Electronic absorption and resonance Raman spectra of methyl viologen radical cation, an important electron transport mediator, are predicted using time-dependent density functional theory. The findings further the understanding of the electronic properties of viologens and related organic redox mediators important in renewable energy applications.

Abstract

Time-dependent density functional theory (TDDFT) was applied to gain insights into the electronic and vibrational spectroscopic properties of an important electron transport mediator, methyl viologen (MV²⁺). An organic dication, MV²⁺ has numerous applications in electrochemistry that include energy conversion and storage, environmental remediation, and chemical sensing and electrosynthesis. MV²⁺ is easily reduced by a single electron transfer to form a radical cation species (MV^•+), which has an intense UV–visible absorption near 600 nm. The redox properties of the MV²⁺/MV^•+ couple and light-sensitivity of MV^•+ have made the system appealing for photo-electrochemical energy conversion (e.g., solar hydrogen generation from water) and the study of photo-induced charge transfer processes through electronic absorption and resonance Raman spectroscopic measurements. The reported work applies leading TDDFT approaches to investigate the electronic and vibrational spectroscopic properties of MV²⁺ and MV^•+. Using a conventional hybrid exchange functional (B3-LYP) and a long-range corrected hybrid exchange functional (ωB97X-D3), including with a conductor-like polarizable continuum model to account for solvation, the electronic absorption and resonance Raman spectra predicted are in good agreement with experiment. Also analyzed are the charge transfer character and natural transition orbitals derived from the TDDFT vertical excitations calculated. The findings and models developed further the understanding of the electronic properties of viologens and related organic redox mediators important in renewable energy applications and serve as a reference for guiding the interpretation of electronic absorption and Raman spectra of the ions.

Recently, synthesized Donor-pyrene (bridge)-Acceptor (DPA) systems were investigated with the ADC(2) method. Five additional donor-acceptor pairs were also studied. The ¹S₁ state is a local excitation in pyrene, while the ¹S₂ state is charge transfer. DFT HOMO and LUMO energies were used to assess the efficiency of the DPA compounds for organic photovoltaics.

Abstract

The alternant polycyclic aromatic hydrocarbon pyrene has photophysical properties that can be tuned with different donor and acceptor substituents. Recently, a D (donor)-Pyrene (bridge)-A (acceptor) system, DPA, with the electron donor N,N-dimethylaniline (DMA), and the electron acceptor trifluoromethylphenyl (TFM), was investigated by means of time-resolved spectroscopic measurements (J. Phys. Chem. Lett. 2021, 12, 2226–2231). DPA shows great promise for potential applications in organic electronic devices. In this work, we used the ab initio second-order algebraic diagrammatic construction method ADC(2) to investigate the excited-state properties of a series of analogous DPA systems, including the originally synthesized DPAs. The additionally investigated substituents were amino, fluorine, and methoxy as donors and nitrile and nitro groups as acceptors. The focus of this work was on characterizing the lowest excited singlet states regarding charge transfer (CT) and local excitation (LE) characters. For the DMA-pyrene-TFM system, the ADC(2) calculations show two initial electronic states relevant for interpreting the photodynamics. The bright S₁ state is locally excited within the pyrene moiety, and an S₂ state is localized ~0.5 eV above S₁ and characterized as a donor to pyrene CT state. HOMO and LUMO energies were employed to assess the efficiency of the DPA compounds for organic photovoltaics (OPVs). HOMO-LUMO and optical gaps were used to estimate power conversion and light-harvesting efficiencies for practical applications in organic solar cells. Considering the systems using smaller D/A substituents, compounds with the strong acceptor NO₂ substituent group show enhanced CT and promising properties for use in OPVs. Some of the other compounds with small substituents are also found to be competitive in this regard.

This article reveals long-range interaction regions, where the long-range correction (LC) affects, in total and orbital densities by comparing to those of the coupled cluster singles and doubles (CCSD) method. As a result, the long-range interaction regions of total density are found to appear in neither core orbitals nor in-between bonds in contrast to the CCSD effect. For orbital density, the long-range interaction regions are surprisingly found to be similar to those of the CCSD effect for unoccupied orbitals, though these are different for occupied orbitals.

Abstract

Total and orbital electron densities of molecules are explored for the effect of the long-range correction (LC) for density functional theory (DFT) exchange functionals by comparing to the effect of the ab initio coupled cluster singles and doubles (CCSD) method. Calculating the LC effect on the total electron densities shows that the LC stabilizes the electrons around the long-range interaction regions of kinetic energy density, which are assumed to be electrons other than free electrons and self-interacting electrons, while the CCSD method stabilizes the electrons in the long-range interaction regions in the vertical molecular planes. As a more precise test, the LC effect on orbital densities are compared to the CCSD effect on Dyson orbital densities. Surprisingly, these effects are similar for the unoccupied orbitals, indicating that the LC covers the effects required to reproduce the CCSD Dyson unoccupied orbitals. For exploring the discrepancies between these effects on the occupied orbitals, the photoionization cross sections are calculated as a direct test for the shapes of the HOMOs to investigate the differences between these effects on the occupied orbitals. Consequently, the LC clearly produces the canonical HOMOs close to the CCSD Dyson and experimental ones, except for the HOMO of benzene molecule that mixes with the HOMO−1 for the CCSD Dyson orbitals. This indicates that the orbital analyses using the photoionization cross sections are available as a direct test for the quality of DFT functionals.

Abstract

Molecular dynamics simulations were performed to study structural and dynamic properties of polar butanamine/water/butanamine, pentanoic acid/water/pentanoic acid, butanethiol/water/butanethiol, and nonpolar pentane/water/pentane systems. The mass density profiles along the interface normal to the organic liquid/water system, the difference in the local structure of H2O molecules in bulk and in the vicinity of interface, as well as the diffusion behavior of water molecules at the interface with above-mentioned organic liquids have been investigated. Our MD simulation has shown that the diffusion of water molecules across the water/organic liquid interface is influenced by the hydrogen bonds nHB between water molecules and the terminal groups of organic liquids. It was found that the loss of the hydrogen bonds nHB in the nonpolar organic liquid leads to a decrease in the value of the normal component of the diffusion coefficient Dz, while the tangential diffusion coefficients, both Dx and Dy, increase.

This work reports on a spin-pure configuration-based implementation of the heatbath configuration interaction algorithm for selective CI calculations in the context of the CASSCF approach. Particular emphasis is put on the details of the implementation that are key to the performance and applicability of the program.

Abstract

This work reports on a spin-pure configuration-based implementation of the heatbath configuration interaction (HCI) algorithm for selective configuration interaction. Besides the obvious advantage of being spin-pure, the presented method combines the compactness of the configurational ansatz with the known efficiency of the HCI algorithm and a variety of algorithmic and conceptual ideas to achieve a high level of performance. In particular, through pruning of the selected configurational space after HCI selection by means of a more strict criterion, a more compact wavefunction representation is obtained. Moreover, the underlying logic of the method allows us to minimize the number of redundant matrix-matrix multiplications while making use of just-in-time compilation to achieve fast diagonalization of the Hamiltonian. The critical search for 2-electron connections within the configurational space is facilitated by a tree-based representation thereof as suggested previously by Gopal et al. Usage of a prefix-based parallelization and batching during the calculation of the PT2-correction leads to a good load balancing and significantly reduced memory requirements for these critical steps of the calculation. In this way, the need for a semistochastic approach to the PT2 correction is avoided even for large configurational spaces. Finally, several test-cases are discussed to demonstrate the strengths and weaknesses of the presented method.

To discover new organic cathode materials, 86 million organic structures were screened. Two thousand three hundred six materials are predicted to have a monoelectronic reduction potential higher than 4 V (vs. Li/Li+), while 626 materials reached an energy density higher than 800 Whkg⁻¹. Successful materials were sorted in families, some of them never proposed before.

Abstract

Efficient and affordable batteries require the design of novel organic electrode materials to overcome the drawbacks of the traditionally used inorganic materials, and the computational screening of potential candidates is a very efficient way to identify prospective solutions and minimize experimental testing. Here we present a DFT high-throughput computational screening where 86 million molecules contained in the PUBCHEM database have been analyzed and classified according to their estimated electrochemical features. The 5445 top-performing candidates were identified, and among them, 2306 are expected to have a one-electron reduction potential higher than 4 V versus (Li/Li⁺). Analogously, one-electron energy densities higher than 800 Whkg⁻¹ have been predicted for 626 molecules. Explicit calculations performed for certain materials show that at least 69 candidates with a two-electron energy density higher than 1300 Whkg⁻¹. Successful molecules were sorted into several families, some of them already commonly used electrode materials, and others still experimentally untested. Most of them are small systems containing conjugated CO, NN, or NC functional groups. Our selected molecules form a valuable starting point for experimentalists exploring new materials for organic electrodes.

First principle investigations of the mechanism of [3+2] cycloaddition reactions between N-benzyl fluoro nitrone and maleimide derivatives, where solvent, temperature effects, and selectivity are screened and allowed explain experimental findings.

Abstract

We present a theoretical study of the [3+2] cycloaddition (32CA) reactions of N-benzyl fluoro nitrone with a series of maleimides producing isoxazolidines. We use the Molecular Electron Density Theory at the MPWB1K/6-311G(d) level. We focus on the reaction mechanism, selectivity, solvent, and temperature effects. In addition, we perform topological analyses at the minimal and transition states to identify the intermolecular interactions. Electron Localization Function approach classifies the N-benzyl fluoro nitrone as zwitterionic (zw-) three-atom components (TACs), associated with a high energy barrier. The low polar character of the reaction is evaluated using the Conceptual Density Functional Theory analysis of the reactants, confirmed by the low global electron density transfer computed at the transition states. Computations show that these 32CA reactions follow a one-step mechanism under kinetic control, with highly asynchronous bond formation and no new covalent bond is formed at the TS. Besides, the potential energy surfaces along the reaction pathways in gas phase and in solvent are mapped. The corresponding Gibbs free energy profiles reveal that the exo-cycloadducts are kinetically and thermodynamically more favored than endo-cycloadducts, in agreement with the exo-selectivity observed experimentally. In particular, we found that solvent and temperature did not affect this selectivity and mainly influence the activation energies and the exothermic character of these 32CA reactions.

This work reports the automated H-BEE code for estimating individual hydrogen bond energies and cooperativity contributions in molecular clusters using MTA-based method employing (i) the actual molecular cluster, (ii) the SS1 model, and (iii) the Frags-in-Frags method. This automated code overcomes the tedious manual fragmentation involved in the respective method.

Abstract

A procedure, derived from the fragmentation-based molecular tailoring approach (MTA), has been proposed and extensively applied by Deshmukh and Gadre for directly estimating the individual hydrogen bond (HB) energies and cooperativity contributions in molecular clusters. However, the manual fragmentation and high computational cost of correlated quantum chemical methods make the application of this method to large molecular clusters quite formidable. In this article, we report an in-house developed software for automated hydrogen bond energy estimation (H-BEE) in large molecular clusters. This user-friendly software is essentially written in Python and executed on a Linux platform with the Gaussian package at the backend. Two approximations to the MTA-based procedure, viz. the first spherical shell (SS1) and the Fragments-in-Fragments (Frags-in-Frags), enabling cost-effective, automated evaluation of HB energies and cooperativity contributions, are also implemented in this software. The software has been extensively tested on a variety of molecular clusters and is expected to be of immense use, especially in conjunction with correlated methods such as MP2, CCSD(T), and so forth.

The R292K mutation in N7 contributes to drug resistance by inducing structural destabilization, resulting in disrupted ligand-protein interactions, perturbed hydrogen bonds, and an increased SASA around K292.

Abstract

At the beginning of the last century, multiple pandemics caused by influenza (flu) viruses severely impacted public health. Despite the development of vaccinations and antiviral medications to prevent and control impending flu outbreaks, unforeseen novel strains and continuously evolving old strains continue to represent a serious threat to human life. Therefore, the recently identified H10N7, for which not much data is available for rational structure-based drug design, needs to be further explored. Here, we investigated the structural dynamics of neuraminidase N7 upon binding of inhibitors, and the drug resistance mechanisms against the oseltamivir (OTV) and laninamivir (LNV) antivirals due to the crucial R292K mutation on the N7 using the computational microscope, molecular dynamics (MD) simulations. In this study, each system underwent long 2 × 1 μs MD simulations to answer the conformational changes and drug resistance mechanisms. These long time-scale dynamics simulations and free energy landscapes demonstrated that the mutant systems showed a high degree of conformational variation compared to their wildtype (WT) counterparts, and the LNV-bound mutant exhibited an extended 150-loop conformation. Further, the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) calculation and MM/GBSA free energy decomposition were used to characterize the binding of OTV and LNV with WT, and R292K mutated N7, revealing the R292K mutation as drug-resistant, facilitated by a decline in binding interaction and a reduction in the dehydration penalty. Due to the broader binding pocket cavity of the smaller K292 mutant residue relative to the wildtype, the drug carboxylate to K292 hydrogen bonding was lost, and the area surrounding the K292 residue was more accessible to water molecules. This implies that drug resistance could be reduced by strengthening the hydrogen bond contacts between N7 inhibitors and altered N7, creating inhibitors that can form a hydrogen bond to the mutant K292, or preserving the closed cavity conformations.