Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions

Looking Inside the Intramolecular C-H∙∙∙O Hydrogen Bond in Lactams Derived from α-Methylbenzylamine

Recently, strong evidence that supports the presence of an intramolecular C−H···O hydrogen bond in amides derived from the chiral auxiliary α-methylbenzylamine was disclosed. Due to the high importance of this chiral auxiliary in asymmetric synthesis, the inadvertent presence of this C−H···O interaction may lead to new interpretations upon stereochemical models in which this chiral auxiliary is present. Therefore, a series of lactams containing the chiral auxiliary α-methylbenzylamine (from three to eight-membered ring) were theoretically studied at the MP2/cc-pVDZ level of theory with the purpose of studying the origin and nature of the C−Hα···O interaction. NBO analysis revealed that rehybridization at C atom of the C−Hα bond (s-character at C is ~23%) and the subsequent bond polarization are the dominant effect over the orbital interaction energy n_(O)→σ*_C−Hα (E(2) < 2 kcal/mol), causing an important shortening of the C−Hα bond distance and an increment in the positive charge in the Hα atom.

New insights into the chemistry of ionic alkylorganic carbonates: a computational study

A library of hydrogenated, perfluorinated aliphatic and aromatic alcohols are selected together with a combination of superbases and metal hydrides to understand the thermodynamics of the binary mixtures once serving as sorbents for the capture of CO₂via ionic organic alkylcarbonate formation.

Conformational differences and intermolecular C-H...N interactions in three polymorphs of a bis(pyridinyl)-substituted benzimidazole

The structural characterization of several polymorphic forms of a compound allow the interplay between molecular conformation and intermolecular interactions to be studied, which can contribute to the development of strategies for the rational preparation of materials with desirable properties and the tailoring of intermolecular interactions to produce solids with predictable characteristics of interest in crystal engineering. The crystal structures of two new polymorphs of 5,6-dimethyl-2-(pyridin-2-yl)-1-[(pyridin-2-yl)methyl]-1H-benzimidazole, C₂₀H₁₈N₄, are reported. The previously reported polymorph, (1) [Geiger & DeStefano (2014). Acta Cryst. E70, o365], exhibits the space group C2/c, whereas polymorphs (2) and (3) presented here are in the Pnma and P-1 space groups, respectively. The molecular structures of the three forms differ in their orientations of the 2-(pyridin-2-yl)- and 1-[(pyridin-2-yl)methyl]- substituents. Density functional theory (DFT) calculations show that the relative energies of the molecule in the three conformations follows the order (1) < (2) < (3), with a spread of 10.6 kJ mol^-1. An analysis of the Hirshfeld surfaces shows that the three polymorphs exhibit intermolecular C-H...N interactions, which can be classified into six types. Based on DFT calculations involving pairs of molecules having the observed interactions, the C-H...N energy in the systems explored is approximately -11.2 to -14.4 kJ mol^-1.

A theoretical study of weak interactions in phenylenediamine homodimer clusters

Utilizing dispersion-corrected density functional theory (DFT) calculations, we demonstrate the weak intermolecular interactions of phenylenediamine dimer (pdd) clusters, emphasizing the local lowest energy structures and decomposition of interaction energies by natural bond orbital (NBO) and atoms in molecule (AIM) analyses.

Noncovalent interactions between the second coordination sphere and the active site of [NiFeSe] hydrogenase

QM/MM studies on seven truncated models of the oxidized as-isolated state of the [NiFeSe] Hases reveal the influence of the residues in the second coordination sphere on the active site.

Influence of the protonation of pyridine nitrogen on pnicogen bonding: competition and cooperativity

Ab initio MP2/aug-cc-pVTZ calculations were performed to investigate the pnicogen-bonded complexes of PyZX₂ (Py = pyridine, Z = P and As, X = H and F) and their protonated analogues.

Weak interactions within nitryl halide heterodimers

Nitryl halides (XNO₂, X = F, Cl, Br and I) are versatile molecules that exhibit several types of interactions within XNO₂:YNO₂ heterodimers mainly governed by dispersion.

Computational evidence that hyperconjugative orbital interactions are responsible for the stability of intramolecular Te⋯O/Te⋯S non-covalent interactions and comparable to hydrogen bonds in quasi-cyclic systems

The intramolecular secondary bonding interactions involving quasi-cyclic tellurium are comparable to H-bond strength and partially governed by orbital interactions.

Weak backbone CH⋯OC and side chain tBu⋯tBu London interactions help promote helix folding of achiral NtBu peptoids

The synthesis and helix folding propensity of achiral all-cis amide (NtBu)-glycine oligomers is reported.

Novel pnicogen bonding interactions with silylene as an electron donor: covalency, unusual substituent effects and new mechanisms

An analogue of carbene, singlet silylene (H3P=N)2Si, was paired with the mono-substituted phosphines XH2Y (X = P, As, and Sb; Y = F, Cl, Br, and I) to form unconventional pnicogen-bonded complexes. All structures have Cs symmetry except the Sb complex, showing a deviation from this symmetry due to the coexistence of H···H interactions. The P and As complexes have different geometries from conventional pnicogen-bonded ones because the Y-X···Si line shows a large deviation from the molecular plane composed of two N atoms and one Si atom of (H3P=N)2Si. This deviation can be attributed to a new formation mechanism of the pnicogen bond due to the combined result of the LPSi→ BD*X-Y and LPX→ LP*Si orbital interactions. Generally, the pnicogen bond becomes stronger in the order of F < Cl < Br < I and weaker in the order of P > As > Sb, exhibiting an unexpected substitution effect and dependence on the nature of the pnicogen atom. These orders are inconsistent with the MEP on the X atom but can be better explained by the above orbital interactions. The Si···X interaction displays a character of covalent or partially covalent interaction, evidenced by the high interaction energy of -59.9 to -105.4 kJ mol(-1) as well as the negative energy density and the great charge transfer.

Linking protein motion to enzyme catalysis

Enzyme motions on a broad range of time scales can play an important role in various intra- and intermolecular events, including substrate binding, catalysis of the chemical conversion, and product release. The relationship between protein motions and catalytic activity is of contemporary interest in enzymology. To understand the factors influencing the rates of enzyme-catalyzed reactions, the dynamics of the protein-solvent-ligand complex must be considered. The current review presents two case studies of enzymes—dihydrofolate reductase (DHFR) and thymidylate synthase (TSase)—and discusses the role of protein motions in their catalyzed reactions. Specifically, we will discuss the utility of kinetic isotope effects (KIEs) and their temperature dependence as tools in probing such phenomena.

Theoretical calculations of π-type pnicogen bonds in the triad intermolecular complexes

The pnicogen bonding interactions of PCl3and π-electron systems (acetylene, ethylene, benzene) were calculated by using MP2/aug-cc-pVDZ method and the effect of hydrogen bond on pnicogen bond systems were investigated. It has been indicated that the hydrogen bonding and the pnicogen bonding interactions have influence on each other and the positively cooperative effect has been detected. The interaction energies of pnicogen bonded supramolecular system were also calculated by using DFT method (M06-2X) and some simple comparisons with those by using MP2 method were made. It has been disclosed from natural bond orbitals (NBO) analysis that more the amount of charge transfer of pnicogen bonding interaction, the greater the stability of the corresponding complex. Through AIM topological analysis, it has been revealed that the electron density of pnicogen bond BCP point is positively correlated with the stability of trimeric complex. Electron localization function (ELF) was also adopted to analyze the nature of pnicogen bonding interactions. Furthermore, density difference function (DDF) method was adopted to analyze the variation of electron density of pnicogen bond system because of hydrogen bond.

Halogen, chalcogen and pnictogen interactions in (XNO2)2homodimers (X = F, Cl, Br, I)

XNO₂(X = F, Cl, Br and I) homodimers present a large variety of interactions. A combination of pnictogen and chalcogen is stronger than single halogen bonds.

Crystallographic and computational investigation of intermolecular interactions involving organic fluorine with relevance to the hybridization of the carbon atom

C–H⋯F–C interaction on the basis of hybridization of the carbon atom participating in the interaction has been analyzed by performing statistical studies using CSD, evaluating the energetics using PIXEL and performing a topological analysis using AIMALL.

Identification of unusual C–Cl⋯π contacts in 2-(alkylamino)-3-chloro-1,4-naphthoquinones: effect of N-substituents on crystal packing, fluorescence, redox and anti-microbial properties

XRD study demonstrates the opening of unusual C–Cl⋯π synthon in 2-(alkylamino)-3-chloro-1,4-naphthoquinone. Notably, compound holding N-pyridylmethyl exhibits enhanced activity against S. aureus and proved to be more potent than ciprofloxacin.

Pnicogen and hydrogen bonds: complexes between PH3X+ and PH2X systems

The charge-assisted complexes between PH₃X⁺ and PH₂X show three potential minima structures, the pnicogen bonded (I) one being the most stable.

The dual role of pnicogen as Lewis acid and base and the unexpected interplay between the pnicogen bond and coordination interaction in H3N⋯FH2X⋯MCN (X = P and As; M = Cu, Ag, and Au)

Ternary systems H₃N⋯FH₂X⋯MCN (X = P and As; M = Cu, Ag, and Au) as well as the corresponding pnicogen-bonded and coordination-bonded binary systems have been studied.

On the properties of S⋯O and S⋯π noncovalent interactions: the analysis of geometry, interaction energy and electron density

We report computational studies on the origin and magnitude of non-covalent S⋯O and S⋯π interactions.

Structural and thermodynamic properties of water-membrane interphases: significance for peptide/membrane interactions

Water appears as a common intermediary in the mechanisms of interaction of proteins and polypeptides with membranes of different lipid composition. In this review, how water modulates the interaction of peptides and proteins with lipid membranes is discussed by correlating the thermodynamic response and the structural changes of water at the membrane interphases. The thermodynamic properties of the lipid-protein interaction are governed by changes in the water activity of monolayers of different lipid composition according to the lateral surface pressure. In this context, different water populations can be characterized below and above the phase transition temperature in relation to the CH₂ conformers' states in the acyl chains. According to water species present at the interphase, lipid membrane acts as a water state regulator, which determines the interfacial water domains in the surface. It is proposed that those domains are formed by the contact between lipids themselves and between lipids and the water phase, which are needed to trigger adsorption-insertion processes. The water domains are essential to maintain functional dynamical properties and are formed by water beyond the hydration shell of the lipid head groups. These confined water domains probably carries information in local units in relation to the lipid composition thus accounting for the link between lipidomics and aquaomics. The analysis of these results contributes to a new insight of the lipid bilayer as a non-autonomous, responsive (reactive) structure that correlates with the dynamical properties of a living system.

Concentration-dependent dynamics of hydrogen bonding between acetonitrile and methanol as determined by 1D vibrational spectroscopy

Solutions of acetonitrile (MeCN) in methanol (MeOH) at various concentrations have been investigated by variable temperature Raman spectroscopy. In the ν(CN) region of the spectrum, the variable temperature spectra at each concentration show two overlapping bands from hydrogen bound and free MeCN. These two species undergo dynamic exchange that gives rise to increasing coalescence of the two bands with increasing temperature. By simulation of the band shape, the rate of exchange was determined at each temperature. Arrhenius plots yielded values for the activation energy, Ea, and the natural log of the pre-exponential factor, ln[A/s(-1)], for the hydrogen bond formation/cleavage. Both of these dynamic parameters were found to depend on the relative amounts of MeCN and MeOH in the solutions. In particular, two different concentration regimes of dynamic hydrogen bonding were observed. First, at low MeCN concentration, the dynamics are largely independent of changes in MeCN concentration. Second, at higher MeCN concentration (above ∼0.2 MeCN mole fraction) the dynamics are strongly dependent on further increases of MeCN content. Over the range of MeCN mole fractions that we studied (0.03-0.5), the ln[A/s(-1)] changes from 32.5 ± 0.1 to 30.1 ± 0.2 and Ea changes from 3.73 ± 0.08 to 2.7 ± 0.1 kcal/mol. We suggest the observed changes in dynamics arise from changes in the local solvent microstructure that occur above a critical mole fraction of MeCN.

C-H…O hydrogen bonds in FK506-binding protein-ligand interactions

Hydrogen bonds are important interaction forces observed in protein structures. They can be classified as stronger or weaker depending on their energy, thereby reflecting on the type of donor. The contribution of weak hydrogen bonds is deemed as an important factor toward structure stability along with the stronger bonds. One such bond, the C-H…O type hydrogen bond, is shown to make a contribution in maintaining three dimensional structures of proteins. Apart from their presence within protein structures, the role of these bonds in protein-ligand interactions is also noteworthy. In this study, we present a statistical analysis on the presence of C-H…O hydrogen bonds observed between FKBPs and their cognate ligands. The FK506-binding proteins (FKBPs) carry peptidyl cis-trans isomerase activity apart from the immunosuppressive property by binding to the immunosuppressive drugs FK506 or rapamycin. Because the active site of FKBPs is lined up by many hydrophobic residues, we speculated that the prevalence of C-H…O hydrogen bonds will be considerable. In a total of 25 structures analyzed, a higher frequency of C-H…O hydrogen bonds is observed in comparison with the stronger hydrogen bonds. These C-H…O hydrogen bonds are dominated by a highly conserved donor, the C(α/β) of Val55 and an acceptor, the backbone oxygen of Glu54. Both these residues are positioned in the β4-α1 loop, whereas the other residues Tyr26, Phe36 and Phe99 with higher frequencies are lined up at the opposite face of the active site. These preferences could be implicated in FKBP pharmacophore models toward enhancing the ligand affinity. This study could be a prelude to studying other proteins with hydrophobic pockets to gain better insights into ligand recognition.

Pnicogen bonds between X═PH3 (X = O, S, NH, CH2) and phosphorus and nitrogen bases

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the pnicogen bonded complexes formed between the acids O═PH3, S═PH3, HN═PH3, and H2C═PH3 and the bases NH3, NCH, N2, PH3, and PCH. All nitrogen and phosphorus bases form complexes in which the bases are lone pair electron donors. The binding energies of complexes involving the stronger bases NH3, NCH, and PH3 differentiate among the acids, but the binding energies of complexes with the weaker bases do not. These complexes are stabilized by charge transfer from the lone pair orbital of N or P to the σ*P═A orbital of X═PH3, where A is the atom of X directly bonded to P. PCH also forms complexes with the X═PH3 acids as a π electron donor to the σ*P═A orbital. The binding energies and the charge-transfer energies of the π complexes are greater than those of the complexes in which PCH is a lone pair donor. Whether the positive charge on P increases, decreases, or remains the same upon complex formation, the chemical shieldings of (31)P decrease in the complexes relative to the corresponding monomers. (1p)J(P-N) and (1p)J(P-P) values correlate best with the corresponding P-N and P-P distances as a function of the nature of the base. (1)J(P-A) values do not correlate with P-A distances. Rather, the absolute values of (1)J(P-O), (1)J(P-S), and (1)J(P-N) decrease upon complexation. Decreasing (1)J(P-A) values correlate linearly with increasing complex binding energies. In contrast, (1)J(P-C) values increase upon complexation and correlate linearly with increasing binding energies.