases read-through and accumulates eRF3 in heavy polysomes in a manner suppressible by overexpressed ABCE1/RLI1. Based on these and other findings we propose that upon stop codon recognition, HCR1 promotes eRF3·GDP ejection from the post-termination complexes to allow binding of its interacting partner ABCE1/RLI1. Furthermore, the fact that high dosage of ABCE1/RLI1 fully suppresses the slow growth phenotype of hcr1? as well as its termination but not initiation defects implies that the termination function of HCR1 is more critical for optimal proliferation than its function in translation initiation. Based on these and other observations we suggest that the assignment of HCR1 as a bona fide eIF3 subunit should be reconsidered. Together our work characterizes novel roles of eIF3 and HCR1 in stop codon recognition, defining a communication bridge between the initiation and termination/recycling phases of translation
Density functional theory study of the oxoperoxo vanadium(V) complexes of glycolic acid. Structural correlations with NMR chemical shifts
The DFT B3LYP/SBKJC method has been used to calculate the gas-phase optimized geometries of the glycolate oxoperoxo vanadium(V) complexes [V2O2(OO)2(gly)2]2-, [V2O3(OO)(gly)2]2- and [VO(OO)(gly)(H2O)]-. The 51V, 17O, 13C and 1H chemical shifts have been calculated for the theoretical geometries in all-electron DFT calculations at the UDFT-IGLO-PW91 level and have been subsequently compared with the experimental chemical shifts in solution. In spite of being applied to the isolated molecules, the calculations allowed satisfactory reproduction of the multinuclear NMR solution chemical shifts of the complexes, suggesting that the theoretical structures are probably close to those in solution. The effects of structural changes on the 51V and 17O NMR chemical shifts have been analysed using the referred computational methodologies for one of the glycolate complexes and for several small molecules taken as models. These calculations showed that structural modifications far from the metal nucleus do not significantly affect the metal chemical shift. This finding explains why it is possible to establish reference scales that correlate the type of complex (type of metal centre associated with a certain type of ligand) with its typical region of metal chemical shifts. It has also been found that the VO bond length is the dominant geometrical parameter determining both 51V and the oxo 17O in this kind of comple