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At least 343 records · Page 19

Photodissociation and Infrared Spectroscopy of Uranium–Nitrogen Cation Complexes

Laser vaporization of uranium in a pulsed supersonic expansion of nitrogen is used to produce complexes of the form U + (N 2 ) n (n = 1–8). These ions are mass selected in a reflectron time-of-flight spectrometer and studied with visible and UV laser fixed-frequency photodissociation and with tunable infrared laser photodissociation spectroscopy. The dissociation patterns and spectroscopy of U + (N 2 ) n indicate that N 2 ligands are intact molecules and that there is no insertion chemistry resulting in UN + or NUN + . Fixed frequency photodissociation at 532 and 355 nm indicate that the U + –N 2 bond dissociation energy varies little with changing coordination. The photon energy and the number of ligands eliminated allow an estimate of the average U + –N 2 dissociation energy of 12 kcal/mol. Infrared bands are observed for these complexes near the N–N stretch vibration via elimination of N 2 molecules. These resonances are observed to be shifted about 130 cm–1 to the red from the free-N 2 frequency for complexes with n = 3–8. Density functional theory indicates that U + is most stable in the sextet state in these complexes and that N 2 molecules bind in end-on configurations. Furthermore, the fully coordinated complex is predicted to be U + (N 2 ) 8 , which has a cubic structure. The vibrational frequencies predicted by theory are consistently lower than those in the experiment, independent of the isomeric structure or spin state of the complexes. Despite its failure to reproduce the infrared spectra, theory provides an average U + –N 2 dissociation energy of 11.8 ± 0.5 kcal/mol, in good agreement with the value from the experiments.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Monofluorination of Naphthyls Promotes the Cofacial π–π Stacking and Increases the Electron Mobility of Non-Planar Zinc(II) Complexes of Di(naphthylethynyl)azadipyrromethene

The homoleptic zinc(II) complex of [2,8-di(1-naphthylethynyl) 3,7-diphenyl 1,9-(4-hexylphenyl)azadipyrromethene (ZnL2) 2 ] is a promising non-planar non-fullerene acceptor for organic photovoltaic applications, but it has a relatively low electron mobility that may limit its performance. Here, we explored the fluorination of peripheral aryl groups to increase intermolecular cofacial π–π stacking interactions, which are desirable for electron transport. Here complexes with fluorine on the distal phenyls [Zn(1F-L2) 2 ], on the naphthyls [Zn(2F-L2) 2 ], and on both [Zn(3F-L2) 2 ] were synthesized and characterized. All three complexes had similar optical and electrochemical properties. The crystal packing structure of Zn(2F-L2) 2 and Zn(3F-L2) 2 revealed cofacial parallel-displaced π–π stacking between the fluorinated 1-naphthylethynyl groups. Such a cofacial orientation was not observed in Zn(L2) 2 crystals, suggesting that fluorination of the naphthyl groups promotes the cofacial π–π stacking orientation. The hole mobility increased from 1.0 × 10 –4 cm 2 V –1 s –1 for Zn(L2) 2 to 0.8–1.0 × 10 –3 cm 2 V –1 s –1 for the fluorinated complexes. Fluorination on the naphthyl groups increased the electron mobility from 4.2 × 10 –5 cm 2 V –1 s –1 for Zn(L2) 2 and Zn(1F-L2) 2 to 2.0 × 10 –4 cm 2 V –1 s –1 for Zn(2F-L2) 2 and Zn(3F-L2) 2 , consistent with cofacial π–π stacking being favorable for electron transport. The three complexes were tested in OPVs using regioregular poly(3-hexylthiophene) (P3HT) as the p-type material, and the best power conversion efficiencies were 5.2, 5.4, and 5.8% for Zn(2F-L2) 2 , Zn(1F-L2) 2 , and Zn(3F-L2) 2 , respectively, compared to 5.5% for Zn(L2) 2 . The fluorination combination found in Zn(3F-L2) 2 resulted in the best device performance. This study points to a viable strategy to increase the electron mobility and performance of non-planar zinc(II) complexes of azadipyrromethene.

36 MATERIALS SCIENCE↗

Strategic Lifetime Tuning of Visible-Light Absorbing Two-Coordinate Metal Complexes

This paper highlights how the singlet and triplet amide ligand centered ( 1,3 LC) and interligand charge transfer ( 1,3 ICT) states in (carbene)M(amide), M = Cu, Au (cMa) complexes influence the excited state properties when the triplet states are close in energy. To that end we prepared a set of five cMa complexes, in which the amide (i.e., 5H-benzo[b]carbazole, H-BnCz) was kept constant giving a 3 LC energy of ca. 2.15 eV. Four different carbene ligands were selected to develop M BnCz Carbene complexes which have energies for the ICT state that vary from being either markedly higher, lower, or close to the energy of the 3 LC state on the amide ligand. Steady-state and time-resolved spectroscopic studies show that the emission spectrum of the cMa complex mirrors the phosphorescence of the parent H-BnCz amide and has a luminescence decay lifetime in the millisecond regime when the lowest energy excited state is 3 LC. When the lowest energy states are 1,3 ICT in nature, the emission band is broad and featureless, giving a lifetime in the nanosecond regime. As the 3 LC and 1,3 ICT states have comparable energies, dynamic equilibrium between the states is observed with the luminescence consisting of a mixture of 3 LC and 1,3 ICT transitions. The measured lifetime of this equilibrating system is between 45 and 350 μs depending on the solvent, for both copper- and gold-based cMa complexes. Furthermore, these complexes demonstrate the ability to “park” the excited state population in the 3 LC state, allowing it to act as a reservoir for thermally activated emission, while still maintaining a very rapid equilibrium between LC and ICT states.

14 SOLAR ENERGY↗

Controlling P–C/C–H Bond Cleavage in Nickel Bis(diphosphine) Complexes: Reactivity Scope, Mechanism, and Computations

The synthesis of heteroleptic [Ni(P 2 N 2 )(diphosphine)][BF 4 ] 2 complexes and the cleavage of P–C and C–H bonds of the P 2 N 2 ligand in those complexes are reported here. The products are five-coordinate complexes in which Ni–C and P–H bonds have formed to give a cyclic moiety containing Ni–CH$=$NR 2 . The reactivity of [Ni(P 2 N 2 )(diphosphine)][BF 4 ] 2 complexes is influenced by the rigidity of the diphosphine, the steric effect of the substituents, and length of the carbon linker of the diphosphine ligands. Diphosphine ligands bearing a rigid backbone (e.g., dmpbz, 1,2-bis(dimethylphosphino)benzene) or aromatic substituents (e.g., dppe, 1,2-bis(diphenylphosphino)ethane) react with [Ni(P t Bu 2 N Bn 2 )(CH 3 CN) 2 ][BF 4 ] 2 to give P–C/C–H bond cleavage products. Both [Ni(P t Bu 2 N Bn 2 )(dmpe)(MeCN)][BF 4 ] 2 and [Ni(P t Bu 2 N Bn 2 )(dmpm)(MeCN)][BF 4 ] 2 (dmpm = 1,2-bis(dimethylylphosphino)methane) were prepared by the reaction of [Ni(P t Bu 2 N Bn 2 )(CH 3 CN) 2 ][BF 4 ] 2 with the corresponding diphosphine ligands. [Ni(P t Bu 2 N Bn 2 )(dmpe)(MeCN)][BF 4 ] 2 readily undergoes P–C/C–H bond cleavage in nitromethane. In sharp contrast, [Ni(P t Bu 2 N Bn 2 )(dmpm)][BF 4 ] 2 is stabilized by dmpm, a diphosphine with small bite angle, and does not show P–C/C–H bond cleavage reactivity. Computational results show that for complexes bearing less bulky diphosphine ligands, such as dmpm, the barriers for the rate-determining transition states are in some examples higher than 30 kcal/mol with the M06 functional, higher than those for complexes bearing more rigid or more bulky ligands, consistent with experimental studies. The calculated barriers for the first transition state correlated with increased values of the dihedral angle formed by the two NiP 2 planes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic Studies of Ligand Substitution, Linkage Isomerism, and Insertion Reactions in Electron Rich Pd(II) Complexes of a Zwitterionic Diimine Ligand

We have prepared cationic palladium complexes possessing a new zwitterionic ligand bis-N,N’–1-(2,4,6-triphenylpyridyl) oxalamide [(N ^ N)Pd(Me)(L)] + [BArF] - , (BArF=3,5-(CF 3 ) 2 C 6 H 3 , L=NCMe, CO). The structure of [(N ^ N)Pd(Me)(CO)] + [BArF] - was determined by X-ray diffraction analysis. Energy Decomposition Analysis (EDA) indi-cates this N ^ N zwitterionic ligand is more electron-donating relative to bidentate diimine ligands. Low temperature NMR analysis shows the existence of linkage isomers with the N ^ N isomer the most stable. Structures were assigned using NMR and DFT analysis. Barriers to interconversion of isomers are ΔG ‡ = 10-12 kcal/mol. Kinetics of acetoni-trile displacement from [(N ^ N)Pd(Me)(NCCH 3 )] + [BArF] - by CD 3 CN, ethylene and t Bu 3 P were measured and mechanisms of exchange determined. The ethylene complex, [(N ^ N)Pd(Me)(C 2 H 4 )] + was generated at -45 °C, and the barrier of migrato-ry insertion determined at 0 °C (ΔG ‡ = 23.4 kcal/mol) and compared to related diimine complexes. The methyl carbonyl complex undergoes migratory insertion in the presence of CO at -70 to -55 °C (ΔG ‡ = ca. 15.7 kcal/mol) to yield the acyl carbonyl complex. Furthermore, the neutral bis-trimethylsilylmethyl complex [(N ^ N)Pd(CH 2 SiMe 3 ) 2 was prepared and characterized by X-ray diffraction analysis. It displays dynamic behavior at very low temperatures in the NMR spectrum (-90 °C, ΔG ‡ =7.9 kcal/mol) which, supported by DFT analysis, is ascribed to rotation of the bulky -CH 2 SiMe 3 groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Alkali Metal Ions Dictate the Structure and Reactivity of an Iron(II) Imido Complex

The presence of redox innocent metal ions has been proposed to modulate the reactivity of metal ligand multiple bonds; however, insight from structure/function relationships is limited. Here, alkali metal reduction of the Fe(III) imido complex [Ph 2 B( t BuIm) 2 Fe=NDipp] (1) provides the series of structurally characterized Fe(II) imido complexes [Ph 2 B( t BuIm) 2 Fe=NDippLi(THF) 2 ] (2), [Ph 2 B( t BuIm) 2 Fe=NDippNa(THF) 3 ] (3), and [Ph 2 B( t BuIm) 2 Fe=NDippK] 2 (4), in which the alkali metal cations coordinate the imido ligand. Structural investigations demonstrate that the alkali metal ions modestly lengthen the Fe=N bond distance from that in the charge separated complex [Ph 2 B( t BuIm) 2 Fe=NDipp][K(18-C-6)THF 2 ] (5), with the longest bond observed for the smallest alkali metal ion. In contrast to 5, the imido ligands in 2–4 can be protonated and alkylated to afford Fe(II) amido complexes. Combined experimental and computational studies reveal that the alkali metal polarizes the Fe=N bond, and the basicity of imido ligand increases according to 5 < 4 ≈ 3 < 2. The basicity of the imido ligands influences the relative rates of reaction with 1,4-cyclohexadiene, specifically by gating access to complex 5, which is the species that is active for HAT. All complexes 2–4 react with benzophenone form metastable Fe(II) intermediates that subsequently eliminate the metathesis product Ph 2 C=NDipp, with relative rates dependent on the alkali metal ion. By contrast, the same reaction with 5 does not lead to the formation of Ph 2 C=NDipp. Furthermore, these results demonstrate that the coordination of alkali metal ions dictate both the structure and reactivity of the imido ligand and moreover can direct the reactivity of reaction intermediates.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

What Is the Right Level of Activation of a High-Spin {FeNO} 7 Complex to Enable Direct N–N Coupling? Mechanistic Insight into Flavodiiron NO Reductases

Flavodiiron nitric oxide reductases (FNORs), found in pathogenic bacteria, are capable of reducing nitric oxide (NO) to nitrous oxide (N 2 O) to detoxify NO released by the human immune system. Previously, we reported the first FNOR model system that mediates direct NO reduction (Dong, H. T.; et al. J. Am. Chem. Soc. 2018, 140, 13429-13440), but no intermediate of the reaction could be characterized. Here, we present a new set of model complexes that, depending on the ligand substitution, can either mediate direct NO reduction or stabilize a highly activated high-spin (hs) {FeNO} 7 complex, the first intermediate of the reaction. The precursors, [{Fe II (MPA-(RPhO) 2 )} 2 ] (1, R = H and 2, R = t Bu, Me), were prepared first and fully characterized. Complex 1 (without steric protection) directly reduces NO to N 2 O almost quantitatively, which constitutes only the second example of this reaction in model systems. Contrarily, the reaction of sterically protected 2 with NO forms the stable mononitrosyl complex 3, which shows one of the lowest N-O stretching frequencies (1689 cm -1 ) observed so far for a mononuclear hs-{FeNO} 7 complex. Here this study confirms that an N-O stretch & LE;1700 cm -1 represents the appropriate level of activation of the FeNO unit to enable direct NO reduction. The higher activation level of these hs-{FeNO} 7 complexes required for NO reduction compared to those formed in FNORs emphasizes the importance of hydrogen bonding residues in the active sites of FNORs to activate the bound NO ligands for direct N-N coupling and N2O formation. The implications of these results for FNORs are further discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Two-Coordinate Coinage Metal Complexes as Solar Photosensitizers

Generating a sustainable fuel from sunlight plays an important role in meeting the energy demands of the modern age. Herein we report two-coordinate carbene-metal-amide (cMa, M = Cu(I) and Au(I)) complexes can be used as sensitizers to promote the light driven reduction of water to hydrogen. The cMa complexes studied here absorb visible photons (ε vis > 10 3 M -1 cm -1 ), maintain long excited state lifetimes (τ ~ 0.2-1 μs) and perform stable photo-induced charge transfer to a target substrate with high photoreducing potential (E +/* up to 2.33 V vs. Fc +/o based on a Rehm-Weller analysis). We pair these coinage metal complexes with a cobalt-glyoxime electrocatalyst to photocatalytically generate hydrogen and compare the performance of the copper- and gold-based cMa complexes. We also find that these two-coordinate complexes presented can perform photo-driven hydrogen production from water without the addition of the cobalt-glyoxime electrocatalyst. In this “catalyst free” system the cMa sensitizer partially decomposes to give metal nanoparticles that catalyze water reduction. Furthermore, this work identifies two-coordinate coinage metal complexes as promising abundant metal, solar fuels photosensitizers that offer exceptional tunability and photoredox properties.

14 SOLAR ENERGY↗

Pursuing Heteroleptic Ligand Design Principles for Photoactive Fe Complexes with Ultrafast X-ray Emission and Variable-Temperature Optical Spectroscopies

Understanding the key parameters that govern the photophysical and photochemical properties of transition metal complexes is essential for the development of efficient photosensitizers for photocatalytic applications. Achieving this objective necessitates clear and detailed investigations of their electronic excited states, for which time-resolved metal Kβ X-ray emission spectroscopy (XES) has proven highly effective. Here, we present a time-resolved Fe Kβ XES study of a heteroleptic Fe(II) polypyridyl carbene complex, [Fe(phen) 2 (C 4 H 10 N 4 )] 2+ (1; phen = 1,10-phenanthroline), utilizing both the valence-to-core and Kβ mainline spectral regions, complemented by variable-temperature transient optical absorption (VT-TA) spectroscopy. Detailed analysis of the time-resolved Kβ XES data, supported by density functional theory (DFT) calculations and an Eyring analysis of the VT-TA data, reveals parallel excited state relaxation dynamics that support an assignment of the long-lived excited state to a triplet metal-centered state. Placing these results in the context of prior studies of heteroleptic Fe(II) polypyridyl cyanide complexes motivated a series of DFT calculations to investigate the effects of ligand structural flexibility and arrangement. These calculations reinforce the experimentally derived conclusion that constraining structural flexibility with multidentate ligands significantly impacts the excited state relaxation dynamics. Furthermore, our study emphasizes that the arrangement of strong field ligands in heteroleptic complexes substantially affects the energy of Jahn–Teller active triplet metal-centered states in low-spin d 6 metal complexes. Together, these findings provide synthetic design principles for extending metal-to-ligand charge transfer excited state lifetimes of heteroleptic Fe complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Strengthening of Calcite Assemblages Through Chemical Complexation Reactions

Abstract Utilization of subsurface reservoirs, including fluid extraction/injection, can induce stress changes and modify in‐situ chemical equilibrium causing subcritical fracturing and deformation. Here, we show that chemical complexation reactions at the newly created fracture surfaces within the crack tip limit fracturing during consolidation of granular calcite assemblages. Previously, we showed that analogous chemical complexation reactions can increase in‐situ fracture toughness in pre‐fractured single crystal calcite. To test the chemical complexation effect under subsurface conditions, we consolidated samples under increasing hydrostatic pressure to induce widespread intergranular fracturing in the presence of fluid containing common anions. Measured consolidation, acoustic emissions, and microfracturing demonstrate that deformation correlates with complexation affinity for calcium in calcite and aqueous anions. We observed that deformation is lowest in the presence of strongly complexing anions (e.g., sulphate), provided sufficient anion diffusion rates. This understanding is important for predicting reservoir effective strength in the presence of complex aqueous fluids.

Choens, R. C.↗

Selecting Appropriate Model Complexity: An Example of Tracer Inversion for Thermal Prediction in Enhanced Geothermal Systems

Abstract A major challenge in the inversion of subsurface parameters is the ill‐posedness issue caused by the inherent subsurface complexities and the generally spatially sparse data. Appropriate simplifications of inversion models are thus necessary to make the inversion process tractable and meanwhile preserve the predictive ability of the inversion results. In this study, we investigate the effect of model complexity on fracture aperture inversion and thermal performance prediction in a field‐scale EGS model. Principal component analysis was used to map the aperture field to a low‐dimensional latent space. The complexity of the inversion model was quantitatively represented by the percentage of total variance in the original aperture fields preserved by the latent space. Tracer, pressure and flow rate data were used to invert for fracture aperture through an ensemble‐based inversion method, and the inferred aperture field was used to predict thermal performance. With an over‐simplified aperture model, ensemble collapse occurred. The inverted aperture models failed to resolve necessary flow and transport features, leading to a biased thermal performance prediction. A complex aperture model involved excessive features and was prone to overinterpreting the inversion data. Both the tracer/pressure/flow rate data reproduction and thermal prediction showed significant uncertainties, making it difficult to properly estimate long‐term thermal performance. Fortunately, our results indicate that there exists an appropriate model complexity which can simultaneously match inversion data and predict thermal performance with an acceptable uncertainty. The quality of the fit of tracer data appears to be a useful indicator of such an appropriate model complexity.

15 GEOTHERMAL ENERGY↗

Atomically precise control of rotational dynamics in charged rare-earth complexes on a metal surface

Abstract Complexes containing rare-earth ions attract great attention for their technological applications ranging from spintronic devices to quantum information science. While charged rare-earth coordination complexes are ubiquitous in solution, they are challenging to form on materials surfaces that would allow investigations for potential solid-state applications. Here we report formation and atomically precise manipulation of rare-earth complexes on a gold surface. Although they are composed of multiple units held together by electrostatic interactions, the entire complex rotates as a single unit when electrical energy is supplied from a scanning tunneling microscope tip. Despite the hexagonal symmetry of the gold surface, a counterion at the side of the complex guides precise three-fold rotations and 100% control of their rotational directions is achieved using a negative electric field from the scanning probe tip. This work demonstrates that counterions can be used to control dynamics of rare-earth complexes on materials surfaces for quantum and nanomechanical applications.

36 MATERIALS SCIENCE↗

Cryo-EM structure of the Saccharomyces cerevisiae Rpd3L histone deacetylase complex

The Rpd3L histone deacetylase (HDAC) complex is an ancient 12-subunit complex conserved in a broad range of eukaryotes that performs localized deacetylation at or near sites of recruitment by DNA-bound factors. Here we describe the cryo-EM structure of this prototypical HDAC complex that is characterized by as many as seven subunits performing scaffolding roles for the tight integration of the only catalytic subunit, Rpd3. The principal scaffolding protein, Sin3, along with Rpd3 and the histone chaperone, Ume1, are present in two copies, with each copy organized into separate lobes of an asymmetric dimeric molecular assembly. The active site of one Rpd3 is completely occluded by a leucine side chain of Rxt2, while the tips of the two lobes and the more peripherally associated subunits exhibit varying levels of flexibility and positional disorder. The structure reveals unexpected structural homology/analogy between unrelated subunits in the fungal and mammalian complexes and provides a foundation for deeper interrogations of structure, biology, and mechanism of these complexes, as well as for the discovery of HDAC complex-specific inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗

The synthesis and characterization of an iron(VII) nitrido complex

Abstract Complexes of iron in high oxidation states are captivating research subjects due to their pivotal role as active intermediates in numerous catalytic processes. Structural and spectroscopic studies of well-defined model complexes often provide evidence of these intermediates. In addition to the fundamental molecular and electronic structure insights gained by these complexes, their reactivity also affects our understanding of catalytic reaction mechanisms for small molecule and bond-activation chemistry. Here, we report the synthesis, structural and spectroscopic characterization of a stable, octahedral Fe(VI) nitrido complex and an authenticated, unique Fe(VII) species, prepared by one-electron oxidation. The super-oxidized Fe(VII) nitride rearranges to an Fe(V) imide through an intramolecular amination mechanism and ligand exchange, which is characterized spectroscopically and computationally. This enables combined reactivity and stability studies on a single molecular system of a rare high-valent complex redox pair. Quantum chemical calculations complement the spectroscopic parameters and provide evidence for a diamagnetic ( S = 0) d 2 Fe(VI) and a genuine S = 1/2, d 1 Fe(VII) configuration of these super-oxidized nitrido complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Metabolic complexity drives divergence in microbial communities

Microbial communities are shaped by environmental metabolites, but the principles that govern whether different communities will converge or diverge in any given condition remain unknown, posing fundamental questions about the feasibility of microbiome engineering. Here, in this work, we studied the longitudinal assembly dynamics of a set of natural microbial communities grown in laboratory conditions of increasing metabolic complexity. We found that different microbial communities tend to become similar to each other when grown in metabolically simple conditions, but they diverge in composition as the metabolic complexity of the environment increases, a phenomenon we refer to as the divergence-complexity effect. A comparative analysis of these communities revealed that this divergence is driven by community diversity and by the assortment of specialist taxa capable of degrading complex metabolites. An ecological model of community dynamics indicates that the hierarchical structure of metabolism itself, where complex molecules are enzymatically degraded into progressively simpler ones that then participate in cross-feeding between community members, is necessary and sufficient to recapitulate our experimental observations. In addition to helping understand the role of the environment in community assembly, the divergence-complexity effect can provide insight into which environments support multiple community states, enabling the search for desired ecosystem functions towards microbiome engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

Structures of the TMC-1 complex illuminate mechanosensory transduction

The initial step in the sensory transduction pathway underpinning hearing and balance in mammals involves the conversion of force into the gating of a mechanosensory transduction channel1. Despite the profound socioeconomic impacts of hearing disorders and the fundamental biological significance of understanding mechanosensory transduction, the composition, structure and mechanism of the mechanosensory transduction complex have remained poorly characterized. Here we report the single-particle cryo-electron microscopy structure of the native transmembrane channel-like protein 1 (TMC-1) mechanosensory transduction complex isolated from Caenorhabditis elegans. The two-fold symmetric complex is composed of two copies each of the pore-forming TMC-1 subunit, the calcium-binding protein CALM-1 and the transmembrane inner ear protein TMIE. CALM-1 makes extensive contacts with the cytoplasmic face of the TMC-1 subunits, whereas the single-pass TMIE subunits reside on the periphery of the complex, poised like the handles of an accordion. A subset of complexes additionally includes a single arrestin-like protein, arrestin domain protein (ARRD-6), bound to a CALM-1 subunit. Single-particle reconstructions and molecular dynamics simulations show how the mechanosensory transduction complex deforms the membrane bilayer and suggest crucial roles for lipid–protein interactions in the mechanism by which mechanical force is transduced to ion channel gating.

59 BASIC BIOLOGICAL SCIENCES↗

Substrate Channeling via a Transient Protein-Protein Complex: The case of D-Glyceraldehyde-3-Phosphate Dehydrogenase and L-Lactate Dehydrogenase

Molecular dynamics studies showed that LDH and GAPDH tetramers can form a complex which can breakdown when the enzymes are saturated with NADH molecules. The interaction sites are conserved between LDH isozymes from heart and muscle cells, and between GAPDH molecules from rabbit and yeast cells. Positive electric fields between the NAD(H) binding sites showed that NAD(H) channeling within LDH-GAPDH complex can be an extension of NAD(H) channeling between the adjacent subunits within LDH and GAPDH tetramers. Analytical ultracentrifugation and enzyme kinetics studies indicated that LDH and GAPDH molecules can form a transient channeling complex. The transient complex can support the channeled and the diffusive paths in parallel, the relative contribution from each path depends on the off-rates for (GAPDH-NADH)-LDH complex and GAPDH-NADH complex. Negative cooperativity in NADH binding to different subunits in GAPDH tetramers can provide allosteric regulation of NADH channeling from GAPDH to LDH.

INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMI↗

DNCON2_Inter: predicting interchain contacts for homodimeric and homomultimeric protein complexes using multiple sequence alignments of monomers and deep learning

Deep learning methods that achieved great success in predicting intrachain residue-residue contacts have been applied to predict interchain contacts between proteins. However, these methods require multiple sequence alignments (MSAs) of a pair of interacting proteins (dimers) as input, which are often difficult to obtain because there are not many known protein complexes available to generate MSAs of sufficient depth for a pair of proteins. In recognizing that multiple sequence alignments of a monomer that forms homomultimers contain the co-evolutionary signals of both intrachain and interchain residue pairs in contact, we applied DNCON2 (a deep learning-based protein intrachain residue-residue contact predictor) to predict both intrachain and interchain contacts for homomultimers using multiple sequence alignment (MSA) and other co-evolutionary features of a single monomer followed by discrimination of interchain and intrachain contacts according to the tertiary structure of the monomer. We name this tool DNCON2_Inter. Allowing true-positive predictions within two residue shifts, the best average precision was obtained for the Top-L/10 predictions of 22.9% for homodimers and 17.0% for higher-order homomultimers. In some instances, especially where interchain contact densities are high, DNCON2_Inter predicted interchain contacts with 100% precision. We also developed Con_Complex, a complex structure reconstruction tool that uses predicted contacts to produce the structure of the complex. Using Con_Complex, we show that the predicted contacts can be used to accurately construct the structure of some complexes. Our experiment demonstrates that monomeric multiple sequence alignments can be used with deep learning to predict interchain contacts of homomeric proteins.

59 BASIC BIOLOGICAL SCIENCES↗