Self-Assembled Two-Dimensional Nanoporous Crystals as Molecular Sieves: Molecular Dynamics Studies of 1,3,5-Tristyrilbenzene-Cn Superstructures.

Due to their unique geometry complex, self-assembled nanoporous 2D molecular crystals offer a broad landscape of potential applications, ranging from adsorption and catalysis to optoelectronics, substrate processes, and future nanomachine applications. Here we report and discuss the results of extensive all-atom Molecular Dynamics (MD) investigations of self-assembled organic monolayers (SAOM) of interdigitated 1,3,5-tristyrilbenzene (TSB) molecules terminated by alkoxy peripheral chains Cn containing n carbon atoms (TSB3,5-Cn) deposited onto highly ordered pyrolytic graphite (HOPG). In vacuo structural and electronic properties of the TSB3,5-Cn molecules were initially determined using ab initio second order Møller-Plesset (MP2) calculations. The MD simulations were then used to analyze the behavior of the self-assembled superlattices, including relaxed lattice geometry (in good agreement with experimental results) and stability at ambient temperatures. We show that the intermolecular disordering of the TSB3,5-Cn monolayers arises from competition between decreased rigidity of the alkoxy chains (loss of intramolecular order) and increased stabilization with increasing chain length (afforded by interdigitation). We show that the inclusion of guest organic molecules (e.g., benzene, pyrene, coronene, hexabenzocoronene) into the nanopores (voids formed by interdigitated alkoxy chains) of the TSB3,5-Cn superlattices stabilizes the superstructure, and we highlight the importance of alkoxy chain mobility and available pore space in the dynamics of the systems and their potential application in selective adsorption.

Intermediate states approach for adsorption studies in flexible metal-organic frameworks.

Adsorption studies in flexible metal-organic frameworks are challenging and time-consuming. It is mainly because the mechanism of adsorption, defined by structural framework properties, is constantly modified during the process, as the framework transformation depends on the adsorption uptake. We propose here a new approach to investigate adsorption in such complex systems, in which the simulations of adsorption in a deforming framework are replaced by the analysis of adsorption in intermediate rigid structures. As a proof of concept we analyze carbon dioxide, hexane, and methane adsorption in MIL-53. 19 intermediate structures were generated using geometrical interpolation between the open and the closed MOF forms and optimized with quantum DFT calculations. The grand canonical Monte Carlo method was applied to calculate adsorption isotherms in all intermediate structures. The comparison with experimental results enabled the identification of the intermediate adsorption states. The analysis of the microscopic configurations of the adsorbed molecules in these structures allowed us to propose a new mechanism of adsorbate evolution over the entire process.

Benchmarking of GGA density functionals for modeling structures of nanoporous, rigid and flexible MOFs.

The adequate choice of the interaction model is essential to reproduce qualitatively and estimate quantitatively the experimentally observed characteristics of materials or phenomena in computer simulations. Here we present the results of a benchmarking of density-functional theory calculations of rigid and flexible metal-organic frameworks (MOFs). The stability of these systems depends on the dispersion interactions. We compare the performance of two functionals, Perdew-Burke-Ernzerhof (PBE) and PBE designed for solids, with and without the dispersion corrections (D2 and TS), in reproducing the high-accuracy low-temperature X-ray and neutron diffraction data for both groups of MOFs. We focus our analysis on the key structural parameters: the lattice parameters, bond lengths, and angles. We show that the dispersion long range correction is essential to stabilize the structures and, in some cases, to converge the system to a geometry that is in line with the experimentally observed structure, especially for breathing MIL-53 structures or zeolitic imidazolate frameworks. We find that for all structures and all analyzed parameters, the D2-corrected PBE functional performs the best, except for bonds involving the metal ions; however, even for these bonds the difference between the experimentally observed and calculated lengths is small. Therefore, we recommend the use of the PBE-D2 functional in further numerical analyses of rigid and flexible nanoporous MOFs.

Adsorption-Induced Structural Phase Transformation in Nanopores.

We report a new type of structural transformation occurring in methane adsorbed in micropores. The observed methane structures are defined by probability distributions of molecular positions. The mechanism of the transformation has been modeled using Monte Carlo method. The transformation is totally determined by a reconstruction of the probability distribution functions of adsorbed molecules. The methane molecules have some freedom to move in the pore but most of the time they are confined to the positions around the high probability adsorption sites. The observed high-probability structures evolve as a function of temperature and pressure. The transformation is strongly discontinuous at low temperature and becomes continuous at high temperature. The mechanism of the transformation is influenced by a competition between different components of the interaction and the thermal energy. The methane structure represents a new state of matter, intermediate between solid and liquid.

Design rules for metal binding biomolecules: understanding of amino acid adsorption on platinum crystallographic facets from density functional calculations.

Understanding the mechanism of biomolecules' interaction with inorganic surfaces might pave the way for the design of material interfaces with controlled and highly predictable properties. Here we have focused on the adsorption mechanism of facet-specific amino acids in the sequence of peptides selected for programmed synthesis of Pt(111) and Pt(100) nanocrystals. Using the first principles calculations we have demonstrated that the specific surface recognition of amino acid side chains occurs due to the combination of multiple processes: electron exchange, partial charge transfer and/or dispersive effects providing a high binding affinity to both polar and non-polar residues against both Pt facets. Our approach points towards promising novel routes for controlled design of material-specific linkers for future materials engineering.

Molecular mechanism of selective binding of peptides to silicon surface.

Despite extensive recent research efforts on material-specific peptides, the fundamental problem to be explored yet is the molecular interactions between peptides and inorganic surfaces. Here we used computer simulations (density functional theory and classical molecular dynamics) to investigate the adsorption mechanism of silicon-binding peptides and the role of individual amino acids in the affinity of peptides for an n-type silicon (n(+)-Si) semiconductor. Three silicon binding 12-mer peptides previously elaborated using phage display technology have been studied. The peptides' conformations close to the surface have been determined and the best-binding amino acids have been identified. Adsorption energy calculations explain the experimentally observed different degrees of affinity of the peptides for n(+)-Si. Our residual scanning analysis demonstrates that the binding affinity relies on both the identity of the amino acid and its location in the peptide sequence.

Unique bonding nature of carbon-substituted Be2 dimer inside the carbon (sp(2)) network.

Controlled doping of active carbon materials (viz., graphenes, carbon nanotubes etc.) may lead to the enhancement of their desired properties. The least studied case of C/Be substitution offers an attractive possibility in this respect. The interactions of Be2 with Be or C atoms are dominated by the large repulsive Pauli exchange contributions, which in turn offsets the attractive interactions leading to relatively small binding energies. The Be2 dimer, e.g., after being doped inside a planar carbon network, undergoes orbital adjustments due to charge transfer and unusual intermolecular interactions and is oriented perpendicular to the plane of the carbon network with the Be-Be bond center located inside the plane. The present theoretical investigation on the nature of bonding in C/Be2 exchange complexes, using state of the art quantum chemical techniques, reveals a sp(2) carbon-like bonding scheme in Be2 arising due to the molecular hybridization of σ and two π orbitals. The perturbations imposed by doped Be2 dimers exhibit a local character of the structural and electronic properties of the complexes, and the separation by two carbon atoms between beryllium active centers is sufficient to consider these centers as independent sites.

Efficient Modeling of Water Adsorption in MOFs Using Interpolated Transition Matrix Monte Carlo.

With the specter of accelerating climate change, securing access to potable water has become a critical global challenge. Atmospheric water harvesting (AWH) through metal-organic frameworks (MOFs) emerges as one of the promising solutions. The standard numerical methods applied for rapid and efficient screening for optimal sorbents face significant limitations in the case of water adsorption (slow convergence and inability to overcome high energy barriers). To address these challenges, we employed grand canonical transition matrix Monte Carlo (GC-TMMC) methodology and proposed an efficient interpolation scheme that significantly reduces the number of required simulations while maintaining accuracy of the results. Through the example of water adsorption in three MOFs: MOF-303, MOF-LA2-1, and NU-1000, we show that the extrapolation of the free energy landscape allows for prediction of the adsorption properties over a continuous range of pressure and temperature. This innovative and versatile method provides rich thermodynamic information, enabling rapid, large-scale computational screening of sorbents for adsorption, applicable for a variety of sorbents and gases. As the presented methodology holds strong applicative potential, we provide alongside this paper a modified version of the RASPA2 code with a ghost swap move implementation and a Python library designed to minimize the user's input for analyzing data derived from the TMMC simulations.

Temperature dependence of the near infrared absorption spectrum of single-wall carbon nanotubes dispersed by sodium dodecyl sulfate in aqueous solution: experiments and molecular dynamics study.

CONTEXT: Single-wall carbon nanotubes (SWCNT) dispersed in water with the help of sodium dodecyl sulfate (SDS) surfactants exhibit a temperature dependent near infrared (NIR) exciton spectrum. Due to their biocompatibility and NIR spectrum falling within the transparent window for biological tissue, SWCNTs hold potential for sensing temperature inside cells. Here, we seek to elucidate the mechanism responsible for this temperature dependence, focusing on changes in the water coverage of the SWCNT as the surfactant structure changes with temperature. We compare optical absorption spectra in the UV-Vis-IR range and fully atomistic molecular dynamics (MD) simulations. The observed temperature dependence of the spectra for various SWCNTs may be attributed to changes in the dielectric environment and its impact on excitons. MD simulations reveal that the adsorbed SDS molecules effectively shield the SWCNT, with ~ 70% of water molecules removed from the first two adlayers; this coverage shows a modest temperature dependence. Although we are not able to directly demonstrate how this influences the NIR spectrum, this represents a potential pathway given the strong influence of the water environment on the excitons in SWCNTs. METHODS: Optical absorption measurements were carried out in the UV-Vis-NIR range using a Varian Cary 5000 spectrophotometer in a temperature-controlled environment. PeakFit™ v. 4.06 was used as peak-fitting program in the spectral range 900-1400 nm (890-1380 meV) as a function of the temperature. Fully atomistic molecular dynamics simulations were conducted using the NAMD2 package. The CHARMM force field comprising two-body bond stretching, three-body angle deformation, four-body dihedral angle deformation, and nonbonded interactions (electrostatic and Lennard-Jones 6-16 potentials) was employed.

Insights on the facet specific adsorption of amino acids and peptides toward platinum.

Engineering shape-controlled bionanomaterials requires comprehensive understanding of interactions between biomolecules and inorganic surfaces. We explore the origin of facet-selective binding of peptides adsorbed onto Pt(100) and Pt(111) crystallographic planes. Using molecular dynamics simulations, we show that upon adsorption the peptides adopt a predictable conformation. We compute the binding energies of the amino acids constituting two adhesion peptides for Pt, S7, and T7 and demonstrate that peptides' surface recognition behavior that makes them unique among populations originates from differential adsorption of their building blocks. We find that the degree of peptide binding is mainly due to polar amino acids and the molecular architecture of the peptides close to the Pt facets. Our analysis is a first step in the prediction of enhanced affinity between inorganic materials and a peptides, toward the synthesis of novel nanomaterials with programmable shape, structure, and properties.

Strongly Emitting Folic Acid-Derived Carbon Nanodots for One- and Two-Photon Imaging of Lyotropic Myelin Figures.

Non-invasive imaging of morphological changes in biologically relevant lipidic mesophases is essential for the understanding of membrane-mediated processes. However, its methodological aspects need to be further explored, with particular attention paid to the design of new excellent fluorescent probes. Here, we have demonstrated that bright and biocompatible folic acid-derived carbon nanodots (FA CNDs) may be successfully applied as fluorescent markers in one- and two-photon imaging of bioinspired myelin figures (MFs). Structural and optical properties of these new FA CNDs were first extensively characterized; they revealed remarkable fluorescence performance in linear and non-linear excitation regimes, justifying further applications. Then, confocal fluorescence microscopy and two-photon excited fluorescence microscopy were used to investigate a three-dimensional distribution of FA CNDs within the phospholipid-based MFs. Our results showed that FA CNDs are effective markers for imaging various forms and parts of multilamellar microstructures.

Hypothetical high-surface-area carbons with exceptional hydrogen storage capacities: open carbon frameworks.

A class of high-surface-area carbon hypothetical structures has been investigated that goes beyond the traditional model of parallel graphene sheets hosting layers of physisorbed hydrogen in slit-shaped pores of variable width. The investigation focuses on structures with locally planar units (unbounded or bounded fragments of graphene sheets), and variable ratios of in-plane to edge atoms. Adsorption of molecular hydrogen on these structures was studied by performing grand canonical Monte Carlo simulations with appropriately chosen adsorbent-adsorbate interaction potentials. The interaction models were tested by comparing simulated adsorption isotherms with experimental isotherms on a high-performance activated carbon with well-defined pore structure (approximately bimodal pore-size distribution), and remarkable agreement between computed and experimental isotherms was obtained, both for gravimetric excess adsorption and for gravimetric storage capacity. From this analysis and the simulations performed on the new structures, a rich spectrum of relationships between structural characteristics of carbons and ensuing hydrogen adsorption (structure-function relationships) emerges: (i) Storage capacities higher than in slit-shaped pores can be obtained by fragmentation/truncation of graphene sheets, which creates surface areas exceeding of 2600 m(2)/g, the maximum surface area for infinite graphene sheets, carried mainly by edge sites; we call the resulting structures open carbon frameworks (OCF). (ii) For OCFs with a ratio of in-plane to edge sites ≈1 and surface areas 3800-6500 m(2)/g, we found record maximum excess adsorption of 75-85 g of H(2)/kg of C at 77 K and record storage capacity of 100-260 g of H(2)/kg of C at 77 K and 100 bar. (iii) The adsorption in structures having large specific surface area built from small polycyclic aromatic hydrocarbons cannot be further increased because their energy of adsorption is low. (iv) Additional increase of hydrogen uptake could potentially be achieved by chemical substitution and/or intercalation of OCF structures, in order to increase the energy of adsorption. We conclude that OCF structures, if synthesized, will give hydrogen uptake at the level required for mobile applications. The conclusions define the physical limits of hydrogen adsorption in carbon-based porous structures.

Quasicontinuous Cooperative Adsorption Mechanism in Crystalline Nanoporous Materials.

The hase behavior of confined fluids adsorbed in nanopores differs significantly from their bulk counterparts and depends on the chemical and structural properties of the confining structures. In general, phase transitions in nanoconfined fluids are reflected in stepwise adsorption isotherms with a pronounced hysteresis. Here, we show experimental evidence and an in silico interpretation of the reversible stepwise adsorption isotherm which is observed when methane is adsorbed in the rigid, crystalline metal-organic framework IRMOF-1 (MOF-5). In a very narrow range of pressures, the adsorbed fluid undergoes a structural and highly cooperative reconstruction and transition between low-density and high-density nanophases, as a result of the competition between the fluid-framework and fluid-fluid interactions. This mechanism evolves with temperature: below 110 K, a reversible stepwise isotherm is observed, which is a result of the bimodal distribution of the coexisting nanophases. This temperature may be considered as a critical temperature of methane confined to nanopores of IRMOF-1. Above 110 K, as the entropy contribution increases, the isotherm shape transforms to a common continuous S-shaped form that is characteristic to a gradual densification of the adsorbed phase as the pressure increases.

Non-toxic Polymeric Dots with the Strong Protein-Driven Enhancement of One- and Two-Photon Excited Emission for Sensitive and Non-destructive Albumin Sensing.

The need for efficient probing, sensing, and control of the bioactivity of biomolecules (e.g., albumins) has led to the engineering of new fluorescent albumins' markers fulfilling very specific chemical, physical, and biological requirements. Here, we explore acetone-derived polymer dots (PDs) as promising candidates for albumin probes, with special attention paid to their cytocompatibility, two-photon absorption properties, and strong ability to non-destructively interact with serum albumins. The PDs show no cytotoxicity and exhibit high photostability. Their pronounced green fluorescence is observed upon both one-photon excitation (OPE) and two-photon excitation (TPE). Our studies show that both OPE and TPE emission responses of PDs are proteinaceous environment-sensitive. The proteins appear to constitute a matrix for the dispersion of fluorescent PDs, limiting both their aggregation and interactions with the aqueous environment. It results in a large enhancement of PD fluorescence. Meanwhile, the PDs do not interfere with the secondary protein structures of albumins, nor do they induce their aggregation, enabling the PD candidates to be good nanomarkers for non-destructive probing and sensing of albumins.

Hydrogen Storage in Pure and Boron-Substituted Nanoporous Carbons-Numerical and Experimental Perspective.

Nanoporous carbons remain the most promising candidates for effective hydrogen storage by physisorption in currently foreseen hydrogen-based scenarios of the world's energy future. An optimal sorbent meeting the current technological requirement has not been developed yet. Here we first review the storage limitations of currently available nanoporous carbons, then we discuss possible ways to improve their storage performance. We focus on two fundamental parameters determining the storage (the surface accessible for adsorption and hydrogen adsorption energy). We define numerically the values nanoporous carbons have to show to satisfy mobile application requirements at pressures lower than 120 bar. Possible necessary modifications of the topology and chemical compositions of carbon nanostructures are proposed and discussed. We indicate that pore wall fragmentation (nano-size graphene scaffolds) is a partial solution only, and chemical modifications of the carbon pore walls are required. The positive effects (and their limits) of the carbon substitutions by B and Be atoms are described. The experimental 'proof of concept' of the proposed strategies is also presented. We show that boron substituted nanoporous carbons prepared by a simple arc-discharge technique show a hydrogen adsorption energy twice as high as their pure carbon analogs. These preliminary results justify the continuation of the joint experimental and numerical research effort in this field.

Pore opening and breathing transitions in metal-organic frameworks: Coupling adsorption and deformation.

Soft porous crystals undergo large structural transformations under a variety of physical stimuli. Breathing-like transformations, occurring with a large volume change, have been associated with an existence of bi-stable or multi-stable crystal structures. Understanding of the mechanism of these transformations is essential for their potential applications in gas adsorption, separation and storage. However, the generic description is still missing. Here, we provide a detailed, multiscale qualitative and quantitative analysis of the adsorption-induced "breathing" transformations in two metal organic frameworks (MOFs): MIL-53(Al) which is a reference case of our approach, and recently synthesized JUK-8, which does not show any bistability without adsorbate. The proposed approach is based on atomistic simulations and does not require any empirical or adjustable parameters. It allows for a prediction of potential structural transformations in MOFs including the adsorption induced deformations derived from adsorption stress model. We also show that the quantitative agreement between calculated and experimental results critically depends on the quality of the dispersion energy correction. Our methodology represents a new, powerful tool for designing and screening of flexible materials, alternative and complimentary to experimental approaches.

Acetone-derived luminescent polymer dots: a facile and low-cost synthesis leads to remarkable photophysical properties.

Carbon-based dots have been attracting much attention as potentially superior alternatives to more conventional semiconductor nanoparticles, due to their fascinating optical properties, chemical and photochemical stability, unique environmental-friendliness, and the versatility of fabrication routes. Many commercial materials and organic compounds have been considered so far as carbon precursors but in many cases the fabrication required high-temperature conditions or led to inhomogeneous final products. Here we report on a simple low-cost synthesis of non-conjugated carbon-rich polymer dots (PDs) that uses acetone as carbon precursor. Both hydrophilic and hydrophobic fractions of PDs were obtained, with the respective average diameters of 2-4 nm and ca. 6 nm. The as-obtained PDs reveal greenish-blue photoluminescence (PL) and high quantum yields (∼5-7%) and complex kinetics of the decays with the average lifetime of ∼3.5 ns. Such luminescent acetone-derived PDs may find application in several fields, including sensing and bioimaging.

Computer modeling of 2D supramolecular nanoporous monolayers self-assembled on graphite.

Nano-porous two-dimensional molecular crystals, self-assembled on atomically flat host surfaces offer a broad range of possible applications, from molecular electronics to future nano-machines. Computer-assisted designing of such complex structures requires numerically intensive modeling methods. Here we present the results of extensive, fully atomistic simulations of self-assembled monolayers of interdigitated molecules of 1,3,5-tristyrilbenzene substituted by C6 alkoxy peripheral chains (TSB3,5-C6), deposited onto highly-ordered pyrolytic graphite. Structural and electronic properties of the TSB3,5-C6 molecules were determined from ab initio calculations, then used in Molecular Dynamics simulations to analyze the mechanism of formation, epitaxy, and stability of the TSB3,5-C6 nanoporous superlattice. We show that the monolayer disordering results from the competition between flexibility of the C6 chains and their stabilization by interdigitation. The inclusion of guest molecules (benzene and pyrene) into superlattice nanopores stabilizes the monolayer. The alkoxy chain mobility and available pore space defines the systems dynamics, essential for potential application.

Boron-neutron Capture on Activated Carbon for Hydrogen Storage.

This work investigates the effects of neutron irradiation on nitrogen and hydrogen adsorption in boron-doped activated carbon. Boron-neutron capture generates an energetic lithium nucleus, helium nucleus, and gamma photons, which can alter the surface and structure of pores in activated carbon. The defects introduced by fission tracks are modeled assuming the slit-shaped pores geometry. Sub-critical nitrogen adsorption shows that nitrogen molecules cannot probe the defects created by fission tracks. Hydrogen adsorption isotherms of irradiated samples indicate higher binding energies compared to their non-irradiated parent samples.

Modeling of low temperature adsorption of hydrogen in carbon nanopores.

We simulated the low temperature (T = 77 K) hydrogen adsorption in carbon slit-shaped nanopores using consecutively united atom (UA) and all atom (AA) representation of hydrogen molecule. We showed that both approximations give comparable estimation of the amount stored, for the wide range of pore width (0.6-2.5 nm). We also showed that at very high pressure (P = 400 bar, corresponding to the fugacity f used in grand canonical Monte Carlo simulations of f = 800 bar) the density of the adsorbed hydrogen structures is larger than the density of bulk liquid at critical temperature (∼76 kg/m3). This result agrees with the experimental observation of the density of the order of 100 kg/m3 for the hydrogen adsorbed in microporous carbons, reported recently in the literature.