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The separation of metal ions can be challenging because of similarities in charge density, size, and binding affinities. Here, we introduce a new photochemical separation strategy that relies on the intrinsically unique photophysical properties of metal ion complexes and the selective transformation of an electroactive ligand.
Here, we report a novel di(imino)guanidinium anion extractant with unparalleled selectivity for sulfate in a liquid–liquid separation system. In addition to a 4.4 order-of-magnitude enhancement in affinity compared to a standard benchmark, our alkylated di(imino)guanidinium receptor is economically synthesized and features good compatibility with application-relevant aliphatic solvents. Small-angle X-ray scattering results reveal the formation of reverse-micelles, which together with the significant organic-phase water content challenge traditional notions of selectivity in extraction of superhydrophilic anions.
Strict monitoring and control of selenium concentrations in freshwater supplies is critical to safeguarding human health and aquatic life. A handful of previously investigated sorbents exhibit noteworthy gravimetric (mg g -1 ) Se uptake capacities; however, often display insufficient volumetric (mg cm -3 ) capacities, thereby requiring large volumes of material for commercial implementation. In this paper, in pursuit of mitigating this material inefficiency, we investigated the selenite (SeO 3 2- ) and selenate (SeO 4 2- ) affinity of MOF-808, a Zr-based metal–organic framework with a high density of potential Se oxyanion binding sites. MOF-808 recorded exceptional volumetric and gravimetric Se oxyanion capacities of 133 mg g -1 (127 mg cm -3 ) and 118 mg g -1 (112 mg cm -3 ) for aqueous selenite and selenate, respectively. Single-crystal X-ray diffraction studies revealed that selenite and selenate can bind at the MOF node via two distinct binding motifs, an η 2 μ 2 motif in which the oxyanion coordinates to two different metal atoms in a single node, and a μ 2 motif in which the oxyanion interacts with only a single metal atom. Finally and furthermore, powder X-ray diffraction (PXRD) patterns and N 2 adsorption/desorption isotherms confirm the retention of bulk crystallinity and porosity after the uptake of Se oxyanions.
We report in this paper a density functional theory study of the nitrogen electroreduction and hydrogen evolution reactions on cubic molybdenum carbide (MoC) in order to investigate the viability of using this material as an electro-catalyst for ammonia synthesis. Free energy diagrams for associative and dissociative Heyrovsky mechanisms showed that nitrogen reduction on cubic MoC(111) can proceed via an associative mechanism and that small negative potentials of -0.3 V vs. standard hydrogen electrode can onset the reduction of nitrogen to ammonia. Kinetic volcano plots for hydrogen evolution showed that the MoC[110] surface is expected to have a high rate for the hydrogen evolution reaction, which could compete with the reduction of nitrogen on cubic MoC. The comparison between the adsorption energies of H-adatoms and N-adatoms also shows that at low potentials adsorption of hydrogen atoms competes with nitrogen adsorption on all the MoC surfaces except the MoC(111) surface. Finally, the hydrogen evolution and accumulation of H-adatoms can be mitigated by introducing carbon vacancies i.e. increasing the ratio of metal to carbon atoms, which will significantly increase the affinity of the catalytic surface for both nitrogen molecules and N-adatoms.
The tetraaza [Co II N 4 H] 2+ complex ( 1 ) is remarkable for its ability to selectively reduce CO 2 to CO with 45% Faradaic efficiency and a CO to H 2 ratio of 3 : 2. We employ density functional theory (DFT) to determine the reasons behind the unusual catalytic properties of 1 and the most likely mechanism for CO 2 reduction. The selectivity for CO 2 over proton reduction is explained by analyzing the catalyst's affinity for the possible ligands present under typical reaction conditions: acetonitrile, water, CO 2 , and bicarbonate. After reduction of the catalyst by two electrons, formation of [Co I N 4 H] + –-CO 2 - is strongly favored. Based on thermodynamic and kinetic data, we establish that the only likely route for producing CO from here consists of a protonation step to yield [Co I N 4 H] + –CO 2 H, followed by reaction with CO 2 to form [Co II N 4 H] 2+ –CO and bicarbonate. This conclusion corroborates the idea of a direct role of CO 2 as a Lewis acid to assist in C–O bond dissociation, a conjecture put forward by other authors to explain recent experimental observations. The pathway to formic acid is predicted to be forbidden by high activation barriers, in accordance with the products that are known to be generated by 1 . Calculated physical observables such as standard reduction potentials and the turnover frequency for our proposed catalytic cycle are in agreement with available experimental data reported in the literature. The mechanism also makes a prediction that may be experimentally verified: that the rate of CO formation should increase linearly with the partial pressure of CO 2 .
Although diamondoids are broadly studied for their fundamental properties and applications, boron-nitride-based diamondoids are scarcely explored.In this report we predict the stability, electronic structure, and optical absorption spectra of six boron-nitride (BN) diamondoids with first-principles methods based on pseudopotential density functional theory and many-body perturbation methods implemented with a real-space formalism. We find that four of them are thermodynamically stable at room temperature, while B10N8H24 and B6N4H16 show thermodynamic instability in molecular dynamics simulations. With the GW approximation, we predicted the ionization energies and electron affinities of BN-diamondoids and find that the evolution of the electronic structure with size does not follow the same trend as diamondoids, owing to the unbalanced numbers of boron and nitrogen atoms. We show strong photoabsorption of BN-triamantane and BN-adamantane in the infrared and visible ranges and analyze the features of low-energy absorption by examining the characteristics of related orbitals.
Here, the dissociative photoionization processes of methyl hydroperoxide (CH 3 OOH) have been studied by imaging Photoelectron Photoion Coincidence (iPEPICO) spectroscopy experiments as well as quantum-chemical and statistical rate calculations. Energy selected CH 3 OOH + ions dissociate into CH 2 OOH + , HCO + , CH 3 + , and H 3 O + ions in the 11.4–14.0 eV photon energy range. The lowest-energy dissociation channel is the formation of the cation of the smallest “QOOH” radical, CH 2 OOH + . An extended RRKM model fitted to the experimental data yields a 0 K appearance energy of 11.647 ± 0.005 eV for the CH 2 OOH + ion, and a 74.2 ± 2.6 kJ mol -1 mixed experimental-theoretical 0 K heat of formation for the CH 2 OOH radical. The proton affinity of the Criegee intermediate, CH 2 OO, was also obtained from the heat of formation of CH 2 OOH + (792.8 ± 0.9 kJ mol -1 ) to be 847.7 ± 1.1 kJ mol - 1, reducing the uncertainty of the previously available computational value by a factor of 4. RRKM modeling of the complex web of possible rearrangement-dissociation processes was used to model the higher-energy fragmentation. Supported by Born–Oppenheimer molecular dynamics simulations, we found that the HCO + fragment ion is produced through a roaming transition state followed by a low barrier. Lastly, H 3 O + is formed in a consecutive process from the CH 2 OOH + fragment ion, while direct C–O fission of the molecular ion leads to the methyl cation.
The intercalation process of binding doxorubicin (DOX) in DNA is studied by extensive MD simulations. Many molecular factors that control the binding affinity of DOX to DNA to form a stable complex are inspected and quantified by employing continuum solvation models for estimating the binding free energy. The modified MM-PB(GB)SA methodology provides a complete energetic profile of Δ G ele , Δ G vDW , Δ G polar , Δ G non-polar , T Δ S total , Δ G deform , Δ G con , and Δ G ion . To identify the sequence specificity of DOX, two different DNA sequences, d(CGATCG) or DNA1 and d(CGTACG) or DNA2, with one molecule (1 : 1 complex) or two molecule (2 : 1 complex) configurations of DOX were selected in this study. Our results show that the DNA deformation energy (Δ G deform ), the energy cost from translational and rotational entropic contributions ( T Δ S tran+rot ), the total electrostatic interactions (Δ G polar-PB/GB + Δ G ele ) of incorporation, the intramolecular electrostatic interactions (Δ G ele ) and electrostatic polar solvation interactions (Δ G polar-PB/GB ) are all unfavorable to the binding of DOX to DNA. However, they are overcome by at least five favorable interactions: the van der Waals interactions (Δ G vDW ), the non-polar solvation interaction (Δ G non-polar ), the vibrational entropic contribution ( T Δ S vib ), and the standard concentration dependent free energies of DOX (Δ G con ) and the ionic solution (Δ G ion ). Specifically, the van der Waals interaction appears to be the major driving force to form a stable DOX–DNA complex. We also predict that DOX has stronger binding to DNA1 than DNA2. The DNA deformation penalty and entropy cost in the 2 : 1 complex are less than those in the 1 : 1 complex, thus they indicate that the 2 : 1 complex is more stable than the 1 : 1 complex. Here, we have calculated the total binding free energy (BFE) (Δ G t-sim ) using both MM-PBSA and MM-GBSA methods, which suggests a more stable DOX–DNA complex at lower ionic concentration. The calculated BFE from the modified MM-GBSA method for DOX–DNA1 and DOX–DNA2 in the 1 : 1 complex is –9.1 and –5.1 kcal mol –1 respectively. The same quantities from the modified MM-PBSA method are –12.74 and –8.35 kcal mol –1 respectively. The value of the total BFE Δ G t-sim in the 1 : 1 complex is in reasonable agreement with the experimental value of –7.7 ± 0.3 kcal mol –1 .
The neutral and charged yttrium metal–ammonia complexes, [Y(NH3)8]0,±, are investigated using state-of-the-art quantum chemical calculations. The electronic structure of these complexes is described as an Y(NH3)83+ core with two, three, and four electrons orbiting in its periphery. Unlike the so far reported solvated electron precursors containing alkali, alkaline earth or first-row transition metals, yttrium complexes are the only ones which can accommodate eight ammonia ligands and up to four peripheral electrons. For the neutral species, two electrons occupy the diffuse s-type orbital (1s) and one diffuse p-type orbital (1p). For the cationic counterpart one electron is removed from the 1p orbital, while for the anion another electron is added to the 1p shell. The calculated low-lying electronic states with excitation energies up to 2.0 eV populate the 1s, 1p, and 1d outer orbitals. The first ionization energy of Y(NH3)8 is 2.74 eV and its electron affinity is 0.64 eV. The present results suggest that saturated yttrium ammonia solutions will turn into solids (liquid or expanded metals), where a grid of Y(NH3)83+ centers will be surrounded by “free” electrons.
The superior Cu( ii ) affinity of human copper transporter 1 (hCtr1) drives copper acquisition from human serum albumin (HSA).
Modifying the ribose ring or the nucleobase within oligonucleotides of RNA is a strategy that has regained attention due to its potential to provide chemical stability, increase affinity towards a target, or introduce groups with bioorthogonal reactivity, among other applications. However introducing groups via synthetic routes can be a daunting process and may result in unexpected physical properties and structural variations. In addition, characterizing the effects of a modification within an oligonucleotide can be time consuming and expensive, e.g., NMR, crystallography. Thus the development of models that are accurate, reasonably priced and carried out over short periods of time is essential to the development of this field. In this paper we report on the development and validation of computational models that explain the nature of the structural and stability changes induced by the presence of a C2'-O-methylthiophene group at various positions within duplexes conformed by two 6-mers of modified RNA as well as random coils containing the same modification(s). Through analysis of the obtained models it was concluded that the presence of the methylthiophene moiety on two strands of RNA induces a conformational change around the torsion angle (κ°) that leads to lower values in the pseudorotational angle (δ°), thus resulting in an A-form α-helix with shorter distances between phosphates than those in canonical RNA. These results provide a reasonable explanation for the experimental observations, which display the thermal stabilization of the duplexes, and are guiding efforts from our groups to control the structure and function of RNA, i.e., via functionalization of the RNA structure for attaining thermal stability while retaining the structural properties of an A-form duplex.
Peptide “cross-stitching” maintains binding affinity and can enhance helical and proteolytic stability.
Stapled-peptides have emerged as an exciting class of molecules which can modulate protein–protein interactions. We have used a structure-guided approach to rationally develop a set of hydrocarbon stapled-peptides with high binding affinities and residence times against the oncogenic eukaryotic translation initiation factor 4E (eIF4E) protein. Crystal structures of these peptides in complex with eIF4E show that they form specific interactions with a region on the protein-binding interface of eIF4E which is distinct from the other well-established canonical interactions. This recognition element is a major molecular determinant underlying the improved binding kinetics of these peptides with eIF4E. The interactions were further exploited by designing features in the peptides to attenuate disorder and increase helicity which collectively resulted in the generation of a distinct class of hydrocarbon stapled-peptides targeting eIF4E. This study details new insights into the molecular basis of stapled-peptide: eIF4E interactions and their exploitation to enhance promising lead molecules for the development of stapled-peptide compounds for oncology.
Molecular clusters are attractive superatomic building blocks for creating materials with tailored properties due to their unique combination of atomic precision, tunability and functionality. The ligands passivating these superatomic clusters offer an exciting opportunity to control their electronic properties while preserving their closed shells and electron counts, which is not achievable in conventional atoms. Here we demonstrate this concept by measuring the anion photoelectron spectra of a series of hexanuclear cobalt sulfide superatomic clusters with different ratios of electron-donating and electron-withdrawing ligands, Co 6 S 8 (PEt 3 ) 6-x (CO) x (x = 0–3). We find that Co 6 S 8 (PEt 3 ) 6 has a low electron affinity (EA) of 1.1 eV, and that the successive replacement of PEt3 ligands with CO gradually shifts its electronic spectrum to lower energy and increases its EA to 1.8 eV. Density functional theory calculations reveal that the increase of EA results from a monotonic lowering of the cluster highest occupied and lowest unoccupied molecular orbitals (HOMO and LUMO). Our work provides unique insights into the electronic structure and tunability of superatomic building blocks.
Serum albumin is the most abundant protein in mammalian blood plasma and is responsible for the transport of metals, drugs, and various metabolites, including hormones. We report the first albumin structure in complex with testosterone, the primary male sex hormone. Testosterone is bound in two sites, neither of which overlaps with the previously suggested Sudlow site I. We determined the binding constant of testosterone to equine and human albumins by two different methods: tryptophan fluorescence quenching and ultrafast affinity extraction. The binding studies and similarities between residues comprising the binding sites on serum albumins suggest that testosterone binds to the same sites on both proteins. Our comparative analysis of albumin complexes with hormones, drugs, and other biologically relevant compounds strongly suggests interference between a number of compounds present in blood and testosterone transport by serum albumin. We discuss a possible link between our findings and some phenomena observed in human patients, such as low testosterone levels in diabetic patients.
An energy dissipation mechanism during deformation is required to impart toughness to hydrogels. Here we describe how in situ small angle X-ray scattering (SAXS) provides insight into possible energy dissipation mechanisms for a tough hydrogel based on an amphiphilic copolymer where nanoscale associations of the hydrophobic moieties act as effective crosslinks. The mechanical properties of the hydrogels are intimately coupled with the nanostructure that provides reversible crosslinks and evolves during deformation. As the extension rate increases, more mechanical energy is dissipated from rearrangements of the crosslinks. The scattering is consistent with hopping of hydrophobes between the nanoscale aggregates as the primary rearrangement mechanism. This rearrangement changes the network conformation that leads to non-affine deformation, where the change in the nanostructure dimension from SAXS is less than 15% of the total macroscopic strain. These nanostructure changes are rate dependent and correlated with the relaxation time of the hydrogel. At low strain rate (0.15% s -1 ), no significant change of the nanostructure was observed, whereas at higher strain rates (1.5% s -1 and 8.4% s -1 ) significant nanostructure anisotropy occurred during extension. These differences are attributed to the ability for the network chains to rearrange on the time scale of the deformation; when the characteristic time for extension is longer than the average segmental relaxation time, no significant change in nanostructure occurs on uniaxial extension. These results illustrate the importance of strain rate in the mechanical characterization and consideration of relaxation time in the design of tough hydrogels with reversible crosslinks.
Effective treatment of disorders of the central nervous system can often be achieved using bioactive molecules of similar moieties to those known to be tolerable. A better understanding of the solid-state characteristics of such molecules could thereby create new opportunities for research on pharmaceutical preparations and drug prescriptions, while information about their rich intramolecular dynamics may well add an important aspect in the field of in silico drug discovery. As such, we have investigated three different antipsychotic drugs: haloperidol (C 21 H 23 ClFNO 2 , HAL), aripiprazole (C 23 H 27 Cl 2 N 3 O 2 , APZ) and quetiapine hemifumarate (C 21 H 25 N 3 O 2 S·0.5C 4 H 4 O 4 , QTP) based on similarities either in their structures, hydrophobic and hydrophilic moieties, or in their modes of action, typical or atypical. Our aim was to test the structural and molecular stability of these three different antipsychotics. To this end, we compared the molecular vibrations observed by inelastic neutron spectroscopy of these systems with those from theoretical periodic calculations of the crystalline antipsychotics using the Vienna ab initio simulation package (VASP). While most of the observed features in the lattice region were reasonably well represented by the calculations, the overall spectra were relatively complex, and hence traditional assignment procedures for the approximately 600 normal modes in the unit cell were not possible. These results indicate that in the search for new drug candidates, not only analysis of the flexibility of the receptor, but also the dynamics of the active molecules play a role in improving the prediction of binding affinities.
The TiO 2 –Pt–water interface is of great relevance in photocatalysis where Pt is widely used as a co-catalyst for The TiO 2 –Pt–water interface is of great relevance in photocatalysis where Pt is widely used as a co-catalyst for enhancing hydrogen evolution in aqueous TiO 2 . Using ab initio molecular dynamics, we investigated this interface focusing on Pt single atoms supported on anatase TiO 2 (101) in a water environment. Based on recent experiments showing a broad distribution of Pt coordination sites in TiO 2 , we examined six distinct single-Pt supported species with different nominal Pt oxidation states, namely: Pt, PtOH, and PtO 2 species adsorbed on the stoichiometric surface; Pt adsorbed at a surface oxygen vacancy (O v ); and Pt substituting a surface Ti cation (PtTi), both without and with an accompanying O v (Pt Ti + O v ). As found for the pristine anatase surface, interfacial water remained intact in the presence of a nearly neutral Pt adatom within the time duration of our simulations (~15 ps). Similarly, no (or only temporary) water dissociation was observed at the Pt Ti + O v and PtO 2 interfaces, due to the formation of very stable planar Pt coordination structures that interact only weakly with water. In contrast, water dissociated with OH – (H + ) on the Pt atom when this substituted a surface Ti (oxygen) ion as well as on PtOH. Lastly, the significant proton affinity of Pt atoms at surface oxygen vacancies suggests that negatively charged Pt species are particularly efficient at catalyzing hydrogen evolution in aqueous TiO 2 .hydrogen evolution in aqueous TiO 2 .