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The understanding of interactions between proteins with silica surface is crucial for a wide range of different applications: from medical devices, drug delivery and bioelectronics to biotechnology and downstream processing. We show the application of EISM (Effective Implicit Surface Model) for discovering the set of peptide interactions with silica surface. The EISM is employed for a high-speed computational screening of peptides to model the binding affinity of small peptides to silica surfaces. The simulations are complemented with experimental data of peptides with silica nanoparticles from microscale thermophoresis and from infrared spectroscopy. The experimental work shows excellent agreement with computational results and verifies the EISM model for the prediction of peptide-surface interactions. 57 peptides, with amino acids favorable for adsorption on Silica surface, are screened by EISM model for obtaining results, which are worth to be considered as a guidance for future experimental and theoretical works. This model can be used as a broad platform for multiple challenges at surfaces which can be applied for multiple surfaces and biomolecules beyond silica and peptides., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

The interaction of proteins and peptides with inorganic surfaces is relevant in a wide array of technological applications. A rational approach to design peptides for specific surfaces would build on amino-acid and surface specific interaction models, which are difficult to characterize experimentally or by modeling. Even with such a model at hand, the large number of possible sequences and the large conformation space of peptides make comparative simulations challenging. Here we present a computational protocol, the effective implicit surface model (EISM), for efficient in silico evaluation of the binding affinity trends of peptides on parameterized surface, with a specific application to the widely studied gold surface. In EISM the peptide surface interactions are modeled with an amino-acid and surface specific implicit solvent model, which permits rapid exploration of the peptide conformational degrees of freedom. We demonstrate the parametrization of the model and compare the results with all-atom simulations and experimental results for specific peptides., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Inc. All rights reserved.)

Multiple linear regression analysis, as a part of machine learning, is employed to develop equations for the quick and accurate prediction of the methane uptake and working capacity of metal-organic frameworks (MOFs). Only three crystal characteristics of MOFs (geometric descriptors) are employed for developing the equations: surface area, pore volume and density of the crystal structure. The values of the geometric descriptors can be obtained much more cheaply in terms of time and other resources compared to running calculations of gas sorption or performing experimental work. Within this work sets of equations are provided for the different cases studied: a series of MOFs with NbO topology, a set of benchmark MOFs with outstanding methane storage and working capacities, and the whole CoRE MOF database (11 000 structures).

Energy-efficient approaches to propylene/propane separation such as molecular sieving are of considerable importance for the petrochemical industry. The metal organic framework NbOFFIVE-1-Ni adsorbs propylene but not propane at room temperature and atmospheric pressure, whereas the isostructural SIFSIX-3-Ni does not exclude propane under the same conditions. The static dimensions of the pore openings of both materials are too small to admit either guest, signalling the importance of host dynamics for guest entrance to and transport through the channels. We use ab initio calculations together with crystallographic and adsorption data to show that the dynamics of the two framework-forming units, polyatomic anions and pyrazines, govern both diffusion and separation. The guest diffusion occurs by opening of the flexible window formed by four pyrazines. In NbOFFIVE-1-Ni, (NbOF 5 ) 2- anion reorientation locates propane away from the window, which enhances propylene/propane separation.

Protein-surface interactions are exploited in various processes in life sciences and biotechnology. Many of such processes are performed in presence of a buffer system, which is generally believed to have an influence on the protein-surface interaction but is rarely investigated systematically. Combining experimental and theoretical methodologies, we herein demonstrate the strong influence of the buffer type on protein-surface interactions. Using state of the art chromatographic experiments, we measure the interaction between individual amino acids and silica, as a reference to understand protein-surface interactions. Among all the 20 proteinogenic amino acids studied, we found that arginine (R) and lysine (K) bind most strongly to silica, a finding validated by free energy calculations. We further measured the binding of R and K at different pH in presence of two different buffers, MOPS (3-(N-morpholino)propanesulfonic acid) and TRIS (tris(hydroxymethyl)aminomethane), and find dramatically different behavior. In presence of TRIS, the binding affinity of R/K increases with pH, whereas we observe an opposite trend for MOPS. These results can be understood using a multiscale modelling framework combining molecular dynamics simulation and Langmuir adsorption model. The modelling approach helps to optimize buffer conditions in various fields like biosensors, drug delivery or bio separation engineering prior to the experiment., (© 2020 Wiley-VCH GmbH.)

Photoreduction of fullerene and the consequent stabilisation of a charge-separated state in a donor-acceptor assembly have been achieved, overcoming the common problem of a fullerene-based triplet state being an energy sink that prevents charge-separation. A route to incorporate a C 60 -fullerene electron acceptor moiety into a catecholate-Pt(ii)-diimine photoactive dyad, which contains an unusually strong electron donor, 3,5-di- tert -butylcatecholate, has been developed. The synthetic methodology is based on the formation of the aldehyde functionalised bipyridine-Pt(ii)-3,5-di- tert -butylcatechol dyad which is then added to the fullerene cage via a Prato cycloaddition reaction. The resultant product is the first example of a fullerene-diimine-Pt-catecholate donor-acceptor triad, C 60 bpy-Pt-cat. The triad exhibits an intense solvatochromic absorption band in the visible region due to catechol-to-diimine charge-transfer, which, together with fullerene-based transitions, provides efficient and tuneable light harvesting of the majority of the UV/visible spectral range. Cyclic voltammetry, EPR and UV/vis/IR spectroelectrochemistry reveal redox behaviour with a wealth of reversible reduction and oxidation processes forming multiply charged species and storing multiple redox equivalents. Ultrafast transient absorption and time resolved infrared spectroscopy, supported by molecular modelling, reveal the formation of a charge-separated state [C 60 ˙ - bpy-Pt-cat˙ + ] with a lifetime of ∼890 ps. The formation of cat˙ + in the excited state is evidenced directly by characteristic absorption bands in the 400-500 nm region, while the formation of C 60 ˙ - was confirmed directly by time-resolved infrared spectroscopy, TRIR. An IR-spectroelectrochemical study of the mono-reduced building block (C 60 -bpy)PtCl 2 , revealed a characteristic C 60 ˙ - vibrational feature at 1530 cm -1 , which was also detected in the TRIR spectra. This combination of experiments offers the first direct IR-identification of C 60 ˙ - species in solution, and paves the way towards the application of transient infrared spectroscopy to the study of light-induced charge-separation in C 60 -containing assemblies, as well as fullerene films and fullerene/polymer blends in various OPV devices. Identification of the unique vibrational signature of a C 60 -anion provides a new way to follow photoinduced processes in fullerene-containing assemblies by means of time-resolved vibrational spectroscopy, as demonstrated for the fullerene-transition metal chromophore assembly with the lowest energy charge-separated excited state.

The key requirement for a portable store of natural gas is to maximize the amount of gas within the smallest possible space. The packing of methane (CH4) in a given storage medium at the highest possible density is, therefore, a highly desirable but challenging target. We report a microporous hydroxyl-decorated material, MFM-300(In) (MFM = Manchester Framework Material, replacing the NOTT designation), which displays a high volumetric uptake of 202 v/v at 298 K and 35 bar for CH4 and 488 v/v at 77 K and 20 bar for H2. Direct observation and quantification of the location, binding, and rotational modes of adsorbed CH4 and H2 molecules within this host have been achieved, using neutron diffraction and inelastic neutron scattering experiments, coupled with density functional theory (DFT) modeling. These complementary techniques reveal a very efficient packing of H2 and CH4 molecules within MFM-300(In), reminiscent of the condensed gas in pure component crystalline solids. We also report here, for the first time, the experimental observation of a direct binding interaction between adsorbed CH4 molecules and the hydroxyl groups within the pore of a material. This is different from the arrangement found in CH4/water clathrates, the CH4 store of nature.

A series of explorative cross-coupling reactions have been developed to investigate the local nanoscale environment around catalytically active Pd(ii)complexes encapsulated within hollow graphitised nanofibers (GNF). Two new fullerene-containing and fullerene-free Pd(ii)Salen catalysts have been synthesised, and their activity and selectivity towards different substrates has been explored in nanoreactors. The catalysts not only show a significant increase in activity and stability upon heterogenisation at the graphitic step-edges inside the GNF channel, but also exhibit a change in selectivity affected by the confinement which alters the distribution of isomeric products of the reaction. Furthermore, the observed selectivity changes reveal unprecedented details regarding the location and orientation of the catalyst molecules inside the GNF nanoreactor, inaccessible by any spectroscopic or microscopic techniques, thus shedding light on the precise reaction environment inside the molecular catalyst-GNF nanoreactor.

The nature and dynamics of bonding between Fe, Ru, Os, and single-walled carbon nanotubes (SWNTs) is studied by aberration-corrected high-resolution transmission electron microscopy (AC-HRTEM). The metals catalyze a wide variety of different transformations ranging from ejection of carbon atoms from the nanotube sidewall to the formation of hollow carbon shells or metal carbide within the SWNT, depending on the nature of the metal. The electron beam of AC-HRTEM serves the dual purpose of providing energy to the specimen and simultaneously enabling imaging of chemical transformations. Careful control of the electron beam parameters, energy, flux, and dose allowed direct comparison between the metals, demonstrating that their chemical reactions with SWNTs are determined by a balance between the cohesive energy of the metal particles and the strength of the metal-carbon σ- or π-bonds. The pathways of transformations of a given metal can be drastically changed by applying different electron energies (80, 40, or 20 keV), thus demonstrating AC-HRTEM as a new tool to direct and study chemical reactions. The understanding of interactions and bonding between SWNT and metals revealed by AC-HRTEM at the atomic level has important implications for nanotube-based electronic devices and catalysis., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The molecular building block approach was employed effectively to construct a series of novel isoreticular, highly porous and stable, aluminum-based metal-organic frameworks with soc topology. From this platform, three compounds were experimentally isolated and fully characterized: namely, the parent Al-soc-MOF-1 and its naphthalene and anthracene analogues. Al-soc-MOF-1 exhibits outstanding gravimetric methane uptake (total and working capacity). It is shown experimentally, for the first time, that the Al-soc-MOF platform can address the challenging Department of Energy dual target of 0.5 g/g (gravimetric) and 264 cm(3) (STP)/cm(3) (volumetric) methane storage. Furthermore, Al-soc-MOF exhibited the highest total gravimetric and volumetric uptake for carbon dioxide and the utmost total and deliverable uptake for oxygen at relatively high pressures among all microporous MOFs. In order to correlate the MOF pore structure and functionality to the gas storage properties, to better understand the structure-property relationship, we performed a molecular simulation study and evaluated the methane storage performance of the Al-soc-MOF platform using diverse organic linkers. It was found that shortening the parent Al-soc-MOF-1 linker resulted in a noticeable enhancement in the working volumetric capacity at specific temperatures and pressures with amply conserved gravimetric uptake/working capacity. In contrast, further expansion of the organic linker (branches and/or core) led to isostructural Al-soc-MOFs with enhanced gravimetric uptake but noticeably lower volumetric capacity. The collective experimental and simulation studies indicated that the parent Al-soc-MOF-1 exhibits the best compromise between the volumetric and gravimetric total and working uptakes under a wide range of pressure and temperature conditions.

The encapsulation of trityl-functionalised C60 molecules inside carbon nanotubes drastically affects the intermolecular interactions for this species. Whilst the orientations of molecules in the crystal are often controlled by thermodynamics, the molecular orientations in nanotubes are a result of kinetic control imposed by the mechanism of entry into and encapsulation within the nanotube.

A robust binary hydrogen-bonded supramolecular organic framework (SOF-7) has been synthesized by solvothermal reaction of 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)dihydropyridyl)benzene (1) and 5,5'-bis-(azanediyl)-oxalyl-diisophthalic acid (2). Single crystal X-ray diffraction analysis shows that SOF-7 comprises 2 and 1,4-bis-(4-(3,5-dicyano-2,6-dipyridyl)pyridyl)benzene (3); the latter formed in situ from the oxidative dehydrogenation of 1. SOF-7 shows a three-dimensional four-fold interpenetrated structure with complementary O-H···N hydrogen bonds to form channels that are decorated with cyano and amide groups. SOF-7 exhibits excellent thermal stability and solvent and moisture durability as well as permanent porosity. The activated desolvated material SOF-7a shows high CO2 adsorption capacity and selectivity compared with other porous organic materials assembled solely through hydrogen bonding.

Solvothermal reaction of H4L (L = biphenyl-3,3',5,5'-tetracarboxylate) and Bi(NO3)3⋅(H2O)5 in a mixture of DMF/MeCN/H2O in the presence of piperazine and nitric acid at 100 °C for 10 h affords the solvated metal-organic polymer [Bi2(L)1.5(H2O)2]⋅(DMF)3.5⋅(H2O)3 (NOTT-220-solv). A single crystal X-ray structure determination confirms that it crystallises in space group P2/c and has a neutral and non-interpenetrated structure comprising binuclear {Bi2} centres bridged by tetracarboxylate ligands. NOTT-220-solv shows a 3,6-connected network having a framework topology with a {4⋅6(2)}2{4(2)⋅6(5)⋅8(8)}{6(2)⋅8} point symbol. The desolvated material NOTT-220a shows exceptionally high adsorption uptakes for CH4 and CO2 on a volumetric basis at moderate pressures and temperatures with a CO2 uptake of 553 g L(-1) (20 bar, 293 K) with a saturation uptake of 688 g L(-1) (1 bar, 195 K). The corresponding CH4 uptake was measured as 165 V(STP)/V (20 bar, 293 K) and 189 V(STP/V) (35 bar, 293 K) with a maximum CH4 uptake for NOTT-220a recorded at 20 bar and 195 K to be 287 V(STP)/V, while H2 uptake of NOTT-220a at 20 bar, 77 K is 42 g L(-1). These gas uptakes have been modelled by grand canonical Monte Carlo (GCMC) and density functional theory (DFT) calculations, which confirm the experimental data and give insights into the nature of the binding sites of CH4 and CO2 in this porous hybrid material., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The porous framework [Cu2(H2O)2L]⋅4 H2O⋅2 DMA (H4L = oxalylbis(azanediyl)diisophthalic acid; DMA = N,N-dimethylacetamide), denoted NOTT-125, is formed by connection of {Cu2(RCOO)4} paddlewheels with the isophthalate linkers in L(4-). A single crystal structure determination reveals that NOTT-125 crystallises in monoclinic unit cell with a = 27.9161(6), b = 18.6627(4) and c = 32.3643(8) Å, β = 112.655(3)°, space group P2(1)/c. The structure of this material shows fof topology, which can be viewed as the packing of two types of cages (cage A and cage B) in three-dimensional space. Cage A is constructed from twelve {Cu2(OOCR)4} paddlewheels and six linkers to form an ellipsoid-shaped cavity approximately 24.0 Å along its long axis and 9.6 Å across its central diameter. Cage B consists of six {Cu2(OOCR)4} units and twelve linkers and has a spherical diameter of 12.7 Å taking into account the van der Waals radii of the atoms. NOTT-125 incorporates oxamide functionality within the pore walls, and this, combined with high porosity in desolvated NOTT-125a, is responsible for excellent CO2 uptake (40.1 wt % at 273 K and 1 bar) and selectivity for CO2 over CH4 or N2. Grand canonical Monte Carlo (GCMC) simulations show excellent agreement with the experimental gas isotherm data, and a computational study of the specific interactions and binding energies of both CO2 and CH4 with the linkers in NOTT-125 reveals a set of strong interactions between CO2 and the oxamide motif that are not possible with a single amide., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In common with rocksalt-type alkali halide phases and also semiconductors such as GeTe and SnTe, SnSe forms all-surface two atom-thick low dimensional crystals when encapsulated within single walled nanotubes (SWNTs) with diameters below ∼1.4 nm. Whereas previous density functional theory (DFT) studies indicate that optimised low-dimensional trigonal HgTe changes from a semi-metal to a semi-conductor, low-dimensional SnSe crystals typically undergo band-gap expansion. In slightly wider diameter SWNTs (∼1.4-1.6 nm), we observe that three atom thick low dimensional SnSe crystals undergo a previously unobserved form of a shear inversion phase change resulting in two discrete strain states in a section of curved nanotube. Under low-voltage (i.e. 80-100 kV) imaging conditions in a transmission electron microscope, encapsulated SnSe crystals undergo longitudinal and rotational oscillations, possibly as a result of the increase in the inelastic scattering cross-section of the sample at those voltages.

A covalently-linked salen-C60 (H2L) assembly binds a range of transition metal cations in close proximity to the fullerene cage to give complexes [M(L)] (M=Mn, Co, Ni, Cu, Zn, Pd), [MCl(L)] (M=Cr, Fe) and [V(O)L]. Attaching salen covalently to the C60 cage only marginally slows down metal binding at the salen functionality compared to metal binding to free salen. Coordination of metal cations to salen-C60 introduces to these fullerene derivatives strong absorption bands across the visible spectrum from 400 to 630 nm, the optical features of which are controlled by the nature of the transition metal. The redox properties of the metal-salen-C60 complexes are determined both by the fullerene and by the nature of the transition metal, enabling the generation of a wide range of fullerene-containing charged species, some of which possess two or more unpaired electrons. The presence of the fullerene cage enhances the affinity of these complexes for carbon nanostructures, such as single-, double- and multiwalled carbon nanotubes and graphitised carbon nanofibres, without detrimental effects on the catalytic activity of the metal centre, as demonstrated in styrene oxidation catalysed by [Cu(L)]. This approach shows promise for applications of salen-C60 complexes in heterogeneous catalysis., (Copyright © 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim.)

Hollow graphitized carbon nanofibres (GNF) are employed as nanoscale reaction vessels for the hydrosilylation of alkynes. The effects of confinement in GNF on the regioselectivity of addition to triple carbon-carbon bonds are explored. A systematic comparison of the catalytic activities of Rh and RhPt nanoparticles embedded in a nanoreactor with free-standing and surface-adsorbed nanoparticles reveals key mechanisms governing the regioselectivity. Directions of reactions inside GNF are largely controlled by the non-covalent interactions between reactant molecules and the nanofibre channel. The specific π-π interactions increase the local concentration of the aromatic reactant and thus promote the formation of the E isomer of the β-addition product. In contrast, the presence of aromatic groups on both reactants (silane and alkyne) reverses the effect of confinement and favours the formation of the Z isomer due to enhanced interactions between aromatic groups in the cis-orientation with the internal graphitic step-edges of GNF. The importance of π-π interactions is confirmed by studying transformations of aliphatic reactants that show no measurable changes in regioselectivity upon confinement in carbon nanoreactors., (Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

The selective capture of carbon dioxide in porous materials has potential for the storage and purification of fuel and flue gases. However, adsorption capacities under dynamic conditions are often insufficient for practical applications, and strategies to enhance CO(2)-host selectivity are required. The unique partially interpenetrated metal-organic framework NOTT-202 represents a new class of dynamic material that undergoes pronounced framework phase transition on desolvation. We report temperature-dependent adsorption/desorption hysteresis in desolvated NOTT-202a that responds selectively to CO(2). The CO(2) isotherm shows three steps in the adsorption profile at 195 K, and stepwise filling of pores generated within the observed partially interpenetrated structure has been modelled by grand canonical Monte Carlo simulations. Adsorption of N(2), CH(4), O(2), Ar and H(2) exhibits reversible isotherms without hysteresis under the same conditions, and this allows capture of gases at high pressure, but selectively leaves CO(2) trapped in the nanopores at low pressure.

The processes of methane adsorption, storage and desorption by the nanocapsule are investigated with molecular-dynamic modeling method. The specific nanocapsule shape defines its functioning uniqueness: methane is adsorbed under 40 MPa and at normal temperature with further blocking of methane molecules the K@C60(1+) endohedral complex in the nanocapsule by external electric field, the storage is performed under normal external conditions, and methane desorption is performed at 350 K. The methane content in the nanocapsule during storage reaches 11.09 mass%. The nanocapsule consists of tree parts: storage chamber, junction and blocking chamber. The storage chamber comprises the nanotube (20,20). The blocking chamber is a short nanotube (20,20) with three holes. The junction consists of the nanotube (10,10) and nanotube (8,8); moreover, the nanotube (8,8) is connected with the storage chamber and nanotube (10,10) with the blocking chamber. The blocking chamber is opened and closed by the transfer of the K@C(60) (1+) endohedral complex under electrostatic field action.

A nanocapsule for safe and effective methane storage is investigated by the method of molecular dynamics. The mass content of methane in the nanocapsule reaches the value of 14.5 mass%. The nanocapsule consists of two parts: a locking chamber and a storage area. The locking chamber is the nanotube (10.10), open at one end, with a K@C(60) (1+) endohedral complex inside it. The storage area is a nanotube (20.20). The locking chamber and the storage area are joined with each other and form T-junction. The locking chamber is opened at the methane filling and the discharge stages, and it is closed at the storage stage. Thanks to the locking chamber, methane molecules are stored in the nanocapsules under normal external conditions. Opening and closing of the locking chamber are carried out by the K@C(60) (1+) endohedral complex displacement, which is done by the electric field action. The specific structure of the nanocapsule allows two aims to be reached: a high methane mass content and significant level of safety.

Because the traditional storage of methane in the condensed state in high-pressure vessels is rather dangerous, and to store a large amount of gas using adsorbents is impossible at normal ambient conditions, we have developed a nanocapsule, which combines the advantages of a high-pressure vessel and adsorbents--a large methane mass content and safe-keeping. A nanocapsule is a system of combined nanotubes forming bottle-like pores, the entrance to which is closed by a positively charged endohedral complex (K@C60) with the help of an electric field. In normal ambient conditions, the nanocapsule can retain the amount of methane adsorbed under charging conditions. The processes taking place during the storage of methane and the methane desorption from the nanocapsule are analysed and the value of the electric field intensity necessary for the transfer of the K@C60 in the nanocapsule is determined. The nanocapsule discussed can retain approximately 17.5 mass% of methane at an internal pressure of 10 MPa and a temperature of 300 K.