Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide

The number of hydrogen bonds and detailed information on the interlayer spacing of graphene oxide (GO) confined water molecules were calculated through experiments and molecular dynamics simulations. Experiments play a crucial role in the modeling strategy and verification of the simulation results. The binding of GO and water molecules is essentially controlled by hydrogen bond networks involving functional groups and water molecules confined in the GO layers. With the increase in the water content, the clusters of water molecules are more evident. The water molecules bounding to GO layers are transformed to a free state, making the removal of water molecules from the system difficult at low water contents. The diffuse behaviors of the water molecules are more evident at high water contents. With an increase in the water content, the functional groups are surrounded by fewer water molecules, and the distance between the functional groups and water molecules increases. As a result, the water molecules adsorbed into the GO interlamination will enlarge the interlayer spacing. The interlayer spacing is also affected by the number of GO layers. These results were confirmed by the calculations of number of hydrogen bonds, water state, mean square displacement, radial distribution function, and interlayer spacing of hydrated GO.

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Graphical Abstract This work research the interaction between GO functional groups and confined water molecules. The state of water molecules and interlayer spacing of graphene oxide were proved to be related to the number of hydrogen bonds.

     

Multiwall Carbon Nanotubes and Nanofibers in Gallionella

This is a report of microbial formation of multiwall carbon nanotubes (MWCNT) and nanofibers at normal pressure and temperature. Our results demonstrate a single cell organism's ability to form complicated material of high industrial interest. The microorganism, Gallionella, is classified as autotrophic and dysoxic. It uses CO₂ for its carbon source and grows in environments with low concentrations of free oxygen. The organisms were taken from a deep bedrock tunnel where water leaking from cracks in the rock formed a precipitate of iron as a bacterial slime on the rock wall. Detailed investigations of the samples by transmission electron microscopy (TEM) revealed several types of MWCNT. The stalk single MWCNT was observed with a diameter of about 10 nm and with an inner diameter of 1.35 nm. The wall of the nanotube is built by graphite layers. The 10 to 20 sheets are used to form the tubes. The measured spacing between the lines is 0.34 nm, which is an average value of interlayer spacing, close to the graphitic distance (0.335 nm). HRTEM images reveal a two-dimensional lattice with a spacing of 0.24 nm, indicating the presence of graphene.     

Enhanced Hydrogen Storage in Graphene Oxide‐MWCNTs Composite at Room Temperature

High hydrogen capacity (up to 2.6 wt%) is reported for highly aligned structures of Graphene oxide‐Multiwalled carbon nanotubes composite at room temperature. It is demonstrated that the scalable liquid crystal route can be employed as a new method to prepare unique 3‐D framework of graphene oxide layers with proper interlayer spacing as building blocks for cost‐effective high‐capacity hydrogen storage media. The strong synergistic effect of the intercalation of MWCNTs as 1‐D spacers within graphene oxide frameworks resulted in unrivalled high hydrogen capacity at ambient temperature. The mechanisms involved in the intercalation procedure are fully discussed. The main concept behind intercalating one‐dimensional spacers in between giant GO sheets represents a versatile and highly scalable route to fabricate devices with superior hydrogen uptake.     

Interlayer energy-optimum stacking registry for two curved graphene sheets of nanometre dimensions

The interlayer energy between two circular graphene sheets of nanometre scale, which is curved into cylindrical shape with different curvature radius, is investigated by a molecular force field based on a registry-dependent interlayer interaction potential. It is found that there is a special interlayer stacking angle near which the interlayer energy is significantly lower. This interlayer energy-minimum stacking registry angle shifts away from the original Bernal (AB) stacking orientation when the curvature radius of curved graphene sheets is less than 20 nm, and increases with decreasing curvature radius beyond this point. The stability of interlayer energy-minimum stacking of the curved graphene sheets decreases with decreasing curvature radius.     

Molecular simulation of cage occupancy and selectivity of binary THF–H2 sII hydrate

The hydrogen capacity of the binary THF–H₂ sII hydrate is determined by the cage occupancy and by the selectivity of guest molecules. Grand canonical Monte Carlo (GCMC) simulation is used to study the cage occupancy and selectivity of guest molecules from the equilibrium configuration of the binary sII hydrate. The cage framework is regarded as a rigid body and the number of guest molecules is varied to preserve the grand canonical ensemble. The occupancy and selectivity were investigated at a temperature of 270 K for pressures ranging from 0.1 to 200 MPa. It was found that most large cages select THF as guest molecules while small cages include only hydrogen molecules. Multiple occupancy of hydrogen, up to four molecules in large cages and two molecules in small cages, was found as the pressure increases. GCMC results show that the hydrogen capacity is approximately 1.1 wt% at 200 MPa.     

Modeling studies on the uptake of hydrogen molecules by graphene

Detailed ab initio molecular orbital calculations on the interactions of molecular hydrogen, H₂, with various poly-aromatic hydrocarbons (PAHs) as a model system for graphene were carried out to accurately describe the physisorption phenomenon. The binding energies corrected for the basis set superposition error, ΔE_bind(BSSE), were obtained using the optimized geometries at the MP2 level with a large basis set and were compared with the single point binding energies, denoted as ΔE_bind(BSSE-s), using large basis sets on the geometries optimized at the small basis sets, such as SVP and TZVP. The calculations showed that the ΔE_bind(BSSE-s) values were similar to those at the MP2 level with the large basis sets. The binding strength increased gradually with increasing size of the PAHs. The ΔE_bind(BSSE-s) for an infinite graphene sheet was estimated to be ?1.70 kcal mol^?1 using the non-linear curve fitting method. The present work could be expected to provide more useful and reliable information on H₂ physisorption.

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Graphical abstract Detailed ab initio molecular orbital calculations on the interactions of molecular hydrogen with various poly-aromatic hydrocarbons as a model system for graphene indicate that the perpendicular type A is the most favorable and the binding energy on an infinite graphene sheet is estimated to be ?1.70 kcal mol^?1.

     

Interaction between an icosahedron Li13 cluster and a graphene layer doped with a hydrogen atom

It is known that graphene reacts with atomic hydrogen to form a hydrogenated sheet of graphene. In order to understand the nature of the interaction between hydrogen and lithium in hydrogenated samples, we have carried out first principle calculations. Density functional theory and molecular dynamics were used to study the interaction between an icosahedron Li₁₃ cluster, and a graphene layer doped with a hydrogen atom. It was found that a hydrogen atom is levitated from the graphene layer and absorbed into the cluster of Li at 300?K and atmospheric pressure, with a binding energy far exceeding that of the adsorption energy of a hydrogen atom on the graphene layer.     

Molecular simulation study of the quantum effects of hydrogen adsorption in metal-organic frameworks: influences of pore size and temperature

In this work a systematic molecular simulation study was performed to investigate the influence of pore size and temperature on the quantum effects of hydrogen adsorption in metal-organic frameworks (MOFs) with temperature varied from 40 to 120 K. To do this, three isoreticular MOFs (IRMOFs) with different pore sizes were adopted, and quadratic Feynman–Hibbs (FH) effective potential was introduced to consider the quantum effect. The results show that quantum effects diminish with increasing pore size of IRMOFs at lower pressure (loading), while the opposite trend appears at higher pressure (loading). Through the simulations it is also found that the quantum effects may be dominantly determined by the adsorbate–adsorbate or adsorbate–MOFs interactions with the varying of pressure (loading). In addition, the results also indicate how the temperature influences the quantum effects of H₂ adsorption in MOFs within the pressure range considered.     

H2‐Directing Strategy on In Situ Synthesis of Co‐MoS2 with Highly Expanded Interlayer for Elegant HER Activity and its Mechanism

MoS₂ has drawn great attention as a promising Pt‐substituting catalyst for the hydrogen evolution reaction (HER). This work utilizes H₂ as the structure directing agent (SDA) to in situ synthesize a range of Co‐MoS₂‐n (n = 0, 0.5, 1.0, 1.4, 2.0) with expanded interlayer spacings (d = 9.2 – 11.1 Å), which significantly boost their HER activities. The Co‐MoS₂‐1.4 with an interlayer spacing of 10.3 Å presents an extremely low overpotential of 56 mV (at 10 mA cm^?2) and a Tafel slope of 32 mV dec^?1, which is superior than most reported MoS₂‐based catalysts. Density function theory calculations are used to gain insights that i) the H₂ can be dissociatively adsorbed on MoS₂ and greatly affect the related surface free energy by regulating the interlayer spacing; ii) the expanded interlayer spacing can significantly decrease the absolute value of ΔG_H, thereby leading to greatly promoted HER activity. Additionally, the large amounts of 1T phase (73.9–79.2%) and Co‐Mo‐S active sites (40.9–91.3%) also contribute to the enhanced HER activity of the synthesized samples. Overall, a simple new strategy for in situ synthesis of Co‐MoS₂ with an expanded interlayer spacing is proposed, which sheds light on other 2D energy material designs.     

The effects of structural parameters of zeolite on the adsorption of hydrogen: a molecular simulation study

The adsorption isotherm of hydrogen in zeolites FAU, LTA, KFI, RWY, RHO and TSC has been simulated employing grand canonical Monte Carlo procedure for a temperature range of 77 to 95 K and different pressures. The effects of structural composition, unit cell volume, framework density and specific surface area of zeolite on hydrogen adsorption in zeolites were investigated. The results clearly show that the adsorption of hydrogen in zeolites with the same silica density is a function of oxygen density at low pressures, and it is approximately the same at intermediate pressures. Nevertheless, at high pressures, the adsorption of hydrogen is a function of pore diameter for zeolites with same silica density. The effect of specific surface area on the adsorption isotherm of hydrogen on zeolites with approximately the same specific surface area is significant at low and high pressures. The results clearly indicate that the adsorption of hydrogen in RWY zeolite has maximum value at 77 K and at high pressures. The optimum condition of pressure for hydrogen adsorption isotherm in RWY zeolite is determined to be 600 bar. At a temperature of 77 K and a pressure of 600 bar, the adsorption of hydrogen in RWY zeolite is 6.93 wt %.     

The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study

Self-diffusion of methanol, ethanol, 1-propanol and 2-propanol has been studied by molecular dynamics simulation in the temperature range between the melting pressure curve and 478 K at pressures up to 300 MPa. The simulation results on self-diffusion of methanol, ethanol and 2-propanol (for 2-propanol, at high temperatures) agree well with experiment, which suggests that the simulation method is a powerful tool to obtain self-diffusion coefficients over wide range of temperature and pressure, under which it is rather difficult for experiments. The local structures of methanol, ethanol and 2-propanol are investigated by calculating the radial distribution functions, H-bond numbers, coordination numbers and the ratios of H-bond number divided by coordination number. The correlation between self-diffusion and structural properties, and the influence of temperature and pressure on them are discussed. The degree of forming H-bond space network in methanol, ethanol and water is higher than that in 2-propanol, and they are all higher than those in ammonia and methylamine. The simulation results demonstrate that the effect of hydrogen bonding on the translational dynamics in methanol and ethanol is more pronounced than that in 2-propanol.     

Tuning hydrogen storage of carbon nanotubes by mechanical bending: theoretical study

The effects of mechanical bending on tuning the hydrogen storage of titanium functionalised (4,0) carbon nanotube have been assessed using density functional theory calculations with reference to the ultimate targets of the US Department of Energy (DOE). The assessment has been carried out in terms of physisorption, gravimetric capacity, projected densities of states, statistical thermodynamic stability and reaction kinetics. The Ti atom binds at the hollow site of the hexagonal ring. The average adsorption energies (?0.54 eV) per hydrogen molecule meet the DOE target for physisorption (?0.20 to ?0.60 eV). The curvature attributed to the bending angle has no effect on the average adsorption energies per H₂ molecule. With no metal clustering, the system gravimetric capacities are expected to be as large as 9.0 wt%. The reactions of the deformed (bent) carbon nanotube have higher probabilities of occurring than those of the un-deformed carbon nanotube. The Gibbs free energies, enthalpies and entropies meet the ultimate targets of the DOE for all temperatures and pressures. The closest reactions to zero free energy occur at (378.15 K/2.961 atm.) and reverse at (340 and 360 K/1 atm.). The translational component is found to exact a dominant effect on the total entropy change with temperature. Favourable kinetics of the reactions at the temperatures targeted by DOE are reported regardless of the applied pressure. The more preferable thermodynamic properties assigned to the bending nanotube imply that hydrogen storage can be improved compared to the nonbending nanotube.     

In vitro study on binding interaction of quinapril with bovine serum albumin (BSA) using multi-spectroscopic and molecular docking methods

The binding interaction between quinapril (QNPL) and bovine serum albumin (BSA) in vitro has been investigated using UV absorption spectroscopy, steady-state fluorescence spectroscopic, synchronous fluorescence spectroscopy, 3D fluorescence spectroscopy, Fourier transform infrared spectroscopy, circular dichroism, and molecular docking methods for obtaining the binding information of QNPL with BSA. The experimental results confirm that the quenching mechanism of the intrinsic fluorescence of BSA induced by QNPL is static quenching based on the decrease in the quenching constants of BSA in the presence of QNPL with the increase in temperature and the quenching rates of BSA larger than 10¹⁰ L mol^?1 s^?1, indicating forming QNPL–BSA complex through the intermolecular binding interaction. The binding constant for the QNPL–BSA complex is in the order of 10⁵ M^?1, indicating there is stronger binding interaction of QNPL with BSA. The analysis of thermodynamic parameters together with molecular docking study reveal that the main binding forces in the binding process of QNPL with BSA are van der Waal’s forces and hydrogen bonding interaction. And, the binding interaction of BSA with QNPL is an enthalpy-driven process. Based on Förster resonance energy transfer, the binding distance between QNPL and BSA is calculated to be 2.76 nm. The results of the competitive binding experiments and molecular docking confirm that QNPL binds to sub-domain IIA (site I) of BSA. It is confirmed there is a slight change in the conformation of BSA after binding QNPL, but BSA still retains its secondary structure α-helicity.     

Modulation of Visible and Near-Infrared Surface Plasmon Resonance of Au Nanoparticles Based on Highly Doped Graphene

We study an active modulation of surface plasmon resonance (SPR) of Au nanoparticles based on highly doped graphene in visible and near-infrared regions. We find that compared to the traditional metal SPR, the SPR of Au nanoparticles based on graphene causes a remarkable blue shift. The field intensity in the gap is redistributed to standing wave. The field intensity of standing wave is about one order of magnitude higher than the traditional model. Moreover, the SPR of Au nanoparticles can be actively modulated by varying the graphene Fermi energy. We find the maximum modulation of field intensity of absorption spectra is more than 21.6 % at λ?=?822?nm and the amount of blue shift is 17.4 nm, which is about 2.14 % of the initial wavelength λ ₀?=?813.4?nm, with increasing monolayer graphene Fermi energy from 1.0 to 1.5 ev. We find that the SPR sensitivity to the refractive index n of the environment is about 642 nm per refractive index unit (RIU). The SPR wavelengths have a big blue shift, which is about 33 nm, with increasing number of graphene layers from 1 to 3, and some shoulders on the absorption spectra are observed in the models with multilayer graphene. Finally, we study the Au nanorod array based on monolayer graphene. We find that the blue shift caused by the graphene increases from 14 to 24 nm, with increasing gap g _y from 10 to 20 nm. Then, it decreases from 24 to 14 nm, with increasing gap g _y from 20 to 50 nm. This study provides a new way for actively modulating the optical and optoelectronic devices.     

Unravelling the binding mechanism and protein stability of human serum albumin while interacting with nefopam analogues: a biophysical and insilico approach

In this study, molecular binding affinity was investigated for Nefopam analogues (NFs), a functionalized benzoxazocine, with human serum albumin (HSA), a major transport protein in the blood. Its binding affinity and concomitant changes in its conformation, binding site and simulations were also studied. Fluorescence data revealed that the fluorescence quenching of HSA upon binding of NFs analogues is based on a static mechanism. The three analogues of NFs binding constants (K_A) are in the order of NF3 > NF2 > NF1 with values of 1.53 ± .057 × 10⁴, 2.16 ± .071 × 10⁴ and 3.6 ± .102 × 10⁵ M^?1, respectively. Concurrently, thermodynamic parameters indicate that the binding process was spontaneous, and the complexes were stabilized mostly by hydrophobic interactions, except for NF2 has one hydrogen bond stabilizes it along with hydrophobic interactions. Circular dichroism (CD) studies revealed that there is a decrease in α-helix with an increase in β-sheets and random coils signifying partial unfolding of the protein upon binding of NFs, which might be due to the formation of NFs-HSA complexes. Further, molecular docking studies showed that NF1, NF2 and NF3 bound to subdomains IIIA, IB and IIA through hydrophobic interactions. However, NF1 have additionally formed a single hydrogen bond with LYS 413. Furthermore, molecular simulations unveiled that NFs binding was in support with the structural perturbation observed in CD, which is evident from the root mean square deviation and R_g fluctuations. We hope our insights will provide ample scope for engineering new drugs based on the resemblances with NFs for enhanced efficacy with HSA.     

Enantioseparation processes and mechanisms in functionalized graphene membranes: Facilitated or retarded transport?

Up to date, functionalized graphene–based membranes have exhibited a promising potential in the enantioseparation. However, since precisely controlling the interlayer distance of two-dimensional materials is a great challenge in practical experiments, the transport mechanism of chiral guests in such membranes, together with various critical parameters that play a controlling role in the transport behaviors of the preferentially binding enantiomer in narrow channels, remains to be explored. The molecular dynamics (MD) simulation, especially using the steered MD (SMD) method, might be an alternative way to investigate the enantioseparation processes and mechanisms of layered membranes with different interlayer distances. In this work, D-alanine modified graphene sheets with different interlayer distances were built as membrane models, whereas D- and L-phenylalanine were selected as chiral probes. The effect of the interlayer distance and the applied external force on the enantioseparation performance was examined. Results show that such two parameters exert a significant influence on the enantioseparation performance: (a) Increasing the interlayer distance would result in a conversion from the retarded to the facilitated mechanism at a proper external force (medium); (b) both the large and small driving forces would only lead to the appearance of the retarded transport for the preferential enantiomer, unlike the moderate force; (c) the interaction energy of L-phenylalanine with D-isomer selector decreases with the rising interlayer distances studied in this work, regardless of what the external force is. Our findings can provide guidance on the practical applications in the membrane-based chiral separation.     

Capecitabine as a minor groove binder of DNA: molecular docking,molecular dynamics,and multi-spectroscopic studies

The interaction mechanism and binding mode of capecitabine with ctDNA was extensively investigated using docking and molecular dynamics simulations, fluorescence and circular dichroism (CD) spectroscopy, DNA thermal denaturation studies, and viscosity measurements. The possible binding mode and acting forces on the combination between capecitabine and DNA had been predicted through molecular simulation. Results indicated that capecitabine could relatively locate stably in the G-C base-pairs-rich DNA minor groove by hydrogen bond and several weaker nonbonding forces. Fluorescence spectroscopy and fluorescence lifetime measurements confirmed that the quenching was static caused by ground state complex formation. This phenomenon indicated the formation of a complex between capecitabine and ctDNA. Fluorescence data showed that the binding constants of the complex were approximately 2 × 10⁴ M^?1. Calculated thermodynamic parameters suggested that hydrogen bond was the main force during binding, which were consistent with theoretical results. Moreover, CD spectroscopy, DNA melting studies, and viscosity measurements corroborated a groove binding mode of capecitabine with ctDNA. This binding had no effect on B-DNA conformation.     

Short‐Range Order in Mesoporous Carbon Boosts Potassium‐Ion Battery Performance

The adequate potassium resource on the earth has driven the researchers to explore new‐concept potassium‐ion batteries (KIBs) with high energy density. Graphite is a common anode for KIBs; however, the main challenge faced by KIBs is that K ions have the larger size than Li and Na ions, hindering the intercalation of K ions into electrodes and thus leading to poor rate performance, low capacity, and cycle stability during the potassiation and depotassiation process. Herein, an amorphous ordered mesoporous carbon (OMC) is reported as a new anode material for high‐performance KIBs. Unlike the well‐crystallized graphite, in which the K ions are squeezed into the restricted interlayer spacing, it is found that the amorphous OMC possesses larger interlayer spacing in short range and fewer carbon atoms in one carbon‐layers cluster, making it more flexible to the deformation of carbon layers. The larger interlayer spacing and the unique layered structure in short range can intercalate more K ions into the carbon layer, accommodate the increase of the interlayer spacing, and tolerate the volume expansion, resulting in a battery behavior with high capacity, high rate capability, and long cycle life.     

Mechanism of Na‐Ion Storage in Hard Carbon Anodes Revealed by Heteroatom Doping

Hard carbon is the leading candidate anode for commercialization of Na‐ion batteries. Hard carbon has a unique local atomic structure, which is composed of nanodomains of layered rumpled sheets that have short‐range local order resembling graphene within each layer, but complete disorder along the c‐axis between layers. A primary challenge holding back the development of Na‐ion batteries is that a complete understanding of the structure–capacity correlations of Na‐ion storage in hard carbon has remained elusive. This article presents two key discoveries: first, the characteristics of hard carbons structure can be modified systematically by heteroatom doping, and second, that these structural changes greatly affect Na‐ion storage properties, which reveals the mechanisms for Na storage in hard carbon. Specifically, via P or S doping, the interlayer spacing is dilated, which extends the low‐voltage plateau capacity, while increasing the defect concentrations with P or B doping leads to higher sloping sodiation capacity. The combined experimental studies and first principles calculations reveal that it is the Na‐ion‐defect binding that corresponds to the sloping capacity, while the Na intercalation between graphenic layers causes the low‐potential plateau capacity. The understanding suggests a new design principle of hard carbon anode: more reversibly binding defects and dilated turbostratic domains, given that the specific surface area is maintained low.     

Molecular modeling of layered double hydroxide intercalated with benzoate,modeling and experiment

The structure of Zn4Al2 Layered Double Hydroxide intercalated with benzencarboxylate (C6H5COO-) was solved using molecular modeling combined with experiment (X-ray powder diffraction, IR spectroscopy, TG measurements). Molecular modeling revealed the arrangement of guest molecules, layer stacking, water content and water location in the interlayer space of the host structure. Molecular modeling using empirical force field was carried out in Cerius(2) modeling environment. Results of modeling were confronted with experiment that means comparing the calculated and measured diffraction pattern and comparing the calculated water content with the thermogravimetric value. Good agreement has been achieved between calculated and measured basal spacing: d(calc) = 15.3 A and d(exp) = 15.5 A. The number of water molecules per formula unit (6H2O per Zn4Al2(OH)12) obtained by modeling (i.e., corresponding to the energy minimum) agrees with the water content estimated by thermogravimetry. The long axis of guest molecules are almost perpendicular to the LDH layers, anchored to the host layers via COO- groups. Mutual orientation of benzoate ring planes in the interlayer space keeps the parquet arrangement. Water molecules are roughly arranged in planes adjacent to host layers together with COO- groups.