High throughput selection of organic cathode materials

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.

Comparative assessment of 9-bromo noscapine ionic liquid and noscapine: Synthesis, in-vitro studies plus computational & biophysical evaluation with human hemoglobin

Noscapine is a proficient anticancer drug active against wide variety of tumors including lung cancer. Over time, several noscapine analogues have been assessed to maximize the efficiency of the drug, amongst which 9-bromo noscapine remains one of the most potent analogues till date. In the present work, we have synthesized 9-bromo noscapine ionic liquid [9-Br-Nos]IBr2, an active pharmaceutical ingredient based ionic liquid (API-IL) to address the existing issues of solubility and targeted drug delivery in the parent alkaloid as well as the synthesized analogues. We have devised a novel two-step synthesis route (first-ever ionic to ionic bromination) to obtain the desired [9-Br-Nos]IBr2 which is advantageous to its organic analogue in terms of increased solubility, lesser reaction time and better yield. Furthermore, we have compared 9-bromo noscapine ionic liquid with noscapine based on its binding interaction with human hemoglobin (Hb) studied via computational along with spectroscopic studies, and bioactivity against non-small cell lung cancer. We inferred formation of a complex between [9-Br-Nos]IBr2 and Hb in the stoichiometric ratio of 1:1, similar to noscapine. At 298 K, [9-Br-Nos]IBr2-Hb binding was found to exhibit Kb and ∆G of 36,307 M-1 and -11.5 KJmol-1, respectively, as compared to 159 M-1 and -12.5 KJmol-1 during Noscapine-Hb binding. This indicates a more stronger and viable interaction between [9-Br-Nos]IBr2 and Hb than the parent compound. From computational studies, the observed higher stability of [9-Br-Nos]I and better binding affinity with Hb with a binding energy of -91.75 kcalmol-1 supported the experimental observations. In the same light, novel [9-Br-Nos]IBr2 was found to exhibit an IC50 = 95.02 ± 6.32 μM compared to IC50 = 128.82 ± 2.87 μM for noscapine on A549 (non-small lung cancer) cell line at 48 h. Also, the desired ionic liquid proved to be more cytotoxic inducing a mortality rate of 87 % relative to 66 % evoked by noscapine at concentrations of 200 μM after 72 h.

A new protocol for the identification of singlet fission sensitizers through computational screening

Although singlet fission presents deep advantages or the generation of solar energy, the list of efficient singlet fission sensitizers is still very short, encouraging the theoreticians to focus their efforts on selecting and designing new candidates. Here, it is presented a computational protocol for the efficient screening of databases to select those species matching the energy requirements for singlet fission. Hence, out of the initial 29,123 species, 254 molecules (0.87%) were found to match singlet fission energy conditions. The consideration of practical concerns such as availability or stability reduced the number to just 24 (0.08%), among which the aminoanthraquinone derivatives are found particularly promising. The proposed protocol correct the deficiencies of the preceding ones, reaching DFT accuracy and minimizing the risk of getting false negatives especially at the early stages of the screening. In addition, this protocol can be used in future high-throughput investigations using datasets composed of millions of species.

Comparative QM/MM Molecular Dynamics and Umbrella Sampling Simulations: Interaction of the Zinc-Bound Intermediate Gem-Diolate Trapoxin A Inhibitor and Acetyl-l-lysine Substrate with Histone Deacetylase 8

Targeting the genetic material without destruction is a priority to develop safe anticancer drugs. Histone deacetylase 8 (HDAC8), which is proved to be involved in carcinogenesis, is an enzyme associated with the chromatin for post-translational deacetylation of acetylated lysine. In this study, HDAC8 co-crystallized with the intermediate state tetrapeptide Trapoxin A (TA) inhibitor and the holoenzyme are utilized to find their conformational ensembles. Furthermore, the co-crystallized intermediate gem-diolate TA was used to find optimum interactions with the active site residues by conventional molecular dynamics (MD) simulation and QM/MM umbrella sampling. Finally, the intermediate state of the acetyl-l-lysine substrate was explored by QM/MM steered MD and compared to the binding of the intermediate state of the inhibitor. This research showed that HDAC8 is flexible and exists in conformational ensembles in its holoenzyme state. Binding of the intermediate state TA stabilizes its conformation. The optimum binding to the active site of HDAC8 for structures of gem-diolate TA (intermediate state) and acetyl-l-lysine (intermediate state) was determined according to the corresponding energy profiles. The use of these models will aid in the design of potentially reversible, potent, and selective inhibitors of HDAC8 for cancer treatment.

Electronic structure, rovibrational, and dipole moment calculations for the AsCl molecule

The potential energy curves of the 19 lowest-lying singlet and triplet electronic states in the (2S+1)Λ((+/-)) representation of the AsCl molecule have been investigated using the complete active space self-consistent field (CASSCF) with multireference configuration interaction (MRCI+Q) method including single and double excitations and with the Davidson correction. The harmonic frequency ω e, the internuclear distance R e, the dipole moment, and the electronic energy with respect to the ground state T e were calculated for the electronic states considered. By using the canonical functions approach, the eigenvalue E v, the rotational constant B v, and the abscissae of the turning points R min and R max were calculated for the electronic states up to the vibrational level v = 60. The values obtained in the present work agree well with corresponding values available in the literature for several electronic states. Fifteen new electronic states were investigated here for the first time.

A combined theoretical and experimental study of chelidamate cadmium (II) complex, [Cd2(dpa)2(chel)2]⋅2[Cd(dpa)(chel)]⋅6H2O

A new chelidamate complex of Cd (II) ion, [Cd2(dpa)2(chel)2]⋅2[Cd(dpa)(chel)]⋅6H2O [(chel: chelidamate or 4-hydroxypyridine-2,6-dicarboxylate, dpa: di (2-picolyl)amine)] was synthesized and characterized by spectroscopic (UV-Vis and FT-IR spectroscopy) and structural (single-crystal X-ray diffraction) methods. Quantum chemical calculations were carried out by using Hartree Fock (HF) and Density Functional Theory (DFT)/B3LYP methods Stuttgart/Dresden (SDD) basis set. The asymmetric unit of the title compound contains two symmetry unrelated monomeric units, one dimeric unit and six water molecules of crystallization. The geometries around the Cd (II) metal centers in the units can be described as distorted octahedral for the monomeric units and distorted monocapped trigonal prism for the dimeric unit. The electronic structure of the complex was calculated using time dependent DFT (TD-DFT) method with polarizable continuum model (PCM). Molecular stability and bond strength were investigated by applying natural bond orbital analysis (NBO). The computed frequencies were compared with experimental frequencies.

Investigation of the valence electronic states of Ti(IV) in Ti silicalite-1 coupling X-ray emission spectroscopy and density functional calculations

We present an application of valence to core X-ray emission spectroscopy to understand the electronic structure of the industrially relevant catalyst titanium silicalite-1. The experimental spectrum was modelled within density functional theory, adopting a one electron approach, investigating the effects of different basis sets, density functionals and cluster sizes. The description of titanium silicalite-1 valence states follows the Kohn-Sham evaluation of the molecular orbitals involved in the computed transitions.

Assessing the performance of density functional theory for the electronic structure of metal-salens: the d2-metals

The performance of three common combinations of density functional theory has been evaluated for the geometries and relative energies of a commonly-employed model complex of the salen ligand [salen = bis(salicylaldehydo)ethylenediamine] with the d2-metals Ti(II), V(III), Cr(IV), Zr(II), Nb(III), and Mo(IV). High-level ab initio methods including complete active-space third-order perturbation theory have been employed both as benchmarks for the density functional theory results and to examine the multireference character of the low-lying electronic states in these systems. The strong multireference character of the systems has been clearly demonstrated. All of the functionals examined provide geometries that are typically within 0.2 A least root mean square deviation from the benchmark geometries. The performance of the density functionals for the relative energies of the low-lying electronic states is significantly worse, providing qualitatively different descriptions in some instances. Of the systems explored, no significant difference is observed in the multireference character or in the reliability of the density functional results when comparing 3d vs 4d transition-metal systems.

Approaching the basis set limit for transition metal compounds with highly polar bonds: A benchmark coupled-cluster study of the ScF3 and FeF3 molecular structures and spectra

The molecular equilibrium geometries, quadratic and cubic force constants, vibrational frequencies, and infrared intensities of scandium and iron trifluorides are determined ab initio with a sequence of atomic natural orbital basis sets using the CCSD(T) treatment of electron correlation. The largest basis set of spdf ghi quality contains 462 contracted Gaussian functions. Relativistic corrections are applied to compute the equilibrium geometries and vibrational frequencies. The cubic force constants are used to estimate vibrational corrections to the effective r(g) internuclear distances determined in the gas electron diffraction experiments. The computed molecular properties are extrapolated to the complete basis-set limit. The predicted values are compared to the available experimental data; uncertainties and inconsistencies in these data are then discussed.

Newly developed basis sets for density functional calculations

Optimized contracted Gaussian basis sets of double-zeta valence polarized (DZVP) quality for first-row transition metals are presented. The DZVP functions were optimized using the PWP86 generalized gradient approximation (GGA) functional and the B3LYP hybrid functional. For a careful analysis of the basis sets performance the transition metal atoms and cations excitation energies were calculated and compared with the experimental ones. The calculated values were also compared with those obtained using the previously available DZVP basis sets developed at the local-density functional level. Because the new basis sets work better than the previous ones, possible reasons of this behavior are analyzed. The newly developed basis sets also provide a good estimation of other atomic properties such as ionization energies.

Exact Gaussian expansions of Slater-type atomic orbitals

Three exact Slater-type function (STO) integral transforms are presented. The STO-NG basis set can then be developed using either only 1s Gaussian functions, the same Gaussian exponents for each shell, or using the first Gaussian of each symmetry. The use of any of these three alternatives depends only on appropriate numerical integration techniques.