Results for “complex” — Page 45

DOE OSTI2012

A structural model of the E. coli PhoB Dimer in the transcription initiation complex

Background: There exist > 78,000 proteins and/or nucleic acids structures that were determined experimentally. Only a small portion of these structures corresponds to those of protein complexes. While homology modeling is able to exploit knowledge-based potentials of side-chain rotomers and backbone motifs to infer structures for new proteins, no such general method exists to extend our understanding of protein interaction motifs to novel protein complexes. Results: We use a Motif Binding Geometries (MBG) approach, to infer the structure of a protein complex from the database of complexes of homologous proteins taken from other contexts (such as the helix-turn-helix motif binding double stranded DNA), and demonstrate its utility on one of the more important regulatory complexes in biology, that of the RNA polymerase initiating transcription under conditions of phosphate starvation. The modeled PhoB/RNAP/s-factor/DNA complex is stereo-chemically reasonable, has sufficient interfacial Solvent Excluded Surface Areas (SESAs) to provide adequate binding strength, is physically meaningful for transcription regulation, and is consistent with a variety of known experimental constraints. Conclusions: Based on a straightforward and easy to comprehend concept, “proteins and protein domains that fold similarly could interact similarly”, a structural model of the PhoB dimer in the transcription initiation complex has been developed. This approach could be extended to enable structural modeling and prediction of other biomolecular complexes. Just as models of individual proteins provide insight into molecular recognition, catalytic mechanism, and substrate specificity, models of protein complexes will provide understanding into the combinatorial rules of cellular regulation and signaling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2012

Transition metal complexes of oxazolinylboranes and cyclopentadienyl-bis(oxazolinyl)borates: Catalysts for asymmetric olefin hydroamination and acceptorless alcohol decarbonylation

The research presented and discussed in this dissertation involves the synthesis of transition metal complexes of oxazolinylboranes and cyclopentadienyl-bis(oxazolinyl)borates, and their application in catalytic enantioselective olefin hydroamination and acceptorless alcohol decarbonylation. Neutral oxazolinylboranes are excellent synthetic intermediates for preparing new borate ligands and also developing organometallic complexes. Achiral and optically active bis(oxazolinyl)phenylboranes are synthesized by reaction of 2-lithio-2-oxazolide and 0.50 equiv of dichlorophenylborane. These bis(oxazolinyl)phenylboranes are oligomeric species in solid state resulting from the coordination of an oxazoline to the boron center of another borane monomer. The treatment of chiral bis(oxazolinyl)phenylboranes with sodium cyclopentadienide provide optically active cyclopentadienyl-bis(oxazolinyl)borates H[PhB(C 5 H 5 )(Ox R ) 2 ] [Ox R = Ox 4S-iPr,Me2 , Ox 4R-iPr,Me2 , Ox 4S-tBu] . These optically active proligands react with an equivalent of M(NMe 2 ) 4 (M = Ti, Zr, Hf) to afford corresponding cyclopentadienyl-bis(oxazolinyl)borato group 4 complexes {PhB(C 5 H 4 )(Ox R ) 2 }M(NMe 2 ) 2 in high yields. These group 4 compounds catalyze cyclization of aminoalkenes at room temperature or below, providing pyrrolidine, piperidine, and azepane with enantiomeric excesses up to 99%. Our mechanistic investigations suggest a non-insertive mechanism involving concerted C-N/C-H bond formation in the turnover limiting step of the catalytic cycle. Among cyclopentadienyl-bis(oxazolinyl)borato group 4 catalysts, the zirconium complex {PhB(C 5 H 4 )(Ox4 S-iPr,Me2 ) 2 }Zr(NMe 2 ) 2 ({S-2}Zr(NMe 2 ) 2 ) displays highest activity and enantioselectivity. Interestingly, S-2 Zr(NMe 2 ) 2 also desymmetrizes olefin moieties of achiral non-conjugated aminodienes and aminodiynes during cyclization. The cyclization of aminodienes catalyzed by S-2 Zr(NMe 2 ) 2 affords diastereomeric mixture of cis and trans cylic amines with high diasteromeric ratios and excellent enantiomeric excesses. Similarly, the desymmetrization of alkyne moieties in S-2 Zr(NMe 2 ) 2 -catalyzed cyclization of aminodiynes provides corresponding cyclic imines bearing quaternary stereocenters with enantiomeric excesses up to 93%. These stereoselective desymmetrization reactions are significantly affected by concentration of the substrate, temperature, and the presence of a noncyclizable primary amine. In addition, both the diastereomeric ratios and enantiomeric excesses of the products are markedly enhanced by N-deuteration of the substrates. Notably, the cationic zirconium-monoamide complex [ S-2 Zr(NMe 2 )][B(C 6 F 5 ) 4 ] obtained from neutral S-2 Zr(NMe 2 ) 2 cyclizes primary aminopentenes providing pyrrolidines with S-configuration; whereas S-2 Zr(NMe 2 ) 2 provides R-configured pyrrolidines. The yttrium complex S-2 YCH 2 SiMe 3 also affords S-configured pyrrolidines by cyclization of aminopentenes, however the enantiomeric excesses of products are low. An alternative optically active yttrium complex {PhB(C 5 H 4 )(Ox 4S-tBu ) 2 }YCH 2 SiMe 3 ({S-3}YCH 2 SiMe 3 ) is synthesized, which displays highly enantioselective in the cyclization of aminoalkenes at room temperature affording S-configured cyclic amines with enantiomeric excesses up to 96%. A noninsertive mechanism involving a six-membered transition state by a concerted C-N bond formation and N-H bond cleavage is proposed for {S-3}YCH 2 SiMe 3 system based on the kinetic, spectroscopic, and stereochemical features. In the end, a series of bis- and tris(oxazolinyl)borato iridium and rhodium complexes are synthesized with bis(oxazolinyl)phenylborane [PhB(Ox Me2 ) 2 ] n , tris(oxazolinyl)borane [B(Ox M ) 3 ]n, and tris(4,4-dimethyl-2-oxazolinyl)phenylborate [To M ] - . All these new and other known rhodium and iridium complexes were examined in acceptorless dehydrogenative decarbonylation of primary alcohols. The catalysts survey shows that the compound To M Ir(η 4 - C 8 H 12 ) is the most active for the conversion of primary alcohols into alkane, H 2 , and CO at 180 °C in toluene. Several aliphatic and aromatic primary alcohols are decarbonylated in the catalytic conditions. Furthermore, To M Ir(η 4 -C 8 H 12 ) is also able to decarbonylate polyols such as ethylene glycol and glycerol to syngas (H 2 and CO) at 180 °C.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

A Historical Evaluation of the U15 Complex, Nevada National Security Site, Nye County, Nevada

This report presents a historical evaluation of the U15 Complex on the Nevada National Security Site (NNSS) in southern Nevada. The work was conducted by the Desert Research Institute at the request of the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office and the U.S. Department of Defense, Defense Threat Reduction Agency. Three underground nuclear tests and two underground nuclear fuel storage experiments were conducted at the complex. The nuclear tests were Hard Hat in 1962, Tiny Tot in 1965, and Pile Driver in 1966. The Hard Hat and Pile Driver nuclear tests involved different types of experiment sections in test drifts at various distances from the explosion in order to determine which sections could best survive in order to design underground command centers. The Tiny Tot nuclear test involved an underground cavity in which the nuclear test was executed. It also provided data in designing underground structures and facilities to withstand a nuclear attack. The underground nuclear fuel storage experiments were Heater Test 1 from 1977 to 1978 and Spent Fuel Test - Climax from 1978 to 1985. Heater Test 1 was used to design the later Spent Fuel Test - Climax experiment. The latter experiment was a model of a larger underground storage facility and primarily involved recording the conditions of the spent fuel and the surrounding granite medium. Fieldwork was performed intermittently in the summers of 2011 and 2013, totaling 17 days. Access to the underground tunnel complex is sealed and unavailable. Restricted to the surface, four buildings, four structures, and 92 features associated with nuclear testing and fuel storage experiment activities at the U15 Complex have been recorded. Most of these are along the west side of the complex and next to the primary access road and are characteristic of an industrial mining site, albeit one with scientific interests. The geomorphological fieldwork was conducted over three days in the summer of 2011. It was discovered that major modifications to the terrain have resulted from four principal activities. These are road construction and maintenance, mining activities related to development of the tunnel complex, site preparation for activities related to the tests and experiments, and construction of drill pads and retention ponds. Six large trenches for exploring across the Boundary geologic fault are also present. The U15 Complex, designated historic district 143 and site 26NY15177, is eligible to the National Register of Historic Places under Criteria A, C, and D of 36 CFR Part 60.4. As a historic district and archaeological site eligible to the National Register of Historic Places, the Desert Research Institute recommends that the area defined for the U15 Complex, historic district 143 and site 26NY15117, be left in place in its current condition. The U15 Complex should also be included in the NNSS cultural resources monitoring program and monitored for disturbances or alterations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

A Historical Evaluation of the U15 Complex, Nevada National Security Site, Nye County, Nevada

This report presents a historical evaluation of the U15 Complex on the Nevada National Security Site (NNSS) in southern Nevada. The work was conducted by the Desert Research Institute at the request of the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office and the U.S. Department of Defense, Defense Threat Reduction Agency. Three underground nuclear tests and two underground nuclear fuel storage experiments were conducted at the complex. The nuclear tests were Hard Hat in 1962, Tiny Tot in 1965, and Pile Driver in 1966. The Hard Hat and Pile Driver nuclear tests involved different types of experiment sections in test drifts at various distances from the explosion in order to determine which sections could best survive in order to design underground command centers. The Tiny Tot nuclear test involved an underground cavity in which the nuclear test was executed. It also provided data in designing underground structures and facilities to withstand a nuclear attack. The underground nuclear fuel storage experiments were Heater Test 1 from 1977 to 1978 and Spent Fuel Test - Climax from 1978 to 1985. Heater Test 1 was used to design the later Spent Fuel Test - Climax experiment. The latter experiment was a model of a larger underground storage facility and primarily involved recording the conditions of the spent fuel and the surrounding granite medium. Fieldwork was performed intermittently in the summers of 2011 and 2013, totaling 17 days. Access to the underground tunnel complex is sealed and unavailable. Restricted to the surface, four buildings, four structures, and 92 features associated with nuclear testing and fuel storage experiment activities at the U15 Complex have been recorded. Most of these are along the west side of the complex and next to the primary access road and are characteristic of an industrial mining site, albeit one with scientific interests. The geomorphological fieldwork was conducted over three days in the summer of 2011. It was discovered that major modifications to the terrain have resulted from four principal activities. These are road construction and maintenance, mining activities related to development of the tunnel complex, site preparation for activities related to the tests and experiments, and construction of drill pads and retention ponds. Six large trenches for exploring across the Boundary geologic fault are also present. The U15 Complex, designated historic district 143 and site 26NY15177, is eligible to the National Register of Historic Places under Criteria A, C, and D of 36 CFR Part 60.4. As a historic district and archaeological site eligible to the National Register of Historic Places, the Desert Research Institute recommends that the area defined for the U15 Complex, historic district 143 and site 26NY15117, be left in place in its current condition. The U15 Complex should also be included in the NNSS cultural resources monitoring program and monitored for disturbances or alterations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

A Historical Evaluation of the U15 Complex, Nevada National Security Site, Nye County, Nevada

This report presents a historical evaluation of the U15 Complex on the Nevada National Security Site (NNSS) in southern Nevada. The work was conducted by the Desert Research Institute at the request of the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office and the U.S. Department of Defense, Defense Threat Reduction Agency. Three underground nuclear tests and two underground nuclear fuel storage experiments were conducted at the complex. The nuclear tests were Hard Hat in 1962, Tiny Tot in 1965, and Pile Driver in 1966. The Hard Hat and Pile Driver nuclear tests involved different types of experiment sections in test drifts at various distances from the explosion in order to determine which sections could best survive in order to design underground command centers. The Tiny Tot nuclear test involved an underground cavity in which the nuclear test was executed. It also provided data in designing underground structures and facilities to withstand a nuclear attack. The underground nuclear fuel storage experiments were Heater Test 1 from 1977 to 1978 and Spent Fuel Test - Climax from 1978 to 1985. Heater Test 1 was used to design the later Spent Fuel Test - Climax experiment. The latter experiment was a model of a larger underground storage facility and primarily involved recording the conditions of the spent fuel and the surrounding granite medium. Fieldwork was performed intermittently in the summers of 2011 and 2013, totaling 17 days. Access to the underground tunnel complex is sealed and unavailable. Restricted to the surface, four buildings, four structures, and 92 features associated with nuclear testing and fuel storage experiment activities at the U15 Complex have been recorded. Most of these are along the west side of the complex and next to the primary access road and are characteristic of an industrial mining site, albeit one with scientific interests. The geomorphological fieldwork was conducted over three days in the summer of 2011. It was discovered that major modifications to the terrain have resulted from four principal activities. These are road construction and maintenance, mining activities related to development of the tunnel complex, site preparation for activities related to the tests and experiments, and construction of drill pads and retention ponds. Six large trenches for exploring across the Boundary geologic fault are also present. The U15 Complex, designated historic district 143 and site 26NY15177, is eligible to the National Register of Historic Places under Criteria A, C, and D of 36 CFR Part 60.4. As a historic district and archaeological site eligible to the National Register of Historic Places, the Desert Research Institute recommends that the area defined for the U15 Complex, historic district 143 and site 26NY15117, be left in place in its current condition. The U15 Complex should also be included in the NNSS cultural resources monitoring program and monitored for disturbances or alterations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2014

A Historical Evaluation of the U15 Complex, Nevada National Security Site, Nye County, Nevada

This report presents a historical evaluation of the U15 Complex on the Nevada National Security Site (NNSS) in southern Nevada. The work was conducted by the Desert Research Institute at the request of the U.S. Department of Energy, National Nuclear Security Administration Nevada Field Office and the U.S. Department of Defense, Defense Threat Reduction Agency. Three underground nuclear tests and two underground nuclear fuel storage experiments were conducted at the complex. The nuclear tests were Hard Hat in 1962, Tiny Tot in 1965, and Pile Driver in 1966. The Hard Hat and Pile Driver nuclear tests involved different types of experiment sections in test drifts at various distances from the explosion in order to determine which sections could best survive in order to design underground command centers. The Tiny Tot nuclear test involved an underground cavity in which the nuclear test was executed. It also provided data in designing underground structures and facilities to withstand a nuclear attack. The underground nuclear fuel storage experiments were Heater Test 1 from 1977 to 1978 and Spent Fuel Test - Climax from 1978 to 1985. Heater Test 1 was used to design the later Spent Fuel Test - Climax experiment. The latter experiment was a model of a larger underground storage facility and primarily involved recording the conditions of the spent fuel and the surrounding granite medium. Fieldwork was performed intermittently in the summers of 2011 and 2013, totaling 17 days. Access to the underground tunnel complex is sealed and unavailable. Restricted to the surface, four buildings, four structures, and 92 features associated with nuclear testing and fuel storage experiment activities at the U15 Complex have been recorded. Most of these are along the west side of the complex and next to the primary access road and are characteristic of an industrial mining site, albeit one with scientific interests. The geomorphological fieldwork was conducted over three days in the summer of 2011. It was discovered that major modifications to the terrain have resulted from four principal activities. These are road construction and maintenance, mining activities related to development of the tunnel complex, site preparation for activities related to the tests and experiments, and construction of drill pads and retention ponds. Six large trenches for exploring across the Boundary geologic fault are also present. The U15 Complex, designated historic district 143 and site 26NY15177, is eligible to the National Register of Historic Places under Criteria A, C, and D of 36 CFR Part 60.4. As a historic district and archaeological site eligible to the National Register of Historic Places, the Desert Research Institute recommends that the area defined for the U15 Complex, historic district 143 and site 26NY15117, be left in place in its current condition. The U15 Complex should also be included in the NNSS cultural resources monitoring program and monitored for disturbances or alterations.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Neutral rhenium(i) tricarbonyl complexes with sulfur-donor ligands: anti-proliferative activity and cellular localization

Rhenium(I) tricarbonyl complexes are widely studied for their cell imaging properties and anticancer and anti-microbial activities, but the complexes with S-donor ligands remain relatively unexplored. A series of six fac-[Re(NN)(CO) 3 (SR)] complexes, where (NN) is 2,2'-bipyridyl (bipy) or 1,10-phenanthroline (phen), and RSH is a series of thiocarboxylic acid methyl esters, have been synthesized and characterized. Cellular uptake and anti-proliferative activities of these complexes in human breast cancer cell lines (MDA-MB-231 and MCF-7) were generally lower than those of the previously described fac-[Re(NN)(CO) 3 (OH 2 )] + complexes; however, one of the complexes, fac-[Re(CO) 3 (phen)(SC(Ph)CH 2 C(O)OMe))] (3b), was active (IC 50 ~ 10 μM at 72 h treatment) in thiol-depleted MDA-MB-231 cells. Moreover, unlike fac- [Re(CO) 3 (phen)(OH 2 )] + , this complex did not lose activity in the presence of extracellular glutathione. Taken together these properties show promise for further development of 3b and its analogues as potential anti-cancer drugs for co-treatment with thiol-depleting agents. Conversely, the stable and non-toxic complex, fac-[Re(bipy)(CO) 3 (SC(Me)C(O)OMe)] (1a), predominantly localized in the lysosomes of MDA-MB-231 cells, as shown by live cell confocal microscopy (λ ex = 405 nm, λ em = 470-570 nm). It is strongly localized in a subset of lysosomes (25 μM Re, 4 h treatment), as shown by co-localization with a Lysotracker dye. Longer treatment times with 1a (25 μM Re for 48 h) resulted in partial migration of the probe into the mitochondria, as shown by co-localization with a Mitotracker dye. These properties make complex 1a an attractive target for further development as an organelle probe for multimodal imaging, including phosphorescence, carbonyl tag for vibrational spectroscopy, and Re tag for X-ray fluorescence microscopy.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2018

Heteroleptic Nickel Complexes of a Bulky Bis(carbene)borate Ligand

Bis(carbene)borate ligand transfer to the nickel nitrosyl synthon Ni(NO)(PPh 3 ) 2 Br provides the new nickel nitrosyl complex Ph 2 B( t BuIm) 2 Ni(NO)(PPh 3 ). The solid state structure reveals a trigonal pyramidal nickel ion with a very long bond to the apical PPh 3 ligand. The complex reversibly dissociates PPh 3 in solution to afford three-coordinate Ph 2 B( t BuIm) 2 Ni(NO), with NMR data providing evidence for PPh 3 binding at low temperatures. Ligand transfer to Ni(PMe 3 ) 2 Cl 2 provides the square planar complex, Ph 2 B( t BuIm) 2 Ni(PMe 3 )Cl, which shows no evidence for rearranging to the form a homoleptic complex with two bis(carbene)borate ligands. This complex is a suitable synthon for the [Ph 2 B( t BuIm) 2 Ni] + fragment, as demonstrated by the synthesis of the π-allyl complex Ph 2 B( t BuIm) 2 Ni(η 3 -C 7 H 7 ). The π-allyl complex reacts with O 2 to provide benzaldehyde and an unstable complex that is tentatively identified as the nickel(II) hydroxide [Ph 2 B( t BuIm) 2 Ni(μ-OH)] 2 .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Tuning Zr 6 Metal–Organic Framework (MOF) Nodes as Catalyst Supports: Site Densities and Electron-Donor Properties Influence Molecular Iridium Complexes as Ethylene Conversion Catalysts

The Zr 6 nodes of the metal–organic frameworks (MOFs) UiO-66 and UiO-67 are metal oxide clusters of atomic precision and can be used as catalyst supports. The bonding sites on these nodes—that is, hydrogen-bonded H 2 O/OH groups on UiO-67 and non-hydrogen-bonded terminal OH groups on UiO-66—were regulated by modulation of the MOF syntheses. Ir(C 2 H 4 ) 2 (C 5 H 7 O 2 ) complexes reacted with these sites to give site-isolated Ir(C 2 H 4 ) 2 complexes, each anchored to the node by two Ir–Onode bonds. The supported iridium complexes on these sites have been characterized by infrared (IR) and extended X-ray absorption fine structure (EXAFS) spectroscopies and density functional theory calculations. The ethylene ligands on iridium are readily replaced by CO, and the ν CO frequencies of the resultant complexes and those of comparable complexes reported elsewhere show that the support electron-donor tendencies increase in the order HY zeolite << UiO-66 < UiO-67 (= NU-1000) < ZrO 2 < MgO. The sharpness of the IR ν CO bands shows that the degree of uniformity of the support bonding sites decreases in the order ZrO 2 ≈ UiO-67 ≈ NU-1000 < MgO < UiO-66 << HY zeolite. The reactivity of supported Ir(CO) 2 complexes with C2H4 to form Ir(C 2 H 4 )(CO) and Ir(C 2 H 4 ) 2 (CO) is influenced by the support electron-donor properties, with the reactivity increasing in the order MgO = ZrO 2 = NU-1000 (not reactive) < UiO-66 < UiO-67 << HY zeolite. Density functional theory calculations characterizing the complexes supported on NU-1000, UiO-66/67, and HY zeolite concur with the use of the calculated ν CO bands as indicators of electron-donor properties of the supported metal catalysts. Our calculations also show that the reactivity of the supported Ir(CO) 2 complexes with C 2 H 4 is correlated with the electron-donor properties of the iridium center. Lastly, the supported Ir(C 2 H 4 ) 2 samples are precatalysts for ethylene hydrogenation and ethylene dimerization, with the activity for each reaction increasing with increasing electron-withdrawing strength of the support.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Photochemical CO 2 Reduction Using Rhenium(I) Tricarbonyl Complexes with Bipyridyl-Type Ligands with and without Second Coordination Sphere Effects

In this study, the effect of phenyl, phenol, aniline, amino, and CF 3 substituents of the 2,2'-bipyridine ligand in fac-ReCl(L)(CO) 3 (L=2,2'-bipyridine derivative) catalysts on photochemical CO 2 reduction in dimethylacetamide is examined, in order to understand the structure-function relationships and to compare the catalytic activities with the previously published electrochemical results. All complexes including ReCl(bpy)(CO) 3 have similar excited-state lifetimes and emission spectra, but complex 1 with the Ph-NH 2 moiety exhibits a significantly larger molar absorption coefficient for its metal-to-ligand charge transfer (MLCT) band. All complexes we tested produce CO with only a negligible amount of H 2 and formate in self-sensitized systems in the presence of triethanolamine (TEOA) and in some cases, BIH (1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]-imidazole). The presence of the Ph-NH 2 moiety (complex 1) has a beneficial effect on both electrochemical and photochemical activity, allowing a turnover number (TON) of 32 and 120 for photochemical CO production (without and with BIH, respectively). In the case of the Ph-OH group in the second coordination sphere (complexes 4 and 6), these complexes are active for photochemical CO 2 reduction, despite the formation of a stable 6-coordinate Re-OPh intermediate via reductive deprotonation as previously observed under electrochemical conditions. Overall, BIH accelerates the rate of formation of the one-electron reduced species (OERS) of the Re catalysts and allows higher turnover frequency (TOF) and TON for CO formation. The X-ray structures of complexes 1 and 4 were determined to have distorted octahedral Re centres, and show π-π stacking interactions with neighboring molecules as well as intramolecular hydrogen bonds to the internal chloride ligands. The unusually high absorptivity of the MLCT absorption of complex 1 has been explained by TD-DFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Quantum chemical study of the structures and dynamic behavior of tricarbonyl complexes of Group 6 metals (Cr, Mo, W) with polyaromatic hydrocarbons using the density functional theory

The quantum chemical study of the mechanism was performed for tricarbonyl η{sup 6}-complexes of coronene I-M and kekulene II-M (M = Cr, Mo, W) by the density functional method. The activation barriers of η{sup 6},η{sup 6}-interring haptotropic rearrangements (IHR), being the migration of the metaltricarbonyl group M(CO){sub 3} from one six-membered aromatic ring to another, were determined. The processes of η{sup 6},η{sup 6}-IHR in the metal tricarbonyl complexes with relatively high polycyclic aromatic hydrocarbons (PAH) I and II occur with close energy barriers (ΔG{sup ≠} ≈ 20—25 kcal mol{sup –1}), which are lower than the barriers (ΔG{sup ≠} ~ 30 kcal mol{sup –1}) of similar transformations measured or calculated earlier for the chromium tricarbonyl complexes of naphthalene and its derivatives and other PAH. For the molybdenum tricarbonyl complexes the activation barriers of η{sup 6},η{sup 6}-IHR decrease additionally by ~ 5 kcal mol{sup –1} compared to those for the chromium tricarbonyl complexes, whereas for the tungsten tricarbonyl complexes they increase again and become approximately equal to the activation barriers of similar chromium tricarbonyl complexes. All stationary states on the potential energy surface determining the mechanism of η{sup 6},η{sup 6}-IHR are characterized by a decrease in hapticity compared to the initial and final complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2014

Electron microscopy and in vitro deneddylation reveal similar architectures and biochemistry of isolated human and Flag-mouse COP9 signalosome complexes

Highlights: • Deneddylation rates of human erythrocyte and mouse fibroblast CSN are very similar. • 3D models of native human and mouse CSN reveal common architectures. • The cryo-structure of native mammalian CSN shows a horseshoe subunit arrangement. - Abstract: The COP9 signalosome (CSN) is a regulator of the ubiquitin (Ub) proteasome system (UPS). In the UPS, proteins are Ub-labeled for degradation by Ub ligases conferring substrate specificity. The CSN controls a large family of Ub ligases called cullin-RING ligases (CRLs), which ubiquitinate cell cycle regulators, transcription factors and DNA damage response proteins. The CSN possesses structural similarities with the 26S proteasome Lid complex and the translation initiation complex 3 (eIF3) indicating similar ancestry and function. Initial structures were obtained 14 years ago by 2D electron microscopy (EM). Recently, first 3D molecular models of the CSN were created on the basis of negative-stain EM and single-particle analysis, mostly with recombinant complexes. Here, we compare deneddylating activity and structural features of CSN complexes purified in an elaborate procedure from human erythrocytes and efficiently pulled down from mouse Flag-CSN2 B8 fibroblasts. In an in vitro deneddylation assay both the human and the mouse CSN complexes deneddylated Nedd8-Cul1 with comparable rates. 3D structural models of the erythrocyte CSN as well as of the mouse Flag-CSN were generated by negative stain EM and by cryo-EM. Both complexes show a central U-shaped segment from which several arms emanate. This structure, called the horseshoe, is formed by the PCI domain subunits. CSN5 and CSN6 point away from the horseshoe. Compared to 3D models of negatively stained CSN complexes, densities assigned to CSN2 and CSN4 are better defined in the cryo-map. Because biochemical and structural results obtained with CSN complexes isolated from human erythrocytes and purified by Flag-CSN pulldown from mouse B8 fibroblasts are very similar, Flag-CSN pulldowns are a proper alternative to CSN preparation from erythrocytes.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2012

Synthesis, structure and luminescence property of 2D lanthanide complexes with 3-fluorophthalate and oxalate

Complexes [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (Ln=Sm 1, Eu 2, Tb 3 and Dy 4; fpht=3-fluorophthalate and ox=oxalate) have been synthesized and structurally characterized by single crystal X-ray diffraction. The four complexes possess similar 2D framework structures constructed from Ln-fpht double-stranded helices and ox linkages. Complexes 2 and 3 display the characteristic emission {sup 5}D{sub 0}{yields}{sup 7}F{sub J} (J=0-4) transitions of Eu(III) ion and {sup 5}D{sub 4}{yields}{sup 7}F{sub J} (J=6-3) transitions of Tb(III) ion, respectively. The emission decay curves reveal a monoexponential behavior yielding the lifetime values of 0.266{+-}0.002 ms for 2 and 0.733{+-}0.002 ms for 3. The emission spectrum of 1 shows three weak bands corresponding to the characteristic emission {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 5/2}, {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 7/2} and {sup 4}G{sub 5/2}{yields}{sup 6}H{sub 9/2} transitions of Sm(III) ion. The emission spectrum of 4 displays a broad band centered at 438 nm, which comes from the {pi}{sup Low-Asterisk }-{pi} transition of the ligand. - Graphical abstract: Complexes [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (fpht=3-fluorophthalate, ox=oxalate) possess 2D structures. Sm(III), Eu(III) and Tb(III) complexes show the characteristic fluorescent emission of the Ln(III). Dy(III) complex displays ligand-based luminescent behavior. Highlights: Black-Right-Pointing-Pointer [Ln{sub 2}(fpht){sub 2}(ox)(H{sub 2}O){sub 4}]{center_dot}H{sub 2}O (fpht=3-fluorophthalate; ox=oxalate) show 2D structures. Black-Right-Pointing-Pointer The 2D structures are constructed from Ln-fpht double-stranded helices and ox linkage. Black-Right-Pointing-Pointer The Sm(III), Eu(III) and Tb(III) complexes show the characteristic emission of the Ln(III) ions. Black-Right-Pointing-Pointer Dy(III) complex displays ligand-based luminescent behavior.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Three complexes of Cu(I) cluster with flexible and rigid ligands: Synthesis, characterization and photoluminescent properties

Three new Cu(I) cluster complexes, viz. [(Cu{sub 4}I{sub 4})(Cu{sub 2}I{sub 2})(dimb){sub 3}]{sub n} (1; dimb=1,4-diimidazol-1-ylbutane), [(Cu{sub 3}I{sub 2})(dimb)(dmtz)]{sub n} (2; dmtz=3,5-dimethyl-1,2,4-triazole), and [Cu{sub 6}(mbt){sub 6}] (3; mbt=2-mercaptobenzothiazole), have been solvothermally synthesized and structurally characterized. In 1, a Cu{sub 4}I{sub 4} cubane core as a 4-connecting node, connects the neighboring nodes either through single dimb or μ{sub 2}-[(Cu{sub 2}I{sub 2})(dimb){sub 2}] linkers, affording an undulated 2D (4,4) net. Parallel interpenetration occurs between the adjacent nets and thus the overall 2D→3D network is formed. Complex 2 is constructed by 2D (4,4) topological plane grid layers of AB stacking. The core, a distorted triangular bipyramidal Cu{sub 3}I{sub 2} cluster, is acted as a 4-connecting node and connected with dimb and μ{sub 3}-dmtz to form the layer. Complex 3 contains a (Cu{sub 6}S{sub 6}) core in discrete paddle-wheel molecule, which serves as a 4-connecting node to link equivalent ones via π···π interaction, forming 2D (4,4) layers. Solid-state luminescence properties and thermogravimetric analyses of 1, 2 and 3 were investigated. - Graphical abstract: Complexes based on Cu(I) clusters possess two-fold 2D→3D parallel interpenetrating (1), triple emissions (2) and near-infrared emission (3). - Highlights: • Complex 1 represents two-fold 2D→3D parallel interpenetrating framework. • Complex 2 shows triple emissions. • Complex 3 displays a quite intense near-infrared (NIR) emission. • These complexes have good thermal stability.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2017

Adenovirus E1A TRRAP-targeting domain-mediated enhancement of MYC association with the NuA4 complex activates a panel of MYC target genes enriched for gene expression and ribosome biogenesis

Cellular transformation by adenovirus E1A requires targeting TRRAP, a scaffold protein which helps assemble histone acetyltransferase complexes, including the NuA4 complex. We recently reported that E1A and E1A 1–80 (N-terminal 80 aa) promote association of the proto-oncogene product MYC with the NuA4 complex. The E1A N-terminal TRRAP-targeting (ET) domain is required for E1A 1–80 to interact with the NuA4 complex. We demonstrate that an ET-MYC fusion associates with the NuA4 complex more efficiently than does MYC alone. Because MYC regulates genes for multiple cellular pathways, we performed global RNA-sequence analysis of cells expressing MYC or ET-MYC, and identified a panel of genes (262) preferentially activated by ET-MYC and significantly enriched in genes involved in gene expression and ribosome biogenesis, suggesting that E1A enhances MYC association with the NuA4 complex to activate a set of MYC target genes likely involved in cellular proliferation and cellular transformation by E1A and by MYC. - Highlights: • E1A N-terminal-MYC chimeric protein associates with the NuA4 complex efficiently. • A panel of MYC-target genes is preferentially activated by E1A N-terminal-MYC fusion. • This panel of genes may be activated by MYC association with NuA4 complex. • This panel of genes may be involved in E1A and MYC-mediated transformation.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Molecular Dynamics Simulations of Complexation of Am(III) with a Preorganized Dicationic Ligand in an Ionic Liquid

Preorganized ligands with imidazolium arms have been found to be highly selective in extracting Am(III) into ionic liquids (ILs), but the detailed structure and mechanism of the complexation process in the ionic solvation environment are unclear. Here, we carry out molecular dynamics simulation of the complexation of Am(III) with a preorganized 1,10-phenanthroline-2,9-dicarboxamide complexant (L) functionalized with alkyl chains and imidazolium cations in the butylmethylimidazolium bistriflimide ([BMIM][NTf 2 ]) IL. Both Am:L (1:1) and Am:L 2 (1:2) complexes are examined. In the absence of the ligand, Am(III) is found to be coordinated by six NTf 2 anions via nine O donors in the first solvation shell. In the Am:L complex, Am(III) is coordinated to the ligand via two O donors and four NTf 2 anions via seven O donors in the first coordination shell. In the Am:L 2 complex, Am(III) is coordinated to the two ligands via four O donors and four NTf 2 anions via five O donors. The imidazolium arms of the ligands play an important role in the secondary solvation environment by attracting NTf 2 anions closer to the metal center. As a result, we find that the binding free energy for the second L 2+ ligand is twice that for the first L 2+ ligand, making the Am:L 2 complex significantly more stable than the Am:L complex. This study highlights the multiple factors and tunability in using preorganized ligands with charged functional groups in an ionic solvation environment, which could hold the key to achieving desired selectivity in ion extraction efficiency.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Cationic α-Diimine Nickel and Palladium Complexes Incorporating Phenanthrene Substituents: Highly Active Ethylene Polymerization Catalysts and Mechanistic Studies of syn/anti Isomerization

α-Diimine palladium complexes incorporating phenanthryl- and 6,7-dimethylphenanthrylimino groups have been synthesized and characterized. The (diimine)PdMeCl complexes prepared from 2,3-butanedione and acenaphthenequinone bearing the unsubstituted phenanthrylimino groups, 12a and 14a, respectively, exist as a mixture syn and anti isomers in a ca. 1:1 ratio. Separation and X-ray diffraction analysis of 14a-syn and 14a-anti isomers confirms the syn/anti assignments. The barrier to interconversion of 14a-syn and 14a-anti via ligand rotation, ΔG ‡ , was found to be 25.5 kcal/mol. The corresponding (diimine)PdMeCl complex prepared from acenaphthenequinone and incorporating the 6,7-dimethylphenanthrylimino group exists solely as the anti isomer, 14b, due to steric crowding which destabilizes the syn isomer. Analogous (diimine)NiBr2 complexes were prepared from 2,3-butanedione incorporating the phenanthrylimino group, 16a, and the 6,7-dimethylphenanthrylimino group, 16b. Nickel-catalyzed polymerizations of ethylene were carried out by activation of the dibromide complexes 16a and 16b using various aluminum alkyl activators. Complex 16a yields a bimodal distribution polymer, the low molecular weight fraction originating from the syn isomer and the high molecular weight fraction arising from the anti isomer. Polymerizations carried out by 16b yield only high molecular weight polymers with monomodal distributions due to the existence of a single isomer (anti) as the active catalyst. All polymers are linear or nearly so. All catalysts are highly active but catalysts derived from 16b are somewhat more active than 16a and exhibit turnover frequencies general over 10 6 and up to 5 × 10 6 per hour (40 °C, 27.2 atm ethylene, 15 min). Here, active palladium ethylene oligomerization catalysts were generated by conversion of the neutral methyl chloride complexes 14a and 14b to the cationic nitrile complexes 15a and 15b via halide abstraction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Complexation behavior of oppositely charged polyelectrolytes: Effect of charge distribution

Complexation behavior of oppositely charged polyelectrolytes in a solution is investigated using a combination of computer simulations and experiments, focusing on the influence of polyelectrolyte charge distributions along the chains on the structure of the polyelectrolyte complexes. The simulations are performed using Monte Carlo with the replica-exchange algorithm for three model systems where each system is composed of a mixture of two types of oppositely charged model polyelectrolyte chains (EGEG){sub 5}/(KGKG){sub 5}, (EEGG){sub 5}/(KKGG){sub 5}, and (EEGG){sub 5}/(KGKG){sub 5}, in a solution including explicit solvent molecules. Among the three model systems, only the charge distributions along the chains are not identical. Thermodynamic quantities are calculated as a function of temperature (or ionic strength), and the microscopic structures of complexes are examined. It is found that the three systems have different transition temperatures, and form complexes with different sizes, structures, and densities at a given temperature. Complex microscopic structures with an alternating arrangement of one monolayer of E/K monomers and one monolayer of G monomers, with one bilayer of E and K monomers and one bilayer of G monomers, and with a mixture of monolayer and bilayer of E/K monomers in a box shape and a trilayer of G monomers inside the box are obtained for the three mixture systems, respectively. The experiments are carried out for three systems where each is composed of a mixture of two types of oppositely charged peptide chains. Each peptide chain is composed of Lysine (K) and glycine (G) or glutamate (E) and G, in solution, and the chain length and amino acid sequences, and hence the charge distribution, are precisely controlled, and all of them are identical with those for the corresponding model chain. The complexation behavior and complex structures are characterized through laser light scattering and atomic force microscopy measurements. The order of the apparent weight-averaged molar mass and the order of density of complexes observed from the three experimental systems are qualitatively in agreement with those predicted from the simulations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗