Long-range effects in anion-π interactions: their crucial role in the inhibition mechanism of Mycobacterium tuberculosis malate synthase.

The glyoxylate shunt is an anaplerotic bypass of the traditional Krebs cycle. It plays a prominent role in Mycobacterium tuberculosis virulence, so it can be exploited for the development of antitubercular therapeutics. The shunt involves two enzymes: isocitrate lyase (ICL) and malate synthase (GlcB). The shunt bypasses two steps of the tricarboxylic acid cycle, allowing the incorporation of carbon, and thus, refilling oxaloacetate under carbon-limiting conditions. The targeting of ICL is complicated; however, GlcB, which accommodates the pantothenate tail of acetyl-CoA in the active site, is easier to target. A catalytic Mg(2+) unit is located at the bottom of the cavity, and plays a very important role. Recently, the development of effective antituberculosis drugs based on phenyldiketo acids (PDKAs) has been reported. Interestingly, all the crystal structures of GlcB-inhibitor complexes exhibit close contact between the carboxylate of Asp633 and the face of the aromatic ring of the inhibitor. Remarkably, the replacement of the phenyl ring in PDKA by aliphatic moieties yields inactive inhibitors, suggesting that the aromatic moiety is crucial for inhibition. However, the aromatic ring of PDKA is not electron-deficient, and consequently, the anion-π interaction is expected to be very weak (dominated only by polarization effects). Herein, through a combination analysis of the recent X-ray structures of GlcB-PDKA complexes retrieved from the protein data bank (PDB) and computational ab initio studies (RI-MP2/def2-TZVP level of theory), we demonstrate the prominent role of the Mg(2+) ion in the active site, which promotes long-range enhancement of the anion-π interaction.

On the importance of anion-π interactions in the mechanism of sulfide:quinone oxidoreductase.

Sulfide:quinone oxidoreductase (SQR) is a flavin-dependent enzyme that plays a physiological role in two important processes. First, it is responsible for sulfide detoxification by oxidizing sulfide ions (S(2-) and HS(-)) to elementary sulfur and the electrons are first transferred to flavin adenine dinucleotide (FAD), which in turn passes them to the quinone pool in the membrane. Second, in sulfidotrophic bacteria, SQRs play a key role in the sulfide-dependent respiration and anaerobic photosynthesis, deriving energy for their growth from reduced sulfur. Two mechanisms of action for SQR have been proposed: first, nucleophilic attack of a Cys residue on the C4 of FAD, and second, an alternate anionic radical mechanism by direct electron transfer from Cys to the isoalloxazine ring of FAD. Both mechanisms involve a common anionic intermediate that it is stabilized by a relevant anion-π interaction and its previous formation (from HS(-) and Cys-S-S-Cys) is also facilitated by reducing the transition-state barrier, owing to an interaction that involves the π system of FAD. By analyzing the X-ray structures of SQRs available in the Protein Data Bank (PDB) and using DFT calculations, we demonstrate the relevance of the anion-π interaction in the enzymatic mechanism.

Is the use of diffuse functions essential for the properly description of noncovalent interactions involving anions?

It is commonly assumed that theoretical DFT or ab initio calculations involving anions require the utilization of diffuse functions in order to obtain reliable results. In large systems, the use of diffuse functions in the calculations increases the computational cost and, more importantly, sometimes provokes self-consistent-field (SCF) convergence problems, especially in open shell systems. Nowadays, the popular and often used bases for studying noncovalent interactions are the correlation-consistent polarized basis sets of Dunning and co-workers, denoted as cc-pVXZ (X = D, T, etc.), and the Turbomole def2 basis set family (def2-SVP and def2-TZVP). In this paper we study the effect of the utilization of diffuse functions on the energetic and geometric features of several noncovalent complexes, including hydrogen, halogen, and pnicogen bonding, lithium bonds, anion-π interactions, and van der Waals interactions.

Anion-π interactions involving [MX(n)](m-) anions: a comprehensive theoretical study.

In this manuscript we perform a systematic study on the geometric and energetic features of anion-π complexes, wherein the anion is a metal complex of variable shapes and charges. Such a study is lacking in the literature. For the calculations we used the ab initio RI-MP2/def2-TZVPP level of theory. A search in the Cambridge Structural Database (CSD) provides the experimental starting point that inspired the subsequent theoretical study. The influence of [MX(n)](m-) on the anion-π interaction was analyzed in terms of energetic, geometric, and charge transfer properties and Bader's theory of "atom-in-molecules" (AIM). The binding energy depends on the coordination index, geometric features and different orientations adopted by the metallic anion. The binding mode resembling a stacking interaction for linear, trigonal planar and square-planar anions is the most favorable. For tetrahedral and octahedral anions the most favorable orientation is the one with three halogen atoms pointing to the ring.

Understanding the forces that govern packing: a density functional theory and structural investigation of anion-π-anion and nonclassical C-H···anion interactions.

The ability of Ni(II) coordinated 4-pyrrolyl-3,5-di(2-pyridyl)-1,2,4-triazole (pldpt) to establish multiple anion-π interactions is analyzed. Experimentally, such complexes were previously shown to form strong anion-π interactions, including "π-pocket" and "π-sandwiched" motifs, in the crystal lattice. In the latter, the triazole ring is "sandwiched" by two anions forming a ternary anion-π-anion assembly (π-sandwich) which, surprisingly, gave about 0.2 Å shorter anion-π distances than in binary assemblies (where only one side of the triazole participates in the anion binding), indicating the possibility of cooperativity. In depth analysis, using dispersion-corrected density functional theory (DFT, BP86-D/def2-TZVP level of theory), shows that this ternary anion-π-anion interaction is slightly less energetically favorable than the binary anion-π interactions in isolation. Hence, the sandwich interaction is not cooperative (E(coop) is positive), but, as E(coop) contributes less than 1.5% of the total interaction energy (which is dominated by the strong electrostatic attraction of the anions to the highly π-acidic Ni(II)-coordinated triazole ring), the presence of nonclassical C-H···anion hydrogen bonds can offset this, making the short anion-π sandwich interactions the most favorable solid state conformation.

Pnicogen-π complexes: theoretical study and biological implications.

The energetic and geometric features of pnicogen-π complexes involving different types of aromatic rings (benzene, trifluorobenzene, hexafluorobenzene and s-triazine) and the heavier pnicogenes (ECl(3), E = As, Sb, Bi) are investigated using theoretical methods (ab initio and DFT-D3). We have analyzed how the interaction energy is affected by the π-acidity of the aromatic moieties and the pnicogen used. In addition, we have found several examples in the Protein Databank where pnicogen-π interactions are present. This likely indicates the potential use of this interaction in the design and synthesis of potential inhibitors of enzymatic reactions. Moreover, in order to know the reliability of the latest version of dispersion termed corrected DFT-D3, we have also compared the energies obtained using the ab initio MP2 method with those obtained using BP86-D3. We have also computed and analyzed the dispersion contribution to the total interaction energy in order to know if it is crucial for the favourable binding. This allows a better understanding of the physical nature of the interaction. Finally, we have used the Bader's theory of "atoms-in-molecules" to demonstrate that the electron density computed at the bond critical point that emerges upon complexation can be used as a measure of bond order in this noncovalent interaction.

Synthesis, X-ray characterization and computational studies of Cu(II) complexes of N-pyrazolyl pyrimidine.

In this manuscript we report the synthesis and X-ray characterization of several complexes of Cu(II) with a 2-(1H-pyrazol-1-yl)-pyrimidine (L) ligand. Complexes CuLCl(2) (1), [CuL(2)(H(2)O)(2)](NO(3))(2) (2) and [CuL(2)H(2)O](NO(3))(2) (3) are mononuclear systems and [CuL(NO(3))(2)](n) (4) is polymeric. In the solid state, complexes 2 and 3 are characterized by the presence of anion-π interactions that are relevant for the final 3D architecture and packing. In complexes 1 and 4, where the counterion is directly bonded to the metal, anion-π interactions are not observed. High level ab initio calculations (RI-MP2/def2-TZVP) have been used to evaluate the noncovalent interactions observed in the solid state and the interplay between them. We also demonstrate that the presence of anions above the aromatic ligand is not due only to strong electrostatic interactions between the counterparts.

Substituent effects in halogen bonding complexes between aromatic donors and acceptors: a comprehensive ab initio study.

Substituent effects in halogen bonding complexes involving aromatic rings are investigated. We have analyzed how the interaction energy (the RI-MP2/aug-cc-pVDZ level of theory) is affected by the substitution in both halogen bond donor and acceptor aromatic moieties. In addition, we have used two different aromatic electron donor molecules pyridine and cyanobenzene, which allow us to study the effect of having the electron donor nitrogen atom forming part of the ring or outside the ring (-CN). Interestingly, the effect of the substituents on the interaction energies is similar in both cases. We have obtained the Hammett's plots for four combinations of aromatic donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammett's σ parameter). We have also studied and compared bifurcated halogen bonds using both possible combinations, that is two donors and one acceptor and vice versa. In addition, we have analyzed the effect of the solvent on the interaction energies using COSMO. Finally, we have used Bader's theory of "atoms-in-molecules" to demonstrate that the electron density computed at the bond critical point that emerges upon complexation can be used as a measure of bond order in this noncovalent interaction.

Theoretical study on cooperativity effects between anion-π and halogen-bonding interactions.

This article analyzes the interplay between lone pair-π (lp-π) or anion-π interactions and halogen-bonding interactions. Interesting cooperativity effects are observed when lp/anion-π and halogen-bonding interactions coexist in the same complex, and they are found even in systems in which the distance between the anion and halogen-bond donor molecule is longer than 9 Å. These effects are studied theoretically in terms of energetic and geometric features of the complexes, which are computed by ab initio methods. Bader's theory of "atoms in molecules" is used to characterize the interactions and to analyze their strengthening or weakening depending upon the variation of charge density at critical points. The physical nature of the interactions and cooperativity effects are studied by means of molecular interaction potential with polarization partition scheme. By taking advantage of all aforementioned computational methods, the present study examines how these interactions mutually influence each other. Additionally, experimental evidence for such interactions is obtained from the Cambridge Structural Database (CSD).

Radical cation (C˙(+)-π) and radical anion (A˙(-)-π) interactions with aromatic rings: energetic, orbitalic and spin density considerations.

Cation and anion-π interactions are important binding forces where aromatic rings are involved. In this manuscript we define and compare two related interactions that have not been reported so far, namely radical cation and radical anion-π interactions (C˙(+)-π and A˙(-)-π, respectively). Moreover, we compare the energetic features of these complexes with the related closed-shell interactions. Interestingly the C˙(+)-π interaction is more favourable than the standard cation-π interaction and the contrary is observed for the A˙(-)-π interaction. Changes in the aromatic character of the ring upon complexation of the ion have been studied using the nucleus-independent chemical shift (NICS) criterion. Orbitalic and spin density calculations of the complexes have been computed in order to investigate if spin transfer effects between the radical ions and the aromatic ring exist. We have analyzed the physical nature of the interactions by means of Bader's theory of "atoms-in-molecules" and partitioning the total interaction energy into individual components using the Molecular Interaction Potential with a polarization partition scheme. Finally, we describe an interesting biological example, which involves the tetrahydrobiopterin cofactor, where the presence of a radical ion-π interaction is important.

Unexpected nonadditivity effects in anion-π complexes.

Several complexes of fluorine-substituted ethyne, ethene, butadiene, benzene, and [n]radialenes (n = 3-5) with two anions have been optimized at the RI-MP2/aug-cc-pVTZ level of theory. The additivity of the anion-π interaction was studied depending on the number of double bonds and fluorine atoms. Interesting nonadditivity effects were observed in the aromatic and antiaromatic complexes, which were analyzed by partitioning the total interaction energy into individual components, using Bader's theory of "atoms in molecules" and changes in the aromatic character of the ring upon complexation.

On the directionality of anion-π interactions.

The directionality of two important noncovalent interactions involving aromatic rings (namely anion-π and cation-π) is investigated. It has been recently published that the anion-π interactions observed in X-ray structures where the anion is located exactly over the center of the ring are scarce compared to cation-π interactions. To explain this behavior, we have analyzed how the interaction energy (RI-MP2/aug-cc-pVDZ level of theory) is affected by moving the anion from the center of the ring to several directions in anion-π complexes of chloride with either hexafluorobenzene or trifluoro-s-triazine. We have compared the results with the directionality of the cation-π interaction in the sodium-benzene complex. The results are useful to explain the experimental differences between both ion-π interactions. We have also computed the van der Waals radii of several halide anions and we have compared them to the neutral halogen atoms.

The role of the ethynyl substituent on the π-π stacking affinity of benzene: a theoretical study.

Herein, we report a high-level theoretical study (SCS-RI-MP2(full)/aug-cc-pVTZ) examining the stacking affinity of 1,3,5-triethynylbenzene. The stacking properties of this compound are compared to those of benzene and 1,3,5-trifluorobenzene. The results indicate that the ethynyl substituent improves the stacking affinity of the arene, since the binding energies for the stacked ethynyl-substituted arene dimers are higher than those of both benzene and the fluoro-substituted arene. This interesting behaviour has been studied by examining the energetics, geometries and electron charge density features of the complexes. A query in the Cambridge Structural Database returned several X-ray crystal structures containing π-π stacking interactions of 1,3,5-triethynylaryls that strongly agree with the theoretical results.

RI-MP2 and MPWB1K Study of π-Anion-π' Complexes: MPWB1K Performance and Some Additivity Aspects.

Several sandwich complexes of hexafluorobenzene, trifluorobenzene, s-triazine, and trifluoro-s-triazine with halides, nitrate, and carbonate anions have been optimized at the RI-MP2/6-31++G** (full and frozen core), B3LYP/6-31++G**, and MPWB1K/6-31++G** levels of theory. All possible combinations of the π-systems and anions (to generate the sandwich π-anion-π' complexes) have been computed and analyzed using the aforementioned levels of theory. This allows us to evaluate the reliability and the performance of the MPWB1K functional to compute the binding energies of the anion-π complexes and to analyze the additivity of the interaction in π-anion-π' complexes where the aromatic rings are of different nature (π-acidity). We have also explored the Cambridge Structural Database and several interesting X-ray structures that support the theoretical calculations that have been found.

New [2 × 2] copper(i) grids as anion receptors. Effect of ligand functionalization on the ability to host counteranions by hydrogen bonds.

Several complexes with a [2 × 2] grid structure have been obtained by the self-assembly of different copper(I) salts and ligands of the type 4,6-bis(pyrazol-1-yl)pyrimidine containing different substituents on the heterocycles. The main goal has been to evaluate the influence over the solid state and solution behavior of the functionalization of the pyrimidine ring with a primary amino substituent. The molecular and crystalline structures of some derivatives have been determined by X-ray diffraction. The grids contain two open voids formed by pairs of ligands facing one another on opposite sides of the grid in a somewhat divergent manner. One counteranion is hosted in each void interacting through hydrogen bonds and anion-π interactions. The presence of the amino group that points toward the inside of the cavity dominates the interactions in the void and apparently determines the orientation of the hosted counteranion and that of the ligands. With the exception of the derivative with chloride as the anion, the grid structure is preserved in solution (NMR and UV-vis) and some cation-anion interaction, increased by the presence of the amino group, exists also in solution (DOSY experiments). The experiments of anion interchange performed in solution indicate that a higher stability is found for the host-guest aggregates with OTs(-) (p-Me-C(6)H(4)SO(3)) and NO(3)(-). While for these anions a 1:2 stoichiometry is reached, for the rest of the anions tested (ReO(4)(-), OTf(-), and PF(6)(-)), only weaker 1:1 complexes are formed. Computational studies support the presence of anion-π interactions.

Experimental and computational study of the interplay between C-H/pi and anion-pi interactions.

The synthesis of octahedral copper and zinc coordination complexes containing ligands of the type 6R,2,4-bis(3,5-dimethylpyrazol-1-yl)triazine is described. They exhibit the simultaneous presence of C-H/pi and anion-pi interactions on both sides of the same triazine ring. When the pyrazolyl groups are not methylated, lone pair-pi and anion-pi interactions coexist on the same triazine ring. In addition, the interplay between C-H/pi and anion-pi interactions is studied by means of high level correlation ab initio calculations. They demonstrate that synergistic effects are present when both interactions coexist. These synergistic effects have been evaluated using the genuine non-additivity energies and symmetry adapted perturbation theory (SAPT).

Substituent effects in ion-pi interactions: fine-tuning via the ethynyl group.

In this work, we report a high level theoretical study (RI-MP2(full)/aug-cc-pVDZ) that deals with the effect of electron-withdrawing substituents on cation-pi and anion-pi interactions in the absence/presence of triple bonds between the substituent and the aromatic ring. The ethynyl group is able to finely tune the interaction energy of the complexes. Interestingly, for the cation-pi complexes, it reduces the effect of the electron withdrawing groups (EWG), improving the interaction. For anion-pi complexes, it boosts the effect of the EWG, improving the interaction as well. This dual behavior has been studied by examining the geometric and energetic features of the complexes, "atoms-in-molecules" analysis and charge transfer effects.

Counterintuitive substituent effect of the ethynyl group in ion-pi interactions.

In this article, we report a high-level theoretical study (SCS-RI-MP2(full)/aug-cc-pVTZ) that deals with the substituent effect of the ethynyl group on ion-pi interactions in 1,3,5-triethynylbenzene systems. The ethynyl group is able to act as an electron-withdrawing group, thus favoring the anion-pi interaction. Unexpectedly, it has little influence on the cation-pi interaction. This behavior has been studied by examining the geometrical and energetic features of the complexes, AIM, and charge analyses and partitioning the interaction energy. The simultaneous interaction of 1,3,5-triethynylbenzene with cations and anions by opposite sides of the ring has also been studied.