Systematic Study of the Performance of Density Functional Theory Methods for Prediction of Energies and Geometries of Organoselenium Compounds

Correlation consistent basis sets designed for density functional theory: Third-row atoms (Ga-Br)

The correlation consistent basis sets (cc-pVnZ with n = D, T, Q, 5) for the Ga-Br elements have been redesigned, tuning the sets for use for density functional approximations. Steps to redesign these basis sets for an improved correlation energy recovery and efficiency include truncation of higher angular momentum functions, recontraction of basis set coefficients, and reoptimization of basis set exponents. These redesigned basis sets are compared with conventional cc-pVnZ basis sets and other basis sets, which are, in principle, designed to achieve systematic improvement with respect to increasing basis set size. The convergence of atomic energies, bond lengths, bond dissociation energies, and enthalpies of formation to the Kohn-Sham limit is improved relative to other basis sets where convergence to the Kohn-Sham limit is typically not observed.

Electrochemical Modification of Polypeptides at Selenocysteine

Mild strategies for the selective modification of peptides and proteins are in demand for applications in therapeutic peptide and protein discovery, and in the study of fundamental biomolecular processes. Herein, we describe the development of an electrochemical selenoetherification (e-SE) platform for the efficient site-selective functionalization of polypeptides. This methodology utilizes the unique reactivity of the 21st amino acid, selenocysteine, to effect formation of valuable bioconjugates through stable selenoether linkages under mild electrochemical conditions. The power of e-SE is highlighted through late-stage C-terminal modification of the FDA-approved cancer drug leuprolide and assembly of a library of anti-HER2 affibody conjugates bearing complex cargoes. Following assembly by e-SE, the utility of functionalized affibodies for in vitro imaging and targeting of HER2 positive breast and lung cancer cell lines is also demonstrated.

N-heterocyclic carbene based Bi-nuclear organoselenium compounds impart a mild biocidal potential compared to their ligands: Synthesis, characterization, computational studies

N-heterocyclic carbene (NHC) based compounds are remarkably known for astonishing biological potentials. Coordination of metal center with these compounds can substantially improve the biological potential for better efficacy. In this context, three binuclear azolium salts (L1-L3) and subsequent selenium adducts L1Se-L3Se were synthesized and assured through analytical techniques. Synthesized compounds were also simulated through computational approach and results were compared with experimental observations that also relatable with biological potentials. Synthesized compounds were screened against bacterial strains and interestingly, the studied compounds showed good antimicrobial potential with MIC values of 7.01, 10.7 and 10.5 µM for S. Aureus (gram positive bacteria) while 12.5, 11.75 and 14.5 µM against E. Coli (gram negative bacteria). The studied compounds showed good antioxidant activity to scavenge DPPH free radicals among which azolium salts were found better in antioxidant potential (IC50 5.75-6.55 µg/mL) than their respective selenium compounds (IC50 9.50-12.75 µg/mL). The hemolytic assay against red blood cells showed that ligands are least toxic comparative to their Se-adducts and can be further trialed for In Vivo studies.

Rethinking Vibrational Stark Spectroscopy: Peak Shifts, Line Widths, and the Role of Non-Stark Solvent Coupling

A vibration's transition frequency is partly determined by the first-order Stark effect, which accounts for the electric field experienced by the mode. Using ultrafast infrared pump-probe and FT-IR spectroscopies, we characterized both the 0 → 1 and 1 → 2 vibrational transitions' field-dependent peak positions and line widths of the CN stretching mode of benzonitrile (BZN) and phenyl selenocyanate (PhSeCN) in ten solvents. We present a theoretical model that decomposes the observed line width into a field-dependent Stark contribution and a field-independent non-Stark solvent coupling contribution (NSC). The model demonstrates that the field-dependent peak position is independent of the line width, even when the NSC dominates the latter. Experiments show that when the Stark tuning rate is large compared to the NSC (PhSeCN), the line width has a field dependence, albeit with major NSC-induced excursions from linearity. When the Stark tuning rate is small relative to the NSC (BZN), the line width is field-independent. BZN's line widths are substantially larger for the 1 → 2 transition, indicating a 1 → 2 transition enhancement of the NSC. Additionally, we examine, theoretically and experimentally, the difference in the 0 → 1 and 1 → 2 transitions' Stark tuning rates. Second-order perturbation theory combined with density functional theory explain the difference and show that the 1 → 2 transition's Stark tuning rate is ∼10% larger. The Stark tuning rate of PhSeCN is larger than BZN's for both transitions, consistent with the theoretical calculations. This study provides new insights into vibrational line shape components and a more general understanding of the vibrational response to external electric fields.

Site-selective photocatalytic functionalization of peptides and proteins at selenocysteine

The importance of modified peptides and proteins for applications in drug discovery, and for illuminating biological processes at the molecular level, is fueling a demand for efficient methods that facilitate the precise modification of these biomolecules. Herein, we describe the development of a photocatalytic method for the rapid and efficient dimerization and site-specific functionalization of peptide and protein diselenides. This methodology, dubbed the photocatalytic diselenide contraction, involves irradiation at 450 nm in the presence of an iridium photocatalyst and a phosphine and results in rapid and clean conversion of diselenides to reductively stable selenoethers. A mechanism for this photocatalytic transformation is proposed, which is supported by photoluminescence spectroscopy and density functional theory calculations. The utility of the photocatalytic diselenide contraction transformation is highlighted through the dimerization of selenopeptides, and by the generation of two families of protein conjugates via the site-selective modification of calmodulin containing the 21^st amino acid selenocysteine, and the C-terminal modification of a ubiquitin diselenide.

Selenium-Catalyzed Reduction of Hydroperoxides in Chemistry and Biology

Among the chalcogens, selenium is the key element for catalyzed H2O2 reduction. In organic synthesis, catalytic amounts of organo mono- and di-selenides are largely used in different classes of oxidations, in which H2O2 alone is poorly efficient. Biological hydroperoxide metabolism is dominated by peroxidases and thioredoxin reductases, which balance hydroperoxide challenge and contribute to redox regulation. When their selenocysteine is replaced by cysteine, the cellular antioxidant defense system is impaired. Finally, classes of organoselenides have been synthesized with the aim of mimicking the biological strategy of glutathione peroxidases, but their therapeutic application has so far been limited. Moreover, their therapeutic use may be doubted, because H2O2 is not only toxic but also serves as an important messenger. Therefore, over-optimization of H2O2 reduction may lead to unexpected disturbances of metabolic regulation. Common to all these systems is the nucleophilic attack of selenium to one oxygen of the peroxide bond promoting its disruption. In this contribution, we revisit selected examples from chemistry and biology, and, by using results from accurate quantum mechanical modelling, we provide an accurate unified picture of selenium's capacity of reducing hydroperoxides. There is clear evidence that the selenoenzymes remain superior in terms of catalytic efficiency.

Computational Modeling of the Catalytic Cycle of Glutathione Peroxidase Nanomimic

To elucidate the role of a derivative of ebselen as a mimic of the antioxidant selenoenzyme glutathione peroxidase, density functional theory and solvent-assisted proton exchange (SAPE) were applied to model the reaction mechanism in a catalytic cycle. This mimic plays the role of glutathione peroxidase through a four-step catalytic cycle. The first step is described as the oxidation of 1 in the presence of hydrogen peroxide, while selenoxide is reduced by methanthiol at the second step. In the third step of the reaction, the reduction of selenenylsulfide occurs by methanthiol, and the selenenic acid is dehydrated at the final step. Based on the kinetic parameters, step 4 is the rate-determining step (RDS) of the reaction. The bond strength of the atoms involved in the RDS is discussed with the quantum theory of atoms in molecules (QTAIM). Low value of electron density, ρ(r), and positive Laplacian values are the evidence for the covalent nature of the hydrogen bonds rupture (O₃₀-H₃₁, O₃₃-H₃₄). A change in the sign of the Laplacian, L(r), from the positive value in the reactant to a negative character at the transition state indicates the depletion of the charge density, confirming the N₅-H₁₀ and O₁₁-Se₁ bond breaking. The analysis of electron location function (ELF) and localized orbital locator (LOL) of the Se₁-N₅ and Se₁-O₁₁ bonds have been done by multi-WFN program. High values of ELF and LOL at the transition state regions between the Se, N, and O atoms display the bond formation. Finally, the main donor-acceptor interaction energies were analyzed using the natural bond orbital analysis for investigation of their stabilization effects on the critical bonds at the RDS.

Density Functional Theory Study of Cyanoetheneselenol: A Molecule of Astrobiological Interest

The interstellar medium has a rich chemistry which involves a wide variety of molecules. Of particular interest are molecules that have a link to prebiotic chemistry which hold the key to understanding of our origins. On the basis of suggestions that selenium may have been involved in the origin and evolution of life, we have studied the selenium analogue of cyanoethenethiol, namely the novel cyanoetheneselenol. Cyanoetheneselenol exhibits conformational and geometrical isomerism. This theoretical work deals with the study of four forms of cyanoetheneselenol in terms of their structural, spectroscopic and thermodynamic parameters. All computations were performed using density functional theory method with the B3LYP functional and the Pople basis set, 6-311 + G(d,p), for all atoms. The relative stability of the four isomers of cyanoetheneselenol was obtained and interpreted. The infrared spectra were generated and assignment of the normal modes of vibration was performed. Probable regions of detection, proposed on the basis of parameters obtained from this study for the four isomers, include comets, the molecular cloud: Sagittarius B2(N), and planetary atmospheres. The molecular and spectroscopic parameters should be useful for future identification of the astrobiological molecule cyanoetheneselenol and the development of the Square Kilometre Array. Graphical Abstract E and Z isomers of cyanoetheneselenol.

Shape-programmed nanofabrication: understanding the reactivity of dichalcogenide precursors

Dialkyl and diaryl dichalcogenides are highly versatile and modular precursors for the synthesis of colloidal chalcogenide nanocrystals. We have used a series of commercially available dichalcogenide precursors to unveil the molecular basis for the outcome of nanocrystal preparations, more specifically, how precursor molecular structure and reactivity affect the final shape and size of II-VI semiconductor nanocrystals. Dichalcogenide precursors used were diallyl, dibenzyl, di-tert-butyl, diisopropyl, diethyl, dimethyl, and diphenyl disulfides and diethyl, dimethyl, and diphenyl diselenides. We find that the presence of two distinctively reactive C-E and E-E bonds makes the chemistry of these precursors much richer and interesting than that of other conventional precursors such as the more common phosphine chalcogenides. Computational studies (DFT) reveal that the dissociation energy of carbon-chalcogen (C-E) bonds in dichalcogenide precursors (R-E-E-R, E=S or Se) increases in the order (R): diallyl<dibenzyl<di-tert-butyl<diisopropyl<diethyl<dimethyl<diphenyl. The dissociation energy of chalcogen-chalcogen (E-E) bonds remains relatively constant across the series. The only exceptions are diphenyl dichalcogenides, which have a much lower E-E bond dissociation energy. An increase in C-E bond dissociation energy results in a decrease in R-E-E-R precursor reactivity, leading to progressively slower nucleation and higher selectivity for anisotropic growth, all the way from dots to pods to tetrapods. Under identical experimental conditions, we obtain CdS and CdSe nanocrystals with spherical, elongated, or tetrapodal morphology by simply varying the identity and reactivity of the dichalcogenide precursor. Interestingly, we find that precursors with strong C-E and weak E-E bond dissociation energies such as Ph-S-S-Ph serve as a ready source of thiol radicals that appear to stabilize small CdE nuclei, facilitating anisotropic growth. These CdS and CdSe nanocrystals have been characterized using structural and spectroscopic methods. An intimate understanding of how molecular structure affects the chemical reactivity of molecular precursors enables highly predictable and reproducible synthesis of colloidal nanocrystals with specific sizes, shapes, and optoelectronic properties for customized applications.