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Title: Coordination characteristics of uranyl BBP complexes: Insights from an electronic structure analysis

Abstract

Here, organic ligand complexes of lanthanide/actinide ions have been studied extensively for applications in nuclear fuel storage and recycling. Several complexes of 2,6-bis(2-benzimidazyl)pyridine (H2BBP) featuring the uranyl moiety have been reported recently, and the present study investigates the coordination characteristics of these complexes using density functional theory-based electronic structure analysis. In particular, with the aid of several computational models, the nonplanar equatorial coordination about uranyl, observed in some of the compounds, is studied and its origin traced to steric effects.

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [2];  [1];  [1]
  1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  2. Univ. of California, Davis, CA (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22)
OSTI Identifier:
1347807
Alternate Identifier(s):
OSTI ID: 1352063; OSTI ID: 1435081
Grant/Contract Number:
AC02-05CH11231
Resource Type:
Journal Article: Published Article
Journal Name:
ACS Omega
Additional Journal Information:
Journal Volume: 2; Journal Issue: 3; Journal ID: ISSN 2470-1343
Publisher:
American Chemical Society (ACS)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; coordination chemistry (organomet.); molecular structure

Citation Formats

Pemmaraju, Chaitanya Das, Copping, Roy, Smiles, Danil E., Shuh, David K., Grønbech-Jensen, Niels, Prendergast, David, and Canning, Andrew. Coordination characteristics of uranyl BBP complexes: Insights from an electronic structure analysis. United States: N. p., 2017. Web. doi:10.1021/acsomega.6b00459.
Pemmaraju, Chaitanya Das, Copping, Roy, Smiles, Danil E., Shuh, David K., Grønbech-Jensen, Niels, Prendergast, David, & Canning, Andrew. Coordination characteristics of uranyl BBP complexes: Insights from an electronic structure analysis. United States. doi:10.1021/acsomega.6b00459.
Pemmaraju, Chaitanya Das, Copping, Roy, Smiles, Danil E., Shuh, David K., Grønbech-Jensen, Niels, Prendergast, David, and Canning, Andrew. Tue . "Coordination characteristics of uranyl BBP complexes: Insights from an electronic structure analysis". United States. doi:10.1021/acsomega.6b00459.
@article{osti_1347807,
title = {Coordination characteristics of uranyl BBP complexes: Insights from an electronic structure analysis},
author = {Pemmaraju, Chaitanya Das and Copping, Roy and Smiles, Danil E. and Shuh, David K. and Grønbech-Jensen, Niels and Prendergast, David and Canning, Andrew},
abstractNote = {Here, organic ligand complexes of lanthanide/actinide ions have been studied extensively for applications in nuclear fuel storage and recycling. Several complexes of 2,6-bis(2-benzimidazyl)pyridine (H2BBP) featuring the uranyl moiety have been reported recently, and the present study investigates the coordination characteristics of these complexes using density functional theory-based electronic structure analysis. In particular, with the aid of several computational models, the nonplanar equatorial coordination about uranyl, observed in some of the compounds, is studied and its origin traced to steric effects.},
doi = {10.1021/acsomega.6b00459},
journal = {ACS Omega},
number = 3,
volume = 2,
place = {United States},
year = {Tue Mar 21 00:00:00 EDT 2017},
month = {Tue Mar 21 00:00:00 EDT 2017}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at 10.1021/acsomega.6b00459

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  • Here, organic ligand complexes of lanthanide/actinide ions have been studied extensively for applications in nuclear fuel storage and recycling. Several complexes of 2,6-bis(2-benzimidazyl)pyridine (H2BBP) featuring the uranyl moiety have been reported recently, and the present study investigates the coordination characteristics of these complexes using density functional theory-based electronic structure analysis. In particular, with the aid of several computational models, the nonplanar equatorial coordination about uranyl, observed in some of the compounds, is studied and its origin traced to steric effects.
  • Organic ligand complexes of lanthanide/actinide ions have been studied extensively for applications in nuclear fuel storage and recycling. Several complexes of 2,6-bis(2-benzimidazyl)pyridine (H2BBP) featuring the uranyl moiety have been reported recently, and the present study investigates the coordination characteristics of these complexes using density functional theory-based electronic structure analysis. In particular, with the aid of several computational models, the nonplanar equatorial coordination about uranyl, observed in some of the compounds, is studied and its origin traced to steric effects.
  • We have captured a preinsertion ternary complex of RB69 DNA polymerase (RB69pol) containing the 3' hydroxyl group at the terminus of an extendable primer (ptO3') and a nonhydrolyzable 2'-deoxyuridine 5'-{alpha},{beta}-substituted triphosphate, dUpXpp, where X is either NH or CH{sub 2}, opposite a complementary templating dA nucleotide residue. Here we report four structures of these complexes formed by three different RB69pol variants with catalytically inert Ca{sup 2+} and four other structures with catalytically competent Mn{sup 2+} or Mg{sup 2+}. These structures provide new insights into why the complete divalent metal-ion coordination complexes at the A and B sites are required formore » nucleotidyl transfer. They show that the metal ion in the A site brings ptO3' close to the {alpha}-phosphorus atom (P{alpha}) of the incoming dNTP to enable phosphodiester bond formation through simultaneous coordination of both ptO3' and the nonbridging Sp oxygen of the dNTP's {alpha}-phosphate. The coordination bond length of metal ion A as well as its ionic radius determines how close ptO3' can approach P{alpha}. These variables are expected to affect the rate of bond formation. The metal ion in the B site brings the pyrophosphate product close enough to P{alpha} to enable pyrophosphorolysis and assist in the departure of the pyrophosphate. In these dUpXpp-containing complexes, ptO3' occupies the vertex of a distorted metal ion A coordination octahedron. When ptO3' is placed at the vertex of an undistorted, idealized metal ion A octahedron, it is within bond formation distance to P{alpha}. This geometric relationship appears to be conserved among DNA polymerases of known structure.« less