Leveraging Curvature on N-Doped Carbon Materials for Hydrogen Storage.

Carbon sorbent materials have shown great promise for solid-state hydrogen (H2) storage. Modification of these materials with nitrogen (N) dopants has been undertaken to develop materials that can store H2 at ambient temperatures. In this work density functional theory (DFT) calculations are used to systematically probe the influence of curvature on the stability and activity of undoped and N-doped carbon materials toward H binding. Specifically, four models of carbon materials are used: graphene, [5,5] carbon nanotube, [5,5] D5d-C120, and C60, to extract and correlate the thermodynamic properties of active sites with varying degrees of sp2 hybridization (curvature). From the calculations and analysis, it is found that graphitic N-doping is thermodynamically favored on more pyramidal sites with increased curvature. In contrast, it is found that the hydrogen binding energy is weakly affected by curvature and is dominated by electronic effects induced by N-doping. These findings highlight the importance of modulating the heteroatom doping configuration and the lattice topology when developing materials for H2 storage.

X-ray absorption spectroscopy and theoretical investigations of the effect of extended ligands in potassium organic matter interaction.

Potassium (K) is an essential nutrient for plant growth, and despite its abundance in soil, most of the K is structurally bound in minerals, limiting its bioavailability and making this soil K reservoir largely inaccessible to plants. Microbial biochemical weathering has been shown to be a promising pathway to sustainably increase plant available K. However, the mechanisms underpinning microbial K uptake, transformation, storage, and sharing are poorly resolved. To better understand the controls on microbial K transformations, we performed K K-edge x-ray absorption near-edge structure (XANES) spectroscopy on K-organic salts, including acetate, citrate, nitrate, oxalate, and tartrate, which are frequently observed as low molecular weight organic acids secreted by soil microbes, as well as humic acid, which acts as a proxy for higher molecular weight organic acids. The organic salts display feature-rich K XANES spectra, each demonstrating numerous unique features spanning ∼13 eV range across the absorption edge. In contrast, the spectra for humic acid have one broad, wide feature across the same energy range. We used a combination of time-dependent density functional theory and the Bethe-Salpeter equation based approach within the OCEAN code to simulate the experimental spectra for K-nitrate (KNO3) and K-citrate [K3(C6H5O7)·H2O] to identify the electronic transitions that give rise to some of the outlying and unique spectral features in the organic salts. KNO3 has both the lowest and highest lying energy features, and K3(C6H5O7)·H2O is produced by several soil microbes and is effective at mineral weathering. Our results analyze the K-organic salt bonding in detail to elucidate why the spectral shapes differ and indicate that the K K-edge XANES spectra are associated with the entire ligand despite similar first-shell bonding environments around the K center. The improved understanding of K bonding environments with organic ligands and their use for interpretation of the K-XANES spectra provides an important toolkit to understand how K is transformed by microbial processes and made bioavailable for plant uptake.

Mechanical coupling in the nitrogenase complex.

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue ß-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing ß-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing ß-188Ser) are important for communication between the two halves.

Analysis of Intermediates and Products from the Dehydrogenation of Mg(BH4)2.

The thermodynamic properties of key compounds Mg(B3H8)2, MgB2H6, MgB10H10, Mg(B11H14)2, Mg3(B3H6)2, and MgB12H12, proposed to be formed in the release of hydrogen from magnesium borohydride Mg(BH4)2 and the uptake of hydrogen by MgB2, have been investigated using solid-state density functional theory (DFT) calculations. More accurate tretment of the cell-size effects with respect to the entropies was also investigated in order to improve the accuracy of the thermodynamic properties of complex borohydrides. We find that the zero-point energy corrections can lower the electronic energies of reaction by 20-30 kJ/(mol H2) for these intermediates, while adding the thermal and entropy contibutions results in a total decrease of up to ∼50 kJ/(mol H2). Although our treatment lowers the calculated formation energy of Mg(B3H8)2, it is still too high to explain the experimental observation of B3H8-. We discuss possible reasons for this disparity and propose that the formation of B3H8- and H- in a disordered amorphous phase has a large energy difference compared to the phase-separated Mg(B3H8)2 and MgH2 considered in calculations. A comparison of the experimental and NMR chemical shifts calculated within a DFT approach for known species Mg(BH4)2, Mg(B3H8)2, Mg(B11H14)2, MgB10H10, and MgB12H12 provides validation for predicting the chemical shifts of the other compounds which are yet to be confirmed experimentally. These include MgB2H6 and the proposed trianion species Mg3(B3H6)2 that both have favorable thermodynamics for reversible hydrogen storage in Mg(BH4)2 without the formation of MgH2 as a coproduct which could phase separate and inhibit rehydrogenation.

Nickel-Sulfonate Mode of Substrate Binding for Forward and Reverse Reactions of Methyl-SCoM Reductase Suggest a Radical Mechanism Involving Long-Range Electron Transfer.

Methyl-coenzyme M reductase (MCR) catalyzes both the synthesis and the anaerobic oxidation of methane (AOM). Its catalytic site contains Ni at the core of cofactor F430. The Ni ion, in its low-valent Ni(I) state, lights the fuse leading to homolysis of the C-S bond of methyl-coenzyme M (methyl-SCoM) to generate a methyl radical, which abstracts a hydrogen atom from coenzyme B (HSCoB) to generate methane and the mixed disulfide CoMSSCoB. Direct reversal of this reaction activates methane to initiate anaerobic methane oxidation. On the basis of the crystal structures, which reveal a Ni-thiol interaction between Ni(II)-MCR and inhibitor CoMSH, a Ni(I)-thioether complex with substrate methyl-SCoM has been transposed to canonical MCR mechanisms. Similarly, a Ni(I)-disulfide with CoMSSCoB is proposed for the reverse reaction. However, this Ni(I)-sulfur interaction poses a conundrum for the proposed hydrogen-atom abstraction reaction because the >6 Å distance between the thiol group of SCoB and the thiol of SCoM observed in the structures appears to be too long for such a reaction. The spectroscopic, kinetic, structural, and computational studies described here establish that both methyl-SCoM and CoMSSCoB bind to the active Ni(I) state of MCR through their sulfonate groups, forming a hexacoordinate Ni(I)-N/O complex, not Ni(I)-S. These studies rule out direct Ni(I)-sulfur interactions in both substrate-bound states. As a solution to the mechanistic conundrum, we propose that both the forward and the reverse MCR reactions emanate through long-range electron transfer from the Ni(I)-sulfonate complexes with methyl-SCoM and CoMSSCoB, respectively.

De novo sequencing and native mass spectrometry revealed hetero-association of dirigent protein homologs and potential interacting proteins in Forsythia × intermedia.

The discovery of dirigent proteins (DPs) and their functions in plant phenol biochemistry was made over two decades ago with Forsythia × intermedia. Stereo-selective, DP-guided, monolignol-derived radical coupling in vitro was then reported to afford the optically active lignan, (+)-pinoresinol from coniferyl alcohol, provided one-electron oxidase/oxidant capacity was present. It later became evident that DPs have several distinct sub-families, presumably with different functions. Some known DPs require other essential enzymes/proteins (e.g. oxidases) for their functions. However, the lack of a fully sequenced genome for Forsythia × intermedia made it difficult to profile other components co-purified with the (+)-pinoresinol forming DP. Herein, we used an integrated bottom-up, top-down, and native mass spectrometry (MS) approach to de novo sequence the extracted proteins via adaptation of our initial report of DP solubilization and purification. Using publicly available transcriptome and genomic data from closely related species, we identified 14 proteins that were putatively associated with either DP function or the cell wall. Although their co-occurrence after extraction and chromatographic separation is suggestive for potential protein-protein interactions, none were found to form stable protein complexes with DPs in native MS under the specific experimental conditions we have explored. Interestingly, two new DP homologs were found and they formed hetero-trimers. Molecular dynamics simulations suggested that similar hetero-trimers were possible between Arabidopsis DP homologs with comparable sequence similarities. Nevertheless, our integrated mass spectrometry method development helped prepare for future investigations directed to the discovery of novel proteins and protein-protein interactions. These advantages can be highly beneficial for plant and microbial research where fully sequenced genomes may not be readily available.

Tuning Catalytic Bias of Hydrogen Gas Producing Hydrogenases.

Hydrogenases display a wide range of catalytic rates and biases in reversible hydrogen gas oxidation catalysis. The interactions of the iron-sulfur-containing catalytic site with the local protein environment are thought to contribute to differences in catalytic reactivity, but this has not been demonstrated. The microbe Clostridium pasteurianum produces three [FeFe]-hydrogenases that differ in "catalytic bias" by exerting a disproportionate rate acceleration in one direction or the other that spans a remarkable 6 orders of magnitude. The combination of high-resolution structural work, biochemical analyses, and computational modeling indicates that protein secondary interactions directly influence the relative stabilization/destabilization of different oxidation states of the active site metal cluster. This selective stabilization or destabilization of oxidation states can preferentially promote hydrogen oxidation or proton reduction and represents a simple yet elegant model by which a protein catalytic site can confer catalytic bias.

Heterolytic Scission of Hydrogen Within a Crystalline Frustrated Lewis Pair.

We report the heterolysis of molecular hydrogen under ambient conditions by the crystalline frustrated Lewis pair (FLP) 1-{2-[bis(pentafluorophenyl)boryl]phenyl}-2,2,6,6-tetramethylpiperidine (KCAT). The gas-solid reaction provides an approach to prepare the solvent-free, polycrystalline ion pair KCATH2 through a single crystal to single crystal transformation. The crystal lattice of KCATH2 increases in size relative to the parent KCAT by approximately 2%. Microscopy was used to follow the transformation of the highly colored red/orange KCAT to the colorless KCATH2 over a period of 2 h at 300 K under a flow of H2 gas. There is no evidence of crystal decrepitation during hydrogen uptake. Inelastic neutron scattering employed over a temperature range from 4-200 K did not provide evidence for the formation of polarized H2 in a precursor complex within the crystal at low temperatures and high pressures. However, at 300 K, the INS spectrum of KCAT transformed to the INS spectrum of KCATH2. Calculations suggest that the driving force is more favorable in the solid state compared to the solution or gas phase, but the addition of H2 into the KCAT crystal is unfavorable. Ab Initio methods were used to calculate the INS spectra of KCAT, KCATH2, and a possible precursor complex of H2 in the pocket between the B and N of crystalline KCAT. Ex-situ NMR showed that the transformation from KCAT to KCATH2 is quantitative and our results suggest that the hydrogen heterolysis process occurs via H2 diffusion into the FLP crystal with a rate-limiting movement of H2 from inactive positions to reactive sites.

Chokepoints in Mechanical Coupling Associated with Allosteric Proteins: The Pyruvate Kinase Example.

Although the critical role of allostery in controlling enzymatic processes is well appreciated, there is a current dearth in our understanding of its underlying mechanisms, including communication between binding sites. One potential key aspect of intersite communication is the mechanical coupling between residues in a protein. Here, we introduce a graph-based computational approach to investigate the mechanical coupling between distant parts of a protein, highlighting effective pathways via which protein motion can transfer energy between sites. In this method, each residue is treated as a node on a weighted, undirected graph, in which the edges are defined by locally correlated motions of those residues and weighted by the strength of the correlation. The method was validated against experimental data on allosteric regulation in the human liver pyruvate kinase as obtained from full-protein alanine-scanning mutagenesis (systematic mutation) studies, as well as computational data on two G-protein-coupled receptors. The method provides semiquantitative information on the regulatory importance of specific structural elements. It is shown that these elements are key for the mechanical coupling between distant parts of the protein by providing effective pathways for energy transfer. It is also shown that, although there are a multitude of energy transfer pathways between distant parts of a protein, these pathways share a few common nodes that represent effective "chokepoints" for the communication.

Structural characterization of the P1+ intermediate state of the P-cluster of nitrogenase.

Nitrogenase is the enzyme that reduces atmospheric dinitrogen (N2) to ammonia (NH3) in biological systems. It catalyzes a series of single-electron transfers from the donor iron protein (Fe protein) to the molybdenum-iron protein (MoFe protein) that contains the iron-molybdenum cofactor (FeMo-co) sites where N2 is reduced to NH3 The P-cluster in the MoFe protein functions in nitrogenase catalysis as an intermediate electron carrier between the external electron donor, the Fe protein, and the FeMo-co sites of the MoFe protein. Previous work has revealed that the P-cluster undergoes redox-dependent structural changes and that the transition from the all-ferrous resting (PN) state to the two-electron oxidized P2+ state is accompanied by protein serine hydroxyl and backbone amide ligation to iron. In this work, the MoFe protein was poised at defined potentials with redox mediators in an electrochemical cell, and the three distinct structural states of the P-cluster (P2+, P1+, and PN) were characterized by X-ray crystallography and confirmed by computational analysis. These analyses revealed that the three oxidation states differ in coordination, implicating that the P1+ state retains the serine hydroxyl coordination but lacks the backbone amide coordination observed in the P2+ states. These results provide a complete picture of the redox-dependent ligand rearrangements of the three P-cluster redox states.

Structural and reorientational dynamics of tetrahydroborate (BH4-) and tetrahydrofuran (THF) in a Mg(BH4)2·3THF adduct: neutron-scattering characterization.

Metal borohydrides are considered promising materials for hydrogen storage applications due to their high volumetric and gravimetric hydrogen density. Recently, different Lewis bases have been complexed with Mg(BH4)2 in efforts to improve hydrogenation/dehydrogenation properties. Notably, Mg(BH4)2·xTHF adducts involving tetrahydrofuran (THF; C4H8O) have proven to be especially interesting. This work focuses on exploring the physicochemical properties of the THF-rich Mg(BH4)2·3THF adduct using neutron-scattering methods and molecular DFT calculations. Structural analysis, based on neutron diffraction measurements of Mg(11BH4)2·3TDF (D - deuterium), has confirmed a lowering of the symmetry upon cooling, from monoclinic C2/c to P1[combining macron] via a triclinic distortion. Vibrational properties are strongly influenced by the THF environment, showing a splitting in spectral features as a result of changes in the bond lengths, force constants, and lowering of the overall symmetry. Interestingly, the orientational mobilities of the BH4- anions obtained from quasielastic neutron scattering (QENS) are not particularly sensitive to the presence of THF and compare well with the mobilities of BH4- anions in unsolvated Mg(BH4)2. The QENS data point to uniaxial 180° jump reorientations of the BH4- anions around a preferred C2 anion symmetry axis. The THF rings are also found to be orientationally mobile, undergoing 180° reorientational jumps around their C2 molecular symmetry axis with jump frequencies about an order of magnitude lower than those for the BH4- anions. In contrast, no dynamical behavior of the THF rings is observed with QENS for a more THF-deficient 2Mg(BH4)2·THF adduct. This lack of comparable THF mobility may reflect a stronger Mg2+-THF bonding interaction for lower THF/Mg(BH4)2 stoichiometric ratios, which is consistent with DFT calculations showing a decrease in the binding energy with each additional THF ring in the adduct. Based on the combined experimental and computational results, we propose that combining THF and Mg(BH4)2 is beneficial to (i) preventing weakly bound THF from coming free from the Mg2+ cation and reducing the concentration of any unwanted impurity in the hydrogen and (ii) disrupting the stability of the crystalline phase, leading to a lower melting point and enhanced kinetics for any potential hydrogen storage applications.

Solid-State NMR Identification of Intermolecular Interactions in Amelogenin Bound to Hydroxyapatite.

Biomineralization processes govern the formation of hierarchical hard tissues such as bone and teeth in living organisms, and mimicking these processes could lead to the design of new materials with specialized properties. However, such advances require structural characterization of the proteins guiding biomineral formation to understand and mimic their impact. In their "active" form, biomineralization proteins are bound to a solid surface, severely limiting our ability to use many conventional structure characterization techniques. Here, solid-state NMR spectroscopy was applied to study the intermolecular interactions of amelogenin, the most abundant protein present during the early stages of enamel formation, in self-assembled oligomers bound to hydroxyapatite. Intermolecular dipolar couplings were identified that support amelogenin dimer formation stabilized by residues toward the C-termini. These dipolar interactions were corroborated by molecular dynamics simulations. A ß-sheet structure was identified in multiple regions of the protein, which is otherwise intrinsically disordered in the absence of hydroxyapatite. To our knowledge, this is the first intermolecular protein-protein interaction reported for a biomineralization protein, representing an advancement in understanding enamel development and a new general strategy toward investigating biomineralization proteins.

Single-Amino Acid Modifications Reveal Additional Controls on the Proton Pathway of [FeFe]-Hydrogenase.

The proton pathway of [FeFe]-hydrogenase is essential for enzymatic H2 production and oxidation and is composed of four residues and a water molecule. A computational analysis of this pathway in the [FeFe]-hydrogenase from Clostridium pasteurianum revealed that the solvent-exposed residue of the pathway (Glu282) forms hydrogen bonds to two residues outside of the pathway (Arg286 and Ser320), implying that these residues could function in regulating proton transfer. In this study, we show that substituting Arg286 with leucine eliminates hydrogen bonding with Glu282 and results in an ∼3-fold enhancement of H2 production activity when methyl viologen is used as an electron donor, suggesting that Arg286 may help control the rate of proton delivery. In contrast, substitution of Ser320 with alanine reduces the rate ∼5-fold, implying that it either acts as a member of the pathway or influences Glu282 to permit proton transfer. Interestingly, quantum mechanics/molecular mechanics and molecular dynamics calculations indicate that Ser320 does not play a structural role or indirectly influence the barrier for proton movement at the entrance of the channel. Rather, it may act as an additional proton acceptor for the pathway or serve in a regulatory role. While further studies are needed to elucidate the role of Ser320, collectively these data provide insights into the complex proton transport process.

Investigating the role of chain and linker length on the catalytic activity of an H2 production catalyst containing a ß-hairpin peptide.

Building on our recent report of an active H2 production catalyst [Ni(PPh 2NProp-peptide)2]2+ (Prop = para-phenylpropionic acid, peptide (R10) = WIpPRWTGPR-NH2, p = D-proline and P2N = 1-aza-3,6-diphosphacycloheptane) that contains structured ß-hairpin peptides, here we investigate how H2 production is effected by: (1) the length of the hairpin (eight or ten residues) and (2) limiting the flexibility between the peptide and the core complex by altering the length of the linker: para-phenylpropionic acid (three carbons) or para-benzoic acid (one carbon). Reduction of the peptide chain length from ten to eight residues increases or maintains the catalytic current for H2 production for all complexes, suggesting a non-productive steric interaction at longer peptide lengths. While the structure of the hairpin appears largely intact for the complexes, NMR data are consistent with differences in dynamic behavior which may contribute to the observed differences in catalytic activity. Molecular dynamics simulations demonstrate that complexes with a one-carbon linker have the desired effect of restricting the motion of the hairpin relative to the complex; however, the catalytic currents are significantly reduced compared to complexes containing a three-carbon linker as a result of the electron withdrawing nature of the -COOH group. These results demonstrate the complexity and interrelated nature of the outer coordination sphere on catalysis.

Controlling Proton Delivery through Catalyst Structural Dynamics.

The fastest synthetic molecular catalysts for H2 production and oxidation emulate components of the active site of hydrogenases. The critical role of controlled structural dynamics is recognized for many enzymes, including hydrogenases, but is largely neglected in designing synthetic catalysts. Our results demonstrate the impact of controlling structural dynamics on H2 production rates for [Ni(PPh2 NC6H4R2 )2 ]2+ catalysts (R=n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl). The turnover frequencies correlate inversely with the rates of chair-boat ring inversion of the ligand, since this dynamic process governs protonation at either catalytically productive or non-productive sites. These results demonstrate that the dynamic processes involved in proton delivery can be controlled through modification of the outer coordination sphere, in a manner similar to the role of the protein architecture in many enzymes. As a design parameter, controlling structural dynamics can increase H2 production rates by three orders of magnitude with a minimal increase in overpotential.

Heterolysis of H2 Across a Classical Lewis Pair, 2,6-Lutidine⋠BCl3 : Synthesis, Characterization, and Mechanism.

We report that 2,6-lutidine⋅trichloroborane (Lut⋅BCl3 ) reacts with H2 in toluene, bromobenzene, dichloromethane, and Lut solvents producing the neutral hydride, Lut⋅BHCl2 . The mechanism was modeled with density functional theory, and energies of stationary states were calculated at the G3(MP2)B3 level of theory. Lut⋅BCl3 was calculated to react with H2 and form the ion pair, [LutH(+) ][HBCl3 (-) ], with a barrier of ΔH(≠) =24.7 kcal mol(-1) (ΔG(≠) =29.8 kcal mol(-1) ). Metathesis with a second molecule of Lut⋅BCl3 produced Lut⋅BHCl2 and [LutH(+) ][BCl4 (-) ]. The overall reaction is exothermic by 6.0 kcal mol(-1) (Δr G°=-1.1). Alternate pathways were explored involving the borenium cation (LutBCl2 (+) ) and the four-membered boracycle [(CH2 {NC5 H3 Me})BCl2 ]. Barriers for addition of H2 across the Lut/LutBCl2 (+) pair and the boracycle BC bond are substantially higher (ΔG(≠) =42.1 and 49.4 kcal mol(-1) , respectively), such that these pathways are excluded. The barrier for addition of H2 to the boracycle BN bond is comparable (ΔH(≠) =28.5 and ΔG(≠) =32 kcal mol(-1) ). Conversion of the intermediate 2-(BHCl2 CH2 )-6-Me(C5 H3 NH) to Lut⋅BHCl2 may occur by intermolecular steps involving proton/hydride transfers to Lut/BCl3 . Intramolecular protodeboronation, which could form Lut⋅BHCl2 directly, is prohibited by a high barrier (ΔH(≠) =52, ΔG(≠) =51 kcal mol(-1) ).

Resolving protein-mineral interfacial interactions during in vitro mineralization by atom probe tomography.

Organic macromolecules exert remarkable control over the nucleation and growth of inorganic crystallites during (bio)mineralization, as exemplified during enamel formation where the protein amelogenin regulates the formation of hydroxyapatite (HAP). However, it is poorly understood how fundamental processes at the organic-inorganic interface, such as protein adsorption and/or incorporation into minerals, regulates nucleation and crystal growth due to technical challenges in observing and characterizing mineral-bound organics at high-resolution. Here, atom probe tomography techniques were developed and applied to characterize amelogenin-mineralized HAP particles in vitro, revealing distinct organic-inorganic interfacial structures and processes at the nanoscale. Specifically, visualization of amelogenin across the mineralized particulate demonstrates protein can become entrapped during HAP crystal aggregation and fusion. Identification of protein signatures and structural interpretations were further supported by standards analyses, i.e., defined HAP surfaces with and without amelogenin adsorbed. These findings represent a significant advance in the characterization of interfacial structures and, more so, interpretation of fundamental organic-inorganic processes and mechanisms influencing crystal growth. Ultimately, this approach can be broadly applied to inform how potentially unique and diverse organic-inorganic interactions at different stages regulates the growth and evolution of various biominerals.

Splitting of multiple hydrogen molecules by bioinspired diniobium metal complexes: a DFT study.

Splitting of molecular hydrogen (H2) into bridging and terminal hydrides is a common step in transition metal chemistry. Herein, we propose a novel organometallic platform for cleavage of multiple H2 molecules, which combines metal centers capable of stabilizing multiple oxidation states, and ligands bearing positioned pendant basic groups. Using quantum chemical modeling, we show that low-valent, early transition metal diniobium(ii) complexes with diphosphine ligands featuring pendant amines can favorably uptake up to 8 hydrogen atoms, and that the energetics are favored by the formation of intramolecular dihydrogen bonds. This result suggests new possible strategies for the development of hydrogen scavenger molecules that are able to perform reversible splitting of multiple H2 molecules.

Visualizing biomolecular electrostatics in virtual reality with UnityMol-APBS.

Virtual reality is a powerful tool with the ability to immerse a user within a completely external environment. This immersion is particularly useful when visualizing and analyzing interactions between small organic molecules, molecular inorganic complexes, and biomolecular systems such as redox proteins and enzymes. A common tool used in the biomedical community to analyze such interactions is the Adaptive Poisson-Boltzmann Solver (APBS) software, which was developed to solve the equations of continuum electrostatics for large biomolecular assemblages. Numerous applications exist for using APBS in the biomedical community including analysis of protein ligand interactions and APBS has enjoyed widespread adoption throughout the biomedical community. Currently, typical use of the full APBS toolset is completed via the command line followed by visualization using a variety of two-dimensional external molecular visualization software. This process has inherent limitations: visualization of three-dimensional objects using a two-dimensional interface masks important information within the depth component. Herein, we have developed a single application, UnityMol-APBS, that provides a dual experience where users can utilize the full range of the APBS toolset, without the use of a command line interface, by use of a simple graphical user interface (GUI) for either a standard desktop or immersive virtual reality experience.

Charge-dependent cavity radii for an accurate dielectric continuum model of solvation with emphasis on ions: aqueous solutes with oxo, hydroxo, amino, methyl, chloro, bromo, and fluoro functionalities.

Dielectric continuum solvation models are widely used because they are a computationally efficacious way to simulate equilibrium properties of solutes. With advances that allow for molecular-shaped cavities, they have reached a high level of accuracy, in particular for neutral solutes. However, benchmark tests show that existing schemes for defining cavities are unable to consistently predict accurately the effects of solvation on ions, especially anions. This work involves the further development of a protocol put forth earlier for defining the cavities of aqueous solutes, with resulting advances that are most striking for anions. Molecular cavities are defined as interlocked spheres around atoms or groups of atoms in the solute, but the sphere radii are determined by simple empirically based expressions involving the effective atomic charges of the solute atoms (derived from molecular electrostatic potential) and base radii. Both of these terms are optimized for the different types of atoms or functional groups in a training set of neutral and charged solutes. Parameters in these expressions for radii were fitted by minimizing residuals between calculated and measured standard free energies of solvation (DeltaG(s)*), weighted by the uncertainty in the measured value. The calculations were performed using density functional theory with the B3LYP functional and the 6-311+G** basis set and the COnductor-like Screening MOdel (COSMO). The optimized radii definitions reproduce DeltaG(s)* of neutral solutes and singly charged ions in the training set to within experimental uncertainty and, more importantly, accurately predict DeltaG(s)* of compounds outside the training set, in particular anions (J. Phys. Chem. A 2003, 107, 5778). Inherent to this approach, the cavity definitions reflect the strength of specific solute-water interactions. We surmise that this feature underlies the success of the model, referred to as the CD-COSMO model for Charge-Dependent (also Camaioni-Dupuis) COSMO model. These findings offer encouragement that we can keep extending this scheme to other functional groups and obtain better accuracy in using continuum solvation models to predict equilibrium properties of aqueous ionic solutes. The approach is illustrated for a number of test cases, including the determination of acidities of an amine base, a study of the tautomerization equilibrium of a zwitterionic molecule (glycine), and calculating solvation energies of transition states toward a full characterization of reaction pathways in aqueous phase, here in S(N)2 exchange reactions. The calculated reaction barriers in aqueous solution are in excellent agreement with experimental values.