Structural Changes of the Trinuclear Copper Center in Bilirubin Oxidase upon Reduction

Geometric and electronic structure changes in the copper (Cu) centers in bilirubin oxidase (BOD) upon a four-electron reduction were investigated by quantum mechanics/molecular mechanics (QM/MM) calculations. For the QM region, the unrestricted density functional theory (UDFT) method was adopted for the open-shell system. We found new candidates of the native intermediate (NI, intermediate II) and the resting oxidized (RO) states, i.e., NIH+ and RO0. Elongations of the Cu-Cu atomic distances for the trinuclear Cu center (TNC) and very small structural changes around the type I Cu (T1Cu) were calculated as the results of a four-electron reduction. The QM/MM optimized structures are in good agreement with recent high-resolution X-ray structures. As the structural change in the TNC upon reduction was revealed to be the change in the size of the triangle spanned by the three Cu atoms of TNC, we introduced a new index (l) to characterize the specific structural change. Not only the wild-type, but also the M467Q, which mutates the amino acid residue coordinating T1Cu, were precisely analyzed in terms of their molecular orbital levels, and the optimized redox potential of T1Cu was theoretically reconfirmed.

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Assessment of the KID Procedure on a Mo–oxo Complex, an Open–Shell System

10.20944/preprints202007.0742.v1 ◽

2020 ◽

Author(s):

Jorge Martínez-Araya ◽

Daniel Glossman-Mitnik

Keyword(s):

Density Functional ◽

Organic Molecules ◽

Open Shell ◽

Density Functionals ◽

Functional Theory ◽

Reactivity Descriptors ◽

Shell System ◽

Global And Local ◽

First Time ◽

Local Reactivity Descriptors

The KID (Koopmans in DFT) procedure usually applies in organic molecules of the closed–shell type. We used the KID procedure in an open–shell system for the first time to choose the most suitable density functional to compute global and local reactivity descriptors coming from the Conceptual Density–Functional Theory. From a set of 18 density functionals spread from the second until the fourth rung of the Jacob’s ladder: BP86, B97-D, BLYP, CAM-B3LYP, M06-L, M11-L, MN12-L, B3LYP, PBE0, N12-SX, M06-2X, M11, MN12-SX, CAM-B3LYP, LC-ωHPBE, ωB97X-D, APFD, MN15 and MN15-L, we concluded that CAM-B3LYP provides the best outcome.

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Formylglycine-generating enzyme binds substrate directly at a mononuclear Cu(I) center to initiate O2activation

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1818274116 ◽

2019 ◽

Vol 116 (12) ◽

pp. 5370-5375 ◽

Cited By ~ 10

Author(s):

Mason J. Appel ◽

Katlyn K. Meier ◽

Julien Lafrance-Vanasse ◽

Hyeongtaek Lim ◽

Chi-Lin Tsai ◽

...

Keyword(s):

Active Site ◽

Density Functional ◽

Structural Data ◽

Type I ◽

Functional Theory ◽

X Ray ◽

Active Site Cysteine ◽

Copper Center ◽

X Ray Absorption ◽

Linear Geometry

The formylglycine-generating enzyme (FGE) is required for the posttranslational activation of type I sulfatases by oxidation of an active-site cysteine to Cα-formylglycine. FGE has emerged as an enabling biotechnology tool due to the robust utility of the aldehyde product as a bioconjugation handle in recombinant proteins. Here, we show that Cu(I)–FGE is functional in O2activation and reveal a high-resolution X-ray crystal structure of FGE in complex with its catalytic copper cofactor. We establish that the copper atom is coordinated by two active-site cysteine residues in a nearly linear geometry, supporting and extending prior biochemical and structural data. The active cuprous FGE complex was interrogated directly by X-ray absorption spectroscopy. These data unambiguously establish the configuration of the resting enzyme metal center and, importantly, reveal the formation of a three-coordinate tris(thiolate) trigonal planar complex upon substrate binding as furthermore supported by density functional theory (DFT) calculations. Critically, inner-sphere substrate coordination turns on O2activation at the copper center. These collective results provide a detailed mechanistic framework for understanding why nature chose this structurally unique monocopper active site to catalyze oxidase chemistry for sulfatase activation.

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Electronic propensity of Cu(II) versus Cu(I) sites in zeolites to activate NO — Spin- and orbital-resolved Cu–NO electron transfer

Canadian Journal of Chemistry ◽

10.1139/cjc-2012-0536 ◽

2013 ◽

Vol 91 (7) ◽

pp. 538-543 ◽

Cited By ~ 8

Author(s):

Mariusz Radoń ◽

Paweł Kozyra ◽

Adam Stępniewski ◽

Jerzy Datka ◽

Ewa Broclawik

Keyword(s):

Electron Transfer ◽

Density Functional ◽

Lone Pair ◽

Blue Shift ◽

Open Shell ◽

Minor Importance ◽

Antibonding Orbital ◽

Spin Manifolds ◽

Copper Center ◽

Nitrogen Lone Pair

Electronic factors responsible for the notable decline of NO activation by Cu(II) with respect to Cu(I) sites in zeolites are investigated within spin-resolved analysis of electron transfer channels between the copper center and the substrate. The results of natural orbitals for chemical valence (NOCV) charge transfer analysis for a minimal model of Cu(II) sites in zeolite ZSM-5 ({T1Cu}+ NO) are compared with those for Cu(I)–NO and referenced to an interaction of NO with bare Cu+ cations. The bonding of NO, which is an open-shell and non-innocent ligand, gives rise to a noticeable nondynamical correlation in the adduct with Cu(II) (reflected in a broken-symmetry solution obtained at the density functional theory (DFT) level). Four distinct components of electron transfer between the copper and NO are identified: (i) donation of an unpaired electron from the NO π∥* antibonding orbital to the Cu species, (ii) backdonation from copper d⊥ to the NO antibonding orbital, (iii) “covalent” donation from NO π∥ and Cu d∥ orbitals to the bonding region, and (iv) donation from the nitrogen lone pair to Cus,d. Large variations in channel identity and significance may be noted among studied systems and between spin manifolds: channel i is effective only in the bonding of NO with either a naked Cu+ cation or Cu(II) site. Channel ii comes into prominence only for the model of the Cu(I) site: it strongly activates the NO bond by populating antibonding π*, which weakens the N–O bond, in contrast to channel i depopulating the antibonding orbital and strengthening the N–O bond. Channels iii and iv, however, may contribute to the strength of the bonding between NO and copper, and are of minor importance for the activation of the NO bond. This picture perfectly matches the IR experiment: interaction with either Cu(II) sites or a naked Cu+ cation imposes a comparable blue-shift of NO stretching frequency, while the frequency becomes strongly red-shifted for a Cu(I) site in ZSM-5 due to enhanced π* backdonation.

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Room Temperature Alkali Metal Reduction of Carbon Dioxide

10.26434/chemrxiv.12665336 ◽

2020 ◽

Author(s):

Lucas A. Freeman ◽

Akachukwu D. Obi ◽

Haleigh R. Machost ◽

Andrew Molino ◽

Asa W. Nichols ◽

...

Keyword(s):

Alkali Metal ◽

Alkali Metals ◽

Room Temperature ◽

Chemical Reduction ◽

Bond Cleavage ◽

Open Shell ◽

Metal Reduction ◽

One Pot ◽

Earth Abundant ◽

Electron Reduction

The reduction of the relatively inert carbon–oxygen bonds of CO2 to access useful CO2-derived organic products is one of the most important fundamental challenges in synthetic chemistry. Facilitating this bond-cleavage using earth-abundant, non-toxic main group elements (MGEs) is especially arduous because of the difficulty in achieving strong inner-sphere interactions between CO2 and the MGE. Herein we report the first successful chemical reduction of CO2 at room temperature by alkali metals, promoted by a cyclic(alkyl)(amino) carbene (CAAC). One-electron reduction of CAAC-CO2 adduct (1) with lithium, sodium or potassium metal yields stable monoanionic radicals clusters [M(CAAC–CO2)]n(M = Li, Na, K, 2-4) and two-electron alkali metal reduction affords open-shell, dianionic clusters of the general formula [M2(CAAC–CO2)]n (5-8). It is notable that these crystalline clusters of reduced CO2 may also be isolated via the “one-pot” reaction of free CO2 with free CAAC followed by the addition of alkali metals – a reductive process which does not occur in the absence of carbene. Each of the products 2-8 were investigated using a combination of experimental and theoretical methods.

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Expression and Solution NMR Study of Multi-site Phosphomimetic Mutant BCL-2 Protein

Protein and Peptide Letters ◽

10.2174/0929866526666190327121225 ◽

2019 ◽

Vol 26 (6) ◽

pp. 449-457

Author(s):

Ting Song ◽

Keke Cao ◽

Yu dan Fan ◽

Zhichao Zhang ◽

Zong W. Guo ◽

...

Keyword(s):

Structural Change ◽

Structural Biology ◽

Quantum Coherence ◽

Structural Changes ◽

Solution Nmr ◽

Flexible Loop ◽

Loop Region ◽

Loop Domain ◽

Nmr Study ◽

Binding Groove

Background: The significance of multi-site phosphorylation of BCL-2 protein in the flexible loop domain remains controversial, in part due to the lack of structural biology studies of phosphorylated BCL-2. Objective: The purpose of the study is to explore the phosphorylation induced structural changes of BCL-2 protein. Methods: We constructed a phosphomietic mutant BCL-2(62-206) (t69e, s70e and s87e) (EEEBCL- 2-EK (62-206)), in which the BH4 domain and the part of loop region was truncated (residues 2-61) to enable a backbone resonance assignment. The phosphorylation-induced structural change was visualized by overlapping a well dispersed 15N-1H heteronuclear single quantum coherence (HSQC) NMR spectroscopy between EEE-BCL-2-EK (62-206) and BCL-2. Results: The EEE-BCL-2-EK (62-206) protein reproduced the biochemical and cellular activity of the native phosphorylated BCL-2 (pBCL-2), which was distinct from non-phosphorylated BCL-2 (npBCL-2) protein. Some residues in BH3 binding groove occurred chemical shift in the EEEBCL- 2-EK (62-206) spectrum, indicating that the phosphorylation in the loop region induces a structural change of active site. Conclusion: The phosphorylation of BCL-2 induced structural change in BH3 binding groove.

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Statistical Approaches to Structural Change in Regional Interindustry Models

Environment and Planning A Economy and Space ◽

10.1068/a181189 ◽

1986 ◽

Vol 18 (9) ◽

pp. 1189-1207

Author(s):

B Ó Huallacháin

Keyword(s):

Structural Change ◽

Structural Changes ◽

Washington State ◽

Multivariate Statistical Analyses ◽

Input Output ◽

Multivariate Statistical ◽

State Data ◽

System A ◽

Statistical Approaches ◽

The Impact

The conventional approach to assessing structural change in regional input – output tables is to measure the impact of coefficient change on the estimation of outputs and multipliers. The methods developed and tested in this paper focus exclusively on the coefficients. Univariate and multivariate statistical analyses can be used to identify and measure various types of changes ranging from coefficient instability to changes in interindustry relationships as a system. A distinction is made between structural changes in input relationships and those in output relationships. The methods are tested by using Washington State data for the years 1963 and 1967. The results are compared with previous analyses of change in these data.

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Defect Processes in Halogen Doped SnO2

Applied Sciences ◽

10.3390/app11020551 ◽

2021 ◽

Vol 11 (2) ◽

pp. 551

Author(s):

Petros-Panagis Filippatos ◽

Nikolaos Kelaidis ◽

Maria Vasilopoulou ◽

Dimitris Davazoglou ◽

Alexander Chroneos

Keyword(s):

Electronic Properties ◽

Tin Oxide ◽

Density Functional ◽

Structural Changes ◽

High Dielectric Constant ◽

Density Functional Theory Calculations ◽

Functional Theory ◽

Optical And Electronic Properties ◽

High Dielectric ◽

Gap States

In the present study, we performed density functional theory calculations (DFT) to investigate structural changes and their impact on the electronic properties in halogen (F, Cl, Br, and I) doped tin oxide (SnO2). We performed calculations for atoms intercalated either at interstitial or substitutional positions and then calculated the electronic structure and the optical properties of the doped SnO2. In all cases, a reduction in the bandgap value was evident, while gap states were also formed. Furthermore, when we insert these dopants in interstitial and substitutional positions, they all constitute a single acceptor and donor, respectively. This can also be seen in the density of states through the formation of gap states just above the valence band or below the conduction band, respectively. These gap states may contribute to significant changes in the optical and electronic properties of SnO2, thus affecting the metal oxide’s suitability for photovoltaics and photocatalytic devices. In particular, we found that iodine (I) doping of SnO2 induces a high dielectric constant while also reducing the oxide’s bandgap, making it more efficient for light-harvesting applications.

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Structural and thermal properties of the amaranth starch granule obtained by high-impact wet milling

International Journal of Food Engineering ◽

10.1515/ijfe-2020-0024 ◽

2020 ◽

Vol 0 (0) ◽

Author(s):

Diego Fernando Roa Acosta ◽

José Fernando Solanilla Duque ◽

Lina Marcela Agudelo Laverde ◽

Héctor Samuel Villada Castillo ◽

Marcela Patricia Tolaba

Keyword(s):

Thermal Properties ◽

Structural Changes ◽

Starch Granule ◽

Amorphous Region ◽

Extraction Yield ◽

High Impact ◽

Degree Of Crystallinity ◽

Wet Milling ◽

Starch Structure ◽

Structure Changes

AbstractIn this study, amaranth starch was extracted by high-impact wet milling and its structural and thermal properties and the effect of NaOH and SDS concentrations on extraction yield were evaluated. The best condition was 55 g of starch/100 g of amaranth, with a decrease from 2.5 to 3.5 kJ/g using different milling energies. The decrease in the protein content of the starch granule is due to an effect of the interaction between surfactant and alkali, preventing the destruction of granules. All starches presented a degree of crystallinity between 21 and 28%. The internal structural changes of the starch granule were monitored by attenuated total reflectance - Fourier-transform infrared (ATR-FTIR) in the region of 990 to 1060 cm−1. Spectra showed significant differences between the peaks at 1032 and 1005 cm−1, corresponding to the crystalline/amorphous region of the starch structure. Changes in viscosity profiles were observed between 0.302 and 1.163 Pa s.

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Effect of chemical modification on electronic transport properties of carbyne

Journal of Computational Electronics ◽

10.1007/s10825-020-01639-7 ◽

2021 ◽

Author(s):

G. R. Berdiyorov ◽

U. Khalilov ◽

H. Hamoudi ◽

Erik C. Neyts

Keyword(s):

Transport Properties ◽

Electronic Transport ◽

Density Functional ◽

Structural Changes ◽

Carbon Chain ◽

Functional Formalism ◽

Functional Theory ◽

Carbon Allotrope ◽

Electronic Transport Properties ◽

Interface Structures

AbstractUsing density functional theory in combination with the Green’s functional formalism, we study the effect of surface functionalization on the electronic transport properties of 1D carbon allotrope—carbyne. We found that both hydrogenation and fluorination result in structural changes and semiconducting to metallic transition. Consequently, the current in the functionalization systems increases significantly due to strong delocalization of electronic states along the carbon chain. We also study the electronic transport in partially hydrogenated carbyne and interface structures consisting of pristine and functionalized carbyne. In the latter case, current rectification is obtained in the system with rectification ratio up to 50%. These findings can be useful for developing carbyne-based structures with tunable electronic transport properties.

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Intercalated architecture of MA2Z4 family layered van der Waals materials with emerging topological, magnetic and superconducting properties

Nature Communications ◽

10.1038/s41467-021-22324-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Lei Wang ◽

Yongpeng Shi ◽

Mingfeng Liu ◽

Ao Zhang ◽

Yi-Lun Hong ◽

...

Keyword(s):

Electronic Properties ◽

Density Functional ◽

Layer Structure ◽

Atomic Layer ◽

Type I ◽

Hybrid Functional ◽

Functional Theory ◽

Valence Electrons ◽

Nonmagnetic Metals ◽

Standard Density

AbstractThe search for new two-dimensional monolayers with diverse electronic properties has attracted growing interest in recent years. Here, we present an approach to construct MA2Z4 monolayers with a septuple-atomic-layer structure, that is, intercalating a MoS2-type monolayer MZ2 into an InSe-type monolayer A2Z2. We illustrate this unique strategy by means of first-principles calculations, which not only reproduce the structures of MoSi2N4 and MnBi2Te4 that were already experimentally synthesized, but also predict 72 compounds that are thermodynamically and dynamically stable. Such an intercalated architecture significantly reconstructs the band structures of the constituents MZ2 and A2Z2, leading to diverse electronic properties for MA2Z4, which can be classified according to the total number of valence electrons. The systems with 32 and 34 valence electrons are mostly semiconductors. Whereas, those with 33 valence electrons can be nonmagnetic metals or ferromagnetic semiconductors. In particular, we find that, among the predicted compounds, (Ca,Sr)Ga2Te4 are topologically nontrivial by both the standard density functional theory and hybrid functional calculations. While VSi2P4 is a ferromagnetic semiconductor and TaSi2N4 is a type-I Ising superconductor. Moreover, WSi2P4 is a direct gap semiconductor with peculiar spin-valley properties, which are robust against interlayer interactions. Our study thus provides an effective way of designing septuple-atomic-layer MA2Z4 with unusual electronic properties to draw immediate experimental interest.

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