Convergent functional groups. X. Molecular recognition of neutral substrates

Non-covalent interactions from a Quantum Chemical Topology perspective

About half a century after its little-known beginnings, the quantum topological approach called QTAIM has grown into a widespread, but still not mainstream, methodology of interpretational quantum chemistry. Although often confused in textbooks with yet another population analysis, be it perhaps an elegant but somewhat esoteric one, QTAIM has been enriched with about a dozen other research areas sharing its main mathematical language, such as Interacting Quantum Atoms (IQA) or Electron Localisation Function (ELF), to form an overarching approach called Quantum Chemical Topology (QCT). Instead of reviewing the latter’s role in understanding non-covalent interactions, we propose a number of ideas emerging from the full consequences of the space-filling nature of topological atoms, and discuss how they (will) impact on interatomic interactions, including non-covalent ones. The architecture of a force field called FFLUX, which is based on these ideas, is outlined. A new method called Relative Energy Gradient (REG) is put forward, which is able, by computation, to detect which fragments of a given molecular assembly govern the energetic behaviour of this whole assembly. This method can offer insight into the typical balance of competing atomic energies both in covalent and non-covalent case studies. A brief discussion on so-called bond critical points is given, highlighting concerns about their meaning, mainly in the arena of non-covalent interactions.

The road to aryl CHanion binding was paved with good intentions: fundamental studies, host design, and historical perspectives in CH hydrogen bonding

Throughout the design and development of supramolecular receptors for anion binding, many different non-covalent anion-binding motifs have been employed. One motif seen in many host-guest systems is the sometimes weaker, 'non-traditional' aryl CH hydrogen bond. From June Sutor's discovery of the interaction and its subsequent dismissal by the field in the 1960s to today's use of the aryl CH hydrogen bond in synthetic anion receptors, the path our lab took to begin studying this interaction has been influenced by many other researchers in the field. This feature article highlights the history and properties of the CH hydrogen bond, with a particular focus on aryl CH hydrogen bonds in anion recognition. We highlight select recent developments in the field of anion receptors utilizing aryl CH hydrogen bonds, with an emphasis on how this has influenced the evolution of our approach in designing fundamental studies on CH hydrogen bonding and exploiting this interaction in efforts aimed toward preferential anion binding.

Why do A·T and G·C self-sort? Hückel aromaticity as a driving force for electronic complementarity in base pairing

Computations reveal that the potential for aromaticity gain and loss in nucleobases play key roles in modulating base pairing strengths.

Sequence-Selective Formation of Synthetic H-Bonded Duplexes

Oligomers equipped with a sequence of phenol and pyridine N-oxide groups form duplexes via H-bonding interactions between these recognition units. Reductive amination chemistry was used to synthesize all possible 3-mer sequences: AAA, AAD, ADA, DAA, ADD, DAD, DDA, and DDD. Pairwise interactions between the oligomers were investigated using NMR titration and dilution experiments in toluene. The measured association constants vary by 3 orders of magnitude (102 to 105 M-1). Antiparallel sequence-complementary oligomers generally form more stable complexes than mismatched duplexes. Mismatched duplexes that have an excess of H-bond donors are stabilized by the interaction of two phenol donors with one pyridine N-oxide acceptor. Oligomers that have a H-bond donor and acceptor on the ends of the chain can fold to form intramolecular H-bonds in the free state. The 1,3-folding equilibrium competes with duplex formation and lowers the stability of duplexes involving these sequences. As a result, some of the mismatch duplexes are more stable than some of the sequence-complementary duplexes. However, the most stable mismatch duplexes contain DDD and compete with the most stable sequence-complementary duplex, AAA·DDD, so in mixtures that contain all eight sequences, sequence-complementary duplexes dominate. Even higher fidelity sequence selectivity can be achieved if alternating donor-acceptor sequences are avoided.

The ANANKE relative energy gradient (REG) method to automate IQA analysis over configurational change

Much chemical insight ultimately comes down to finding out which fragment of a total system behaves like the total system, in terms of an energy profile. A simple example is that of the water dimer, where this system is regarded as held together by a hydrogen bond. The hydrogen bond consists of two atoms (H···O), which energetically behave similarly to the total system (H₂O)₂. However, from a quantum mechanical point of view, each atom in the total system interacts with any other atom. Thus, the view that the hydrogen bond by itself governs the energetic stability of the water dimer needs rigorous justification. In this work, we propose a method that provides such a justification, in general, but only illustrated on the water dimer here. This method is based on the topological energy partitioning method called interacting quantum atoms (IQA). The method is implemented in the program ANANKE, which calculates correlations between the energy profile of the total system and those of subsystems (or fragments). ANANKE acts on the IQA energy contributions obtained for a sequence of full-system geometries controlled by a coordinate of interest (e.g. the O···H distance in the water dimer). Although applied only for the water dimer in this work, the method is general and able to explain the gauche effect, the torsional barrier in biphenyl, the arrow-pushing scheme of an enzymatic reaction (peptide hydrolysis in the HIV-1 Protease active site), and halogen-alkane nucleophilic substitution (S_N2) reactions. Those applications will appear elsewhere as separate and elaborated case studies; here we focus on the details of the ANANKE method and its justification, using the water dimer as a concrete case.

Exploiting directional long range secondary forces for regulating electrostatics-dominated noncovalent interactions

It has been well established that long range secondary electrostatic interactions (SEIs) have a significant effect on the stability of supramolecular complexes. However, general rules for exploiting SEIs in the rational design of diverse supramolecular complexes have been difficult to obtain. In this work, we outline a quantum chemical approach for understanding the strength of electrostatic interactions. This approach is seen to provide excellent correlation between the electrostatic force and the binding energy between two partners in hydrogen-bonded complexes, as well as that between two ions in ion-pair complexes. Furthermore, we illustrate how the understanding of the binding allows for the rational design of new complexes where the association constant between the two partners can be increased or decreased, as desired, by several orders of magnitude. Hence, the current work showcases a general, simple and powerful method of understanding and exploiting long range secondary electrostatic interactions.

A Porphyrin-Anthracene Supramolecular System Assembled via Complementary Nucleic Acid Base Pairing

Covalently linked porphyrin–adenine (meso-5(4-(9-(2-oxyethyl)adenine)phenyl)-10,15,20-tritolylporphyrin, 1) and anthracene–thymine (1-(9-methylanthracene)thymine, 2) conjugates have been synthesized and fully characterized by elemental analysis, FAB mass, UV-vis, 1 H NMR, fluorescence and cyclic voltammetric methods. Detailed 1 H NMR studies reveal that 1 and 2 self-assemble in CDCl 3 solutions at 293 ± 3 K to form a two-point hydrogen-bonded, bichromophoric, supramolecular system 3 with a binding constant of 47 ± 5 M−1 and that both Hoogsteen- and Watson–Crick-type A–T assemblies exist in solution under these experimental conditions. Spectral and electrochemical data point out the possibility of occurrence of both energy and electron transfer reactions from the singlet excited state of 2 to 1 in the ensemble 3. The singlet state activity of the ensemble 3 has been probed mainly by the time-resolved fluorescence method and the results have been discussed in the light of those obtained earlier on similar ‘non-covalently’ or covalently bound bichromophoric systems.

Dinuclear organoplatinum(II) complexes containing N-methylbenzamide

The preparation and characterization of cationic, dinuclear complexes of the type trans-[Pt(PPh3)2(σ-C6H4NHMe)-µ-L-Pt(PPh3)2(σ-C6H4NHMe)](OTf)2 (L = 4,4′-bipyridine, 4,7-phenanthroline, 4,4′-dipyrazolylmethane, and 1,1′-diphenyl-4,4′-dipyrazolylmethane; OTf = trifluoromethanesulfonate (triflate)) containing two C3-N-methylbenzamide ligands are described. The key structural feature of the cationic complexes is the presence of two convergent amide groups that may allow for charge-assisted, H-bonding interactions in solution with suitable heteroaromatic guest molecules such as nucleobases.Key words: organoplatinum(II) complex, organometallic host, dinuclear complex, N-methylbenzamide.

Highly selective recognition of adenine nucleobases by synthetic hosts with a linked five-six-five-membered triheteroaromatic structure and the application to potentiometric sensing of the adenine nucleotide

A new structure for an adenine-selective host molecule, featuring the pertinent link of five-six-five-membered heteroaromatic rings and two carbamoyl NH sites, was developed. This structure provides a correctly oriented array of complementary hydrogen bonding sites for the adenine nucleobase, which exploits both Watson-Crick and Hoogsteen-type interactions. The complexation with adenine nucleobases by multiple hydrogen bonding was supported by (1)H NMR spectroscopy. This type of host displayed high selectivity in complexation, with an accompanying fluorescent response to lipophilized adenosine in CHCl(3). Furthermore, a remarkably selective potentiometric response was attained for adenosine 5'-monophosphate over 5'-GMP, 5'-CMP, and 5'-UMP by using an ion-selective electrode with a PVC-supported solvent polymeric membrane. This indicates recognition of water-soluble nucleotide guests through the membrane-water interface. These findings are expected to form a reliable basis for the development of artificial sensing systems for mononucleotides in biological systems.

Synthesis and characterization of a platinum(II) complex tethered to a ligand of the peripheral benzodiazepine receptor

A peripheral benzodiazepine receptor (PBR) ligand (TZ6, 5) has been selected as receptor-mediated carrier for antitumor cisplatin-like compounds. Compound 5, containing a thiazole ring in position 2 of the imidazopyridine nucleus, is able to act as a dinitrogen chelate toward platinum. The resulting complex, cis-[PtCl2(5)], that is, compound 8, has been fully characterized by NMR techniques and has been shown to possess affinity and selectivity for the PBR comparable to those of 5 (IC50 of 4.6 and 2.81 nM for 8 and 5, respectively; selectivity indexes for PBR greater than 10,000 for both compounds). Hence, a platinum moiety cross-linking the imidazopyridine and the thiazole aromatic rings does not alter the affinity for PBR. The same cross-linking could be responsible for the tendency of 8 to associate in dimers. The equilibrium between monomer and dimer has been investigated by NMR spectroscopy and the corresponding constant determined.

NMR and Computational Studies of Chiral Discrimination by Amylose Tris(3,5-dimethylphenylcarbamate)

Proton NMR and simulations were combined to study the origin of chiral selectivity by a polysaccharide used in a commercial chromatographic stationary phase: amylose tris(3,5-dimethylphenylcarbamate). This material has unusually high enantioselectivity for p-O-tert-butyltyrosine allyl ester, which is activated by the presence of an acid. Proton NMR spectra agreed with the HPLC in showing that the l-enantiomer interacts much more strongly with the polysaccharide and that acidity switches on the selectivity. 2D NOESY spectra revealed which protons of each enantiomer and the polysaccharide were in proximity, and these spectra revealed folding of the l-enantiomer. Computations generated energy-minimized structures for the polysaccharide-enantiomer complexes, independently predicting folding of the l-enantiomer. Molecular dynamics simulations 2 ns in duration, repeated for three different energy-minimized structures, generated pair distribution functions that are in excellent agreement with the 2D NOESY spectra. The modeling studies revealed why acidity switches on chiral selectivity and minimally affects the chromatographic retention time of the unfavored d-enantiomer. The results comprise the first case of a chiral separation by a commercial polysaccharide stationary phase being explained using a combination of 2D NOESY and simulations, providing excellent agreement between experiment and computation and lending detailed molecular insight into enantioselectivity for this system.

Does the A·T or G·C Base-Pair Possess Enhanced Stability? Quantifying the Effects of CH···O Interactions and Secondary Interactions on Base-Pair Stability Using a Phenomenological Analysis and ab Initio Calculations

An empirically based relationship between overall complex stability (-DeltaG degrees ) and various possible component interactions is developed to probe the question of whether the A.T/U and G.C base-pairs exhibit enhanced stability relative to similarly hydrogen-bonded complexes. This phenomenological approach suggests ca. 2-2.5 kcal mol-1 in additional stability for A.T owing to a group interaction containing a CH...O contact. Pairing geometry and the role of the CH...O interaction in the A.T base-pair were also probed using MP2/6-31+G(d,p) calculations and a double mutant cycle. The ab initio studies indicated that Hoogsteen geometry is preferred over Watson-Crick geometry in A.T by ca. 1 kcal mol-1. Factors that might contribute to the preference for Hoogsteen geometry are a shorter CH...O contact, a favorable alignment of dipoles, and greater distances between secondary repulsive sites. The CH...O interaction was also investigated in model complexes of adenine with ketene and isocyanic acid. The ab initio calculations support the result of the phenomenological approach that the A.T base-pair does have enhanced stability relative to hydrogen-bonded complexes with just N-H...N and N-H...O hydrogen bonds.

Direct experimental observation of the effect of the base pairing on the oxidation potential of Guanine

The effect of complementary base pairing on the oxidation potential of a guanosine derivative has been determined by cyclic and differential pulse voltammetry in CHCl3. The formation of the Watson-Crick H-bonded complex lowers the oxidation potential of the free molecule by 0.34 V, which compares well with the value obtained by DFT/B3LYP/6-311++g** computations.

Direct Assignment of Enantiofacial Discrimination on Single Heterocyclic Substrates by Self-induced CD

The first direct assignment of highly dynamic enantiofacial discrimination acting on a single heterocyclic substrate has been achieved by a combination of experimental and theoretical CD spectroscopy. The interaction of chirally modified hosts based on triphenylene ketals with appropriate prochiral guests can lead to the preferential formation of one diastereomeric host-guest complex. This reversible stereoselective binding transmits the chiral information from remote chiral groups in the host to the strongly absorbing triphenylene chromophore, which gives rise to self-induced CD. This effect was exploited for the determination of the enantiofacial recognition in various host-guest systems. Inversion of the steric demand either of the chiral substituents at the host or of the prochiral guest leads to almost complete inversion of the resulting CD spectra. For the assignment of the absolute stereochemistry of the complexes, a combined molecular dynamics/quantum-chemical approach was successfully employed. Despite the size and the highly dynamic character of the supramolecular systems, fundamental properties of the systems and details of the spectra were simulated accurately, providing access to fast and reliable assignment of the enantiofacial preference. The results are highly consistent with available X-ray data.

With Regard to the Hydrogen Bonding in Complexes of Pyridylureas, Less Is More. A Role for Shape Complementarity and CH···O Interactions?

A pyridylurea.tetraazaanthracenedione complex with three hydrogen bonds is more stable than an analogous complex with four hydrogen bonds. An X-ray analysis and modeling suggests a steric mismatch destabilizing the latter and a CH...O contact enhancing the stability of the former.

Molecular Imprinting Inside Dendrimers

Synthetic hosts capable of binding porphyrins have been produced by a mixed-covalent-noncovalent imprinting process wherein a single binding site is created within cross-linked dendrimers. Two synthetic hosts were prepared, using as templates 5,10,15,20-tetrakis(4-hydroxyphenyl)porphyrin and 5,10,15,20-tetrakis(3,5-dihydroxyphenyl)porphyrin. These two templates were esterified with, respectively, fourth- and third-generation Fréchet-type dendrons containing homoallyl end-groups. The resulting tetra- and octadendron macromolecules underwent the ring-closing metathesis reaction using Grubbs' Type I catalyst, RuCl(2)(P(C(6)H(5))(3))(2)(CHCH(2)C(6)H(5)), to give extensive interdendron cross-linking. Hydrolytic removal of the porphyrin cores afforded imprinted hosts whose ability to bind porphyrins with various peripheral substituents was investigated by UV-visible spectrophotometric titrations and size exclusion chromatography. The results indicate a high yield of imprinted sites that show high selectivity for binding of porphyrins capable of making at least four hydrogen bonds, but only a moderate degree of shape selectivity.

The elusive atomic rationale for DNA base pair stability

A systematic analysis of the electrostatic interaction between 27 natural DNA base pairs was carried out, based on ab initio correlated wave functions and the topology of the electron density. Using high rank multipole moments we show that the atomic partitioning of the interaction energy contains many substantial contributions between distant atoms. Profiles of cumulative energy versus internuclear distance show large fluctuations and provide an electrostatic fingerprint of the partitioning of interaction energy in a complex. A quantified comparison between each pair of energy profiles, one for each base pair, makes clear that there is no correlation between the total base pair interaction energy and the shape of the profile. In other words, base pairs with similar interaction energy are not stable for the same reasons in terms of atomic partitioning. In summary, simple rules to rationalize the pattern of energetic stability of naturally occurring base pairs in terms of subsets of atoms are elusive. Our work cautions against inappropriate use of Jorgensen's secondary interaction hypothesis.

Rebek imides and their adenine complexes: preferences for Hoogsteen binding in the solid state and in solution

Rebek imides (3), formed from Kemp's triacid, were developed in the mid-1980's as model receptors for adenine derivatives. We report here the first account of their hydrogen-bonding preferences upon binding 9-ethyladenine (1a) in the solid state. Structural analysis begins with simple imides 3a-e that form discrete dimers, while bis-imide 4 forms ribbon-like structures in the crystalline phase. The hydrogen-bonding interface within each of the representative assemblies features short intermolecular N(3)imide...O(8*)imide* distances (ca. 2.95 A), indicative of two-point hydrogen bonding. Imides 3f-h could be co-crystallized with 1a; single-crystal X-ray analysis of the resulting complexes reveals hydrogen-bonding geometries nearly identical to those observed in nucleobase complexes of adenine and pyrimidine derivatives. Imides 3f and 3g form 2:1 ternary assemblies with 1a; the complex of the former, (3f)2 x 1a, displays both Watson-Crick- and Hoogsteen-type hydrogen bonding, whereas the complex of the latter, (3g)2 x 1a, shows the Hoogsteen motif and imide hydrogen bonding to N(3) of the purine base (N(3)adenine...N(3'')imide = 3.07(1) A). Imide 3h forms a 1:1 complex with 1a (3h x 1a x CHCl3) and displays Hoogsteen binding exclusively. All of the 3 x 1a assemblies show C(adenine)...O(imide) distances (3.38-3.75 A) that are consistent with C-H...O hydrogen bonding. Base-pairing preferences for the Rebek imides are further explored in solution by 1H NMR one-dimensional NOE experiments and by computational means; in all cases the Hoogsteen motif is modestly favored relative to its Watson-Crick counterpart.

A new versatile receptor platform

We prepared a molecular receptor based on the molecular tweezer concept. Our system offers versatility, an extremely short synthetic route, good yield, large quantities, and finally having binding constants that equal the best known tweezer molecules when it comes to binding various nitroaromatics such as 1,3,5-trinitrotoluene (24 M(-1)), 1,3,5-trinitrobenzene (182 M(-1)), and 2,4,7-trinitrofluorenone (490 M(-1)) as determined using 1H NMR in CDCl3. It is notable that these binding constants are achieved although the molecular framework is not locked in a fixed and rigid conformation. The rigidity has been claimed to be the governing factor when it comes to achieving a large binding constant. We propose that our molecular tweezer system may be preorganized and that this explains the high binding constants observed. Further, we investigated the crystal structures of both the neutral receptor molecule and a complex with 1,3,5-trinitrobenzene and found that the molecule forms a pocket suited to accommodate flat aromatic analytes.

Interaction of ferrocenoyl-dipeptides with 3-aminopyrazole derivatives: beta-sheet models? A synthetic, spectroscopic, structural, and electrochemical study

The use of 3-aminopyrazole derivatives as beta-sheet templates is investigated using a series of ferrocenoyl (Fc)-dipeptides (Fc-Gly(2)-OEt, Fc-Ala(2)-OBzl, Fc-Leu-Phe-OMe, Fc-Val-Phe-OMe, Fc-Phe(2)-OMe, Fc-Leu(2)-OMe, Fc-Val(2)-OMe). The synthesis and full characterization are reported. The solid-state structures of Fc-Gly(2)-OMe and Fc-Leu-Phe-OMe show extensive hydrogen bonding of the podand peptide substituents, resulting in the formation of supramolecular Fc-dipeptide assemblies. For Fc-Gly(2)-OMe, this can be described as a parallel beta-sheet, whereas intermolecular interactions in Fc-Leu-Phe-OMe result in the formation of supramolecular helical structures. The saturation titrations of Fc-dipeptides with 3-amino-5-methylpyrazole (3-AMP) and 3-trifluoroacetylamido-5-methylpyrazole (3-TFAc-AMP) show a 1:1 interaction of the Fc-peptide with the aminopyrazole derivatives. IR measurements in solution confirm binding to the top face of the Fc-dipeptide and the involvement of the Fc-C=O and the ester C=O groups in establishing H-bonding interactions with the 3-TFAc-AMP. However, binding constants in chloroform are low and range from 8 to 27 M(-1), which correspond to binding energies of 5-7 kJ mol(-1). In higher polarity solvents, such as acetonitrile or acetone, the binding constants are below 5 M(-1), emphasizing the limited utility of 3-AMP derivatives as beta-sheet templates. Electrochemical measurements confirm the weak interactions between the various Fc-dipeptides and 3-TFAc-AMP. Typical shifts in the redox potential of the Fc moiety are in the range 0-20 mV. Attempts to modify 3-AMP at the 3-position by carbodiimide coupling with amino acid derivatives and, thus, enhance the binding to the Fc-peptides resulted in 2-amino acid substituted 3-AMP derivatives. Substitution at the 2-position blocks the binding site, and no interactions with Fc-dipeptides are observed.

Catalytic enantioselective protonation of lithium enolates with chiral imides

The catalytic enantioselective protonation of simple enolates was achieved using a catalytic amount of chiral imides and stoichiometric amount of achiral proton sources. Among the achiral proton sources examined in the protonation of the lithium enolate of 2,2,6-trimethylcyclohexanone catalyzed by (S,S)-imide 1, 2, 6-di-tert-butyl-p-cresol (BHT) and its derivatives gave the highest enantiomeric excess. For example, 90% ee of (R)-enriched ketone was obtained when (S,S)-imide 1 (0.1 equiv) and BHT (1 equiv) were used. Use of 0.01 equiv of the chiral catalyst still caused a high level of asymmetric induction. For catalytic protonation of the lithium enolate of 2-methylcyclohexanone, chiral imide 6 possessing a chiral amide portion was superior to (S,S)-imide 1 as a chiral proton source and the enolate was effectively protonated with up to 82% ee.