Machine learning recognition of protein secondary structures based on two-dimensional spectroscopic descriptors.

Protein secondary structure discrimination is crucial for understanding their biological function. It is not generally possible to invert spectroscopic data to yield the structure. We present a machine learning protocol which uses two-dimensional UV (2DUV) spectra as pattern recognition descriptors, aiming at automated protein secondary structure determination from spectroscopic features. Accurate secondary structure recognition is obtained for homologous (97%) and nonhomologous (91%) protein segments, randomly selected from simulated model datasets. The advantage of 2DUV descriptors over one-dimensional linear absorption and circular dichroism spectra lies in the cross-peak information that reflects interactions between local regions of the protein. Thanks to their ultrafast (∼200 fs) nature, 2DUV measurements can be used in the future to probe conformational variations in the course of protein dynamics.

Understanding the Interface Enhancement Mechanisms of CFRP with the Polydopamine-Polyetheramine Interphase at the Molecular Level.

In this work, polydopamine (PDA) and polyetheramine D230 were selected to construct the PDA-D230 interphase between the carbon fiber (CF) and epoxy matrix. Density functional theory (DFT) and molecular dynamics (MD) simulations were performed to explore the interface enhancement mechanisms of a carbon fiber reinforced polymer (CFRP) with the PDA-D230 interphase from the molecular level. The adsorption characteristics of a PDA molecule on the CF surface were investigated using the DFT method. The results show that stronger π-π stacking interactions are formed due to the structure and orientation preference of the PDA molecule. The interfacial structures and properties of CFRP with the PDA-D230 interphase are derived from MD simulations. The PDA-D230 interphase on the CF surface induces stronger interfacial interaction energy, leading to the better load transfer between the CF and epoxy matrix. The existence of the PDA-D230 interphase on the CF surface can decrease the mean-square displacement (MSD) value and the free volume fraction of CFRP, which restricts the movement of epoxy atoms and inhibits the translational and rotational motion of epoxy chains. Compared with the epoxy using pristine CFs as reinforcement, the interfacial shear stress (ISS) of CFRP with the PDA-D230 interphase is improved by 13.1%. Our results provide valuable insights into the interface characteristics of CFRP with the PDA-D230 interphase, which are of great significance for exploring the strengthening mechanisms for CFRPs with the PDA-D230 interphase.

Theoretical mechanism study on the electrochemical benzylation of [60]fullerene derivatives.

The electrochemical methodology is available for the functionalization of fullerenes. However, intricate and ambiguous issues remain to be identified for some electrochemical reactions. In this work, density functional theory (DFT) calculations reveal that the electron delocalization of C60 in fullerobenzofuran (RF5) and the C60-fused lactone (RL6) declines with the electron injection of electrochemistry, and clear active sites can be obtained to react with the electrophilic agent. Furthermore, the selectivity of the addition reaction depends on the Oδ- site, which is inclined to react with the Cδ+ of C60 after electron injection or the Cδ+ of PhCH2+, forming a new C-O bond.

First principles terahertz spectroscopy of molecular crystals: the crucial role of periodic boundary conditions benchmarked with experimental L-ascorbic acid spectra.

The terahertz (THz) region vibration spectral signatures of molecular crystals can usually be ascribed to the low-frequency vibrational modes related to weak intermolecular interactions, e.g. van der Waals (vdW) interactions or hydrogen bonding. These interactions collectively dictate the compositional units deviating from their equilibrium configurations. The collective movements are intrinsically long-range, and hence the boundary conditions used for theoretical calculation can affect the corresponding potential energy gradients and alter the vibrational features. In this work, we constructed a series of finite-sized cluster models with varying sizes and an extended periodic crystal model for L-ascorbic acid (L-AA) crystals. Density functionals with both semi-local contributions and nonlocal vdW terms, implemented with either atom-centered Gaussian basis or plane waves, were tested. By comparing first principles calculations with experimental time-domain spectra (TDS), we found that the non-local vdW functional opt-B88 combined with a periodic boundary condition is capable of assigning all the experimental features in the 0.2-1.6 THz region. Calculations with cluster models failed in this task. Even worse, the deficiency of the cluster models varied with cluster sizes, and did not converge as the cluster size grew. Our results demonstrate that an appropriate periodic boundary condition is essential to correctly assign and analyze the THz vibration spectra of molecular crystals.

Two-dimensional metal-organic frameworks as bifunctional electrocatalysts for the oxygen evolution reaction and oxygen reduction reaction (OER/ORR): a theoretical study.

Effective bifunctional catalysts are needed for the two main processes in metal-air batteries (oxygen evolution reaction and oxygen reduction reaction (OER/ORR)) to increase efficiency. Herein, we systematically investigate the stability, electronic structure, and catalytic performance of the OER/ORR of two-dimensional (2D) conducting metal-organic frameworks (MOFs) M3(C6Se6)2 (M = Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zr, Nb, Mo, Ru, Rh, Pd, Ir, and Pt) by first-principles calculations. The results show that Co3(C6Se6)2 has an overpotential of 0.51 V and 0.3 V for the OER and ORR, respectively, and Rh3(C6Se6)2 has an overpotential of 0.53 V and 0.29 V for the OER and ORR, respectively, which are very promising bifunctional catalysts. In addition, Ir3(C6Se6)2 is a very promising ORR catalyst with a low overpotential of 0.34 V. Volcano plots and contour maps of OER/ORR activity versus intermediate adsorption strength were established to describe the activity trend of M3(C6Se6)2 based on the relationship of adsorbed intermediates. Furthermore, the d-band center theory and crystal orbital Hamilton populations (COHPs) were used to relate the OER/ORR activity to the d-electrons of the central metal. Our study not only provides a novel bifunctional electrocatalyst but also provides some references for other 2D MOFs as electrocatalysts.

Can N, S Cocoordination Promote Single Atom Catalyst Performance in CO2 RR? Fe-N2 S2 Porphyrin versus Fe-N4 Porphyrin.

Single atom catalysts (SACs) are promising electrocatalysts for CO2 reduction reaction (CO2 RR), in which the coordination environment plays a crucial role in intrinsic catalytic activity. Taking the regular Fe porphyrin (Fe-N4 porphyrin) as a probe, the study reveals that the introduction of opposable S atoms into N coordination (Fe-N2 S2 porphyrin) allows for an appropriate electronic structural optimization on active sites. Owing to the additional orbitals around the Fermi level and the abundant Fe dz2 orbital occupation after S substitution, N, S cocoordination can effectively tune SACs and thus facilitating protonation of intermediates during CO2 RR. CO2 RR mechanisms lead to possible C1 products via two-, six-, and eight-electron pathways are systematically elucidated on Fe-N4 porphyrin and Fe-N2 S2 porphyrin. Fe-N4 porphyrin yields the most favorable product of HCOOH with a limiting potential of -0.70 V. Fe-N2 S2 porphyrin exhibits low limiting potentials of -0.38 and -0.40 V for HCOOH and CH3 OH, respectively, surpassing those of most Cu-based catalysts and SACs. Hence, the N, S cocoordination might provide better catalytic environment than regular N coordination for SACs in CO2 RR. This work demonstrates Fe-N2 S2 porphyrin as a high-performance CO2 RR catalyst, and highlights N, S cocoordination regulation as an effective approach to fine tune high atomically dispersed electrocatalysts.

Ultrafast stimulated resonance Raman signatures of lithium polysulfides for shuttling effect characterization: An ab initio study.

The shuttling effect is a crucial obstacle to the practical deployment of lithium sulfur batteries (LSBs). This can be ascribed to the generation of lithium polysulfide (LiPS) redox intermediates that are soluble in the electrolyte. The detailed mechanism of the shuttling, including the chemical structures responsible for the loss of effective mass and the dynamics/kinetics of the redox reactions, are not clear so far. To obtain this microscopic information, characterization techniques with high spatial and temporal resolutions are required. Here, we propose that resonance Raman spectroscopy combined with ultrafast broadband pulses is a powerful tool to reveal the mechanism of the shuttling effect. By combining the chemical bond level spatial resolution of resonance Raman and the femtosecond scale temporal resolution of the ultrafast pulses, this novel technique holds the potential of capturing the spectroscopic fingerprints of the LiPS intermediates during the working stages of LSBs. Using ab initio simulations, we show that, in addition to the excitation energy selective enhancement, resonance Raman signals of different LiPS intermediates are also characteristic and distinguishable. These results will facilitate the real-time in situ monitoring of LiPS species and reveal the underlying mechanism of the shuttling effect.

One-step Ethylene Purification from an Acetylene/Ethylene/Ethane Ternary Mixture by Cyclopentadiene Cobalt-Functionalized Metal-Organic Frameworks.

The separation of ethylene (C2 H4 ) from a mixture of ethane (C2 H6 ), ethylene (C2 H4 ), and acetylene (C2 H2 ) at normal temperature and pressure is a significant challenge. The sieving effect of pores is powerless due to the similar molecular size and kinetic diameter of these molecules. We report a new modification method based on a stable ftw topological Zr-MOF platform (MOF-525). Introduction of a cyclopentadiene cobalt functional group led to new ftw-type MOFs materials (UPC-612 and UPC-613), which increase the host-guest interaction and achieve efficient ethylene purification from the mixture of hydrocarbon gases. The high performance of UPC-612 and UPC-613 for C2 H2 /C2 H4 /C2 H6 separation has been verified by gas sorption isotherms, density functional theory (DFT), and experimentally determined breakthrough curves. This work provides a one-step separation of the ternary gas mixture and can further serve as a blueprint for the design and construction of function-oriented porous structures for such applications.

ZIF-8@ZIF-67-Derived Nitrogen-Doped Porous Carbon Confined CoP Polyhedron Targeting Superior Potassium-Ion Storage.

Potassium ion batteries (KIB) have become a compelling energy-storage system owing to their cost effectiveness and the high abundance of potassium in comparison with lithium. However, its practical applications have been thwarted by a series of challenges, including marked volume expansion and sluggish reaction kinetics caused by the large radius of potassium ions. In line with this, the exploration of reliable anode materials affording high electrical conductivity, sufficient active sites, and structural robustness is the key. The synthesis of ZIF-8@ZIF-67 derived nitrogen-doped porous carbon confined CoP polyhedron architectures (NC@CoP/NC) to function as innovative KIB anode materials is reported. Such composites enable an outstanding rate performance to harvest a capacity of ≈200 mAh g-1 at 2000 mA g-1 . Additionally, a high cycling stability can be gained by maintaining a high capacity retention of 93% after 100 cycles at 100 mA g-1 . Furthermore, the potassium ion storage mechanism of the NC@CoP/NC anode is systematically probed through theoretical simulations and experimental characterization. This contribution may offer an innovative and feasible route of emerging anode design toward high performance KIBs.

Quantum Chemical Study of the Carbon Dioxide-Philicity of Surfactants: Effects of Tail Functionalization.

Carbon dioxide (CO2)-philic surfactants have broad application prospects in organic synthesis, fracture-enhanced oil recovery, polymerization, extraction, and other fields and can be used to enhance the viscosity of supercritical CO2 (scCO2). In this work, the relationship between the functional group of the surfactant tail and CO2-philicity is studied from a new perspective using density functional theory. Three common functional group types (fluorinated, oxidative, and methyl groups) were investigated. The analysis of binding energy demonstrates that all three types of functional groups can improve the CO2-philicity of the surfactant. Among these three kinds of functional groups, the strongest interaction with CO2 molecules is observed for oxidative functional groups followed by semifluorinated, fluorinated, and methyl groups. However, the CO2 molecules tend to be adsorbed onto the middle segment of the oxidative group, and the intrusion of the CO2 molecules results in the low solubility of oxidative surfactants. In contrast, fluorinated and methyl groups interact with CO2 at the end of the surfactant tail. As a result, the fluorinated surfactants show the best solubility in CO2. Therefore, the solubility of a surfactant in CO2 is not only related to the interaction strength between the surfactant and CO2, it also depends on the interaction structure. The results of this study provide a new strategy for evaluating surfactant CO2-philicity and provide guidance for the design of surfactants with high solubility in scCO2.

Adsorption and dehydrogenation of C2-C6n-alkanes over a Pt catalyst: a theoretical study on the size effects of alkane molecules and Pt substrates.

Adsorption and dehydrogenation of C2-C6n-alkanes are investigated on a Pt substrate using density functional theory (DFT) calculations, and the size effects of alkane molecules and Pt substrates are discussed in detail. The Pt(111) surface and Pt55 cluster are chosen to represent large and small Pt nanoparticles, respectively. The C2-C6 straight-chain alkanes show no site preference on Pt(111) drifting over the surface, but prefer to locate along the edge sites of Pt55. Our results suggest that a linear relationship holds for the adsorption energies of n-alkanes against the chain length on Pt(111), in accordance with the experimental observations. Pt55 also exhibits a similar linear relationship for n-alkanes but with larger adsorption energies due to the low-coordinated Pt atoms at the edge site. For the two-step dehydrogenation from alkanes to alkenes, the first dehydrogenation reaction is the rate-determining step (RDS) on Pt(111), and a larger size of alkane molecule will lead to a lower dehydrogenation activity. While on Pt55, no RDS is present and the dehydrogenation activity oscillates slightly as the chain length of n-alkane increases. Generally, Pt55 involves lower energy barriers for most dehydrogenation steps compared to Pt(111), indicating that small Pt particles with more low-coordinated Pt atoms are more active towards alkane dehydrogenation. In addition, a clear BEP relationship is identified for all the dehydrogenation reactions of C2-C6n-alkanes on Pt substrates, and this linear relationship is independent of the particle size of the Pt substrate and the chain length of alkanes.

General Nondestructive Passivation by 4-Fluoroaniline for Perovskite Solar Cells with Improved Performance and Stability.

Hybrid perovskite thin films are prone to producing surface vacancies during the film formation, which degrade the stability and photovoltaic performance. Passivation via post-treatment can heal these defects, but present methods are slightly destructive to the bulk of 3D perovskite due to the solvent effect, which hinders fabrication reproducibility. Herein, nondestructive surface/interface passivation using 4-fluoroaniline (FAL) is established. FAL is not only an effective antisolvent candidate for surface modification, but also a large dipole molecule (2.84 Debye) with directional field for charge separation. Density functional theory calculation reveals that the nondestructive properties are attributed to both the conjugated amine in aromatic ring and the para-fluoro-substituent. A hot vapor assisted colloidal process is employed for the post-treatment. The molecular passivation yields an ultrathin protection layer with a hydrophobic fluoro-substituent tail and thus enhances the stability and optoelectronic properties. FAL post-treated perovskite solar cell (PSC) delivers a 20.48% power conversion efficiency under ambient conditions. Micro-photoluminescence reveals that passivation activates the dark defective state at the surface and interface, delivering the impact picture of boundary on the local carriers. This work demonstrates a generic nondestructive chemical approach for improving the performance and stability of PSCs.

Insight into thiophene hydrodesulfurization on clean and S-modified MoP(010): a periodic density functional theory study.

The hydrodesulfurization (HDS) of thiophene on clean and S-modified MoP(010) is investigated to understand the HDS mechanism as well as the surface sulfur (S) atom effect using periodic density functional theory (DFT). The results show that thiophene prefers strongly flat adsorption on both the clean and S-modified surfaces, in either the molecular state or the dissociative state breaking simultaneously one C-S bond, and the adsorption of thiophene can be slightly weakened by the surface S atom. Thermodynamic and kinetic analysis indicates that the HDS of thiophene in both the molecular and dissociative adsorption states prefers to take place along the direct desulfurization (DDS) pathway rather than hydrogenation on both the clean and S-modified MoP(010) surfaces. Surface S shows a promotion effect on the HDS catalytic activity of MoP(010), because the energy barrier/rate constant of the rate-determining step on the DDS pathway is decreased/enlarged under the S modification. Compared with the situation of MoP(001), MoP(010) should have relatively low HDS activity, since a higher energy barrier as well as weaker exothermicity is involved in the reaction on the latter surface.

Metallic Iron-Nickel Sulfide Ultrathin Nanosheets As a Highly Active Electrocatalyst for Hydrogen Evolution Reaction in Acidic Media.

We report on the synthesis of iron-nickel sulfide (INS) ultrathin nanosheets by topotactic conversion from a hydroxide precursor. The INS nanosheets exhibit excellent activity and stability in strong acidic solutions as a hydrogen evolution reaction (HER) catalyst, lending an attractive alternative to the Pt catalyst. The metallic α-INS nanosheets show an even lower overpotential of 105 mV at 10 mA/cm(2) and a smaller Tafel slope of 40 mV/dec. With the help of DFT calculations, the high specific surface area, facile ion transport and charge transfer, abundant electrochemical active sites, suitable H(+) adsorption, and H2 formation kinetics and energetics are proposed to contribute to the high activity of the INS ultrathin nanosheets toward HER.

Theoretical Investigation of the Methanol Decomposition by Fe+)and Fe(C2H4)+: A π-Type Ligand Effect.

Density functional theory has been used to probe the mechanism of gas-phase methanol decomposition by bare Fe(+) and ligated Fe(C(2)H(4))(+) in both quartet and sextet states. For the Fe(+)/methanol system, Fe(+) could directly attach to the O and methyl-H atoms of methanol, respectively, forming two encounter isomers. The methanol reaction with Fe(+) prefers initial C-O bond activation to yield methyl with slight endothermicity, whereas CH(4) elimination is hindered by the strong endothermicity and high-energy barrier of hydroxyl-H shift. For the Fe(C(2)H(4))(+)/methanol system, the major product of H(2)O is formed through six elementary steps: encounter complexation, C-O bond activation, C-C coupling, ß-H shift, hydride H shift, and nonreactive dissociation. Both ligand exchange and initial C-O bond activation mechanisms could account for ethylene elimination with the ion products Fe(CH(3)OH)(+) and (CH(3))Fe(OH)(+), respectively. With the assistance of a π-type C(2)H(4) ligand, the metal center in the Fe(C(2)H(4))(+)/CH(3)OH system avoids formation of unfavorable multi-σ-type bonding and thus greatly enhances the reactivity compared to that of bare Fe(+).

Trapping and structure determination of an intermediate in the allosteric transition of aspartate transcarbamoylase.

X-ray crystallography and small-angle X-ray scattering (SAXS) in solution have been used to show that a mutant aspartate transcarbamoylase exists in an intermediate quaternary structure between the canonical T and R structures. Additionally, the SAXS data indicate a pH-dependent structural alteration consistent with either a pH-induced conformational change or a pH-induced alteration in the T to R equilibrium. These data indicate that this mutant is not a model for the R state, as has been proposed, but rather represents the enzyme trapped along the path of the allosteric transition between the T and R states.

The adsorption behaviour of CH4 on microporous carbons: effects of surface heterogeneity.

The effects of chemical and structural surface heterogeneity on the CH4 adsorption behaviour on microporous carbons have been investigated using a hybrid theoretical approach, including the use of density functional theory (DFT), molecular dynamics (MD), and grand canonical Monte Carlo (GCMC) simulations. Bader charge analysis is first performed to analyze the surface atomic partial charges. The CH4 adsorption densities in defective and functionalized graphite slit pores are lower than that in the perfect pore according to the MD simulations. Finally, the CH4 adsorption isotherms for the perfect, defective and functionalized slit pores are analyzed using the GCMC simulations in combination with the DFT and MD results. For pores with a defective surface, the adsorption capacities decrease; the embedded functional groups decrease the adsorption capacity at low pressure and enhance it at high pressure. Our results demonstrate the significant effects of chemical and structural surface heterogeneity on the CH4 adsorption and provide a systematic approach to understand the gas adsorption behaviour.

Density Functional Theory Study of Methanol Steam Reforming on Pt3Sn(111) and the Promotion Effect of a Surface Hydroxy Group.

Methanol steam reforming (MSR) is studied on a Pt3Sn surface using the density functional theory (DFT). An MSR network is mapped out, including several reaction pathways. The main pathway proposed is CH3OH + OH → CH3O → CH2O → CH2O + OH → CH2OOH → CHOOH → COOH → COOH + OH → CO2 + H2O. The adsorption strengths of CH3OH, CH2O, CHOOH, H2O and CO2 are relatively weak, while other intermediates are strongly adsorbed on Pt3Sn(111). H2O decomposition to OH is the rate-determining step on Pt3Sn(111). The promotion effect of the OH group is remarkable on the conversions of CH3OH, CH2O and trans-COOH. In particular, the activation barriers of the O-H bond cleavage (e.g., CH3OH → CH3O and trans-COOH → CO2) decrease substantially by ~1 eV because of the involvement of OH. Compared with the case of MSR on Pt(111), the generation of OH from H2O decomposition is more competitive on Pt3Sn(111), and the presence of abundant OH facilitates the combination of CO with OH to generate COOH, which accounts for the improved CO tolerance of the PtSn alloy over pure Pt.

Catalytic System-Controlled Regioselective 1,2- and 1,4-Carboannulations of [60]Fullerene.

Selective functionalization of fullerenes is an important but challenging topic in fullerene chemistry and synthetic chemistry. Here we present the first example of catalytic system-controlled regioselective 1,2- and 1,4-addition reactions for the flexible and efficient synthesis of novel 1,2- and 1,4-carbocycle-fused fullerenes via a palladium-catalyzed decarboxylative carboannulation process.

Understanding and controlling the formation of single-atom site from supported Cu10 cluster by tuning CeO2 reducibility: Theoretical insight into the Gd-doping effect on electronic metal-support interaction.

Controlling the formation of single-atom (SA) sites from supported metal clusters is an important and interesting issue to effectively improve the catalytic performance of heterogeneous catalysts. For extensively studied CO oxidation over metal/CeO2 systems, the SA formation and stabilization under reaction conditions is generally attributed to CO adsorption, however, the pivotal role played by the reducible CeO2 support and the underlying electronic metal-support interaction (EMSI) are not yet fully understood. Based on a ceria-supported Cu10 catalyst model, we performed density functional theory calculations to investigate the intrinsic SA formation mechanism and discussed the synergistic effect of Gd-doped CeO2 and CO adsorption on the SA formation. The CeO2 reducibility is tuned with doped Gd content ranging from 12.5 % ∼ 25 %. Based on ab initio thermodynamic and ab initio molecular dynamics, the critical condition for SA formation was identified as 21.875 % Gd-doped CeO2 with CO-saturated adsorption on Cu10. Electronic analysis revealed that the open-shell lattice Oδ- (δ < 2) generated by Gd doping facilitates the charge transfer from the bottom-corner Cu (Cubc) to CeO2. The CO-saturated adsorption further promotes this charge transfer process and enhances the EMSI between Cubc and CeO2, leading to the disintegration of Cubc from Cu10 and subsequent formation of the active SA site.