Structural Basis for Long Residence Time c-Src Antagonist: Insights from Molecular Dynamics Simulations

c-Src is involved in multiple signaling pathways and serves as a critical target in various cancers. Growing evidence suggests that prolonging a drug's residence time (RT) can enhance its efficacy and selectivity. Thus, the development of c-Src antagonists with longer residence time could potentially improve therapeutic outcomes. In this study, we employed molecular dynamics simulations to explore the binding modes and dissociation processes of c-Src with antagonists characterized by either long or short RTs. Our results reveal that the long RT compound DAS-DFGO-I (DFGO) occupies an allosteric site, forming hydrogen bonds with residues E310 and D404 and engaging in hydrophobic interactions with residues such as L322 and V377. These interactions significantly contribute to the long RT of DFGO. However, the hydrogen bonds between the amide group of DFGO and residues E310 and D404 are unstable. Substituting the amide group with a sulfonamide yielded a new compound, DFOGS, which exhibited more stable hydrogen bonds with E310 and D404, thereby increasing its binding stability with c-Src. These results provide theoretical guidance for the rational design of long residence time c-Src inhibitors to improve selectivity and efficacy.

Solution Dynamics of Covalent Open-[60]Fullerene Dimers

The translational diffusivity of covalent open-[60]fullerene dimers in an organic solvent was found to be well describable by a prolate ellipsoid model while a monomeric open-[60]fullerene behaves like a sphere model. The water association dynamics were examined for two open-[60]fullerene dimers, showing a higher water affinity for the sp3-linked dimer relative to sp2-linked dimer owing to an effective orbital-orbital overlap identified by π(fullerene)→σ*(H2O) interactions as suggested by theoretical calculations.

Deprotonation of formic, acetic acids and bicarbonate ion in slit silica nanopores at infinite dilution and in the presence of electrolytes

Dielectric effects and the coupled electrostatics between the nanoconfined and the internal/external aqueous media contribute to the observed deviations of chemistry within the nanoconfined environment when compared with unconfined systems. A systematic understanding has remained elusive, especially with respect to background salt concentration and boundary condition effects like the nanopore surface chemistry and the reference state used to calculate free energies. We utilize molecular dynamics simulations along with thermodynamic integration to determine the free energy difference associated with acid-base chemistry in 2 nm and 4 nm slit pores open to a bulk-like reservoir. pKa increases are predicted when confining acetic acid, formic acid, and bicarbonate in the slits at infinite dilution conditions. We find that confinement weakens the acids, and the modulation of outer pore surface dipole magnitudes can tune the pKa shift values, suggesting that purely "intrinsic" electrostatic effect on confinement may not exist. At sufficiently high salt concentrations, the dielectric/electrostatic effects on pKa values diminish due to charge screening effects. These discoveries enable future modifications of nanopore chemistries to achieve desirable properties for industrial applications.

Direct Through-Space Substituent-π Interactions in Noncovalent Arene-Fullerene Assemblies

The arene-arene interactions between electron-rich and deficient aromatics have been less understood. Herein, we focus on a [60]fullerene π-surface as an electron-deficient aromatics. Using a 1H signal of H2O@C60 as a magnetic probe, the presence of benzene-fullerene interactions was confirmed. To investigate substituent effects on the noncovalent arene-fullerene interactions, NMR titration experiments were carried out using an open-[60]fullerene and a series of substituted benzenes, i. e., PhX (X=NO2, CN, Cl, OMe, H, CH3, and NH2), demonstrating a 1 : 2 stoichiometry with a positive correlation between stabilization energies upon the first association (ΔG1) and Hammet constants (σm). The destabilization of the self-assembled structure for X=OMe with a σ-withdrawing nature clearly showed direct through-space substituent-π interactions describable by the Wheeler-Houk model while the second association was suggested to be considerably perturbed by the secondary effects.

Water Adsorption on π-Surfaces of Open-Fullerenes

Understanding the water adsorptive behavior of fullerenes is of particular importance for their material application in aqueous media. The conventional fullerenols usually provide complex physical pictures of water adsorption due to their uncontrollable hydroxylation degree and substitution pattern. Herein, we focus on poorly hydroxylated fullerenes with well-defined structures. The water adsorptive behavior was examined by synchrotron IR spectroscopy and computational studies. As a result, three types of IR bands were observed for adsorbed water. The population of the three states was considerably altered by the orientational difference of the hydroxy groups. Nevertheless, water adsorption could not occur for 9-fluorenol and catechol. This indicates that the Lewis acidic fullerene π-surface plays a prominent role in water adsorption, while the rather Lewis basic π-surface of 9-fluorenol is unable to attract much water at a boundary with humid air.

Molecular CO2 Storage: State of a Single-Molecule Gas

CO2 evolution is one of the urgent global issues; meanwhile, understanding of sorptive/dynamic behavior is crucial to create next-generation encapsulant materials with stable sorbent processes. Herein, we showcase molecular CO2 storage constructed by a [60]fullerenol nanopocket. The CO2 density reaches 2.401 g/cm3 within the nanopore, showing strong intramolecular interactions, which induce nanoconfinement effects such as forbidden translation, restricted rotation, and perturbed vibration of CO2. We also disclosed an equation of state for a molecular CO2 gas, revealing a very low pressure of 3.14 rPa (1 rPa = 10-27 Pa) generated by the rotation/vibration at 300 K. Curiously enough, the CO2 capture enabled to modulate an external property of the encapulant material itself, i.e., association of the [60]fullerenol via intercage hydrogen-bonding.

Water Self-Dissociation is Insensitive to Nanoscale Environments

Nanoconfinement effects on water dissociation and reactivity remain controversial, despite their importance to understand the aqueous chemistry at interfaces, pores, or aerosols. The pKw in confined environments has been assessed from experiments and simulations in a few specific cases, leading to dissimilar conclusions. Here, with the use of carefully designed ab initio simulations, we demonstrate that the energetics of bulk water dissociation is conserved intact to unexpectedly small length-scales, down to aggregates of only a dozen molecules or pores of widths below 2 nm. The reason is that most of the free-energy involved in water autoionization comes from breaking the O-H covalent bond, which has a comparable barrier in the bulk liquid, in a small droplet of nanometer size, or in a nanopore in the absence of strong interfacial interactions. Thus, dissociation free-energy profiles in nanoscopic aggregates or in 2D slabs of 1 nm width reproduce the behavior corresponding to the bulk liquid, regardless of whether the corresponding nanophase is delimited by a solid or a gas interface. The present work provides a definite and fundamental description of the mechanism and thermodynamics of water dissociation at different scales with broader implications on reactivity and self-ionization at the air-liquid interface.

Open-Cage Fullerene as a Macrocyclic Ligand for Na, Pt, and Rh Metal Complexes

An open-cage [60]fullerene derivative was prepared through Malaprade oxidation of a vicinal triol moiety as the key step. Above the 17-membered orifice, there is one carboxyl group. Three ketone carbonyl groups and one lactone carbonyl group are located on the rim of the orifice. The carboxylic and carbonyl oxygen atoms around the orifice act as strong polydentate ligands for a sodium ion. These oxygen atoms also react with [Rh(CO)2Cl]2 to form various isomeric rhodium complexes with comparable stability. The fullerene C═C bond on the rim of the orifice forms a stable platinum complex when treated with Pt(PPh3)4. Single crystal X-ray diffraction data reveal that one of the carboxylic oxygen atoms above the orifice forms a H-bond with the water molecule trapped in the cage.

C2-insertion into a fullerene orifice

The embedment of a C_n-unit into a carbon network constituting fullerene(s) potentially enables a cage-expansion. Herein, we report a C2-insertion into a fullerene orifice in which the mechanism was examined computationally. The C2-embedded open-[60]fullerene possesses an orifice enlarged from an octagon to a decagon, while the inner space was notably expanded as confirmed by the dynamic motion of the incarcerated H₂O molecule.

π-Extended Fullerenes with a Reactant Inside

Fullerene-graphene hybrids potentially exhibit unprecedented properties owing to interactive communication between the two units through a linkage. However, most of their discrete molecular structures have been still undisclosed thus far. With the recent rise in the awareness of facile access to molecular nanocarbon hybrids, we showcase novel π-extended fullerenes with a fused pyrazine or imidazole. Owing to the effective planar-curved π-conjugation, their absorption coefficients significantly increased in the visible region. Curiously enough, during the formation of π-extended fullerenes, an in situ generated NH₃ molecule was spontaneously encapsulated inside the fullerene cavity. The NH₃ molecule then underwent a timed orifice-expansion triggered by its sustained release. This is the first demonstration that fullerene captures a reactant inside, suggesting their potential usage for a sustained dosing and/or material delivery toward postfunctionalization of fullerene-graphene hybrids.

Hydrogenation of cage-opened C60 derivatives mediated by frustrated Lewis pairs

Multiply-carbonylated fullerene derivatives were found to work as one component in frustrated Lewis pairs which caused an Si-H bond activation in the presence of B(C₆F₅)₃, leading to the carbonyl hydrogenation in up to 99% yield. The Lewis acid-mediated reductive arylation also took place to furnish a corresponding ketal derivative.

An H2 O2 Molecule Stabilized inside Open-Cage C60 Derivatives by a Hydroxy Stopper

An H₂ O₂ molecule was isolated inside hydroxylated open-cage fullerene derivatives by mixing an H₂ O₂ solution with a precursor molecule followed by reduction of one of carbonyl groups on its orifice. Depending on the reduction site, two structural isomers for H₂ O₂ @open-fullerenes were obtained. A high encapsulation ratio of 81 % was attained at low temperature. The structures of the peroxosolvate complexes thus obtained were studied by ¹ H NMR spectroscopy, X-ray analysis, and DFT calculations, showing strong hydrogen bonding between the encapsulated H₂ O₂ and the hydroxy group located at the center of the orifice. This OH group was found to act as a kinetic stopper, and the formation of the hydrogen bonding caused thermodynamic stabilization of the H₂ O₂ molecule, both of which prevent its escape from the cage. One of the peroxosolvates was isolated by HPLC, affording H₂ O₂ @open-fullerene with 100 % encapsulation ratio, likely due to the intramolecular hydrogen-bonding interaction.

Structure and dynamics of nanoconfined water and aqueous solutions

This review is devoted to discussing recent progress on the structure, thermodynamic, reactivity, and dynamics of water and aqueous systems confined within different types of nanopores, synthetic and biological. Currently, this is a branch of water science that has attracted enormous attention of researchers from different fields interested to extend the understanding of the anomalous properties of bulk water to the nanoscopic domain. From a fundamental perspective, the interactions of water and solutes with a confining surface dramatically modify the liquid's structure and, consequently, both its thermodynamical and dynamical behaviors, breaking the validity of the classical thermodynamic and phenomenological description of the transport properties of aqueous systems. Additionally, man-made nanopores and porous materials have emerged as promising solutions to challenging problems such as water purification, biosensing, nanofluidic logic and gating, and energy storage and conversion, while aquaporin, ion channels, and nuclear pore complex nanopores regulate many biological functions such as the conduction of water, the generation of action potentials, and the storage of genetic material. In this work, the more recent experimental and molecular simulations advances in this exciting and rapidly evolving field will be reported and critically discussed.

Cage-Expansion of Fullerenes

Despite the first proposal on the cage inflation of fullerenes in 1991, the chemical expansion of fullerenes has been still a formidable challenge. Herein, we provide an efficient methodology to expand [60] and [70]fullerene cages by the inclusion of totally C5N unit, giving nitrogen-containing closed structures as C₆₅N and C₇₅N with double fused heptagons. This method consists of two steps commenced with the construction of an opening by the reaction with triazine as a C3N source, followed by the cage reformation using N-phenylmaleimide as a C2 source. We also synthesized endohedral cages, demonstrating that the encapsulated H₂O molecule inside the C₇₅N cage prefers the orientation which maximizes the intramolecular interaction with the carbon wall. Additionally, we revealed the existence of a through-space magnetic dipolar interaction between the encapsulated H₂ molecule and the embedded N atom.

Photochemical Orifice Expansion of a Cage-Opened C60 Derivative

Upon light irradiation, a tetraketosulfoxide derivative of C₆₀ was transformed into a diketosulfide carboxylic anhydride via intermolecular nucleophilic addition of the sulfoxide moiety. The thus-formed 18-membered ring enables a spontaneous insertion of an Ar atom. In this encapsulation/release process, the phenyl ring on the orifice works as a dynamic stopper, which potentially adopts three conformations: an open form reduces distortion energy at the transition state while semiopen and closed forms reduce the orifice size.

Dynamics and magnetic properties of NO molecules encapsulated in open-cage fullerene derivatives evidenced by low temperature heat capacity

Low-temperature heat capacity analyses for an NO-encapsulated fullerene derivative revealed (i) low-energy motion and (ii) strong magnetic anisotropy of the NO molecule due to its orbital angular momentum. The low-energy motion was attributed to reorientational motions of the NO molecules, in which only a small number (n ∼ 0.04) of NO molecules were found to participate. The NO molecules were confirmed to be paramagnetic even at 1 K. Ab-initio calculation indicated that the magnetic properties of the NO unit strongly depended on its surroundings, allowing the conformation of the fullerene cage to be estimated.

Synthesis of Ar@C60 using molecular surgery

Synthesis of Ar@C60 is described, using a route in which high-pressure argon filling of an open-fullerene and photochemical desulfinylation are the key steps for >95% encapsulation of the noble gas. Enrichment by recycling HPLC leads to quantitative incorporation of argon in the product endofullerene, with a mass recovery of tens of milligrams, allowing the first characterisation of fine structure in the solution 13C NMR spectrum.

Nonclassical Abramov Products Formed on Orifices of Cage-Opened C60 Derivatives

By nucleophilic addition of phosphite P(OMe)₃ to a cage-opened C₆₀ derivative, α-hydrophosphate and enol phosphate were obtained as kinetic and thermodynamic products, respectively. Different from classical Abramov products bearing a phosphorus-carbon bond, these products have a phosphorus-oxygen bond. The observed anomaly originates from the fully conjugated π system, which significantly stabilizes zwitterionic intermediates bearing a phosphorus-oxygen bond. The thus formed enol phosphate was found to exhibit an intense absorption band that extended to 730 nm, reflecting the intramolecular charge-transfer transitions. We also report domino phosphorylation reactions, which gave a cage-opened C₆₀ derivative bearing a direct P-C bond.

Pressure-induced annulative orifice closure of a cage-opened C60 derivative

A cage-opened C60 derivative was found to undergo an unusual annulative orifice-closure reaction under high-pressure conditions, in which the orifice size changed from a 16- to a 13-membered ring. The structure was different from that obtained by the reaction at 1 atm. The theoretical calculations suggested that the formation of the former one is thermodynamically favored.

Synthesis of a Dihydroxylated Open-Cage [70]Fullerene by a Reductive Ring-Closure Reaction

Upon heating an open-cage diketo C₇₀ derivative in carbon disulfide, the 1,2-dihydroxylated compound was unprecedentedly formed via a reductive ring-closure reaction. The crystallographic analysis of the diketo derivative revealed a benzenoid character on its orifice which suppresses the nucleophilic addition. The 1,2-dihydroxylated derivative could be transformed into a 1,4-substituted one by an acid-catalyzed reaction. The observed unique reactivity of the diketo derivative is inherently different from those of structurally related C₇₀ isomers as well as a C₆₀ analogue.

Cation recognition on a fullerene-based macrocycle

Heterocyclic orifices in cage-opened fullerene derivatives are regarded as potential ligands toward metals or ions, being reminiscent of truncated fullerenes as a hypothetical class of macrocycles with spherical π-conjugation. Among a number of cage-opened examples reported thus far, the coordination ability and dynamic behavior in solution still remained unclear due to difficulties in structural determination with multiple coordination sites on the macrocycles. Herein, we present the detailed solution dynamics of a cage-opened C60 derivative bearing a diketo bis(hemiketal) moiety in the presence of alkali metal ions. The NMR spectroscopy disclosed the coordination behavior which is identified as a two-step process with a 1 : 2 stoichiometry. Upon coordination to the Li+ ion, the macrocycle largely varies its properties, i.e., increased absorption coefficients in the visible region due to weakly-allowed charge transfer transitions as well as the inner potential field from neutral to positive by the charge delocalization along with the spherical π-surface. The Li+-complexes formed in situ underwent unprecedented selective dehydroxyhydrogenation under high-pressure conditions. These findings would facilitate further studies on fullerene-based macrocycles as metal sensors, bulky ligands in organic reactions, and ion carriers in batteries and biosystems.

EPR study of NO radicals encased in modified open C60 fullerenes

Using pulsed electron paramagnetic resonance (EPR) techniques, the low-temperature magnetic properties of the NO radical being confined in two different modified open C 60 -derived cages are determined. It is found that the smallest principal g value g 3 , being assigned to the axis of the radical, deviates strongly from the free electron value. This behaviour results from partial compensation of the spin and orbital contributions to the g 3 value. The measured g 3 values in the range of 0.7 yield information about the deviation of the locking potential for the encaged NO from axial symmetry. The estimated 17 meV asymmetry is quite small compared to the situation found for the same radical in polycrystalline or amorphous matrices ranging from 300 to 500 meV. The analysis of the temperature dependence of spin relaxation times resulted in an activation temperature of about 3 K, assigned to temperature-activated motion of the NO within the modified open C 60 -derived cages with coupled rotational and translational degrees of freedom in a complicated three-dimensional locking potential.

Molecular Containers Derived from [60]Fullerene through Peroxide Chemistry

Molecular containers can keep guest molecules in a confined space that is completely separated from the solution. They have wide potential applications, including selective trapping of reactive intermediates, catalysis within the cavity, and molecular delivery. Numerous molecular containers have been prepared through covalent bonds, metal-ligand interactions and H-bonding or hydrophobic interactions. Fullerenes are all-carbon molecules with a spherical structure. Partial opening of the cage structure results in open-cage fullerenes, which can serve as molecular containers for various small molecules and atoms. Compared with classical molecular containers, open-cage fullerenes exhibit some unusual phenomena because of the unique structure of the fullerene cage. The synthesis of an open-cage fullerene with a large enough orifice as a molecular container requires consecutive cleavage of multiple fullerene skeleton bonds within a local area on the cage surface. In spite of the difficulty, remarkable progress has been achieved. Several reactions have been reported to cleave fullerene C-C bonds selectively to form open-cage fullerenes, some of which have been successfully used as molecular containers for molecules such as H₂O. The size and shape of the orifice play a key role in the encapsulation of the guest molecule. To date the focus in this area has been the preparation of open-cage fullerenes and encapsulation of small molecules. Little information has been reported about the functional properties of these host-guest systems. Potential applications of these systems need to be explored. This Account mainly presents our results on the encapsulation of small molecules in open-cage fullerenes prepared in my group. The preparation of our open-cage fullerenes is based on fullerene-mixed peroxides, which are briefly mentioned herein. The encapsulation and release of a single molecule of water is discussed in detail. Quantitative water encapsulation was achieved by heating the open-cage fullerene in a homogeneous CDCl₃/H₂O/EtOH mixture at 80 °C for 18 h. The kinetics of the water release process was studied by blackbody IR radiation-induced dissociation (BIRD) and theoretical calculations. The trapped water could also be released by H-bonding with HF. To control the encapsulation and release processes, we prepared open-cage fullerenes with a switchable stopper on the rim of the orifice. Besides H₂O, encapsulations of H₂, HF, CO, O₂, and H₂O₂ were also achieved by using different open-cage fullerenes. The encapsulation of CO is quite unusual in that the trapped CO is derived from a fullerene skeleton carbon that was pushed into the cavity by oxidation under ambient conditions at room temperature. The trapped O₂/H₂O₂ could be released slowly under mild conditions, and these systems are now being studied as a new type of oxygen-releasing materials for biomedical research. The present results demonstrate that open-cage fullerenes are suitable molecular containers for small molecules. Our future work will focus on optimizing the conditions for the preparation of open-cage fullerenes and applications of open-cage fullerenes in areas such as oxygen delivery for photodynamic therapy.

Synthesis of an open-cage fullerene-based unidirectional H-bonding network and its coordination with titanium

Hydroxyl groups formed a unidirectional H-bond network on the rim of an orifice and showed a weak interaction with a water molecule trapped inside a fullerene cage.