Recent Progress in Polyaniline and its Composites for Supercapacitors.

Polyaniline (PANI) has piqued the interest of nanotechnology researchers due to its potential as an electrode material for supercapacitors. Despite its ease of synthesis and ability to be doped with a wide range of materials, PANI's poor mechanical properties have limited its use in practical applications. To address this issue, researchers investigated using PANI composites with materials with highly specific surface areas, active sites, porous architectures, and high conductivity. The resulting composite materials have improved energy storage performance, making them promising electrode materials for supercapacitors. Here, we provide an overview of recent developments in PANI-based supercapacitors, focusing on using electrochemically active carbon and redox-active materials as composites. We discuss challenges and opportunities of synthesizing PANI-based composites for supercapacitor applications. Furthermore, we provide theoretical insights into the electrical properties of PANI composites and their potential as active electrode materials. The need for this review stems from the growing interest in PANI-based composites to improve supercapacitor performance. By examining recent progress in this field, we provide a comprehensive overview of the current state-of-the-art and potential of PANI-based composites for supercapacitor applications. This review adds value by highlighting challenges and opportunities associated with synthesizing and utilizing PANI-based composites, thereby guiding future research directions.

Structural and Thermodynamic Control of Supramolecular Polymers and DNA Assemblies with Cyanuric Acid: Influence of Substituents and Intermolecular Interactions.

Understanding the interactions and thermodynamic parameters that govern the structure and stability of supramolecular polymers is challenging because of their flexible nature and high sensitivity to weak intermolecular interactions. The application of both experimental and computational analyses reveals the role that substituents on cyanuric acid (Cy), and other nitrogen-containing heterocycles, play in the formation of novel helical supramolecular structures. In this report, we focus on how noncovalent interactions, including steric and stacking interactions, modulate the structural and physical properties of these assemblies. In-depth analyses and several examples of critical steric and electrostatic effects provide insight into the relationship between intermolecular interactions of Cy with nucleic acids and the structure and thermodynamic stability of the supramolecular polymers they form.

Helicene Structure between DNA and Cyanuric Acid: The Role of Noncovalent Interactions.

The self-assembly between DNA and small organic molecules can expand the structural space of and introduce novel functionalities to DNA nanomaterials. In particular, it was demonstrated that poly(adenosine) DNA self-assembles with cyanuric acid (CA) to form a triplex helical structure. Previous molecular dynamics simulations showed that the DNA-CA assemblies adopt a novel noncovalent helicene structure that has a continuous helical hydrogen bond network. This article explores why the assemblies adopt the helicene geometry instead of an alternative planar hexameric rosette geometry. Analysis of the hydrogen bonding and stacking interaction energies indicates that constraining the system to the hexameric rosette geometry strains the hydrogen bonds without significantly improving the interaction energy. Molecular dynamics simulations for the assemblies between adenosine nucleosides and CA confirm that the formation of helicene structure is primarily driven by base-pair interactions and not because of the DNA backbone.

Structural Analysis of the Poly(thymidine)-Melamine Assembly.

Hydrogen bonding between the DNA nucleobases and small organic molecules, such as melamine, is a new strategy for the design of novel DNA materials. Poly(thymidine) DNA and melamine self-assemble into a duplex structure containing two antiparallel DNA strands hydrogen bonded to central melamine units. In this Article, molecular dynamics simulations rationalize the observed antiparallel duplex structure. Alternative duplex and triplex structures with parallel and antiparallel strand orientations are shown to be unstable because of the increase in unfavorable interactions between the DNA backbones.

Quantum Chemistry Common Driver and Databases (QCDB) and Quantum Chemistry Engine (QCEngine): Automation and interoperability among computational chemistry programs.

Community efforts in the computational molecular sciences (CMS) are evolving toward modular, open, and interoperable interfaces that work with existing community codes to provide more functionality and composability than could be achieved with a single program. The Quantum Chemistry Common Driver and Databases (QCDB) project provides such capability through an application programming interface (API) that facilitates interoperability across multiple quantum chemistry software packages. In tandem with the Molecular Sciences Software Institute and their Quantum Chemistry Archive ecosystem, the unique functionalities of several CMS programs are integrated, including CFOUR, GAMESS, NWChem, OpenMM, Psi4, Qcore, TeraChem, and Turbomole, to provide common computational functions, i.e., energy, gradient, and Hessian computations as well as molecular properties such as atomic charges and vibrational frequency analysis. Both standard users and power users benefit from adopting these APIs as they lower the language barrier of input styles and enable a standard layout of variables and data. These designs allow end-to-end interoperable programming of complex computations and provide best practices options by default.

Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics.

Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.

X-ray Fiber Diffraction and Computational Analyses of Stacked Hexads in Supramolecular Polymers: Insight into Self-Assembly in Water by Prospective Prebiotic Nucleobases.

Aqueous solutions of equimolar mixtures of 2,4,6-triaminopyrimidine (TAP) and carboxylic acid substituted cyanuric acid (CyCo6 or R-4MeCyCo6) monomers self-assemble into gel-forming supramolecular polymers. Macroscopic fibers drawn from these mixtures were analyzed by X-ray diffraction to determine their molecular structures. Computational methods were used to explore the intrinsic intermolecular interactions that contribute to the structure and stability of these assemblies. Both polymers are formed by the stacking of hexameric rosettes, (TAP/CyCo6)3 or (TAP/R-4MeCyCo6)3, respectively, into long, stiff, twisted stacks of essentially planar rosettes. Chiral, left-handed supramolecular polymers with a helical twist angle of -26.7° per hexad are formed when the pure enantiomer R-4MeCyCo6 is used. These hexad stacks pack into bundles with a hexagonal crystalline lattice organization perpendicular to the axis of the macroscopic fiber. Polymers formed from TAP and CyCo6, both of which are achiral, assemble into macroscopic domains that are packed as a centered rectangular lattice. Within these domains, the individual polymers exist as either right-handed or left-handed helical stacks, with twist angles of +15° or -15° per hexad, respectively. The remarkable ability of TAP and cyanuric acid derivatives to self-assemble in water, and the structural features of their supramolecular polymers reported here, provide additional support for the proposal that these heterocycles could have served as recognition units for an early form of nucleic acids, before the emergence of RNA.

The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs.

The helical structures of DNA and RNA were originally revealed by experimental data. Likewise, the development of programs for modeling these natural polymers was guided by known structures. These nucleic acid polymers represent only two members of a potentially vast class of polymers with similar structural features, but that differ from DNA and RNA in the backbone or nucleobases. Xeno nucleic acids (XNAs) incorporate alternative backbones that affect the conformational, chemical, and thermodynamic properties of XNAs. Given the vast chemical space of possible XNAs, computational modeling of alternative nucleic acids can accelerate the search for plausible nucleic acid analogs and guide their rational design. Additionally, a tool for the modeling of nucleic acids could help reveal what nucleic acid polymers may have existed before RNA in the early evolution of life. To aid the development of novel XNA polymers and the search for possible pre-RNA candidates, this article presents the proto-Nucleic Acid Builder (https://github.com/GT-NucleicAcids/pnab), an open-source program for modeling nucleic acid analogs with alternative backbones and nucleobases. The torsion-driven conformation search procedure implemented here predicts structures with good accuracy compared to experimental structures, and correctly demonstrates the correlation between the helical structure and the backbone conformation in DNA and RNA.

Noncovalent Helicene Structure between Nucleic Acids and Cyanuric Acid.

Cyanuric acid (CA), a triazine heterocycle, is extensively utilized for noncovalent self-assembly. The association between poly(adenine) and CA into micron-length fibers was a remarkable observation made by Sleiman and co-workers, who proposed that adenine and CA adopt a hexameric rosette configuration in analogy with previously reported structures for CA assemblies. However, recent experimental observations from the Krishnamurthy group led to a reevaluation of the hexameric rosette model, wherein they have proposed a hydrogen-bonded helicene model as an alternative. Our molecular dynamics simulations show that the hexad model is indeed unlikely and that this novel noncovalent helicene geometry, where the adenine and CA bases form an extended helical hydrogen-bond network across the system, is a more probable structural motif. The existence of noncovalent helicene compounds may have wide-ranging applications in DNA nanotechnology and helicene chemistry.

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

PSI4 is a free and open-source ab initio electronic structure program providing implementations of Hartree-Fock, density functional theory, many-body perturbation theory, configuration interaction, density cumulant theory, symmetry-adapted perturbation theory, and coupled-cluster theory. Most of the methods are quite efficient, thanks to density fitting and multi-core parallelism. The program is a hybrid of C++ and Python, and calculations may be run with very simple text files or using the Python API, facilitating post-processing and complex workflows; method developers also have access to most of PSI4's core functionalities via Python. Job specification may be passed using The Molecular Sciences Software Institute (MolSSI) QCSCHEMA data format, facilitating interoperability. A rewrite of our top-level computation driver, and concomitant adoption of the MolSSI QCARCHIVE INFRASTRUCTURE project, makes the latest version of PSI4 well suited to distributed computation of large numbers of independent tasks. The project has fostered the development of independent software components that may be reused in other quantum chemistry programs.

Psi4NumPy: An Interactive Quantum Chemistry Programming Environment for Reference Implementations and Rapid Development.

Psi4NumPy demonstrates the use of efficient computational kernels from the open-source Psi4 program through the popular NumPy library for linear algebra in Python to facilitate the rapid development of clear, understandable Python computer code for new quantum chemical methods, while maintaining a relatively low execution time. Using these tools, reference implementations have been created for a number of methods, including self-consistent field (SCF), SCF response, many-body perturbation theory, coupled-cluster theory, configuration interaction, and symmetry-adapted perturbation theory. Furthermore, several reference codes have been integrated into Jupyter notebooks, allowing background, underlying theory, and formula information to be associated with the implementation. Psi4NumPy tools and associated reference implementations can lower the barrier for future development of quantum chemistry methods. These implementations also demonstrate the power of the hybrid C++/Python programming approach employed by the Psi4 program.

Assessment of Density Functional Methods for Geometry Optimization of Bimolecular van der Waals Complexes.

We explore the suitability of three popular density functionals (B97-D3, B3LYP-D3, M05-2X) for producing accurate equilibrium geometries of van der Waals (vdW) complexes with diverse binding motifs. For these functionals, optimizations using Dunning's aug-cc-pVDZ basis set best combine accuracy and a reasonable computational expense. Each DFT/aug-cc-pVDZ combination produces optimized equilibrium geometries for 21 small vdW complexes of organic molecules (up to four non-hydrogen atoms total) that agree with high-level CCSD(T)/CBS reference geometries to within ±0.1 Å for the averages of the center-of-mass displacement and the mean least root-mean-squared displacement. The DFT/aug-cc-pVDZ combinations are also able to reproduce the optimal center-of-mass displacements interpolated from CCSD(T)/CBS radial potential energy surfaces in both NBC7x and HBC6 test sets to within ±0.1 Å. We therefore conclude that each of these denisty functional methods, together with the aug-cc-pVDZ basis set, is suitable for producing equilibrium geometries of generic nonbonded complexes.