Binod Nepal

Sulfur–Oxygen Chalcogen Bonding Mediates AdoMet Recognition in the Lysine Methyltransferase SET7/9

Recent studies have demonstrated that carbon-oxygen (CH···O) hydrogen bonds have important roles in S-adenosylmethionine (AdoMet) recognition and catalysis in methyltransferases. Here, we investigate noncovalent interactions that occur between the AdoMet sulfur cation and oxygen atoms in methyltransferase active sites. These interactions represent sulfur-oxygen (S···O) chalcogen bonds in which the oxygen atom donates a lone pair of electrons to the σ antibonding orbital of the AdoMet sulfur atom. Structural, biochemical, and computational analyses of an asparagine mutation in the lysine methyltransferase SET7/9 that abolishes AdoMet S···O chalcogen bonding reveal that this interaction enhances substrate binding affinity relative to the product S-adenosylhomocysteine. Corroborative quantum mechanical calculations demonstrate that sulfonium systems form strong S···O chalcogen bonds relative to their neutral thioether counterparts. An inspection of high-resolution crystal structures reveals the presence of AdoMet S···O chalcogen bonding in different classes of methyltransferases, illustrating that these interactions are not limited to SET domain methyltransferases. Together, these results demonstrate that S···O chalcogen bonds contribute to AdoMet recognition and can enable methyltransferases to distinguish between substrate and product.

Substituent Effects on the Binding of Halides by Neutral and Dicationic Bis(triazolium) Receptors.

The effects of substituent and overall charge upon the binding of a halide anion by a bis(triazolium) receptor are studied by M06-2X DFT calculations, with the aug-cc-pVDZ basis set. Comparison is also made between a receptor that engages in H-bonds, with a halogen-bonding species. Fluoride is clearly most strongly bound, followed by Cl(-), Br(-), and I(-) in that order. The dicationic receptor engages in stronger complexes, but not by a very wide margin compared to its neutral counterpart. The binding is enhanced as the substituent on the two triazolium rings becomes progressively more electron-withdrawing. Halogen-substituted receptors, whether neutral or cationic, display a greater sensitivity to substituent than do their H-bonding counterparts. Both Coulombic and charge transfer factors obey the latter trends but do not correctly reproduce the stronger halogen vs hydrogen bonding. Both H-bonds and halogen bonds are nearly linear within the complexes, due in part to bond rotations within the receptor that bring the two triazole rings closer to coplanarity with the central benzene ring.

Competitive Halide Binding by Halogen Versus Hydrogen Bonding: Bis‐triazole Pyridinium

The binding of F(-) , Cl(-) , Br(-) , and I(-) anions by bis-triazole-pyridine (BTP) was examined by quantum chemical calculations. There is one H atom on each of the two triazole rings that chelate the halide via H bonds. These H atoms were replaced by halogens Cl, Br, and I, thus substituting H bonds by halogen bonds. I substitution strongly enhances the binding; Br has a smaller effect, and Cl weakens the interaction. The strength of the interaction is sensitive to the overall charge on the BTP, rising as the binding agent becomes singly and then doubly positively charged. The strongest preference of a halide for halogenated as compared to unsubstituted BTP, as much as several orders of magnitude, is observed for I(-) . Both unsubstituted and I-substituted BTP could be used to selectively extract F(-) from a mixture of halides.

Anionic CH⋅⋅⋅X− Hydrogen Bonds: Origin of Their Strength, Geometry, and Other Properties

CF3H as a proton donor was paired with a variety of anions, and its properties were assessed by MP2/aug-cc-pVDZ calculations. The binding energy of monoanions halide, NO3(-), formate, acetate, HSO4(-), and H2PO4(-) lie in the 12-17 kcal mol(-1) range, although F(-) is more strongly bound, by 26 kcal mol(-1). Dianions SO4(2-) and HPO4(2-) are bound by 27 kcal mol(-1), and trianion PO4(3-) by 45 kcal mol(-1). When two O atoms are available on the anion, the CH⋅⋅⋅O(-) H-bond (HB) is usually bifurcated, although asymmetrically. The CH bond is elongated and its stretching frequency redshifted in these ionic HBs, but the shift is reduced in the bifurcated structures. Slightly more than half of the binding energy is attributed to Coulombic attraction, with smaller contributions from induction and dispersion. The amount of charge transfer from the anions to the σ*(CH) orbital correlates with many of the other indicators of bond strength, such as binding energy, CH bond stretch, CH redshift, downfield NMR spectroscopic chemical shift of the bridging proton, and density at bond critical points.

Effect of Ionic Charge on the CH···π Hydrogen Bond

The CH···π hydrogen bonds (HBs) between trimethylamine (TMA) and an assortment of π-systems are generally weaker than those in which CF3H serves as a proton donor, despite the larger number of CH groups available to serve as donors in the amine. The added positive charge of tetramethylammonium (TMA+) enhances the binding energy by a factor between 4 and 7. The strongest such interaction for TMA+ occurs with indole, bound by 15.5 kcal/mol. Changing from ionic CH···π to NH···π further strengthens the interaction. Conjugation of the π-system improves its proton-accepting capacity, which is further enhanced by aromaticity. Dispersion plays a major role in CH···π HBs: It is the prime contributor in the neutral HBs of TMA, and comparable to Coulombic forces for CF3H and even in ionic CH···π HBs of TMA+. Many of the results can be understood on the basis of a combination of electrostatic potentials and charge transfers.

Building a Better Halide Receptor: Optimum Choice of Spacer, Binding Unit, and Halosubstitution

Quantum calculations are used to measure the binding of halides to a number of bipodal dicationic receptors, constructed as a pair of binding units separated by a spacer group. A number of variations are studied. A H atom on each binding unit (imidazolium or triazolium) is replaced by Br or I. Benzene, thiophene, carbazole, and dimethylnaphthalene are considered as spacer groups. Each receptor is paired with halides F(-) , Cl(-) , Br(-) , and I(-) . Substitution with I on the binding unit yields a large enhancement of binding, as much as 13 orders of magnitude; a much smaller increase occurs for substitution with Br. Imidazolium is a more effective binding agent than is triazolium. Benzene and dimethylnaphthalene represent the best spacers, followed by thiophene and carbazole. F(-) binds much more strongly than do the other halides, which obey the order Cl(-) >Br(-) >I(-) .

Enhancing the Reduction Potential of Quinones via Complex Formation.

Quantum calculations are used to study the manner in which quinones interact with proton-donating molecules. For neutral donors, a stacked geometry is favored over a H-bond structure. The former is stabilized by charge transfers from the N or O lone pairs to the quinones π* orbitals. Following the addition of an electron to the quinone, the radical anion forms strong H-bonded complexes with the various donors. The presence of the donor enhances the electron affinity of the quinone. This enhancement is on the order of 15 kcal/mol for neutral donors, but up to as much as 85 kcal/mol for a cationic donor. The increase in electron affinity is larger for electron-rich quinones than for their electron-deficient counterparts, containing halogen substituents. Similar trends are in evidence when the systems are immersed in aqueous solvent.