A Perspective on Sustainable Computational Chemistry Software Development and Integration.

The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.

Role of hydrogen bonding in bulk aqueous phase decomposition, complexation, and covalent hydration of pyruvic acid.

Pyruvic acid (PA) is a model for amphiphilic oxygenated organic compounds, and together with its hydrogen-bonded (H-bonded) water complexes, their presence can alter atmospheric aerosol formation. However, the fundamental understanding of PA reaction mechanisms in different environments is still being debated. Here, the role of H-bonding on PA's degradation, complexation, and covalent hydration in bulk aqueous phase is investigated theoretically. Using CCSD(T)-F12/aug-cc-pVDZ-F12 on B2PLYP-D3BJ structures with solvation model based on density, we revealed the stabilization by intramolecular H-bonding of an intermediate, PA hydrogen-transferred tautomer, altered the PA degradation mechanisms compared to gas phase. We also found that the intramolecular H-bonding in the most stable gas phase conformer (Tc) is weakened due to bulk solvation, leading to slower acetaldehyde production rate. Natural bond orbital analysis characterized the primary intermolecular H-bond in PA-water complexes as electron donation of an Owater lone pair (p) to the σ* orbital of the OH group of PA. Stronger H-bonding is correlated to p to σ* interaction, wider OH-O angles, and larger differences in the H-bond lengths between phases. The less charge difference between phases on H-bonded atoms also indicates aggressive competition of H-bonding with solvation. Water's cooperative behavior was observed by lowering the water-complexed 2,2-dihydroxypropanoic acid (DHPA-H2O) barrier from PA-water complexes compared to DHPA in both phases, stabilizing the transition state and product with intermolecular H-bonding. PA is vital in atmospheric keto-acid chemistry; thus, changes in PA reaction mechanisms in different environments due to H-bond behavior will affect aerosol formation.

Influence of dityrosine nanotubes on the expression of dopamine and differentiation in neural cells.

In this study, we report the synthesis of self-assembled dityrosine nanotubes as a biologically functional scaffold and their interactions with neural cells. Quantum chemical methods were used to determine the forces involved in the self-assembly process. The physicochemical properties of the nanostructures relevant to their potential as bioactive scaffolds were characterized. The morphology, secondary structure, crystallinity, mechanical properties, and thermal characteristics of YY nanotubes were analyzed. The influence of these nanotubes as scaffolds for neural cells was studied in vitro to understand their effects on cell proliferation, morphology, and gene expression. The scanning electron microscopy and fluorescence confocal microscopy demonstrated the feasibility of nanotube scaffolds for enhanced adhesion to rat and human neural cells (PC12 and SH-SY5Y). Preliminary ELISA and qPCR analyses demonstrate the upregulation of dopamine synthesis and genes involved in dopamine expression and differentiation. The expression levels of DßH, AADC, VMAT2 and MAOA in SH-SY5Y cells cultured on the nanotube scaffolds for 7 days were elevated in comparison to the control cells.

Designing high energy density flow batteries by tuning active-material thermodynamics.

The cost of electricity generated by wind and solar installations has become competitive with that generated by burning fossil fuels. While this paves the way for a carbon-neutral electrical grid, short- and long-term intermittency necessitates energy storage. Flow batteries are a promising technology to accommodate this need, with numerous advantages, including decoupled power and energy ratings, which imparts flexibility, thermal stability, and safety. Further, development of robust nonaqueous systems has the potential to greatly improve energy density, approaching that of lithium-ion batteries, while maintaining the advantages of flow systems. Herein we report a breakthrough on a bio-inspired nonaqueous redox flow battery (NRFB) electrolyte, which contains high-concentration active-material and maintains stability during deep cycling for extended time-periods. These advances are reinforced by thermodynamic considerations and computational investigations, which provide a clear path to further improvements. Electrochemical studies confirm that the active-material maintains its high stability at high concentration. This molecular scaffold clears two important hurdles in designing active-materials for nonaqueous electrolytes - low solubility and poor stability - providing an in-road to development of high-performance NRFB systems.

Computational and experimental investigation of the effect of cation structure on the solubility of anionic flow battery active-materials.

Recent advances in clean, sustainable energy sources such as wind and solar have enabled significant cost improvements, yet their inherent intermittency remains a considerable challenge for year-round reliability demanding the need for grid-scale energy storage. Nonaqueous redox flow batteries (NRFBs) have the potential to address this need, with attractive attributes such as flexibility to accommodate long- and short-duration storage, separately scalable energy and power ratings, and improved safety profile over integrated systems such as lithium-ion batteries. Currently, the low-solubility of NRFB electrolytes fundamentally limits their energy density. However, synthetically exploring the large chemical and parameter space of NRFB active materials is not only costly but also intractable. Here, we report a computational framework, coupled with experimental validation, designed to predict the solubility trends of electrolytes, incorporating both the lattice and solvation free energies. We reveal that lattice free energy, which has previously been neglected, has a significant role in tuning electrolyte solubility, and that solvation free energies alone is insufficient. The desymmetrization of the alkylammonium cation leading to short-chain, asymmetric cations demonstrated a modest increase in solubility, which can be further explored for NRFB electrolyte development and optimization. The resulting synergistic computational-experimental approach provides a cost-effective strategy in the development of high-solubility active materials for high energy density NRFB systems.

Probing the Nature of Noncovalent Interactions in Dimers of Linear Tyrosine-Based Dipeptides.

Tyrosine-based dipeptides self-assemble to form higher order structures. To gain insights into the nature of intermolecular interactions contributing to the early stages of the self-assembly of aromatic dipeptides, we study the dimers of linear dityrosine (YY) and tryptophan-tyrosine (WY) using quantum-chemical methods with dispersion corrections and universal solvation model based on density in combination with energy decomposition and natural bond orbital (NBO) analyses. We find that hydrogen bonding is a dominant stabilizing force. The lowest energy structure for the linear YY dimer is characterized by Ocarboxyl···H(O)tyr. In contrast, the lowest energy dimer of linear WY is stabilized by Ocarboxyl···H(N)trp and πtyr···πtyr. The solvent plays a critical role as it can change the strength and nature of interactions. The lowest energy for linear WY dimer in acetone is stabilized by Ocarboxyl···H(O)tyr, πtrp···H(C), and πtrp···H(N). The ΔG of dimerization and stabilization energies of solvated dipeptides reveal that the dipeptide systems are more stable in the solvent phase than in gas phase. NBO confirms increased magnitudes for donor-acceptor interaction for the solvated dipeptides.

Molecular Mechanisms of Tryptophan-Tyrosine Nanostructures Formation and their Influence on PC-12 Cells.

The discovery of self-assembling peptides, which can form well-ordered structures, has opened a realm of opportunity for the design of tailored short peptide-based nanostructures. In this study, a combined experimental and computational approach was utilized to understand the intramolecular and intermolecular interactions contributing to the self-assembly of linear and cyclic tryptophan-tyrosine (WY) dipeptides. The density functional tight binding (DFTB) calculations with empirical dispersive corrections assisted the identification of the lowest energy conformers. Conformer analysis and the prediction of the electronic structure for the monomeric, dimeric, and hexameric forms of the cyclic and linear WY confirmed the contributions of hydrogen bonding, π-π stacking, and CH-π interactions in the stability of the self-assembled nanotubes. The influence of the processing conditions on the morphological and thermal characteristics, as well as the secondary structures of the synthesized nanostructures, were analyzed. Preliminary studies of the influence of the nanotubes on the fate of neuronal cell lines such as, PC-12 cells indicate that the nanotubes promote cellular proliferation, and differentiation in the absence of growth factors. The aspect ratio of the nanotubes played an essential role in cellular interactions where a higher cellular uptake was observed in nanotubes of lower aspect ratios. These results provide insight for future applications of such nanotubes as scaffolds for tissue engineering and nerve regeneration and in drug delivery.

Importance of Three-Body Interactions in Molecular Dynamics Simulations of Water Demonstrated with the Fragment Molecular Orbital Method.

The analytic first derivative with respect to nuclear coordinates is formulated and implemented in the framework of the three-body fragment molecular orbital (FMO) method. The gradient has been derived and implemented for restricted second-order Møller-Plesset perturbation theory, as well as for both restricted and unrestricted Hartree-Fock and density functional theory. The importance of the three-body fully analytic gradient is illustrated through the failure of the two-body FMO method during molecular dynamics simulations of a small water cluster. The parallel implementation of the fragment molecular orbital method, its parallel efficiency, and its scalability on the Blue Gene/Q architecture up to 262,144 CPU cores are also discussed.

Modeling the electron-impact dissociation of methane.

The product yield of the electron-impact dissociation of methane has been studied with a combination of three theoretical methods: R-matrix theory to determine the electronically inelastic collisional excitation cross sections, high-level electronic structure methods to determine excited states energies and derivative couplings, and trajectory surface hopping (TSH) calculations to determine branching in the dissociation of the methane excited states to give CH(3), CH(2), and CH. The calculations involve the lowest 24 excited-state potential surfaces of methane, up to the ionization energy. According to the R-matrix calculations, electron impact preferentially produces triplet excited states, especially for electron kinetic energies close to the dissociation threshold. The potential surfaces of excited states are characterized by numerous avoided and real crossings such that the TSH calculations show rapid cascading down to the lowest excited singlet or triplet states, and then slower the dissociation of these lowest states. Product branching for electron-impact dissociation was therefore estimated by combining the electron-impact excitation cross sections with TSH product branching ratios that were obtained from the lowest singlet and triplet states, with the singlet dissociation giving a comparable formation of CH(2) and CH(3) while triplet dissociation gives CH(3) exclusively. The overall branching in electron-impact dissociation is dominated by CH(3) over CH(2). A small branching yield for CH is also predicted.

Experimental-computational study of shear interactions within double-walled carbon nanotube bundles.

The mechanical behavior of carbon nanotube (CNT)-based fibers and nanocomposites depends intimately on the shear interactions between adjacent tubes. We have applied an experimental-computational approach to investigate the shear interactions between adjacent CNTs within individual double-walled nanotube (DWNT) bundles. The force required to pull out an inner bundle of DWNTs from an outer shell of DWNTs was measured using in situ scanning electron microscopy methods. The normalized force per CNT-CNT interaction (1.7 ± 1.0 nN) was found to be considerably higher than molecular mechanics (MM)-based predictions for bare CNTs (0.3 nN). This MM result is similar to the force that results from exposure of newly formed CNT surfaces, indicating that the observed pullout force arises from factors beyond what arise from potential energy effects associated with bare CNTs. Through further theoretical considerations we show that the experimentally measured pullout force may include small contributions from carbonyl functional groups terminating the free ends of the CNTs, corrugation of the CNT-CNT interactions, and polygonization of the nanotubes due to their mutual interactions. In addition, surface functional groups, such as hydroxyl groups, that may exist between the nanotubes are found to play an unimportant role. All of these potential energy effects account for less than half of the ~1.7 nN force. However, partially pulled-out inner bundles are found not to pull back into the outer shell after the outer shell is broken, suggesting that dissipation is responsible for more than half of the pullout force. The sum of force contributions from potential energy and dissipation effects are found to agree with the experimental pullout force within the experimental error.

Confined propagation of covalent chemical reactions on single-walled carbon nanotubes.

Covalent chemistry typically occurs randomly on the graphene lattice of a carbon nanotube because electrons are delocalized over thousands of atomic sites, and rapidly destroys the electrical and optical properties of the nanotube. Here we show that the Billups-Birch reductive alkylation, a variant of the nearly century-old Birch reduction, occurs on single-walled carbon nanotubes by defect activation and propagates exclusively from sp(3) defect sites, with an estimated probability more than 1,300 times higher than otherwise random bonding to the 'π-electron sea'. This mechanism quickly leads to confinement of the reaction fronts in the tubular direction. The confinement gives rise to a series of interesting phenomena, including clustered distributions of the functional groups and a constant propagation rate of 18 ± 6 nm per reaction cycle that allows straightforward control of the spatial pattern of functional groups on the nanometre length scale.