Binding energies of five molecular pincers calculated by explicit and implicit solvent models

We perform Replica Exchange Molecular Dynamics (REMD) simulations on a silk-like protein design with amino-acid sequence [(Gly-Ala)3-Gly-Glu]5 to investigate the stability of a single protein, a dimer, a trimer and a tetramer made up of these proteins starting from β-roll and β-sheet structures in both explicit (TIP3P) and implicit (GBSA) solvent models. Our simulation results for the implicit solvent model agree with those for the explicit solvent model for simulation times up to the longest tested, being 30 ns per replica. From this we infer that the implicit solvent model that we use is reliable, allowing us to reach much longer time scales (up to 200 ns per replica). We find that the self-assembly of fibers of these proteins in solution must be a nucleated process, involving nuclei made up of at least three monomers. We also find that the conformation of the protein changes upon assembly, i.e., there is a transition from a disordered globular state to an ordered β-sheet structure in the self-assembled state of aggregates containing more than two monomers. This indicates that autosteric effects must be important in the polymerization of this protein, reminiscent of what is observed for β-amyloids. Our findings are consistent with recent experimental results on a protein with an amino acid sequence similar to that of the protein we study.

Magnetic interactions in a series of tetranuclear Fe(3+) complexes with the butterfly core structure have been studied with semiempirical ZILSH and density functional theory (DFT) calculations (B3LYP functional). A theoretical analysis of a previously used method of estimating exchange constants from a restricted number of spin configurations reveals systematic errors arising from asymmetry in the complexes, which cause large variations in results with different choices of spin configurations. Correction factors are derived that yield the correct results obtained from full configuration space (FCS) calculations. Exchange constants obtained from DFT FCS calculations for the "body-body" interaction were large and ferromagnetic, in disagreement with values obtained from empirical fits of magnetic susceptibility data for the complexes, established magnetostructural correlations in polynuclear Fe(3+) complexes, and ZILSH calculations. DFT calculations also gave unreasonably large antiferromagnetic exchange constants for interaction between "wingtip" ions that are not directly bridged, again in disagreement with ZILSH calculations. Estimates of exchange constants for interaction of body and wingtip ions obtained with ZILSH and DFT were similar, with the ZILSH values in slightly better agreement with empirical fits. Considering all interactions, the ZILSH method provides results in better accord with experiment than DFT for these complexes. Additional comparisons of exchange constants obtained with different spin coupling schemes showed that values appropriate for two-center spin eigenfunctions gave consistently better results than values calculated with the local spin operator. The effect of basis set was found to be very small. A brief analysis of these findings is given.

Vibrational absorption (VA) and vibrational circular dichroism (VCD) spectra of methyl mandelate, a prototype chiral molecule, in a series of organic solvents, namely methanol (MeOH-d(4)), dimethyl sulfoxide (DMSO-d(6)), and chloroform (CDCl(3)), have been measured in the finger print region from 1800 to 1150 cm(-1). Implicit solvation models in the form of polarizable continuum model and explicit solvation models have been employed independently and simultaneously. The goal is to evaluate their efficiencies in dealing with solvent effects in each solution and to establish a general strategy to adequately account for effects of solvents. Molecular dynamics (MD) simulation and radial distribution function analysis have been performed to aid the construction of the explicit solvation models. Initial geometry searches have been carried out at the B3LYP/6-31G(d) level for the methyl mandelate monomer and its explicit 1 : 1 and 1 : 2 solute-solvent hydrogen-bonded complexes. B3LYP/cc-pVTZ has been used for all the final geometry optimizations, the vibrational frequency, VA and VCD intensity, and optical rotation dispersion (ORD) calculations. The results show that inclusion of solvent explicitly and implicitly at the same time has significant impacts on the appearance of the VA and VCD spectra, and is crucial for reliable spectral assignments when solvents are capable of hydrogen-bonding interactions with solutes. When no strong solvent-solute hydrogen-bonding interactions in the case of chloroform are expected, the gas phase monomer model is adequate for spectral interpretation, while inclusion of implicit solvation improves the frequency agreement with experiment. ORD spectra of methyl mandelate in the aforementioned solvents at different concentrations under 5 excitation wavelengths have also been measured. The comparison between the calculated and the experimental ORD spectra supports the conclusions drawn from the VA and VCD investigations.

Most theoretical studies of an electrical double layer, which is formed by an electrolyte in contact with a charged electrode, employ a primitive model in which the solvent is represented by a dielectric continuum. This implicit-solvent model is convenient because computations are comparatively simple. However, it suppresses oscillations in the density profiles of ionic species that result from the discreteness of the solvent molecules. Furthermore, the implicit-solvent model yields poor results for the capacitance. In comparison with experiment at fixed electrode charge density, it predicts a too small electrode potential, and the resultant capacitance is too large. This latter discrepancy can be compensated in part by postulating the existence of an often fictitious inner layer whose properties are parametrized to agree best with experiment. The use of an implicit solvent model and an inner layer helps in correlating experimental results but rests on a faulty microscopic picture. Unfortunately, explicit consideration of solvent molecules poses both theoretical and numerical difficulties and, as a result, studies using an explicit solvent model have been few and far between. In this study, we consider a simple nonprimitive or explicit solvent model in which each solvent molecule is represented by a dimer composed of touching positive and negative hard spheres, with a resulting dipole moment that is equal to that of a water molecule, and the ions are represented by charged hard spheres. The density profiles and charge-potential relationship of this model are examined using the classical density functional theory. We find that the introduction of an explicit solvent increases the electrode potential, at fixed electrode charge, without the need to postulate a parametrized inner layer. Because of the solvent polarity, the ion profiles become strong oscillatory and show local charge inversion near a highly charged electrode surface at all ion concentrations.

Sumanene as a delivery system for 5-fluorouracil drug – DFT, SAPT and MD study

Watching the defectives: DFT studies on the growth of nickel clusters on different graphene substrates shows that graphene defects essentially determine the morphology of the clusters. Defects greatly improve the catalytic reactivity of the larger clusters Nin (5≤n≤10). Smaller clusters Nin (n<4) efficiently open the band gap of defective graphene, allowing a way to modulate the electronic properties of the graphene. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

We study numerically, by means of density functional theory (DFT) calculations complemented with an implicit solvation model, a novel chemical probe bearing urea and aromatic phenyl groups. We probe the interaction in water of the latter with a wide variety of ions relevant to water quality. We perform geometry minimizations using PBE0 functional and aug‐cc‐pVDZ basis set, and a polarizable continuum model (PCM) to take into account the aqueous solvent. We underline for the first time several methodological details concerning the definition of thebindingorinteractionenergy, and the basis set superposition error definition in the context of implicit solvation models. We observe two competing interaction modes for this probe: a urea‐enhanced, cation‐πinteraction (with cations only), and hydrogen bonding occurring between the urea group and anions, the former being more favorable than the latter. A Generalized Kohn–Sham Energy Decomposition Analysis (GKS‐EDA) in implicit solvent is performed to analyze the nature of the ions–probe interactions. Magnesium and sodium ions, and respectively glyphosate and hypochlorite ions, are found as the cations (resp. anions) having the largest binding free energies with the probe. This is the first time such an exhaustive study, investigating the selectivity of an organic probe toward a wide variety of ions in water, is carried out in the context of DFT/PCM models. Computer‐aided sensor design needs reliable and efficient methods. Our methodology can be used as a general way to gain a valuable insight into the sensitivity of organic ligands toward a variety of ions or pesticides in water, without the need of an explicit solvent description, but still going beyond the state‐of‐the‐art DFT in vacuo approach. By predicting possible competitive interactions, and understanding their nature, this methodology can thus help to better design functional groups selective to specific targets.

Open AccessCCS ChemistryRESEARCH ARTICLES22 Oct 2022Decrypting the Influence of Axial Coordination on the Electronic Microenvironment of Co-N5 Site for Enhanced Electrocatalytic Reaction Bingyu Huang†, Senhe Huang†, Chenbao Lu, Longbin Li, Judan Chen, Ting Hu, Dirk Lützenkirchen-Hecht, Kai Yuan, Xiaodong Zhuang and Yiwang Chen Bingyu Huang† Institute of Polymers and Energy Chemistry (IPEC), College of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031 , Senhe Huang† Themeso-Entropy Matter Lab, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240 , Chenbao Lu Themeso-Entropy Matter Lab, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240 , Longbin Li Institute of Polymers and Energy Chemistry (IPEC), College of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031 , Judan Chen Institute of Polymers and Energy Chemistry (IPEC), College of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031 , Ting Hu School of Materials Science and Engineering, Nanchang University, Nanchang 330031 , Dirk Lützenkirchen-Hecht Faculty of Mathematics and Natural Sciences-Physics Department, Bergische Universität Wuppertal, Wuppertal D-42119 , Kai Yuan *Corresponding authors: E-mail Address: [email protected] E-mail Address: [email protected] E-mail Address: [email protected] Institute of Polymers and Energy Chemistry (IPEC), College of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031 , Xiaodong Zhuang *Corresponding authors: E-mail Address: [email protected] E-mail Address: [email protected] E-mail Address: [email protected] Themeso-Entropy Matter Lab, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240 and Yiwang Chen *Corresponding authors: E-mail Address: [email protected] E-mail Address: [email protected] E-mail Address: [email protected] Institute of Polymers and Energy Chemistry (IPEC), College of Chemistry and Chemical Engineering, Nanchang University, Nanchang 330031 Institute of Advanced Scientific Research (iASR), Key Lab of Fluorine and Silicon for Energy Materials and Chemistry of Ministry of Education, Jiangxi Normal University, Nanchang 330022 https://doi.org/10.31635/ccschem.022.202202241 SectionsSupplemental MaterialAboutAbstractPDF ToolsAdd to favoritesDownload CitationsTrack Citations ShareFacebookTwitterLinked InEmail Metal porphyrins are star molecules that possess well-defined coordination metal centers for versatile catalytic reactions. However, most previous work has focused on the correlations between in-plane symmetric configuration of metal-N4 sites and their catalytic performance. Addressing the catalytic contribution of additional axial coordination to such symmetric configuration remains a challenge. Theoretical calculations revealed that axially anchoring an extra pyridine on the tetra-coordinated cobalt porphyrin (Co-N4) to construct penta-coordinated cobalt porphyrin (Co-N5) renders cobalt a higher electron density, thereby favoring the rate-determining O2 adsorption/activation and reducing the oxygen electroreduction barrier. Therefore, a well-defined Co-N5 site is rationally introduced into the azo-linked polymer framework for a fundamental structure–catalytic performance correlation study. As-prepared Co-N5 catalyst exhibits a 26 mV positive shift in half-wave potential compared with the pyridine-free Co-N4 counterpart, discloses a markedly higher power density (141.4 mW cm−2), and possesses better long-term durability (over 160 h cycles) in a Zn-air battery. Moreover, such a Co-N5 catalyst also showcases potential applications for CO2 reduction with high CO2-to-CO conversion faradic efficiency and better selectivity than the Co-N4 counterpart because coordination of the fifth pyridine evokes electronic localization that suppresses a competitive side reaction. This work proves the positive electrocatalytic contribution of axial penta-coordination on well-defined metal-porphyrin-based catalysts and offers atomic understanding of the structure–performance correlation on single atom catalysts for future catalyst design. Download figure Download PowerPoint Introduction Currently, many advanced electrocatalysts have been developed to facilitate the sluggish kinetics of the multiple-electron transfer process in energy conversion reactions, such as the oxygen reduction reaction (ORR) and CO2 reduction reaction (CO2RR).1–4 Due to maximized atom utilization, mainstream research has focused on the isolated transition metal/nitrogen coordinated (M-N-C) single-atom catalysts (SACs) with high catalytic activity and selectivity.5–9 Despite extensive investigations, the rational design and controllable and precise synthesis of M-N-C catalysts continues to be the main obstacle to multiple-electron transfer processes.10–12 The preparation of M-N-C catalysts normally needs high-temperature pyrolysis to increase the graphitization degree for better conductivity.13–17 Unfortunately, the pyrolysis process inevitably evokes metal aggregation due to the thermal decomposition of metal precursors and high surface energy of single metal atoms, posing challenges for maintaining atomic-metal isolation.13,18,19 The inhomogeneity and indistinction of the catalytic environment of carbonaceous materials give rise to tremendous difficulties in simultaneously enhancing the catalysts' activity and selectivity. In addition, the inherently less-defined active sites formed after pyrolysis leaves an ambiguous structure–performance relationship and seriously precludes us from exploring the in-depth mechanism for different electrocatalytic reactions.20–24 Therefore, the above-mentioned challenges stimulate the vigorous search for developing cost-effective and high-performance pyrolysis-free electrocatalysts with well-defined active sites. Transition-metal macrocycles, such as cobalt porphyrins, which possess the distinct tetra-coordinated cobalt porphyrin (Co-N4) site, have been heavily studied.25–28 Benefitting from the production of fewer radical oxygen species during the electrocatalytic process, the Co-N4 structure is more robust and advantageous for electrocatalysis of ORR.16,20,29–31 However, the representative plane-symmetric electron configuration of Co-N4 is not the optimal structure for the chemisorption and activation of reactants.32–34 Breaking the structure symmetry with penta-coordination to regulate the charge redistribution of Co-N4 sites could promote the electrocatalytic process, but the accurate synthesis of this structural motif is still a noteworthy challenge. Besides, the role of penta-coordination and the exact local microenvironment of such active sites have not yet been ascertained.35,36 In view of this, offering a model catalyst as an ideal platform is urgently required to elucidate the contribution of axial penta-coordination on catalytic activity, selectivity, and durability of Co-N4 sites. In this work, we probed the positive effect of axial pyridinic penta-coordinated cobalt porphyrin (Co-N5) to achieve optimized electronic localization on the Co-N5 site for boosting ORR through density functional theory (DFT) calculations as well as electrochemical analysis. DFT calculations indicate Co-N5 with axial pyridinic coordination possesses obviously higher electronic density on the Co center in comparison with Co-N4. Taking advantage of the electronic-push effect of penta-coordination, the ORR rate-determining step of O2 adsorption/activation can be significantly promoted, ensuring better ORR performance of Co-N5 than the Co-N4 model. Hence, we innovatively designed and synthesized an azo-linked polymer framework with atomically dispersed electron-rich Co-N5 sites for ORR through a pyrolysis-free axial-pyridinic coordination strategy. The Co-N5 catalyst displays impressive ORR performance with a more positive half-wave potential of 0.811 V and lower Tafel slope of 39 mV dec−1 than the Co-N4 counterpart (0.785 V and 50 mV dec−1), which support the theoretical predictions. Encouragingly, such a penta-coordination-induced electronic localization strategy also promises the potential for improving the CO2-to-CO conversion faradic efficiency and selectivity of electrocatalytic CO2 reduction. This work provides new design strategies toward well-defined single-atom electrocatalysts with axial coordination and offers new models for fundamentally understanding the catalytic mechanism of asymmetric coordination systems. Experimental Methods Synthesis of [email protected] catalysts First, 20 mg (27.3 μmol) of CoTAPP and 80 mg of G-py were redispersed in 20 mL of dimethyl sulfoxide (DMSO). Then, the mixture was stirred for 15 h to ensure CoTAPP was fully coordinated to G-py. Immediately after the coordination, 35.2 mg (0.11 mmol, 4 equiv to CoTAPP) of PhI(OAc)2 was added to the mixed solution, and the mixture was stirred for 24 h. The resultant precipitate was filtered and washed with DMSO, methanol, deionized water, and ethanol for three times, and dried at 60 °C overnight. [email protected] was harvested as a black powder (86.8 mg, 87% yield). [email protected] and [email protected] were prepared with a procedure similar to [email protected] Experimental details, materials characterization methods, and synthesis of other samples are available in the Supporting Information. Results and Discussion Theoretical calculations and catalytic mechanism Based on cobalt porphyrin, two models with different coordination environments, axial pyridinic Co-N5 model and Co-N4 model were designed (Figure 1a and Supporting Information Figure S1). The elementary steps and corresponding ORR adsorption configurations on the two models are presented in Supporting Information Figure S2. The Gibbs free energies at different potentials for all elementary steps were evaluated to illustrate how the penta-coordination affects intrinsic ORR activity. As given in Figure 1b, all elementary steps are distinctly downhill at U = 0 V, thus the reaction is exothermic and able to proceed spontaneously. When the potential rises to 1.23 V, the rate-determining step of Co-N4 is the first step (* + O2 + H2O + e− → *OOH + OH−) with a high energy barrier of 0.34 eV. In contrast, the final release step (*OH + e− → OH− + *) of the Co-N5 model is the rate-determining step, and its free energy can be distinctly reduced to only 0.26 eV. The thermodynamic limiting potentials, which represent the maximum potential to ensure all steps downhill are 0.97 and 0.89 V for Co-N5 and Co-N4 models, respectively (Figure 1c and Supporting Information Figure S3), revealed the Co-N5 model requires the minimum overpotential to drive the oxygen reduction. This result implies that the axial pyridine coordination plays a crucial role in regulating the ORR intermediates adsorption strength and decreasing the reaction barrier of the rate-determining step. Similarly, axial pyridine coordination can also alter the Fe electronic microenvironment, thereby enhancing the catalytic activity of the Fe-N5 model ( Supporting Information Figures S4–S7), further validating the universality of additional axial coordination. Figure 1 | (a) DFT calculation models of Co-N5 and Co-N4 for the electrochemically catalyzed ORR. (b) Free energy diagrams at U = 0 V and U = 1.23 V, and (c) free energy diagrams for the thermodynamic limiting potentials of Co-N5 model and Co-N4 model. (d) PDOS of Co atom for Co-N5 model (top) and Co-N4 model (bottom); the d-band center is denoted by the dashed gray line. Differential charge density distribution after O2 absorption on (e) Co-N5 model and (f) Co-N4 model. Download figure Download PowerPoint To further study axial coordination induced changes in the Co center's electronic configuration and interaction with oxygen-containing intermediates, projected density of states (PDOS) was conducted. The axial coordination obviously tunes the Co 3d orbital according to the PDOS in Figure 1d. The d-band center of the Co-N5 model at −1.59 eV is closer to the Fermi level than that of Co-N4 at −1.76 eV, thereby leading to an increase in O-containing intermediates' adsorption.37 The enhanced adsorption ensures subsequent ORR steps proceed through a more efficient four-electron pathway. Hence, the thermodynamic onset potentials improvement can be ascribed to fine-tuned adsorption strength of the ORR intermediates, which directly determines the activity and selectivity of catalysts. In addition, the higher PDOS near the Fermi level represents more abundant charge carriers and better electronic conductivity for the Co-N5 model. During the ORR process, the activated Co d orbitals and their hybridization with O p orbitals co-determine the adsorption strength for oxygen-containing adsorbates.38–42 After O2 adsorption and *OH formation, the increased overlapping degree of the strong σ-bond that originates from the Co dz2 orbital and O p orbital, along with the decreased O2 antibonding orbital filling degree that appears above the Fermi level for Co-N5 model, can be observed. It theoretically suggests that the extra fifth pyridine coordination assures a tighter connection between Co centers and O2 ( Supporting Information Figures S8 and S9), thus enabling higher ORR selectivity towards the four-electron pathway.43 As verified by charge density differences ( Supporting Information Figure S10), obvious asymmetrical charge distribution caused by axial coordination can be found for the Co-N5 model in comparison with the symmetric Co-N4 model. An apparent charge accumulation on the Co center is found to form the electron-rich Co-N5 site due to the electronic-push effect of axial pyridine. As expected, the O2 only absorbs on the individual Co center (Figure 1e,f), which can provide superior ORR electrocatalytic sites. Furthermore, the axial pyridine can construct an electronic pathway that renders adequate charge transfer to oxygen molecules from the conductive graphene layer. In general, the electron-rich Co-N5 site promises stable chemisorption and activation of O2, which facilitates O–O bond cleavage, thus offering better selectivity for the four-electron reduction pathway. Therefore, the axial-pyridine coordination-induced electronic localization strategy is viable to efficaciously enhance the ORR kinetics. Synthesis and structural characterization To experimentally confirm the calculation results and demonstrate the significance of penta-coordination architecture in ORR, an azo-linked penta-coordinated cobalt porphyrin-based polymer (CoTAPP-Azo) anchored on pyridine functionalized graphene (G-py) ([email protected]) was synthesized. The synthesis route and structure of [email protected] and the counterpart [email protected] (directly grown CoTAPP-Azo on pristine graphene) are schematically revealed in Figure 2a. Tetrakis(4-aminophenyl) porphyrin (TAPP) was first chelated with cobalt cation to obtain CoTAPP ( Supporting Information Figure S11). TAPP coordinating with Fe (FeTAPP) and Ni (NiTAPP) were also successfully obtained using the same procedure. The formation of CoTAPP, FeTAPP, and NiTAPP were confirmed by mass spectrometry ( Supporting Information Figure S12) and Fourier-transform infrared (FTIR) spectroscopy ( Supporting Information Figure S13). The successful pyridine functionalization in G-py was confirmed by thermogravimetric analysis ( Supporting Information Figure S14), Raman spectroscopy ( Supporting Information Figure S15), and X-ray photoelectron spectroscopy (XPS) ( Supporting Information Figure S16). Subsequently, CoTAPP was anchored on G-py through axial pyridine coordination; following an azo-coupling reaction, [email protected] was finally obtained (see details in Supporting Information Scheme S1). For comparison, FeTAPP-based polymer hybridized with G-py ([email protected]) and graphene ([email protected]) and NiTAPP-based polymer hybridized with G-py ([email protected]), were synthesized by similar routes. Figure 2 | (a) Synthetic route of CoTA[email protected]y and [email protected] (b) HAADF-STEM image of [email protected] (c) High-resolution Co 2p XPS spectra of [email protected] and [email protected] Download figure Download PowerPoint The morphology of [email protected] was first identified by scanning electron microscopy (SEM). Compared with the thin-layered sheet structure of G-py, a thicker layer was observed, indicating G-py was covered by CoTAPP-Azo ( Supporting Information Figures S17 and 18). The transmission electron microscopy (TEM) image of [email protected] also presented representative lamellar plate morphology ( Supporting Information Figure S18c). To further discern the structural features at the atomic level, high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) was carried out. HAADF-STEM images and the corresponding energy dispersive spectroscopy (EDS) of [email protected] indicated homogeneous spatial distribution of C, N, Co elements ( Supporting Information Figure S19). The abundant bright points (highlighted by red circles) offer direct evidence for the uniform distribution of single Co atoms (Figure 2b). Similarly, [email protected], [email protected], and [email protected] all exhibited similar lamella morphology with homogeneously distributed elements ( Supporting Information Figures S20–S22). The chemical structures of [email protected] were preliminarily examined by FTIR spectroscopy ( Supporting Information Figure S23). Compared with CoTAPP, the corresponding FTIR spectrum of [email protected] displayed a significant intensity increase of N=N stretching signals (1570 cm−1, 1215 cm−1) along with an obviously weakened N–H peak at 3400 cm−1, proving the successful polymerization of CoTAPP. The increased ID/IG ratio of 0.94 for [email protected] to 1.07 for [email protected] in the Raman spectra ( Supporting Information Figure S24) verifies surface lattice interference caused by penta-coordination. X-ray diffraction (XRD) confirmed that G-py was coated by CoTAPP-Azo, and the absence of crystalline cobalt species diffraction peaks demonstrated the highly dispersed state of Co atoms ( Supporting Information Figure S25), agreeing well with the HAADF-STEM observations. [email protected] and [email protected] both show similar XRD patterns ( Supporting Information Figures S26 and S27). Furthermore, XPS was extracted to unravel the nature of the chemical bonding of [email protected] and [email protected] ( Supporting Information Figures S28–S31). Compared with [email protected], the N 1s XPS spectrum for [email protected] displayed an obvious pyridinic N peak (398.3 eV, Supporting Information Figure S29). The C 1s XPS spectrum of [email protected] showed that the C–N peak shifts to higher binding energy (BE) than that of [email protected] (ΔBE = 0.4 eV), revealing the decreased electron density of C atom. In the Co 2p spectra (Figure 2c), [email protected] underwent a shift to lower BE for Co 2p3/2 (780.3 eV) and Co 2p1/2 (795.6 eV) peaks, relative to that of [email protected] (780.8 and 796.0 eV for Co 2p3/2 and Co 2p1/2, respectively), providing evidence for the electronic localization on the Co with penta-coordination.44,45 This result confirms that axial pyridine ligands act as channels between G-py and CoTAPP-Azo and boost the charge transfer from graphene to Co centers, which is consistent with the electron-rich Co-N5 model in theoretical calculations. Importantly, similar phenomena were found in [email protected] and [email protected], suggesting the universality of such an electron localization approach. The UV–vis spectrum of [email protected] revealed a clear porphyrin Soret band at 448 nm ( Supporting Information Figure S32). Interestingly, an appreciable peak change to 438 nm in [email protected] was observed due to the penta-coordination-induced electron transfer. Meanwhile, photoluminescence spectroscopy was conducted to explore the charge separation behaviors ( Supporting Information Figure S33). Significantly increased quenching occurred in [email protected] compared with [email protected], further demonstrating that axial pyridine can enhance the charge transfer between G-py and CoTAPP-Azo. The work function, which represents the minimum energy needed to draw one inner electron from the nucleus, was obtained by ultraviolet photoelectron spectroscopy. [email protected] showed a 0.51 eV shift to higher BE than [email protected] in the second electron cut-off edge ( Supporting Information Figure S34). Hence, with respect to 4.49 eV for [email protected], the smaller work function for [email protected] (3.98 eV) indicated that the electrons are more likely to be activated and transferred outward.46,47 We assessed the porosity of the samples by nitrogen physisorption isotherms ( Supporting Information Figure S35). [email protected] and [email protected] both displayed the typical type-IV isotherms with an evident hysteresis loop, indicative of the coexistence of micropores and mesopores. The Brunauer–Emmett–Teller specific surface areas for [email protected] and [email protected] were calculated to be 506.6 and 440.3 m²/g, respectively. Pore size distribution demonstrated by nonlocalized DFT showed the pore widths centered at 1.9 and 4.8 nm for [email protected] ( Supporting Information Figure S36). These results demonstrate the improved surface area and hierarchical porous structure of [email protected], which are conducive to increase the quantity of accessible active sites and enhance the mass transport. To investigate the local coordination environment of the Co center, X-ray absorption near-edge structure (XANES) and extended X-ray absorption fine structure (EXAFS) analyses were examined. The stronger white-line peak intensity of [email protected] (7727 eV) compared with [email protected] was assigned to the larger coordination number of the Co center for [email protected] than [email protected] (Figure 3a).48 The quantitative fits ( Supporting Information Table S1) showed a Co atom in [email protected] was straightforwardly connected by N atoms with a coordination number of 5.1 and the average bond length of 1.98 Å. From the Co K-edge Fourier-transformed EXAFS spectra (Figure 3b), the first shell peak for [email protected] around 1.43 Å corresponded to the Co–N scattering path, accompanying the absent Co–Co peak at 2.18 Å, jointly signifying the isolated Co atoms' configuration. [email protected] displayed an obviously positive shift for the Co–N first shell in than [email protected], suggesting an Co–N bond length caused by the to the EXAFS results (Figure and Supporting Information Figures and in to an of for [email protected], the first shell intensity for [email protected] was enhanced with an to revealing the larger number of N coordination The was also for the coordination In Figure the intensity maximum at for [email protected] was assigned to Co–N Co–Co and corresponding coordination was demonstrating the of the Co The shift of [email protected] maximum compared with that of CoTAPP is caused by the in [email protected] Hence, on and EXAFS as well as the XPS we that [email protected] by Co-N5 sites was successfully synthesized. Figure | (a) Co K-edge spectra and (b) the of Co K-edge EXAFS spectra of [email protected] with Co and CoTAPP as (c) The corresponding EXAFS of [email protected] model with Co N and C (d) of [email protected] in comparison with Co and CoTAPP. Download figure Download PowerPoint Electrocatalytic ORR performance To how axial penta-coordination affects ORR [email protected] and [email protected] were first evaluated with a In ( Supporting Information Figure significant peaks in for [email protected], but a peak was observed in The (Figure and Supporting Information Figure that [email protected] the ORR performance with the most positive half-wave potential of 0.811 V which is 26 mV more positive than that of [email protected] (0.785 V These results indicate that [email protected] possesses superior catalytic performance that from the electron localization caused by pyridine penta-coordination. in comparison with [email protected], the density for [email protected] was enhanced because the axial pyridine as between G-py and CoTAPP-Azo, thus boosting the charge transfer from graphene to CoTAPP layer. Figure 4 | (a) ORR of [email protected] and [email protected] catalysts at (b) Tafel (c) density by electrochemically active surface and (d) comparison of Tafel and for [email protected] and [email protected] catalysts. (e) The of [email protected] and [email protected] and after (f) and power density specific for Zn-air at and long-term performance of Zn-air at a density of using [email protected], [email protected], and as catalysts. Download figure Download PowerPoint To further into the reaction kinetics of [email protected], the at from to were ( Supporting Information Figure The ( Supporting Information Figure which were from at different potentials, revealed the toward the of Based on the the number for [email protected] was which with the This proves that the Co-N5 site a four-electron pathway towards ORR, [email protected] has a smaller of ( Supporting Information Figure We the enhanced ORR selectivity to the Co-N5 configuration that can be with because of the effect between Co and pyridinic the resultant O–O bond with stronger stretching is thus providing higher selectivity for four-electron ORR. [email protected] has a more positive than [email protected] ( Supporting Information Figures that ORR activity can be improved by microenvironment through extra axial penta-coordination on different metal Moreover, the Tafel slope of 39 mV dec−1 the process of [email protected] for oxygen reduction (Figure and Supporting Information Figure by the of electrochemical spectroscopy ( Supporting Information Figure the decreased in the for [email protected], indicating the optimized and electron toward ORR kinetics. In addition, [email protected] exhibited the electrochemically active surface area ( Supporting Information Figure which is conducive to more active sites. density with an in the ORR can be found (Figure the intrinsic activity for [email protected] For further comparison, the performance density Tafel density and for different electrocatalysts are (Figure and

To evaluate the accuracy of density functional theory (DFT) for describing van der Waals interaction between rare‐gas atoms, we performed coupled‐cluster theory restricted to single, double, and noniterative triple excitations [CCSD(T)], fourth‐order perturbation theory including single, double, and quadruple substitutions [MP4(SDQ)], and several DFT calculations for He, Ne, Ar, and Kr dimers. The results clarified that (1) CCSD(T) and MP4(SDQ) with an “adjusted” diffuse basis‐set reproduce the experimental trend in binding energies as well as equilibrium distances of these dimers, (2) MP3 and MP2 underestimate the binding energies, (3) Becke's three‐parameter exchange functional and the gradient‐corrected functional of Lee, Yang, and Paar (B3LYP) and B3PW91 completely fail to describe the binding, and (4) Perdew–Wang exchange‐correlation functional (PW91PW91) and its modified ones (MPWPW91 and MPW1PW91) can provide the binding states, although the calculated binding energies cannot reproduce the experimental trend in binding energies. Therefore, we conclude that the above DFT functionals cannot quantitatively describe the van der Waals interaction between rare‐gas atoms and that the Perdew‐Wang–type exchange functional needs further improvement to describe the interaction. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003

A theoretical study is presented on the adsorption of the sarin molecule, a nerve agent, on three model solid surfaces: aliphatic (graphane), aromatic (graphene), and ionic (CaO). Calculations are carried out using accurate electronic structure methods based on configuration interaction (CI) as well as complementary density functional theory (DFT) and time dependent (TD) DFT calculations. The objective is to describe surface interactions accurately in order to identify factors that affect adsorption of sarin. Potential energy curves are calculated and compared between surface types. Computed CI binding energies to graphane, graphene, and calcium oxide surfaces are 2.2, 4.5, and 13.2 kcal/mol, respectively. The corresponding DFT binding energies are 6.4, 4.8, and 18.8 kcal/mol, respectively. Excited states of free sarin as well as sarin bound to the surfaces are examined using TDDFT and CI. Low-lying excited states of the adsorption complexes involving excitations from the surface to sarin are calculated.

The prevalence of salt bridges across protein binding interfaces is surprising given the significant costs of desolvating the two charged groups upon binding. These desolvation costs, which are difficult to examine using laboratory experiments, have been computed in previous studies using the Poisson−Boltzmann (PB) implicit solvent model. Here, for the first time, we directly compare the PB implicit solvent model with several explicit water models in computing the desolvation penalties of salt bridges across protein−protein interfaces. We report both overall agreement as well as significant differences between the implicit and explicit solvent results. These differences highlight challenges to be faced in the application of implicit solvent methods.

In recent years, first principles periodic Density Functional Theory (DFT) calculationhas been used to investigate heterogeneous catalytic reactions and examine catalyststructures as well as adsorption properties in a variety of systems. The increasingcontribution to give detailed understanding of elementary reaction mechanism is critical toprovide fundamental insights into the catalyst design. It is a link to the fundamentalknowledge and a bridge to the practical application. DFT calculations is also a powerfultool to predict and yield promising catalysts which is time- and cost-saving in the practicalend.Because of the recent boom in natural shale gas deposit, there is an increasing interestin developing more efficient ways to transform light alkanes into desired and high-valuechemicals, such as propylene. Propylene is a valuable raw material in the petrochemicalapplication to make value-added commodities, such as plastics, paints, and fibers, etc. Theconventional cracking, steam cracking (SC) and fluid catalytic cracking (FCC), could notmeet the growing demand of propylene. Thus, it has motivated extensive research ofproduction technologies. On the other hand, the abundance of light alkanes extracted fromthe shale gas makes on-purpose production an appealing method which is economicallycompetitive. Non-oxidative dehydrogenation of propane (PDH) is a one of ways to makeup the supply and solve the issue.xiiiAccording to the current research and industrial work, platinum (Pt) shows promisingperformance for the PDH. However, it suffered from some major drawbacks, such asthermodynamic limitation, rapid deactivation leading to poor catalytic performance andfrequent regeneration. In addition, it is a relatively high cost noble metal. Consequently,many efforts have been devoted to the enhancement of the catalytic performance. It wasfound that the stability and the selectivity of Pt-based catalysts can be improved viamodifying its properties with transition metals as promoters.In this thesis, DFT calculations were performed for propane dehydrogenation overtwo different catalyst systems, bimetallic platinum-zinc alloy and monometallic platinumcatalysts. The work provides insights into the catalyst crystal structures, the adsorptioncharacteristics of diverse adsorbates as well as the energy profiles regarding to theselectivity of the propane dehydrogenation. Bulk calculation signifies a stable tetragonalconfiguration of the PtZn catalyst which is in accordance with the experimental result. Thethermodynamic stability regarding to the stability of bulk and surface alloys are studiedwith the consideration of physical constrains. We have identified the thermodynamicstability of several PtZn low-index surface facets, (101), (110), (001), (100) flat surfacesand stepped surface (111), at certain chemical potential environmental conditions throughthe surface energy phase diagram. Stoichiometric and symmetric (101) slab isthermodynamically stable under the region of high Pt chemical potential, and the offstoichiometricand symmetric (100 Zn-rich) slab under the low Pt chemical potential.In this work, PtZn(101) is used as a model surface to demonstrate the effect on thecatalytic performance with zinc promotion of platinum. In comparison with Pt(111) surface,an elimination of 3-fold Pt hollow site on PtZn(101) is of important and it leads to thexivchange of binding site preferences. The divalent groups (1-propenyl, 2-propenyl) changefrom Pt top site on PtZn(101) to 3-fold site on Pt(111), which is because of the lack of Pt3-fold site on alloyed surface. As for propylene, it changes from di-σ site on PtZn to 𝜋 siteon Pt. The surface reaction intermediates are found to bond more weakly on PtZn(101)than on the Pt surface. Especially, the binding energy of propylene reduces from -1.09 to -0.16 eV. The weaker binding strength facilitates the activity of propylene on alloyedsurfaces.Through a complete and classic reaction network analysis, the introduction of Znshows an increase in the endothermicity and the energy barrier of each elementary reactionon the alloy surface. With the consideration of entropy for kinetic under real experimentalcondition, the alloying of Zn is found to lower the energy barrier for the propylene productdesorption and increases that for propylene dehydrogenation. Meanwhile, the competitionbetween desired C-H and undesired C-C cleavages is investigated. It is found that thecleavage of C-H is energetically favorable than that of C-C. These positive factorspotentially lead to a high selectivity toward propylene production on PtZn(101).Subsequently, Microkinetic modeling is performed to estimate kinetic parametersincluding the reaction order, rate-determining step to build a possible reaction mechanism.Finally, conclusions brought out about the comparison between bimetallic andmonometallic catalyst, and suggestions for future work are presented.

A mechanism of the adhesion between carbon fiber and epoxy resin is studied by using density functional theory (DFT) calculations. Surface structures of carbon fiber were modeled by the armchair-edge structure of graphite functionalized with OH and COOH groups. DFT calculations were performed to construct two realistic models of adhesion interface consisting of the functionalized carbon surface and a fragment of epoxy resin. Adhesive properties of the model interfaces were evaluated based on the binding energy (Eb) between the carbon surface and the resin as well as the maximum adhesive force (Fmax) acting at the interface. Calculated values of Eb are 13.8 kcal/mol for the OH-functionalized surface and 19.1 kcal/mol for the COOH-functionalized surface. The binding energy per hydrogen bond is calculated to be 6.9 kcal/mol (OH model; two H-bonds) and 6.3 kcal/mol (COOH model; three H-bonds), both of which are virtually similar and reasonable for the bond energy of a typical OH···O hydrogen bond. Analysis of adhesive force–displacement curves derived from energy–displacement plots revealed that Fmax is 0.52 nN for the OH model and 0.70 nN for the COOH model. Calculated adhesive properties are in good agreement with those previously reported for the interface between an aluminum oxide surface and an epoxy resin [J. Phys. Chem. C 2011, 115, 11701], strongly suggesting that hydrogen bonds between the oxygen-containing functional groups play a crucial role in the adhesive interaction in the carbon fiber/epoxy resin system.

The possibilities and problems to predict excited-state acidities and basicities in water with electronic structure calculations combined with a continuum solvation model are investigated for a test set of photoacids and photobases. Different error sources, like errors in the ground-state values, the excitation energies in solution for the neutral and (de-)protonated species, basis set effects, and contributions beyond implicit solvation are investigated and their contributions to the total error in are discussed. Density functional theory in combination with the conductor like screening model for real solvents and an empirical linear Gibbs free energy relationship are used to predict the ground-state values. For the test set, this approach gives more accurate values for the acids than for the bases. Time-dependent density-functional theory (TD-DFT) and second-order wave function methods in combination with the conductor like screening model are applied to compute excitation energies in water. Some TD-DFT functionals fail for several species to predict correctly the order of the lowest excitations. Where experimental data for absorption maxima in water is available, the implicit solvation model leads with the applied electronic structure methods in most cases for the excitation energies in water to an overestimation for the protonated and to an underestimation for the deprotonated species. The magnitude and sign of the errors depend on the hydrogen bond donating and accepting ability of the solute. We find that for aqueous solution this results generally in an underestimation in the changes from the ground to the excited state for photoacids and an overestimation for photobases.

• Novel cellulose-based biosorbent from Cistus albidus L leaves for BF dye removal. • Adsorption capacity for BF dye: 12.01 mg/g at C 0 = 100 mg/L after 60 minutes. • DFT and NCI calculations show cellulose contribute to adsorption BF dye. • Adsorption mechanism involves hydrogen bonding and van der Waals forces. • Kinetic, thermodynamic, and isothermic studies conducted for BF dye adsorption. Synthetic dyes are widely used in various industries, but the discharge of dye-contaminated effluents poses significant environmental and health hazards due to the persistence and toxicity of many dyes. Traditional remediation methods often face challenges regarding cost, efficiency, and environmental impact. This study introduces a novel, unmodified bioadsorbent derived from the powdered leaves of Cistus albidus L . (CSP) for the removal of Basic Fuchsin (BF) dye from aqueous solutions. The bioadsorbent was characterized using scanning electron microscopy (SEM) and Brunauer-Emmett-Teller (BET) analysis, revealing a well-structured mesoporous architecture with a surface area of 10.93 m²/g. Under optimal conditions (21°C, pH 10, initial BF concentration of 100 mg/L, contact time of 60 minutes, and a CSP dose of 5 g/L), the maximum adsorption capacity for BF dye reached 12.01 mg/g, demonstrating competitive efficiency relative to other plant-based adsorbents. The adsorption process was best described by the Freundlich isotherm model and pseudo-second-order kinetics, indicating multilayer adsorption on a heterogeneous surface. Density Functional Theory (DFT) calculations revealed that BF dye adsorbs onto the cellulose structure of CSP (R-CSP), with an interaction energy of E I n t e r a c t i o n = − 0.13 eV, confirming that the adsorption is thermodynamically favorable and exothermic. This energy therefore yields E b i n d i n g = 0.13 eV indicates a stable configuration for the R-CSP-BF complex. Furthermore, Non-Covalent Interaction (NCI) analysis highlighted the critical roles of hydrogen bonding and van der Waals forces in the adsorption of BF dye. These results underscore the potential of CSP as an effective and environmentally friendly bioadsorbent for removing dyes from wastewater.