Carbonyl-carbonyl Interactions Research Articles

Experimental and theoretical analyses and investigation of intermolecular interactions and antibacterial activity of a novel proton transfer compound:8-hydroxyquinolinium oxalate monohydrate

A novel proton transfer compound, 8-hydroxyquinolinium oxalate monohydrate was synthesised by solid state grinding of 8-hydroxyquinoline and oxalic acid. The resulting compound is characterised by single crystal X-ray diffraction (SXRD), FT-IR, UV–Visible, TG/DTG, DTA and DSC analyses. The compound crystallizes in monoclinic crystal system with space group P21/n. The carboxylate oxygen O2 which acts as a tetrafurcated acceptor of four hydrogen bonds is the main feature of the crystal structure. The molecules are linked together by O–H⋯O, N–H⋯O and C–H⋯O hydrogen bonds. Carbonyl-carbonyl interactions play a crucial role in stabilising the crystal packing. Hirshfeld surface analysis and the associated finger print plots facilitates the comparison of intermolecular interactions. The nature of charge density distribution and topological parameters of the proton transfer region N1–H1A⋯O2 hydrogen bond reveals that the bond has considerable covalent character. Natural Bond Orbital (NBO) has been extended to analyse the nature and strength of intermolecular interactions. Topology analysis using ELF and LOL reveals electron localisation and depletion regions. ADMET analysis reveals that the compound satisfies Lipinski’s rule of five and drug likeness. Antibacterial activity was screened against 3 g positive - Bacillus subtilis, Enterococcus faecalis, Staphylococcus aureus and 2 g negative strains- Klebsiella pneumonia and Salmonella typhi by employing disc diffusion method.

Synthesis and Characterization of Novel [2 + 1] Tricarbonyl Rhenium Complexes with the Hydrophilic Phosphine Ligands PTA and CAP.

In the pursuit of hydrophilic model fac-[Re(CO)3]+ complexes for (radio) pharmaceutical applications, six novel [2 + 1] mixed-ligand complexes of the general type fac-[Re(CO)3(bid)P] were synthesized and characterized, where bid is a bidentate ligand bearing either (N, O) or (S, S′) donor atom sets and P is the hydrophilic phosphine 1,3,5-triaza-7-phosphoadamantane (PTA) or its macrocyclic homologue 1,4,7-triaza-9-phosphatricyclo[5.3.2.1]tridecane (CAP). The (N, O) ligands used in this study were picolinic and quinaldic acid, while the (S, S′) ligand was diethyldithiocarbamate. The complexes were synthesized in generally high yields and purity and the characterization was performed by spectroscopic methods, IR, NMR, and elemental analysis. Detailed X-ray crystallographic study of molecular packing by using Hirshfeld analysis tools revealed a plethora of intermolecular interactions such as hydrogen bond, π⋯π, C-H⋯π, and carbonyl-carbonyl interactions. To our knowledge, the CAP complexes reported herein are the first example of [2 + 1] mixed-ligand fac-[Re(CO)3]+ complexes with CAP. The new complexes might have the potential to serve as platforms for the design of target-specific complexes with favorable pharmacokinetics.

Intermolecular Carbonyl···Carbonyl Interactions in Transition-Metal Complexes.

We performed a comprehensive analysis of intermolecular carbonyl-carbonyl interactions in transition-metal complexes. Those interactions can be classified in two main types depending on the organometallic or organic nature of the donor carbonyl: M-CO···CO and R-CO···CO, respectively. By means of a combined structural and computational study we unraveled their geometrical features and strength. Moreover, electronic structure, natural bond orbitals, energy decomposition analysis, and quantum theory of atoms in molecules calculations were performed to try to understand their nature. Remarkably, we discovered that these carbonyl-carbonyl contacts have several features of the n → π* interaction. The charge transfer from an oxygen lone pair to an empty antibonding π orbital of the acceptor carbonyl is also accompanied by an electrostatic Oδ-···Cδ+ interaction. To the best of our knowledge this is the first report of an intermolecular n → π* interaction in metal complexes. These results might be significant, for instance, for the catalytic activation of carbonyl-containing small molecules with metal compounds or in the design of hybrid organic-inorganic materials, metal-organic frameworks, and other extended structures.

Reciprocal carbonyl\u2013carbonyl interactions in small molecules and proteins

Carbonyl-carbonyl n→π* interactions where a lone pair (n) of the oxygen atom of a carbonyl group is delocalized over the π* orbital of a nearby carbonyl group have attracted a lot of attention in recent years due to their ability to affect the 3D structure of small molecules, polyesters, peptides, and proteins. In this paper, we report the discovery of a “reciprocal” carbonyl-carbonyl interaction with substantial back and forth n→π* and π→π* electron delocalization between neighboring carbonyl groups. We have carried out experimental studies, analyses of crystallographic databases and theoretical calculations to show the presence of this interaction in both small molecules and proteins. In proteins, these interactions are primarily found in polyproline II (PPII) helices. As PPII are the most abundant secondary structures in unfolded proteins, we propose that these local interactions may have implications in protein folding.

Conformational analysis of short polar side-chain amino-acids through umbrella sampling and DFT calculations.

Molecular and quantum mechanics calculations were carried out in a series of tripeptides (GXG, where X = D, N and C) as models of the unfolded states of proteins. The selected central amino acids, especially aspartic acid (D) and asparagine (N) are known to present significant average conformations in partially allowed areas of the Ramachandran plot, which have been suggested to be important in unfolded protein regions. In this report, we present the calculation of the propensity values through an umbrella sampling procedure in combination with the calculation of the NMR J-coupling constants obtained by a DFT model. The experimental NMR observations can be reasonably explained in terms of a conformational distribution where PPII and β basins sum up propensities above 0.9. The conformational analysis of the side chain dihedral angle (χ1), along with the computation of 3J(HαHβ), revealed a preference for the g - and g + rotamers. These may be connected with the presence of intermolecular H-bonding and carbonyl-carbonyl interactions sampled in the PPII and β basins. Taking into account all those results, it can be established that these residues show a similar behavior to other amino acids in short peptides regarding backbone φ,ψ dihedral angle distribution, in agreement with some experimental analysis of capped dipeptides.

A Unique Conformational Behaviour of Glutamine Peptides

Trinucleotide repeat expansions (CAG) lead to increase in glutamine residues and hence increase in glutamine stretch. This leads to number of neurodegenerative diseases. Therefore, the conformation of poly Q of varying chain lengths has been investigated by quantum mechanical and molecular dynamics approaches. Glutamine contains amide linkage in the side chain. It is the interaction between side chain amide linkage and the peptide bond of the backbone which dictates the conformational behaviour. Some of the glutamine residues adopt phi psi values corresponding to poly-L-proline type II structure. Not more than three glutamine residues are found to have the same set of values and hence polyglutamine is adopting random coil structure. Carbonyl-carbonyl, CH-O interactions and hydrogen bond formation involving backbone and side chain amide chain linkages are found to contribute to the stability of the adopted structure. In simulation studies due to interaction of water molecules with the amide linkages the values undergo change and this leads to weakening of carbonyl-carbonyl interactions and hydrogen bonds. The conformational behaviour of polyglutamine peptides is shown to be chain length dependent and this may provide some insight regarding the aggregation behaviour of proteins containing poly Q stretch. Possibly this is the first systematic study of the conformational behaviour of polyglutamine peptides.

An n→π* interaction reduces the electrophilicity of the acceptor carbonyl group

Carbonyl-carbonyl (C=O···C'=O') interactions are ubiquitous in both small and large molecular systems. This interaction involves delocalization of a lone pair (n) of a donor oxygen into the antibonding orbital (π*) of an acceptor carbonyl group. Analyses of high-resolution protein structures suggest that these carbonyl-carbonyl interactions prefer to occur in pairs, that is, one donor per acceptor. Here, the reluctance of the acceptor carbonyl group (C'=O') to engage in more than one n→π* electron delocalization is probed using imidazolidine-based model systems with one acceptor carbonyl group and two equivalent donor carbonyl groups. The data indicate that the electrophilicity of the acceptor carbonyl group is reduced when it engages in n→π* electron delocalization. This diminished electrophilicity discourages a second n→π* interaction with the acceptor carbonyl group.

Conformational behavior of stereo regular substituted polyglycolides is side chain dependent

Substituted polyglycolides having two asymmetric centers are attractive alternatives to materials derived from petroleum because of their biocompatibility and biodegradability. The conformational behavior of various substituted polyglycolides has been investigated by both quantum mechanical and molecular dynamics approaches. Polymethylglycolide (polylactide) and polyphenylmethylglycolide in RS or SR forms are predicted to adopt 27 ribbon type structures with φ, ψ values of ±30, ±50 or +30 or +50 respectively stabilised by carbonyl-carbonyl interactions. Isopropylglycolide and isobutyl-glycolide having branching at β & γ positions respectively in their side chains can be realized in all SS form with φ, ψ values lying in right handed helical region. In addition to carbonyl-carbonyl interactions, the hydrophobic interactions between the side chains in isopropylgly-colide the C-H-O interactions also contributes to the stability. With cyclic side chains directly attached to Cα of backbone, polyphenylglycolide (polymandelide) and polycyclohexylglycolide are found to adopt left handed helical structure without hydrogen bonds in RR form, stabilised by stacking interactions and hydrophobic interactions respectively. In all the forms of polyphenylglycolide & polycyclohexylglycolide, the cyclic side chains are found to be locked into unfavourable gauche plus conformation. The stability of substituted polyglycolides has been analyzed in terms of various interactions. The carbonyl-carbonyl interactions in all the conformations of all forms of substituted polyglycolides are found to be of highly shielded parallel motif with only one short carbon-oxygen interaction. Simulation studies of substituted polyglycolides in water give a good insight of the approach of water molecules to the backbone.

Peptoids with aliphatic sidechains as helical structures without hydrogen bonds and collagen/ inverse-collagen type structures

Aliphatic homo-polypeptoids of NAla, NVal, NIle and NLeu both in the presence and absence of protecting groups adopt helical structures without hydrogen bonds with Φ, Ψ values of ~ 0, ± 90° with trans amide bonds. These structures are stabilized by carbonyl-carbonyl interactions and characterized by ~ 3.16 residues per turn with a pitch of ~ 6.13 Å. It has been shown that like polyvaline and polyleucine peptides, poly-peptoids can also be exploited for the construction of potential surfactant like molecules by incorporating charged amino acid residues at the N terminal. A single-handed template with Φ, Ψ values of ~ 0, 90° can be attained by incorporating L-leu or L-val at the C-terminal of poly-NIle. Analysis of the simulation results in water as a function of time reveals that the opening of helical structures without hydrogen bonds takes place at sub-picosecond time scale starting from the N-terminal. This leads to the formation of collagen or inverse-collagen type structures (Φ, Ψ ~ -60, 145° and 60, -145° respectively) stabilized by interactions of water molecules with the backbone carbonyl groups.

Control of Channel Size for Selective Guest Inclusion with Inlaid Anionic Building Blocks in a Porous Cationic Metal–Organic Host Framework

Step by step: By attaching anionic building blocks of variable bulk to a cationic metal-organic framework, stepwise channel-size adjustment of the resulting porous three-dimensional host framework is achieved (see picture). This method is a new and viable approach for materials with predesigned nanopores for application in molecular recognition and selective guest inclusion.Through the introduction of perfluorocarboxylates as counteranions that line the inner surface of each channel in a host cationic metal-organic open framework, stepwise channel-size control has been realized, resulting in wide guest compatibility for [{Ag(L)(CF(3)CO(2))}(6)6 G](infinity) (1 supersetG; G=guest, L=ligand), selective guest recognition for [{Ag(L)(C(2)F(5)CO(2))}(6)4 G'](infinity) (2 supersetG'), and a lack of inclusion behavior for [{Ag(L)(C(3)F(7)CO(2))}(6)](infinity) (3; G and G' represent the same or different guest molecules). The cationic frameworks in 1-3 are constructed from the linkage of hexameric inorganic-organic hybrid macrocycles through multiple argentophilic interaction plus pi-pi interactions between pyridyl rings and carbonyl-carbonyl interactions, to which corresponding counteranions are attached. With different anions as intrachannel arms, similar frameworks in complexes 1 supersetG, 2 supersetG', and 3 exhibit percentages of guest-accessible voids of approximately 30-35, 25, and 18 % for 1-3, respectively. The highly flexible framework 1 in 1 supersetG contains stretchable channels with up to 21.7 % effective-volume change of the solvent-accessible void for inclusion of various guest species in the series of solvates 1 a-m. The pair of complexes 1 supersetG and [Ag(L)(CF(3)CO(2))](infinity) (4), and likewise the pair 2 supersetG' and [Ag(L)(C(2)F(5)CO(2))](infinity) (5), are interconvertible through distinct controllable processes.

Nonmerohedrally twinned 6-amino-3-methyluracil-5-carbaldehyde: a hydrogen-bonded ribbon containing four types of ring

In the title compound [systematic name: 6-amino-5-formyl-3-methylpyrimidine-2,4(1H,3H)-dione], C(6)H(7)N(3)O(3), the intramolecular dimensions provide evidence for some polarization of the electronic structure. There is an intramolecular N-H...O hydrogen bond; this and a combination of three intermolecular N-H...O hydrogen bonds generate an almost planar ribbon containing S(6), R(2)(2)(4), R(2)(1)(6) and R(4)(4)(16) rings. These ribbons are linked into sheets by a dipolar carbonyl-carbonyl interaction. The structure was refined as a nonmerohedral twin, with twin fractions 0.7924 (1) and 0.2076 (10).

New Type of Helix and 27Ribbon Structure Formation in Poly ΔLeu Peptides: Construction of a Single-Handed Template

alpha,beta-Dehydroamino acid residues due to the presence of Calpha = Cbeta double bond influences the main chain and the side chain conformations. These residues have interesting chemical features including the increased resistance to enzymatic degradation. The chain length dependent conformational behavior of poly alpha,beta-dehydroleucine (DeltaLeu) peptides in both the pure forms Z and E and their various combinations like alternate ZE/EZ etc. have been investigated by using quantum mechanical method PCILO (perturbative configuration interaction of localized orbitals). The conformational states in alternate Z and E forms, with Phi, Psi values of -10 degrees , 105 degrees /1 degrees , -88 degrees for Z form and 35 degrees , 22 degrees /-34 degrees , -27 degrees for the E form are found to be the most stable and degenerate than the states in pure Z and E forms and the EZ form etc. The repeated Phi, Psi values give rise to altogether new types of left and right handed helices, and their stability increases with increasing chain length. These structures are stabilized by intramolecular hydrogen bonding, carbonyl-carbonyl interactions and hydrophobic interactions between the side chains of DeltaZLeu and DeltaELeu residues. The 2(7) ribbon structure (seven-membered hydrogen-bonded ring involving two consecutive amino acid residues) is found to be most stable and degenerate in the pentapeptide Ac-DeltaELeu5-NHMe, due to the formation of maximum hydrogen bonds. A right-handed template from achiral DeltaLeu peptides has been achieved by incorporating L-Leu at the C-terminal or D-Leu at the N-terminal.

(3S)-BenzylN-(1-hydroxy-2,5-dioxopyrrolidin-3-yl)carbamate: two-dimensional sheets built from O—H...O, N—H...O, C=O...C=O and C—H...O interactions linked into a three-dimensional complex frameworkviaC—H...π(arene) interactions

The title compound, C(10)H(12)O(5)N(2), crystallizes with two independent molecules in the asymmetric unit. The molecules in the crystal structure are arranged into one-dimensional substructural ribbon motifs stabilized by a combination of two O-H...O and three N-H...O intermolecular hydrogen bonds, and also augmented by short C=O...C=O carbonyl-carbonyl interactions. Two intermolecular C-H...O short contacts between adjacent ribbons generate complex two-dimensional sheets on the ab plane. Adjacent sheets are linked via C-H...pi(arene) interactions, resulting in a complex three-dimensional framework.

Carbonyl-carbonyl interactions in first-row transition metal complexes

Carbonyl-carbonyl interactions in first-row transition metal complexes

Chains of edge-fused hydrogen-bondedR33(12) rings inN-phenyl-4-nitrophthalimide

Molecules of the title compound [systematic name: 5-nitro-1H-isoindole-1,3(2H)-dione], C14H8N2O4, adopt a conformation in the solid state which renders them chiral, and they are linked by three distinct types of direction-specific intermolecular interaction. The molecules are linked by two C-H...O hydrogen bonds [H...O = 2.50 and 2.52 A, C...O = 3.118 (7) and 3.294 (7) A, and C-H...O = 123 and 139 degrees ] into chains of edge-fused R(3)(3) (12) rings, which are themselves weakly linked into sheets by a combination of an aromatic pi-pi stacking interaction and a sheared-parallel carbonyl-carbonyl interaction.

Conformation of peptides constructed from achiral amino acid residues Aib and ΔZPhe: Computational study of the effect of L/D‐ Leu at terminal positions

Conformational studies of the peptides constructed from achiral amino acid residues Aib and Delta(Z)Phe (I) Ac-Aib-Delta(Z)Phe-NHMe (II), and Ac-(Aib-Delta(Z)Phe)(3)-NHMe; peptides III-VI having L-Leu or D-Leu at either the N- or the C-terminal position and of peptides VII-X having Leu residues in different enantiomeric combinations at both the N- and the C-terminal positions in peptide II have been studied to design the peptide with the required helical sense. Peptide II, as expected, adopts degenerate left- and right-handed helical structures. It has been shown that the peptides IV and VI having D-Leu at either the N or the C terminus can be realized in the right-handed helical structure with the phi,psi values of -20 degrees and -60 degrees for the Aib/Delta(Z)Phe residues. L-Leu and D- Leu at both the terminals in peptides VII and VIII, respectively, have hardly any effect as both the left- and the right-handed structures are found to be degenerate. Peptides III and IX can be realized in right- and left-handed helical structures, respectively, in solvents of low polarity whereas peptides V and X are predicted to be in the right-handed helical structures stabilized by carbonyl-carbonyl interactions without the formation of hydrogen bonds. The conformational states with the phi,psi values of 0 degrees and -85 degrees in peptide V are characterized by rise per residue of 2.03 A, rotation per residue of 117.5 degrees , and 3.06 residues per turn. In all peptides having Leu residue at the N terminus, the methyl moiety of the acetyl group is involved in the CH/pi interactions with the Cepsilon--Cdelta edge of the aromatic ring of Delta(Z)Phe (3) and the amino group NH of Delta(Z)Phe is involved in the NH/pi interactions with its own aromatic ring. The CH(3) groups of the Aib residues are also involved in CH/pi interactions with the i + 1th and i + 3th Delta(Z)Phe's aromatic side chains.

The sesquiterpenoid nootkatone and the absolute configuration of a dibromo derivative.

Nootkatone, or (4R,4aS,6R)-4,4a,5,6,7,8-hexahydro-4,4a-dimethyl-6-(1-methylethenyl)naphthalen-2(3H)-one, C(15)H(22)O, a sesquiterpene with strong repellent properties against Formosan subterranean termites and other insects, has the valencene skeleton. The dibromo derivative (1S,3R,4S,4aS,6R,8aR)-1,3-dibromo-6-isopropyl-4,4a-dimethyl-1,2,3,4,5,6,7,8-octahydronaphthalen-2-one, C(15)H(24)Br(2)O, has two independent molecules in the asymmetric unit, which differ in the rotation of the isopropyl group with respect to the main skeleton. The C-Br distances are in the range 1.950 (4)-1.960 (4) A. Both independent molecules form zigzag chains, with very short intermolecular carbonyl-carbonyl interactions, having the perpendicular motif and O...C distances of 2.886 (6) and 2.898 (6) A. These chains are flanked by intermolecular Br...Br interactions of distances in the range 4.067 (1)-4.218 (1) A. The absolute configuration of the dibromo derivative was determined, from which that of nootkatone was inferred.

Use of Relibase for retrieving complex three-dimensional interaction patterns including crystallographic packing effects.

Relibase is a database system that has been specially designed to handle protein-ligand data. Included within Relibase is a tool that can be used to systematically analyse protein-ligand interaction patterns specified by three-dimensional (3D) constraints, revealing favorable combinations of interacting functional groups and their preferred interaction geometries. This paper describes the Relibase 3D query tools, including novel extensions (Relibase+) for handling crystallographic packing effects. Examples illustrating the broad range of functionality for defining 3D interaction patterns and the application of such queries in drug design comprise carbonyl-carbonyl interactions, zinc binding site environments, and ligand-ligand interactions in the crystal packing.

Carbonyl-carbonyl interactions stabilize the partially allowed Ramachandran conformations of asparagine and aspartic acid.

Asparagine and aspartate are known to adopt conformations in the left-handed alpha-helical region and other partially allowed regions of the Ramachandran plot more readily than any other non-glycyl amino acids. The reason for this preference has not been established. An examination of the local environments of asparagine and aspartic acid in protein structures with a resolution better than 1.5 A revealed that their side-chain carbonyls are frequently within 4 A of their own backbone carbonyl or the backbone carbonyl of the previous residue. Calculations using protein structures with a resolution better than 1.8 A reveal that this close contact occurs in more than 80% of cases. This carbonyl-carbonyl interaction offers an energetic sabilization for the partially allowed conformations of asparagine and aspartic acid with respect to all other non-glycyl amino acids. The non-covalent attractive interactions between the dipoles of two carbonyls has recently been calculated to have an energy comparable to that of a hydrogen bond. The preponderance of asparagine in the left-handed alpha-helical region, and in general of aspartic acid and asparagine in the partially allowed regions of the Ramachandran plot, may be a consequence of this carbonyl-carbonyl stacking interaction.

Coulombic interactions between partially charged main-chain atoms not hydrogen-bonded to each other influence the conformations of α-helices and antiparallel β-sheet. A new method for analysing the forces between hydrogen bonding groups in proteins includes all the Coulombic interactions

An angle named γ has been employed to describe the geometry at a hydrogen bond between main-chain atoms of polypeptides. In antiparallel β-sheet, γ is normally positive, whereas, in parallel β-sheet and α-helices, it is negative. Although intriguing, no particular explanation has been offered to explain this result. We provide evidence that, in each case, the angular preference maximises the favourable Coulombic interaction between the partial negative charge on the carbonyl oxygen atom and the partial positive charge on the carbonyl carbon atom adjacent to the NH group to which it is hydrogen-bonded. Analyses of helices and β-sheets in native proteins using Lennard-Jones potentials suggest that these carbonyl-carbonyl interactions are significant components of the attractive forces holding main-chain CONH groups together and are even in some cases larger than the hydrogen bonds themselves. A novel technique for analysing the forces holding together hydrogen bonding groups in proteins is presented. It can be regarded as a development of the Kabsch and Sander method of calculating the energy of hydrogen bonds between main-chain atoms. In their program, electrostatic interactions are calculated between appropriate pairs of atoms, i.e. NH binding to CO. Instead, in our method, the four N, H, C, and O atoms, in a peptide bond are taken as a unit and the interaction between two NHCO groups calculated. We also use a Lennard-Jones potential, rather than just measuring the Coulombic interaction. With this approach, account is taken of all types of interactions between partially charged atoms, not only the hydrogen bonds.