Showing papers in "Physical Chemistry Chemical Physics in 2016"
TL;DR: The internal surface terminations of Ti3C2Tx MXene are identified and quantified and there are found to be significantly fewer -OH terminations than -F and -O, with the proportions highly dependent on the synthesis method.
Abstract: 1H and 19F NMR experiments have identified and quantified the internal surface terminations of Ti3C2Tx MXene. –F and –OH terminations are shown to be intimately mixed and there are found to be significantly fewer –OH terminations than –F and –O, with the proportions highly dependent on the synthesis method.
613 citations
TL;DR: Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs.
Abstract: As one of the most popular computational approaches in modern structure-based drug design, molecular docking can be used not only to identify the correct conformation of a ligand within the target binding pocket but also to estimate the strength of the interaction between a target and a ligand. Nowadays, as a variety of docking programs are available for the scientific community, a comprehensive understanding of the advantages and limitations of each docking program is fundamentally important to conduct more reasonable docking studies and docking-based virtual screening. In the present study, based on an extensive dataset of 2002 protein–ligand complexes from the PDBbind database (version 2014), the performance of ten docking programs, including five commercial programs (LigandFit, Glide, GOLD, MOE Dock, and Surflex-Dock) and five academic programs (AutoDock, AutoDock Vina, LeDock, rDock, and UCSF DOCK), was systematically evaluated by examining the accuracies of binding pose prediction (sampling power) and binding affinity estimation (scoring power). Our results showed that GOLD and LeDock had the best sampling power (GOLD: 59.8% accuracy for the top scored poses; LeDock: 80.8% accuracy for the best poses) and AutoDock Vina had the best scoring power (rp/rs of 0.564/0.580 and 0.569/0.584 for the top scored poses and best poses), suggesting that the commercial programs did not show the expected better performance than the academic ones. Overall, the ligand binding poses could be identified in most cases by the evaluated docking programs but the ranks of the binding affinities for the entire dataset could not be well predicted by most docking programs. However, for some types of protein families, relatively high linear correlations between docking scores and experimental binding affinities could be achieved. To our knowledge, this study has been the most extensive evaluation of popular molecular docking programs in the last five years. It is expected that our work can offer useful information for the successful application of these docking tools to different requirements and targets.
582 citations
TL;DR: In this article, a regularized entropy match (REMatch) approach was proposed to describe the similarity of both molecular and bulk periodic structures, introducing powerful metrics that enable the navigation of alchemical and structural complexities within a unified framework.
Abstract: Evaluating the (dis)similarity of crystalline, disordered and molecular compounds is a critical step in the development of algorithms to navigate automatically the configuration space of complex materials. For instance, a structural similarity metric is crucial for classifying structures, searching chemical space for better compounds and materials, and driving the next generation of machine-learning techniques for predicting the stability and properties of molecules and materials. In the last few years several strategies have been designed to compare atomic coordination environments. In particular, the smooth overlap of atomic positions (SOAPs) has emerged as an elegant framework to obtain translation, rotation and permutation-invariant descriptors of groups of atoms, underlying the development of various classes of machine-learned inter-atomic potentials. Here we discuss how one can combine such local descriptors using a regularized entropy match (REMatch) approach to describe the similarity of both whole molecular and bulk periodic structures, introducing powerful metrics that enable the navigation of alchemical and structural complexities within a unified framework. Furthermore, using this kernel and a ridge regression method we can predict atomization energies for a database of small organic molecules with a mean absolute error below 1 kcal mol(-1), reaching an important milestone in the application of machine-learning techniques for the evaluation of molecular properties.
533 citations
TL;DR: The Z-scheme heterostructure mechanism can well explain the improved photocatalytic activity of the g-C3N4/TiO2 heterost structure.
Abstract: Constructing a TiO2 based heterostructure is a very effective strategy for enhancing photocatalytic performance. The details of the electronic structure, interfacial interaction, and photogenerated carrier separation are important for explaining the photocatalytic properties of a heterostructure. Herein, the density of states, charge distribution, and the band offset of the monolayer g-C3N4/TiO2 heterojunction are systematically investigated through the hybrid DFT method. Results indicated that the valence band offset and the conduction band offset of the g-C3N4/TiO2 heterostructure were 0.40 and 0.18 eV, respectively. Interfacial interaction made the TiO2 surface with negative charge, whereas the g-C3N4 surface with positive charge, which led to the formation of a built-in electric field at the interface. Under illumination, the built-in electric field accelerates the transfer of photoexcited electrons in the CB of TiO2 into the VB of g-C3N4, thus resulting in the photoexcited electrons and holes naturally accumulating in the CB of g-C3N4 and the VB of TiO2, respectively. The photoexcited electrons and holes gathering in different surface regions efficiently prolonged the lifetime of photogenerated carriers. Meanwhile, electrons in the CB of g-C3N4 and holes in the VB of TiO2 had a stronger redox ability. Therefore, g-C3N4/TiO2 is a direct Z-scheme photocatalyst, and the Z-scheme heterostructure mechanism can well explain the improved photocatalytic activity of the g-C3N4/TiO2 heterostructure.
423 citations
TL;DR: Electrochemical findings showed that inhibitors impart high resistance towards charge transfer across the metal-electrolyte interface and behaved as mixed type inhibitors.
Abstract: In order to evaluate the effect of the functional group present in the ligand backbone towards corrosion inhibition performances, three Schiff-base molecules namely, (E)-4-((2-(2,4-dinitrophenyl)hydrazono)methyl)pyridine (L(1)), (E)-4-(2-(pyridin-4-ylmethylene)hydrazinyl)benzonitrile (L(2)) and (E)-4-((2-(2,4-dinitrophenyl)hydrazono)methyl)phenol (L(3)) were synthesized and used as corrosion inhibitors on mild steel in 1 M HCl medium. The corrosion inhibition effectiveness of the studied inhibitors was investigated by weight loss and several sophisticated analytical tools such as potentiodynamic polarization and electrochemical impedance spectroscopy measurements. Experimentally obtained results revealed that corrosion inhibition efficiencies followed the sequence: L(3) > L(1) > L(2). Electrochemical findings showed that inhibitors impart high resistance towards charge transfer across the metal-electrolyte interface and behaved as mixed type inhibitors. Scanning electron microscopy (SEM) was also employed to examine the protective film formed on the mild steel surface. The adsorption as well as inhibition ability of the inhibitor molecules on the mild steel surface was investigated by quantum chemical calculation and molecular dynamic (MD) simulation. In quantum chemical calculations, geometry optimized structures of the Schiff-base inhibitors, electron density distribution in HOMO and LUMO and Fukui indices of each atom were employed for their possible mode of interaction with the mild steel surfaces. MD simulations revealed that all the inhibitors molecules adsorbed in parallel orientation with respect to the Fe(110) surface.
352 citations
TL;DR: If the addition of KCl to such solutions can improve conductivity and hence jCO is investigated, Electrolytes containing KCl in combination with EMIM Cl, choline Cl, or DESs showed a two to three fold improvement in jCO in comparison to those without KCl.
Abstract: The electroreduction of CO2 to C1–C2 chemicals can be a potential strategy for utilizing CO2 as a carbon feedstock. In this work, we investigate the effect of electrolytes on the electroreduction of CO2 to CO on Ag based gas diffusion electrodes. Electrolyte concentration was found to play a major role in the process for the electrolytes (KOH, KCl, and KHCO3) studied here. Several fold improvements in partial current densities of CO (jCO) were observed on moving from 0.5 M to 3.0 M electrolyte solution independent of the nature of the anion. jCO values as high as 440 mA cm−2 with an energy efficiency (EE) of ≈ 42% and 230 mA cm−2 with EE ≈ 54% were observed when using 3.0 M KOH. Electrochemical impedance spectroscopy showed that both the charge transfer resistance (Rct) and the cell resistance (Rcell) decreased on moving from a 0.5 M to a 3.0 M KOH electrolyte. Anions were found to play an important role with respect to reducing the onset potential of CO in the order OH− (−0.13 V vs. RHE) < HCO3− (−0.46 V vs. RHE) < Cl− (−0.60 V vs. RHE). A decrease in Rct upon increasing electrolyte concentration and the effect of anions on the cathode can be explained by an interplay of different interactions in the electrical double layer that can either stabilize or destabilize the rate limiting CO2˙− radical. EMIM based ionic liquids and 1 : 2 choline Cl urea based deep eutectic solvents (DESs) have been used for CO2 capture but exhibit low conductivity. Here, we investigate if the addition of KCl to such solutions can improve conductivity and hence jCO. Electrolytes containing KCl in combination with EMIM Cl, choline Cl, or DESs showed a two to three fold improvement in jCO in comparison to those without KCl. Using such mixtures can be a strategy for integrating the process of CO2 capture with CO2 conversion.
331 citations
TL;DR: The results illustrate that the MM/GBSA rescoring has better capability to distinguish the correct binding structures from the decoys than the ZDOCK scoring and may be a good choice for predicting the binding affinities and identifying correctbinding structures for protein-protein systems.
Abstract: Understanding protein–protein interactions (PPIs) is quite important to elucidate crucial biological processes and even design compounds that interfere with PPIs with pharmaceutical significance. Protein–protein docking can afford the atomic structural details of protein–protein complexes, but the accurate prediction of the three-dimensional structures for protein–protein systems is still notoriously difficult due in part to the lack of an ideal scoring function for protein–protein docking. Compared with most scoring functions used in protein–protein docking, the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) methodologies are more theoretically rigorous, but their overall performance for the predictions of binding affinities and binding poses for protein–protein systems has not been systematically evaluated. In this study, we first evaluated the performance of MM/PBSA and MM/GBSA to predict the binding affinities for 46 protein–protein complexes. On the whole, different force fields, solvation models, and interior dielectric constants have obvious impacts on the prediction accuracy of MM/GBSA and MM/PBSA. The MM/GBSA calculations based on the ff02 force field, the GB model developed by Onufriev et al. and a low interior dielectric constant (ein = 1) yield the best correlation between the predicted binding affinities and the experimental data (rp = −0.647), which is better than MM/PBSA (rp = −0.523) and a number of empirical scoring functions used in protein–protein docking (rp = −0.141 to −0.529). Then, we examined the capability of MM/GBSA to identify the possible near-native binding structures from the decoys generated by ZDOCK for 43 protein–protein systems. The results illustrate that the MM/GBSA rescoring has better capability to distinguish the correct binding structures from the decoys than the ZDOCK scoring. Besides, the optimal interior dielectric constant of MM/GBSA for re-ranking docking poses may be determined by analyzing the characteristics of protein–protein binding interfaces. Considering the relatively high prediction accuracy and low computational cost, MM/GBSA may be a good choice for predicting the binding affinities and identifying correct binding structures for protein–protein systems.
325 citations
TL;DR: Spin-polarized calculations, combined with self-consistently determined Hubbard U that accounts for strong correlation energy, demonstrate that CrX3 (X = Cl, Br, I) monolayers are ferromagnetic and that Cr is trivalent and carries a magnetic moment of 3 μ(B); the resulting Cr(3+) ions are biocompatible.
Abstract: In addition to spintronics another motivation for exploring ferromagnetic two-dimensional materials is for biomedical applications such as magnetic labeling and hyperthermia treatment of tumors. Unfortunately, the widely studied Mn-containing monolayer is not biocompatible, although it is ferromagnetic. Here using first principles calculations combined with Monte Carlo simulations based on the Ising model, we systematically study a class of 2D ferromagnetic monolayers CrX3 (X = Cl, Br, I). The feasibility of exfoliation from their layered bulk phase is confirmed by the small cleavage energy and high in-plane stiffness. Spin-polarized calculations, combined with self-consistently determined Hubbard U that accounts for strong correlation energy, demonstrate that CrX3 (X = Cl, Br, I) monolayers are ferromagnetic and that Cr is trivalent and carries a magnetic moment of 3 μB; the resulting Cr3+ ions are biocompatible. The corresponding Curie temperatures for CrCl3, CrBr3 and CrI3 are found to be 66, 86, and 107 K, respectively, which can be increased to 323, 314, and 293 K by hole doping. The biocompatibility and ferromagnetism render these Cr-containing trihalide monolayers unique for applications.
292 citations
TL;DR: The major part of the observed overall specific capacity loss is reversible and induced by kinetic limitations, namely an impeded lithiation reaction during discharge, and the impact of parasitic reactions, such as oxidative electrolyte decomposition, on the irreversible capacity is negligible.
Abstract: The 1st cycle Coulombic efficiency (CE) of LiNi1/3Co1/3Mn1/3O2 (NCM) at 4.6 V vs. Li/Li(+) has been extensively investigated in NCM/Li half cells. It could be proven that the major part of the observed overall specific capacity loss (in total 36.3 mA h g(-1)) is reversible and induced by kinetic limitations, namely an impeded lithiation reaction during discharge. A measure facilitating the lithiation reaction, i.e. a constant potential (CP) step at the discharge cut-off potential, results in an increase in specific discharge capacity of 22.1 mA h g(-1). This capacity increase during the CP step could be proven as a relithiation process by Li(+) content determination in NCM via an ICP-OES measurement. In addition, a specific capacity loss of approx. 4.2 mA h g(-1) could be determined as an intrinsic reaction to the NCM cathode material at room temperature (RT). In total, less than 10.0 mA h g(-1) (=28% of the overall capacity loss) can be attributed to irreversible reactions, mainly to irreversible structural changes of NCM. Thus, the impact of parasitic reactions, such as oxidative electrolyte decomposition, on the irreversible capacity is negligible and could also be proven by on-line MS. As a consequence, the determination of the amount of extracted Li(+) ("Li(+) extraction ratio") so far has been incorrect and must be calculated by the charge capacity (=delithiation amount) divided by the theoretical capacity. In a NCM/graphite full cell the relithiation amount during the constant voltage (CV) step is smaller than in the half cell, due to irreversible Li(+) loss at graphite.
282 citations
TL;DR: The photophysical/chemical properties of MOFs are introduced; various strategies of modification ofMOFs towards better photocatalytic activity will be presented; the challenge and further perspective in MOF-based photocatalysis are addressed.
Abstract: Photocatalysis is a promising technology to convert solar energy into chemical energy. Recently, metal–organic frameworks (MOFs) have emerged as novel photocatalysts owing to their inherent structural characteristics of a large surface area and a well-ordered porous structure. Most importantly, via modulation of the organic linker/metal clusters or incorporation with metal/complex catalysts, not only the reactant adsorption and light absorption but also the charge separation and reactant activation will be largely promoted, leading to superior photocatalytic performance. In this article, we will first introduce the photophysical/chemical properties of MOFs; then various strategies of modification of MOFs towards better photocatalytic activity will be presented; finally, we will address the challenge and further perspective in MOF-based photocatalysis.
279 citations
TL;DR: It is revealed that light could greatly reduce the ion migration energy barrier in both polycrystalline and single crystalline OIHP, which is much shorter than what it was thought to take.
Abstract: Understanding the influence of light on ion migration in organic–inorganic halide perovskite (OIHP) materials is important to understand the photostability of perovskite solar cells. We reveal that light could greatly reduce the ion migration energy barrier in both polycrystalline and single crystalline OIHP. The activation energies derived from conductivity measurement under 0.25 Sun decrease to less than one half of the values in the dark. A typical ion drift velocity in CH3NH3PbI3 polycrystalline films is 1.2 μm s−1 under 1 Sun, compared with 0.016 μm s−1 under 0.02 Sun. Ion migration across the photoactive layers in most OIHP devices thus takes only subseconds under 1 Sun illumination, which is much shorter than what it was thought to take. Most important of all, ion migration through a single crystal surface is still too slow to be observed even after illumination for two days due to the large ion diffusion activation energy, >0.38 eV.
TL;DR: This investigation reveals a pre-edge feature in the O K-edge of highly catalytically active X-ray amorphous iridium oxides that is identified as O 2p hole states forming in conjunction with Ir(III) and these electronic defects in the near-surface region of the anionic and cationic framework are likely critical for the enhanced activity of amorphously irium oxides relative to their crystalline counterparts.
Abstract: Iridium oxide based electrodes are among the most promising candidates for electrocatalyzing the oxygen evolution reaction, making it imperative to understand their chemical/electronic structure. However, the complexity of iridium oxide's electronic structure makes it particularly difficult to experimentally determine the chemical state of the active surface species. To achieve an accurate understanding of the electronic structure of iridium oxide surfaces, we have combined synchrotron-based X-ray photoemission and absorption spectroscopies with ab initio calculations. Our investigation reveals a pre-edge feature in the O K-edge of highly catalytically active X-ray amorphous iridium oxides that we have identified as O 2p hole states forming in conjunction with IrIII. These electronic defects in the near-surface region of the anionic and cationic framework are likely critical for the enhanced activity of amorphous iridium oxides relative to their crystalline counterparts.
TL;DR: In this article, the authors present Raman and terahertz absorbance spectra of methylammonium lead halide single crystals (MAPbX3, X = I, Br, Cl) at temperatures between 80 and 370 K.
Abstract: We present Raman and terahertz absorbance spectra of methylammonium lead halide single crystals (MAPbX3, X = I, Br, Cl) at temperatures between 80 and 370 K. These results show good agreement with density-functional-theory phonon calculations. Comparison of experimental spectra and calculated vibrational modes enables confident assignment of most of the vibrational features between 50 and 3500 cm−1. Reorientation of the methylammonium cations, unlocked in their cavities at the orthorhombic-to-tetragonal phase transition, plays a key role in shaping the vibrational spectra of the different compounds. Calculations show that these dynamic effects split Raman peaks and create more structure than predicted from the independent harmonic modes. This explains the presence of extra peaks in the experimental spectra that have been a source of confusion in earlier studies. We discuss singular features, in particular the torsional vibration of the C–N axis, which is the only molecular mode that is strongly influenced by the size of the lattice. From analysis of the spectral linewidths, we find that MAPbI3 shows exceptionally short phonon lifetimes, which can be linked to low lattice thermal conductivity. We show that optical rather than acoustic phonon scattering is likely to prevail at room temperature in these materials.
TL;DR: The pairwise interactions of the constituent components of the choline chloride-urea DES are examined and it is found that the covalency of doubly ionic H-bonds can be greater than, or comparable with, neutral and ionic examples.
Abstract: Deep eutectic solvents (DESs) are exemplars of systems with the ability to form neutral, ionic and doubly ionic H-bonds. Herein, the pairwise interactions of the constituent components of the choline chloride-urea DES are examined. Evidence is found for a tripodal CHCl doubly ionic H-bond motif. Moreover it is found that the covalency of doubly ionic H-bonds can be greater than, or comparable with, neutral and ionic examples. In contrast to many traditional solvents, an "alphabet soup" of many different types of H-bond (OHO[double bond, length as m-dash]C, NHO[double bond, length as m-dash]C, OHCl, NHCl, OHNH, CHCl, CHO[double bond, length as m-dash]C, NHOH and NHNH) can form. These H-bonds exhibit substantial flexibility in terms of number and strength. It is anticipated that H-bonding will have a significant impact on the entropy of the system and thus could play an important role in the formation of the eutectic. The 2 : 1 urea : choline-chloride eutectic point of this DES is often associated with the formation of a [Cl(urea)2](-) complexed anion. However, urea is found to form a H-bonded urea[choline](+) complexed cation that is energetically competitive with [Cl(urea)2](-). The negative charge on [Cl(urea)2](-) is found to remain localised on the chloride, moreover, the urea[choline](+) complexed cation forms the strongest H-bond studied here. Thus, there is potential to consider a urea[choline](+)·urea[Cl](-) interaction.
TL;DR: ABCluster was extended to the optimization of clusters of rigid molecules, where "rigid" means that all internal degrees of freedom of the constituent molecules are frozen.
Abstract: The global optimization of molecular clusters is an important topic encountered in many fields of chemistry. In our previous work (Phys. Chem. Chem. Phys., 2015, 17, 24173), we successfully applied the recently introduced artificial bee colony (ABC) algorithm to the global optimization of atomic clusters and introduced the corresponding software “ABCluster”. In the present work, ABCluster was extended to the optimization of clusters of rigid molecules. Here “rigid” means that all internal degrees of freedom of the constituent molecules are frozen. The algorithm was benchmarked by TIP4P water clusters (H2O)N (N ≤ 20), for which all global minima were successfully located. It was further applied to various clusters of different chemical nature: 10 microhydration clusters, 4 methanol microsolvation clusters, 4 nonpolar clusters and 2 ion–aromatic clusters. In all the cases we obtained results consistent with previous experimental or theoretical studies.
TL;DR: This second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above, and all have non-trivial complete basis set limits.
Abstract: An energy decomposition analysis (EDA) separates a calculated interaction energy into as many interpretable contributions as possible; for instance, permanent and induced electrostatics, Pauli repulsions, dispersion and charge transfer. The challenge is to construct satisfactory definitions of all terms in the chemically relevant regime where fragment densities overlap, rendering unique definitions impossible. Towards this goal, we present an improved EDA for Kohn-Sham density functional theory (DFT) with properties that have previously not been simultaneously attained. Building on the absolutely localized molecular orbital (ALMO)-EDA, this second generation ALMO-EDA is variational and employs valid antisymmetric electronic wavefunctions to produce all five contributions listed above. These contributions moreover all have non-trivial complete basis set limits. We apply the EDA to the water dimer, the T-shaped and parallel-displaced benzene dimer, the p-biphthalate dimer "anti-electrostatic" hydrogen bonding complex, the biologically relevant binding of adenine and thymine in stacked and hydrogen-bonded configurations, the triply hydrogen-bonded guanine-cytosine complex, the interaction of Cl(-) with s-triazine and with the 1,3-dimethyl imidazolium cation, which is relevant to the study of ionic liquids, and the water-formaldehyde-vinyl alcohol ter-molecular radical cationic complex formed in the dissociative photoionization of glycerol.
TL;DR: A multi-peak deconvolution system and spectral band assignment were proposed based on the chemical and structural modifications identified by X-ray photoelectron spectroscopy, thermogravimetry,X-ray diffraction, specific surface areas and the comparative analysis of the first and second order regions of the Raman spectra.
Abstract: Raman spectroscopy is highly sensitive to the morphology and electronic structures of graphitic materials, but a convenient interpretation model has been lacking for multiwalled carbon nanotubes (MWCNTs), in particular for the discrimination of spectral changes induced by covalent functionalization. The present work describes a systematic investigation of the Raman analysis of covalently functionalized MWCNTs by diazonium chemistry and oxidation methodologies, with typically different mechanisms and reaction sites. A multi-peak deconvolution system and spectral band assignment were proposed based on the chemical and structural modifications identified by X-ray photoelectron spectroscopy, thermogravimetry, X-ray diffraction, specific surface areas and the comparative analysis of the first and second order regions of the Raman spectra. Diazonium functionalization takes place mainly in the π-system of the external sidewall, while oxidation occurs on defects and leads to structure burning. This allowed us to distinguish between spectral features related to aromaticity disruptions within the sidewalls and spectral features related to changes within the inner tubes. The model was validated extending the studies to the functionalization of MWCNTs by the Bingel reaction.
TL;DR: This work focuses on nanoporous carbon materials prepared by direct carbonization of zeolitic imidazolate frameworks (ZIF-8) towards supercapacitor applications, and demonstrates the effects of various factors on the performance.
Abstract: Nanoporous carbon materials are a versatile source of carbons that would be useful in applications ranging from electronics to electrochemical energy storage. Here, we focus on nanoporous carbon materials prepared by direct carbonization of zeolitic imidazolate frameworks (ZIF-8) towards supercapacitor applications. Several types of nanoporous carbons have been prepared by varying the applied carbonization temperature. The symmetric devices assembled using nanoporous carbon electrodes were tested for their optimal performance in the electrolyte of sulfuric acid solution. We demonstrate the effects of various factors (e.g., surface area, nitrogen content, degree of graphitization, and relative percentage of micropores) on the performance.
TL;DR: It is demonstrated that the substitution of methylammonium with the formamidinium cations inside the in organic cage gives greater robustness to the overall lattice and extends the material durability due to a different interaction between the organic molecules and the inorganic cage, which supports the use of FAPbI3 in applications, provided its structure can be stabilized in the dark phase at room temperature.
Abstract: We provide a semi-empirical model based on in situ degradation measurements to predict the durability of hybrid perovskite materials under simulated thermal operation conditions. In the model, the degradation path of MAPbI3 layers is proved to follow an Arrhenius-type law. The predictive role is played by the activation energy combined with its pre-exponential factor. Our comparative study under moisture conditions with respect to vacuum and nitrogen treatments has assessed the occurrence of an intrinsic dynamic exchange of protons between the organic cations and the inorganic cage with a direct impact on the lattice stability, for which the presence of water molecules is not mandatory. This mutual interaction produces defects inside the material and volatile species, such as HI, CH3NH2 or MAI, with an associated experimental activation energy of 1.54 eV measured under vacuum conditions in dark. This value is comparable to that calculated by the density functional theory for defect generation in MAPbI3. In air, the action of water molecules reduces the activation energy for proton exchanges in dark to 0.96 eV. As an alternative solution to increase the material stability, we demonstrate that the substitution of methylammonium (MA(+)) with the formamidinium (FA(+)) cations inside the inorganic cage gives greater robustness to the overall lattice and extends the material durability due to a different interaction between the organic molecules and the inorganic cage. This definitely supports the use of FAPbI3 in applications, provided its structure can be stabilized in the dark phase at room temperature.
TL;DR: The significant cocatalyst shape-sensitive photocatalytic activity in the Pt/g-C3N4 hybrids is revealed, revealing the disparity of active sites and adsorption energies in photoc atalytic reactions.
Abstract: Cubic, octahedral and spherical platinum (Pt) nanoparticles (NPs) ex situ supported on a graphitic carbon nitride (g-C3N4) substrate are synthesized using a colloidal adsorption–deposition method for photocatalytic hydrogen evolution reactions. These Pt NPs of different shapes have similar sizes of around 10 nm but have different facets exposed. It is found that the visible-light-driven photocatalytic activities for the Pt/g-C3N4 hybrid photocatalysts follow the order as: cubic Pt/g-C3N4 < octahedral Pt/g-C3N4 < spherical Pt/g-C3N4, revealing the significant cocatalyst shape-sensitive photocatalytic activity in the Pt/g-C3N4 hybrids. This is mainly due to the different surface atomic structures of different exposed facets of Pt NPs, which lead to the disparity of active sites and adsorption energies in photocatalytic reactions.
TL;DR: This perspective briefly describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics and provides numerous examples showing how computational methods have provided new insights into the physical and chemical features of complex systems including graphene and graphene derivatives.
Abstract: Graphene has attracted great interest because of its remarkable properties and numerous potential applications. A comprehensive understanding of its structural and dynamic properties and those of its derivatives will be required to enable the design and optimization of sophisticated new nanodevices. While it is challenging to perform experimental studies on nanoscale systems at the atomistic level, this is the ‘native’ scale of computational chemistry. Consequently, computational methods are increasingly being used to complement experimental research in many areas of chemistry and nanotechnology. However, it is difficult for non-experts to get to grips with the plethora of computational tools that are available and their areas of application. This perspective briefly describes the available theoretical methods and models for simulating graphene functionalization based on quantum and classical mechanics. The benefits and drawbacks of the individual methods are discussed, and we provide numerous examples showing how computational methods have provided new insights into the physical and chemical features of complex systems including graphene and graphene derivatives. We believe that this overview will help non-expert readers to understand this field and its great potential.
TL;DR: The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods and an improved, parameter-free scaling for the (T) contribution is proposed.
Abstract: The S66x8 dataset for noncovalent interactions of biochemical relevance has been re-examined by means of MP2-F12 and CCSD(F12*)(T) methods. We deem our revised benchmark data to be reliable to about 0.05 kcal mol−1 RMS. Most levels of DFT perform quite poorly in the absence of dispersion corrections: somewhat surprisingly, that is even the case for the double hybrids and for dRPA75. Analysis of optimized D3BJ parameters reveals that the main benefit of dRPA75 and DSD double hybrids alike is the treatment of midrange dispersion. dRPA75-D3BJ is the best performer overall at RMSD = 0.10 kcal mol−1. The nonlocal VV10 dispersion functional is especially beneficial for the double hybrids, particularly in DSD-PBEP86-NL (RMSD = 0.12 kcal mol−1). Other recommended dispersion-corrected functionals with favorable price/performance ratios are ωB97X-V, and, surprisingly, B3LYP-D3BJ and BLYP-D3BJ (RMSDs of 0.23, 0.20 and 0.23 kcal mol−1, respectively). Without dispersion correction (but parametrized for midrange interactions) M06-2X has the lead (RMSD = 0.45 kcal mol−1). A collection of three energy-based diagnostics yields similar information to an SAPT analysis about the nature of the noncovalent interaction. Two of those are the percentages of Hartree–Fock and of post-MP2 correlation effects in the interaction energy; the third, CSPI = [IE(2)ss − IE(2)ab]/[IE(2)ss + IE(2)ab] or its derived quantity DEBC = CSPI/(1 + CSPI2)1/2, describes the character of the MP2 correlation contribution, ranging from 0 (purely dispersion) to 1 (purely other effects). In addition, we propose an improved, parameter-free scaling for the (T) contribution based on the Ecorr[CCSD-F12b]/Ecorr[CCSD] and Ecorr[CCSD(F12*)]/Ecorr[CCSD] ratios. For Hartree–Fock and conventional DFT calculations, full counterpoise generally yields the fastest basis set convergence, while for double hybrids, half-counterpoise yields faster convergence, as previously established for correlated ab initio methods.
TL;DR: It is found that CH2OO does not substantially affect the lifetime of SO2 or HCOOH in the Southeast US, and the mechanism proposes a comprehensive reaction mechanism that can be incorporated into atmospheric models, which reproduces laboratory data over a wide range of relative humidities.
Abstract: We use a large laboratory, modeling, and field dataset to investigate the isoprene + O3 reaction, with the goal of better understanding the fates of the C1 and C4 Criegee intermediates in the atmosphere. Although ozonolysis can produce several distinct Criegee intermediates, the C1 stabilized Criegee (CH2OO, 61 ± 9%) is the only one observed to react bimolecularly. We suggest that the C4 Criegees have a low stabilization fraction and propose pathways for their decomposition. Both prompt and non-prompt reactions are important in the production of OH (28% ± 5%) and formaldehyde (81% ± 16%). The yields of unimolecular products (OH, formaldehyde, methacrolein (42 ± 6%) and methyl vinyl ketone (18 ± 6%)) are fairly insensitive to water, i.e., changes in yields in response to water vapor (≤4% absolute) are within the error of the analysis. We propose a comprehensive reaction mechanism that can be incorporated into atmospheric models, which reproduces laboratory data over a wide range of relative humidities. The mechanism proposes that CH2OO + H2O (k(H2O) ∼ 1 × 10−15 cm3 molec−1 s−1) yields 73% hydroxymethyl hydroperoxide (HMHP), 6% formaldehyde + H2O2, and 21% formic acid + H2O; and CH2OO + (H2O)2 (k(H2O)2 ∼ 1 × 10−12 cm3 molec−1 s−1) yields 40% HMHP, 6% formaldehyde + H2O2, and 54% formic acid + H2O. Competitive rate determinations (kSO2/k(H2O)n=1,2 ∼ 2.2 (±0.3) × 104) and field observations suggest that water vapor is a sink for greater than 98% of CH2OO in a Southeastern US forest, even during pollution episodes ([SO2] ∼ 10 ppb). The importance of the CH2OO + (H2O)n reaction is demonstrated by high HMHP mixing ratios observed over the forest canopy. We find that CH2OO does not substantially affect the lifetime of SO2 or HCOOH in the Southeast US, e.g., CH2OO + SO2 reaction is a minor contribution (<6%) to sulfate formation. Extrapolating, these results imply that sulfate production by stabilized Criegees is likely unimportant in regions dominated by the reactivity of ozone with isoprene. In contrast, hydroperoxide, organic acid, and formaldehyde formation from isoprene ozonolysis in those areas may be significant.
TL;DR: This review summarizes the advances in electrochemical biosensors based on Conducting polymer (CP) materials, which include recognition probe immobilisation techniques, transduction mechanisms and detection of various target biomolecules.
Abstract: Conducting polymer (CP)-based electrochemical biosensors have gained great attention as such biosensor platforms are easy and cost-effective to fabricate, and provide a direct electrical readout for the presence of biological analytes with high sensitivity and selectivity. CP materials themselves are both sensing elements and transducers of the biological recognition event at the same time, simplifying sensor designs. This review summarizes the advances in electrochemical biosensors based on CPs. Recognition probe immobilisation techniques, transduction mechanisms and detection of various target biomolecules have been discussed in detail. Efforts to miniaturize CP-based electrochemical biosensors and fabrication of sensor arrays are also briefly reviewed.
TL;DR: In this paper, it was shown that borophane has direction-dependent Dirac cones, which are mainly caused by the in-plane px and py orbitals of boron atoms and possess an ultrahigh Fermi velocity of up to 3.5 × 106 m s−1 under the HSE06 level, which is 4 times higher than that of graphene.
Abstract: The recent synthesis of monolayer borophene (triangular boron monolayer) on a substrate has opened the era of boron nanosheets (Science, 2015, 350, 1513), but the structural instability and a need to explore the novel physical properties are still open issues. Here we demonstrated that borophene can be stabilized by full surface hydrogenation (borophane), from first-principles calculations. Most interestingly, our calculations show that borophane has direction-dependent Dirac cones, which are mainly caused by the in-plane px and py orbitals of boron atoms. The Dirac fermions possess an ultrahigh Fermi velocity of up to 3.5 × 106 m s−1 under the HSE06 level, which is 4 times higher than that of graphene. The Young's moduli are calculated to be 190 and 120 GPa nm along two different directions, which are comparable to those of steel. The ultrahigh Fermi velocity and good mechanical features render borophane ideal for nanoelectronic applications.
TL;DR: These two kinds of upconversion processes are reviewed and their respective characteristics and merits are compared, with particular emphasis on molecular engineering of these two active upconverted materials.
Abstract: Organic upconversion is a unique process in which low-energy light (usually NIR light) is converted to high-energy light through either the two-photon absorption (TPA) mechanism or the triplet–triplet annihilation (TTA) mechanism. Both TPA upconversion (TPA-UC) and TTA upconversion (TTA-UC) have been actively investigated in recent years due to their intriguing applications in optics, biophotonics, and solar energy utilization. Although they show some similarity (i.e., belonging to the nonlinear two-quantum process and needing focused excitation light), TPA-UC and TTA-UC are very different, such as in mechanism, characteristics involved, molecular design and potential applications. Here, we collectively reviewed these two kinds of upconversion processes and compared their respective characteristics and merits. We also present recent advances made in the areas of TPA- and TTA-UC, the remaining challenges and opportunities, with particular emphasis on molecular engineering of these two active upconversion materials.
TL;DR: A first-principles quality high-dimensional neural network potential built from dispersion-corrected density functional theory data in molecular dynamics simulations is used to investigate water-copper interfaces as a prototypical case and finds that in general the copper-water interaction is rather weak.
Abstract: Solid–liquid interfaces have received considerable attention in recent years due to their central role in many technologically relevant fields like electrochemistry, heterogeneous catalysis and corrosion. As the chemical processes in these examples take place primarily at the interface, understanding the structural and dynamical properties of the interfacial water molecules is of vital importance. Here, we use a first-principles quality high-dimensional neural network potential built from dispersion-corrected density functional theory data in molecular dynamics simulations to investigate water–copper interfaces as a prototypical case. After performing convergence tests concerning the required supercell size and water film diameter, we investigate numerous properties of the interfacial water molecules at the low-index copper (111), (100) and (110) surfaces. These include density profiles, hydrogen bond properties, lateral mean squared displacements and residence times of the water molecules at the surface. We find that in general the copper–water interaction is rather weak with the strongest interactions observed at the Cu(110) surface, followed by the Cu(100) and Cu(111) surfaces. The distribution of the water molecules in the first hydration layer exhibits a double peak structure. In all cases, the molecules closest to the surface are predominantly allocated on top of the metal sites and are aligned nearly parallel with the oxygen pointing slightly to the surface. The more distant molecules in the first hydration layer at the Cu(111) and Cu(100) surfaces are mainly found in between the top sites, whereas at the Cu(110) surface most of these water molecules are found above the trenches of the close packed atom rows at the surface.
TL;DR: The graphene-family are promising materials for extracting s-DCF from wastewater effluents and the general-order kinetic model shows the best fit to the experimental data compared with pseudo-first order and pseudo-second order kinetic adsorption models.
Abstract: The interactions of sodium diclofenac drug (s-DCF) with different graphene species were investigated using both first principles calculations based on Density Functional Theory (DFT) and adsorption experiments. Through batch adsorption experiments, it was found that rGO was a good adsorbent for removing the s-DCF drug from aqueous solutions. The general-order kinetic model shows the best fit to the experimental data compared with pseudo-first order and pseudo-second order kinetic adsorption models. The equilibrium data (at 25 °C) were fitted to the Liu isotherm model. The maximum sorption capacity for adsorption of the s-DCF drug was 59.67 mg g−1 for rGO. The s-DCF adsorption onto pristine graphene, graphene with a vacancy, reduced oxide graphene (rGO) and functionalized graphene nanoribbons were simulated providing a good understanding of the adsorption process of this molecule on graphene-family surfaces. The results predict a physisorption regime in all cases. Based on these results, the ab initio calculations and the adsorption experiments point out that the graphene-family are promising materials for extracting s-DCF from wastewater effluents.
TL;DR: The composition of the lithium cation (Li(+)) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born-Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)-LiPF6 as a model system.
Abstract: The composition of the lithium cation (Li+) solvation shell in mixed linear and cyclic carbonate-based electrolytes has been re-examined using Born–Oppenheimer molecular dynamics (BOMD) as a function of salt concentration and cluster calculations with ethylene carbonate:dimethyl carbonate (EC:DMC)–LiPF6 as a model system. A coordination preference for EC over DMC to a Li+ was found at low salt concentrations, while a slightly higher preference for DMC over EC was found at high salt concentrations. Analysis of the relative binding energies of the (EC)n(DMC)m–Li+ and (EC)n(DMC)m–LiPF6 solvates in the gas-phase and for an implicit solvent (as a function of the solvent dielectric constant) indicated that the DMC-containing Li+ solvates were stabilized relative to (EC4)–Li+ and (EC)3–LiPF6 by immersing them in the implicit solvent. Such stabilization was more pronounced in the implicit solvents with a high dielectric constant. Results from previous Raman and IR experiments were reanalyzed and reconciled by correcting them for changes of the Raman activities, IR intensities and band shifts for the solvents which occur upon Li+ coordination. After these correction factors were applied to the results of BOMD simulations, the composition of the Li+ solvation shell from the BOMD simulations was found to agree well with the solvation numbers extracted from Raman experiments. Finally, the mechanism of the Li+ diffusion in the dilute (EC:DMC)LiPF6 mixed solvent electrolyte was studied using the BOMD simulations.
TL;DR: This work presents SREFLEX, a hybrid modeling approach that uses normal mode analysis (NMA) to explore the conformational space of high-resolution models and refine the structure guided by the agreement with the experimental SAXS data.
Abstract: Structural flexibility and conformational rearrangements are often related to important functions of biological macromolecules, but the experimental characterization of such transitions with high-resolution techniques is challenging. At a lower resolution, small angle X-ray scattering (SAXS) can be used to obtain information on biomolecular shapes and transitions in solution. Here, we present SREFLEX, a hybrid modeling approach that uses normal mode analysis (NMA) to explore the conformational space of high-resolution models and refine the structure guided by the agreement with the experimental SAXS data. The method starts from a given conformation of the protein (which does not agree with the SAXS data). The structure is partitioned into pseudo-domains either using structural classification databases or automatically from the protein dynamics as predicted by the NMA. The algorithm proceeds hierarchically employing NMA to first probe large rearrangements and progresses into smaller and more localized movements. At the large rearrangements stage the pseudo-domains stay as rigid bodies allowing one to avoid structural disruptions inherent to the earlier NMA-based algorithms. To validate the approach, we compiled a representative benchmark set of 88 conformational states known experimentally at high resolution. The performance of the algorithm is demonstrated in the simulated data on the benchmark set and also in a number of experimental examples. SREFLEX is included into the ATSAS program package freely available to the academic users, both for download and in the on-line mode.