Challenges in first-principles NPT molecular dynamics of soft porous crystals: A case study on MIL-53(Ga)

Pressure induced topochemical polymerization of solid acrylamide facilitated by anisotropic response of the hydrogen bond network

The pressure induced polymerization of molecular solids is an appealing route to obtain pure, crystalline polymers without the need for radical initiators. Here, we report a detailed density functional theory (DFT) study of the structural and chemical changes that occur in defect free solid acrylamide, a hydrogen bonded crystal, when it is subjected to hydrostatic pressures. While our calculations are able to reproduce experimentally measured pressure dependent spectroscopic features in the 0-20 GPa range, our atomistic analysis predicts polymerization in acrylamide at a pressure of ∼23 GPa at 0 K albeit through large enthalpy barriers. Interestingly, we find that the two-dimensional hydrogen bond network in acrylamide templates topochemical polymerization by aligning the atoms through an anisotropic response at low pressures. This results not only in conventional C-C, but also unusual C-O polymeric linkages, as well as a new hydrogen bonded framework, with both N-HO and C-HO bonds. Using a simple model for thermal effects, we also show that at 300 K, higher pressures significantly accelerate the transformation into polymers by lowering the barrier. Thus, application of pressure offers an alternative route for topochemical polymerization when higher temperatures are undesirable.

In Silico Study Identified Methotrexate Analog as Potential Inhibitor of Drug Resistant Human Dihydrofolate Reductase for Cancer Therapeutics

Drug resistance is a core issue in cancer chemotherapy. A known folate antagonist, methotrexate (MTX) inhibits human dihydrofolate reductase (hDHFR), the enzyme responsible for the catalysis of 7,8-dihydrofolate reduction to 5,6,7,8-tetrahydrofolate, in biosynthesis and cell proliferation. Structural change in the DHFR enzyme is a significant cause of resistance and the subsequent loss of MTX. In the current study, wild type hDHFR and double mutant (engineered variant) F31R/Q35E (PDB ID: 3EIG) were subject to computational study. Structure-based pharmacophore modeling was carried out for wild type (WT) and mutant (MT) (variant F31R/Q35E) hDHFR structures by generating ten models for each. Two pharmacophore models, WT-pharma and MT-pharma, were selected for further computations, and showed excellent ROC curve quality. Additionally, the selected pharmacophore models were validated by the Guner-Henry decoy test method, which yielded high goodness of fit for WT-hDHFR and MT-hDHFR. Using a SMILES string of MTX in ZINC¹⁵ with the selections of 'clean', in vitro and in vivo options, 32 MTX-analogs were obtained. Eight analogs were filtered out due to their drug-like properties by applying absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment tests and Lipinski's Rule of five. WT-pharma and MT-pharma were further employed as a 3D query in virtual screening with drug-like MTX analogs. Subsequently, seven screening hits along with a reference compound (MTX) were subjected to molecular docking in the active site of WT- and MT-hDHFR. Through a clustering analysis and examination of protein-ligand interactions, one compound was found with a ChemPLP fitness score greater than that of MTX (reference compound). Finally, a simulation of molecular dynamics (MD) identified an MTX analog which exhibited strong affinity for WT- and MT-hDHFR, with stable RMSD, hydrogen bonds (H-bonds) in the binding site and the lowest MM/PBSA binding free energy. In conclusion, we report on an MTX analog which is capable of inhibiting hDHFR in wild type form, as well as in cases where the enzyme acquires resistance to drugs during chemotherapy treatment.

Water Adsorption in Soft and Heterogeneous Nanopores

ConspectusLiquids under confinement differ in behavior from their bulk counterparts and can acquire properties that are specific to the confined phase and linked to the nature and structure of the host matrix. While confined liquid water is not a new topic of research, the past few years have seen a series of intriguing novel features for water inside nanoscale pores. These unusual properties arise from the very specific nature of nanoporous materials, termed "soft porous crystals"; they combine large-scale flexibility with a heterogeneous internal surface. This creates a rich diversity of behavior for the adsorbed water, and the combination of different experimental characterization techniques along with computational chemistry at various scales is necessary to understand the phenomena observed and their microscopic origins. The range of systems of interest span the whole chemical range, from the inorganic (zeolites, imogolites) to the organic (microporous carbons, graphene, and its derivatives), and even encompass the hybrid organic-inorganic systems (such as metal-organic frameworks).The combination of large scale flexibility with the strong physisorption (or even chemisorption) of water can lead to unusual properties (belonging to the "metamaterials" category) and to novel phenomena. One striking example is the recent elucidation of the mechanism of negative hydration expansion in ZrW₂O₈, by which adsorption of ∼10 wt % water in the inorganic nonporous framework leads to large shrinkage of its volume. Another eye-catching case is the occurrence of multiple water adsorption-driven structural transitions in the MIL-53 family of materials: the specific interactions between water guest molecules and the host framework create behavior that has not been observed with any other adsorbate. Both are counterintuitive phenomena that have been elucidated by a combination of experimental in situ techniques and molecular simulation.Another important direction of research is the shift in the systems and phenomena studied, from physical adsorption toward studies of reactivity, hydrothermal stability, and the effect of confinement on aqueous phases more complex than pure water. There have been examples of water adsorption in highly flexible metal-organic frameworks being able to compete with the materials' coordination bonds, thereby limiting its hydrothermal stability, while tweaking the functional groups of the same framework can lead to increased stability while retaining the flexibility of the material. However, this additional complexity and tunability in the macroscopic behavior can occur from changes in the confined fluid rather than the material. Very recent studies have shown that aqueous solutions of high concentration (such as LiCl up to 20 mol L^-1) confined in flexible nanoporous materials can have specific properties different from pure water and not entirely explained by osmotic effects. There, the strong ordering of the confined electrolyte competes with the structural flexibility of the framework to create an entirely new behavior for the {host, guest} system.

In Silico Study Probes Potential Inhibitors of Human Dihydrofolate Reductase for Cancer Therapeutics

Dihydrofolate reductase (DHFR) is an essential cellular enzyme and thereby catalyzes thereduction of dihydrofolate to tetrahydrofolate (THF). In cancer medication, inhibition of humanDHFR (hDHFR) remains a promising strategy, as it depletes THF and slows DNA synthesis and cellproliferation. In the current study, ligand-based pharmacophore modeling identified and evaluatedthe critical chemical features of hDHFR inhibitors. A pharmacophore model (Hypo1) was generatedfrom known inhibitors of DHFR with a correlation coefficient (0.94), root mean square (RMS)deviation (0.99), and total cost value (125.28). Hypo1 was comprised of four chemical features,including two hydrogen bond donors (HDB), one hydrogen bond acceptor (HBA), and onehydrophobic (HYP). Hypo1 was validated using Fischer's randomization, test set, and decoy setvalidations, employed as a 3D query in a virtual screening at Maybridge, Chembridge, Asinex,National Cancer Institute (NCI), and Zinc databases. Hypo1-retrieved compounds were filtered byan absorption, distribution, metabolism, excretion, and toxicity (ADMET) assessment test andLipinski's rule of five, where the drug-like hit compounds were identified. The hit compounds weredocked in the active site of hDHFR and compounds with Goldfitness score was greater than 44.67(docking score for the reference compound), clustering analysis, and hydrogen bond interactionswere identified. Furthermore, molecular dynamics (MD) simulation identified three compounds asthe best inhibitors of hDHFR with the lowest root mean square deviation (1.2 Å to 1.8 Å), hydrogenbond interactions with hDHFR, and low binding free energy (-127 kJ/mol to -178 kJ/mol). Finally,the toxicity prediction by computer (TOPKAT) affirmed the safety of the novel inhibitors of hDHFRin human body. Overall, we recommend novel hit compounds of hDHFR for cancer and rheumatoidarthritis chemotherapeutics.

Thermodynamics of the Flexible Metal-Organic Framework Material MIL-53(Cr) From First Principles

We use first-principles density functional theory total energy and linear response phonon calculations to compute the Helmholtz and Gibbs free energy as a function of temperature, pressure, and cell volume in the flexible metal-organic framework material MIL-53(Cr) within the quasiharmonic approximation. GGA and metaGGA calculations were performed, each including empirical van der Waals (vdW) forces under the D2, D3, or D3(BJ) parameterizations. At all temperatures up to 500 K and pressures from -30 MPa to 30 MPa, two minima in the free energy versus volume are found, corresponding to the narrow pore (np) and large pore (lp) structures. Critical positive and negative pressures are identified, beyond which there is only one free energy minimum. While all results overestimated the stability of the np phase relative to the lp phase, the best overall agreement with experiment is found for the metaGGA PBEsol+RTPSS+U+J approach with D3 or D3(BJ) vdW forces. For these parameterizations, the calculated free energy barrier for the np-lp transition is only 3 to 6 kJ per mole of Cr₄(OH)₄(C₈H₄O₄)₄.

Ab initio molecular dynamics determination of competitive O₂ vs. N₂ adsorption at open metal sites of M₂(dobdc)

The separation of oxygen from nitrogen using metal-organic frameworks (MOFs) is of great interest for potential pressure-swing adsorption processes for the generation of purified O2 on industrial scales. This study uses ab initio molecular dynamics (AIMD) simulations to examine for the first time the pure-gas and competitive gas adsorption of O2 and N2 in the M2(dobdc) (M = Cr, Mn, Fe) MOF series with coordinatively unsaturated metal centers. Effects of metal, temperature, and gas composition are explored. This unique application of AIMD allows us to study in detail the adsorption/desorption processes and to visualize the process of multiple guests competitively binding to coordinatively unsaturated metal sites of a MOF.

Recent advances in the computational chemistry of soft porous crystals

We highlight recent progress in the field of computational chemistry of nanoporous materials, focusing on methods and studies that address the extraordinary dynamic nature of these systems: the high flexibility of their frameworks, the large-scale structural changes upon external physical or chemical stimulation, and the presence of defects and disorder.

Thermodynamic Insight in the High-Pressure Behavior of UiO-66: Effect of Linker Defects and Linker Expansion

In this Article, we present a molecular-level understanding of the experimentally observed loss of crystallinity in UiO-66-type metal-organic frameworks, including the pristine UiO-66 to -68 as well as defect-containing UiO-66 materials, under the influence of external pressure. This goal is achieved by constructing pressure-versus-volume profiles at finite temperatures using a thermodynamic approach relying on ab initio derived force fields. On the atomic level, the phenomenon is reflected in a sudden drop in the number of symmetry operators for the crystallographic unit cell because of the disordered displacement of the organic linkers with respect to the inorganic bricks. For the defect-containing samples, a reduced mechanical stability is observed, however, critically depending on the distribution of these defects throughout the material, hence demonstrating the importance of judiciously characterizing defects in these materials.

Adsorption deformation of microporous composites

We study here the behavior of flexible adsorbent materials, or soft porous crystals, when used in practical applications as nanostructured composites such as core-shell particles or mixed matrix membranes. Based on simple models and the well-established laws of elasticity, we demonstrate how the presence of a binder results in an attenuation of the adsorption-induced stress and deformation. In the case where the adsorbent undergoes adsorption-induced structural transitions, such as the gate opening phenomenon occurring in some metal-organic frameworks, we show that the presence of the binder will result in shifts of the adsorption-induced transition pressures.

Hydrothermal Breakdown of Flexible Metal-Organic Frameworks: A Study by First-Principles Molecular Dynamics

Flexible metal-organic frameworks, also known as soft porous crystals, have been proposed for a vast number of technological applications, because they respond by large changes in structure and properties to small external stimuli, such as adsorption of guest molecules and changes in temperature or pressure. While this behavior is highly desirable in applications such as sensing and actuation, their extreme flexibility can also be synonymous with decreased stability. In particular, their performance in industrial environments is limited by a lack of stability at elevated temperatures and in the presence of water. Here, we use first-principles molecular dynamics to study the hydrothermal breakdown of soft porous crystals. Focusing on the material MIL-53(Ga), we show that the weak point of the structure is the bond between the metal center and the organic linker and elucidate the mechanism by which water lowers the activation free energy for the breakdown. This allows us to propose strategies for the synthesis of MOFs with increased heat and water stability.

Defect-dependent colossal negative thermal expansion in UiO-66(Hf) metal-organic framework

Thermally-densified hafnium terephthalate UiO-66(Hf) is shown to exhibit the strongest isotropic negative thermal expansion (NTE) effect yet reported for a metal-organic framework (MOF). Incorporation of correlated vacancy defects within the framework affects both the extent of thermal densification and the magnitude of NTE observed in the densified product. We thus demonstrate that defect inclusion can be used to tune systematically the physical behaviour of a MOF.