An Unprecedented Interconversion Between Non-covalent and Covalent Interactions Driven by Halogen Bonding.

The spontaneous interconversion between covalent forces and noncovalent counterparts remains an unexplained mystery to date. Here we have discovered a marvelous transformation between them through halogen bonding using NI3 as a prototype. Our results show that the interaction strength of the NI3 dimer is 7.01 kcal mol-1 , demonstrating that it is a quite strong halogen bond. Molecular orbital analyses indicate that the frontier molecular orbitals result from strong mixing of the fragment orbitals, which may be the electronic structure basis for interconversion. Further studies on a series of NI3 oligomers (5-, 10-, 15-, 20-, 26-, 30-mer) show that the interconversion occurs approximately at 26-mer on the basis on bond distance, ELF, etc.; the interconversion is a gradual transformation and not a sudden one. This study provides more insights into the halogen bonding and the high explosivity of NI3 containing species.

An improved DNA force field for ssDNA interactions with gold nanoparticles.

The widespread applications of single-stranded DNA (ssDNA) conjugated gold nanoparticles (AuNPs) have spurred an increasing interest in the interactions between ssDNA and AuNPs. Despite extensive studies using the most sophisticated experimental techniques, the detailed molecular mechanisms still remain largely unknown. Large scale molecular dynamics (MD) simulations can thus be used to supplement experiments by providing complementary information about ssDNA-AuNP interactions. However, up to now, all modern force fields for DNA were developed based on the properties of double-stranded DNA (dsDNA) molecules, which have hydrophilic outer backbones "protecting" hydrophobic inner nucleobases from water. Without the double-helix structure of dsDNA and thus the "protection" by the outer backbone, the nucleobases of ssDNA are directly exposed to solvent, and their behavior in water is very different from that of dsDNA, especially at the interface with nanoparticles. In this work, we have improved the force field of ssDNA for use with nanoparticles, such as AuNPs, based on recent experimental results and quantum mechanics calculations. With the new improved force field, we demonstrated that a poly(A) sequence adsorbed on a AuNP surface is much more stable than a poly(T) sequence, which is consistent with recent experimental observations. On the contrary, the current standard force fields, including AMBER03, CHARMM27, and OPLSAA, all gave erroneous results as compared to experiments. The current improved force field is expected to have wide applications in the study of ssDNA with nanomaterials including AuNPs, which might help promote the development of ssDNA-based biosensors and other bionano-devices.

The aromatic amino acid phenylalanine: a versatile tool for binding transition metal ions.

CONTEXT: The human body contains many different types of transition metal ions, such as Zn2+, Cu2+, which are involved in many physiological processes. An excess or deficiency of these ions can cause diseases, such as Alzheimer's disease, which is closely related to the levels of these ions in the body. In-depth understanding of various physiological and pathological mechanisms related to metal ions requires understanding the interaction between metal ions and nearby amino acids at the atomic level. This article selected four transition metal ions: Zn2+, Cu2+, Fe2+, and Mn2+ and the aromatic amino acid Phe, known for its strong coordination capability, as study subjects, comprehensively examining their binding situations. The results show that there are multiple binding modes between them and Phe, and most of the binding modes involve benzene ring coordination. The coordination strength order of the four metal ions with benzene ring, carbonyl O, hydroxyl O and amino N is different. For the lowest energy structure formed by each ion with Phe, all four ions are bound to N, carbonyl O, and benzene ring. Zn2+ is combined with two C's of the benzene ring, Cu2+ with four C's of the benzene ring, and Fe2+ and Mn2+ with the benzene ring as a whole. Part of the reason for this phenomenon may be derived from the tendency of transition metal ions to reach 18e stable structures when bound to ligands. There is a strong binding force between the four ions and Phe, and the binding trend is Cu2+(-294.9 kcal/mol) > Zn2+(-261.3 kcal/mol) > Fe2+(-247.5 kcal/mol) > Mn2+(-220.2 kcal/mol). Mayer bond order analysis and molecular orbital localization analysis found that there are very strong chemical interactions between transition metal ions and surrounding atoms, especially with N and carbonyl O. METHODS: Several initial structures with different coordination modes to Phe were created according to chemical intuition for each divalent cation. Then semiempirical MD simulations at GFN2 level were run on these structures. The numerous generated structures were classified according to some criteria, then representative geometries were preliminarily optimized by TPSSh/6-31G*/LanL2DZ. To get more accurate electronic energies, high-precision quantum chemistry calculations at the level of TPSSh/def2TZVPP//TPSSh/def2QZVPP were carried out on the selected low-lying structures. All the optimized structures were confirmed to be minima without imaginary frequency by performing frequency analyses. Further electronic structure analyses such as IRI, Mayer bond order, IBSI etc. were performed to get more insights into the binding between the transition metal ions and Phe.

Insight into the interaction between amino acids and SO2: Detailed bonding modes.

CONTEXT: Amino acids are a highly effective and environmentally friendly adsorbent for SO2. However, there has been no comprehensive study of the binding modes between amino acids and SO2 at the molecular level. In this paper, the binding modes of three amino acids (Asp, Lys, and Val) with SO2 are studied comprehensively and in detail using quantum chemical calculations. The results indicate that each amino acid has multiple binding modes: 22 for Asp, 49 for Lys, and 10 for Val. Both the amino and carboxyl groups in amino acids, as well as those in side chains, can serve as binding sites for chalcogen bonds. The binding energies range from - 6.42 to - 1.06 kcal/mol for Asp, - 12.43 to - 1.63 kcal/mol for Lys, and - 7.42 to - 0.60 kcal/mol for Val. Chalcogen and hydrogen bonds play a crucial role in the stronger binding modes. The chalcogen bond is the strongest when interacting with an amino group, with an adiabatic force constant of 0.475 mDyn/Å. Energy decomposition analysis indicates that the interaction is primarily electrostatic attraction, with the orbital and dispersive interactions dependent on the binding mode. METHODS: Amino acids and complexes of amino acids with SO2 were used to do semi-empirical MD using Molclus combined with xtb at the GFN2 level. Optimization and frequency calculations of the structures were conducted using density-functional theory (DFT) B3LYP/6-311G* (with DFT-D3 correction). Single-point energy calculations were performed for all structures using DLPNO-CCSD(T)/aug-cc-pVTZ with tightPNO. Further analysis of the structures was conducted using ESP, AIM, IGMH, and sob-EDA to gain a deeper understanding of the interactions between amino acids and SO2.

Iron clusters regulate local charge distribution in Fe-N4 sites to boost oxygen electroreduction.

The atomically-dispersed and nitrogen-coordinated iron (FeNC) on a carbon catalyst is a potential non-noble metal catalyst that can replace precious metal electrocatalysts. However, its activity is often unsatisfactory owing to the symmetric charge distribution around the iron matrix. In this study, atomically- dispersed Fe-N4 and Fe nanoclusters loaded with N-doped porous carbon (FeNCs/FeSAs-NC-Z8@34) were rationally fabricated by introducing homologous metal clusters and increasing the N content of the support. FeNCs/FeSAs-NC-Z8@34 exhibited a half-wave potential of 0.918 V, which exceeded that of the commercial benchmark Pt/C catalyst. Theoretical calculations verified that introducing Fe nanoclusters can break the symmetric electronic structure of Fe-N4, thus inducing charge redistribution. Furthermore, it can optimize a part of Fe 3d occupancy orbitals and accelerate OO fracture in OOH* (rate-determining step), thus significantly improving oxygen reduction reaction activity. This work provides a reasonably advanced pathway to modulate the electronic structure of the single-atom center and optimize the catalytic activity of single-atom catalysts.

Synergies of Atomically Dispersed Mn/Fe Single Atoms and Fe Nanoparticles on N-Doped Carbon toward High-Activity Eletrocatalysis for Oxygen Reduction.

PGM-free (platinum group metal) electrocatalysts are intensively investigated and used as low-cost catalysts for the oxygen reduction reaction (ORR) in the field of fuel cells, but further studying their performance improvement methods and actual reaction mechanism is still a big a challenge. In this work, a novel eletrocatalyst containing atomically dispersed Mn/Fe single atoms (SAs) and Fe nanoparticles (NPs) on N-doped carbonaceous (nanosheet/nanotube hybrids) is fabricated via a simple pyrolysis method. This high-activity ORR electrocatalyst has higher half-wave potential (E1/2 = 0.91 V) and superior long-term durability in alkaline solutions and outperforms Pt/C catalysts, which can be ascribed to the synergetic interaction between Mn/Fe SAs and Fe-NPs. FeNPs/MnFeSAs-NC-25 has stronger reactant adsorption ability and a lower dissociation energy barrier than FeNPs/FeSAs-NC, which is conducive to breaking the O-O bond and accelerating ORR kinetics. This work presents a method to synthesize carbon-based electrocatalysts with high ORR activity and stability and shows that a variety of active sites encapsulated in N-doped carbonaceous materials can be a class of competitive candidates for PGM-free electrocatalysts.

Highly Dispersed CoO Embedded on Graphitized Ordered Mesoporous Carbon as an Effective Catalyst for Selective Fischer-Tropsch Synthesis of C5+ Hydrocarbons.

Herein, we report the high Fischer-Tropsch synthesis performance of the Co-based catalysts supported on graphitized ordered mesoporous carbon (GMC-900) by using a facile strategy. Compared with CMK-3 and active carbon (AC), the obtained GMC-900 by using pollution-free soybean oil as a carbon source exhibited enhanced catalytic performance after loading Co species due to its highly crystallized graphitic structure and uniform dispersion of CoO. As a result, Co/GMC-900 was an effective catalyst with the maximum C5+ selectivity of 52.6%, which much outperformed Co/CMK-3 and Co/AC. This research provides an approach to produce advanced Co-based catalysts with satisfactory performance for efficient Fischer-Tropsch synthesis.

Precise constructed atomically dispersed Fe/Ni sites on porous nitrogen-doped carbon for oxygen reduction.

Exploring highly-efficient noble-metal-free electrocatalysts for oxygen reduction reaction (ORR) is crucial for preparation of rechargeable metal-air batteries. Herein, FeNi-mIm (guest) was loaded on the surface of ZIF-8 (host) via a novel host-guest strategy, and the resulting ZIF-8@FeNi(mIm)X precursors can be converted to FeNi SAs/NC catalysts with controllable structures. Robust metal-organic framework (MOF)-derived atomically dispersed Fe/Ni dual single atom electrocatalysts for ORR were developed, followed by pyrolysis of the precursors. Characterizations showed that the atomically-dispersed Fe/Ni active sites were uniformly embedded in the N-doped carbon framework. As a result, the ORR performance was obviously improved with lower half-wave potential (E1/2 = 0.91 V) in alkaline media. Such improvement is mainly attributed to the synergy of fully-exposed bimetallic single atom active sites caused by the interaction of Fe/Ni 3d orbitals. The lower adsorption energy of intermediate hydroxyl groups on the active sites and the smaller ORR energy barrier were calculated by the density functional theory. The novelty FeNi SAs/NC catalysts showed faster ORR dynamics in the rate-determining step of four-electron transfer. The synthesis strategy reported here provides an efficient approach to construct high performance dual single-atom catalysts with fully-exposed active sites on the surface.

Boron/nitrogen co-doped carbon synthesized from waterborne polyurethane and graphene oxide composite for supercapacitors.

We report B/N co-doped carbon materials synthesized by an efficient and easy one-step carbonization method with ferric catalyst treatment from a precursor with boric acid treatment after the formation of the composite between waterborne polyurethane (WPU) and graphene oxide (GO). The nitrogen content was improved with the introduction of numerous melamine in the synthetic process of WPU. In addition, WPU possessed a repetitive basic unit urethane bond (-NHCOO); thus, nitrogen heteroatom could be efficiently introduced into the WPU/GO composite from WPU as a nitrogen-rich carbon. In addition, the specific surface area was increased by the boric acid treatment and washing process. The ferric catalyst treatment could prevent the formation of inert B-N bonds. Thus, the synthesized B/N co-doped carbon materials exhibited high specific capacitance (330 F g-1 at 0.5 A g-1), superior rate performance, and excellent cycling stability. Furthermore, the assembled symmetric supercapacitor displayed a good energy density (7.9 W h kg-1 at 505 W kg-1) and a good capacitance retention of about 89.9% after 5000 charge-discharge cycles in 6 M KOH electrolyte. Therefore, the as-prepared B/N co-doped carbon materials show a promising future in supercapacitor application.

Bistable electrical switching and nonvolatile memory effects by doping different amounts of GO in poly(9,9-dioctylfluorene-2,7-diyl).

Poly(9,9-dioctylfluorene-2,7-diyl) (PFO) was synthesized under a Suzuki coupling reaction, and its structure was proved by Fourier transform infrared (FT-IR) spectroscopy, and hydrogen and carbon nuclear magnetic resonance (1H-NMR and 13C-NMR). A nonvolatile organic memristor, based on active layers of PFO and PFO:GO composite, was prepared by spin-coating and the influence of GO concentration on the electrical characteristics of the memristor was investigated. The results showed that the device had two kinds of conductance behavior: electric bistable nonvolatile flash memory behavior and conductor behavior. With an increase in GO concentration, the device has an increased ON/OFF current ratio, increasing from 2.1 × 101 to 1.9 × 103, a lower threshold voltage (V SET), decreasing from -1.1 V to -0.7 V, and better stability. The current remained stable for 3 hours in both the ON state and OFF state, and the ON and OFF state current of the device did not change substantially after 9000 read cycles.

Reversible Hydrophobicity-Hydrophilicity Transition Modulated by Surface Curvature.

Wettability (hydrophobicity and hydrophilicity) is of fundamental importance in physical, chemical, and biological behaviors, resulting in widespread interest. Herein, by modulating surface curvature, we observed a reversible hydrophobic-hydrophilic transition on a model referred to a platinum surface. The underlying mechanism is revealed to be the competition between strong water-solid attraction and interfacial water orderliness. On the basis of the competition, we further propose an equation of wetting transition in the presence of an ordered interfacial liquid. It quantitatively reveals the relation of solid wettability with interfacial water orderliness and solid surface curvature, which can be used for predicting the critical point of the wetting transition. Our findings thus provide an innovative perspective on the design of a functional device demonstrating a reversible wettability transition and even a molecular-level understanding of biological functions.

Enhanced generation of hydroxyl radicals on well-crystallized molybdenum trioxide/nano-graphite anode with sesame cake-like structure for degradation of bio-refractory antibiotic.

Anodic electro-catalysis oxidation is a highly effective way to solve the pollution problem of antibiotics in wastewater and receiving water bodies. In this study, for the first time, molybdenum trioxide/Nano-graphite (MoO3/Nano-G) composites are synthesized as anodic catalysts by a surfactant-assisted solvothermal method followed by low-temperature calcination. The effects of the proportion of MoO3 to Nano-G (10, 30 and 50%) on the properties of composites are investigated through structural characterizations and electrochemical measurements. Results indicate that MoO3(30)/Nano-G electrode displays the electro-catalysis degradation efficiency of 99.9% towards ceftazidime, which is much higher than those of Nano-G (46.7%) and dimensionally stable anode (69.2%). The degradation mechanism for ceftazidime is studied by investigating the yields and kinds of active species. Results show that all of the OH, O2- and H2O2 are responsible for the electro-catalytic degradation process, and the produced OH radicals are the major active species for ceftazidime degradation. The synergistic effects between MoO3 and Nano-G greatly contribute to the activation of H2O molecules to produce OH, meanwhile the special sesame cake-like structure facilitates to the exposure of contaminants to OH on active sites to enhance the degradation efficiency. These results suggest that MoO3/Nano-G electrodes can be considered as the promising catalysts for treating bio-refractory organic wastewater.

Anomalous behavior of membrane fluidity caused by copper-copper bond coupled phospholipids.

Membrane fluidity, essential for cell functions, is obviously affected by copper, but the molecular mechanism is poorly understood. Here, we unexpectedly observed that a decrease in phospholipid (PL) bilayer fluidity caused by Cu2+ was more significant than those by Zn2+ and Ca2+, while a comparable reduction occurred in the last two ions. This finding disagrees with the placement in the periodic table of Cu just next to Zn and far from Ca. The physical nature was revealed to be an anomalous attraction between Cu+ cations, as well as the induced motif of two phospholipids coupled by Cu-Cu bond (PL-diCu-PL). Namely, upon Cu2+ ion binding to a negatively charged phosphate group of lipid, Cu2+ was reduced to Cu+. The attraction of the cations then caused one Cu+ ion simultaneously binding to two lipids and another Cu+, resulting in the formation of PL-diCu-PL structure. In contrast, this attraction cannot occur in the cases of Zn and Ca ions. Remarkably, besides lipids, the phosphate group also widely exists in other biological molecules, including DNA, RNA, ADP and ATP. Our findings thus provide a new view for understanding the biological functions of copper and the mechanism underlying copper-related diseases, as well as lipid assembly.

Denaturation of dsDNA Induced by Specific Major Groove Binding of Cadmium Ion to Thymine.

The toxicity of cadmium causes varying degrees of risk to organisms. The underlying mechanism has been conventionally attributed to Cd2+-ion-induced oxidative stress. Here, we propose that the Cd2+ ion directly and stably binds with the thymine specifically in the major groove and causes denaturation of dsDNA. Using molecular dynamics simulations, it was found that the Cd2+ ion preferred to bind to the thymine exposed in the major groove. This then destroyed the hydrogen bonds between adenine and thymine, resulting in a mismatched structure of dsDNA. Our findings are expected to promote the understanding of cadmium-induced direct destruction of genomic stability and may also be helpful for the facilitation of the experimental detection of the binding sites.

Isomers Identification of 2-hydroxyglutarate acid disodium salt (2HG) by Terahertz Time-domain Spectroscopy.

2-Hydroxyglutaric acid disodium salt (2HG) is a unique biomarker existing in glioma, which can be used for recognizing cancer development stage and identifying the boundary between the ordinary tissue and cancer tissue. However, the most efficient detection method for 2HG now is Magnetic Resonance Spectroscopy (MRS), whose testing time is at least twenty minutes and the variability of 2HG (continuous synthesis and decomposition) determines it cannot be used as the real-time image in medical surgery. In this paper, by using the Terahertz Time-domain Spectroscopy (THz-TDS) System, we investigate the vibration spectra of 2HG isomers and further distinguish their physical properties by using Density Functional Theory. The differences between isomers are mainly attributed to the proton transfer inside the carbon chain. These results indicate that terahertz technology can identify the isomers of 2HG accurate and fast, which has important significance for the further investigation of glioma and clinical surgery.