Topological analysis of aromatic halogen/hydrogen bonds by electron charge density and electrostatic potentials

In this work, the intermolecular distribution of the electronic charge density in the aromatic hydrogen/halogen bonds is studied within the framework of the atoms in molecules (AIM) theory and the molecular electrostatic potentials (MEP) analysis. The study is carried out in nine complexes formed between benzene and simple lineal molecules, where hydrogen, fluorine and chlorine atoms act as bridge atoms. All the results are obtained at MP2 level theory using cc-pVTZ basis set. Attention is focused on topological features observed at the intermolecular region such as bond, ring and cage critical points of the electron density, as well as the bond path, the gradient of the density maps, molecular graphs and interatomic surfaces. The strength of the interaction increases in the following order: F⋅⋅⋅π < Cl⋅⋅⋅π < H⋅⋅⋅π. Our results show that the fluorine atom has the capability to interact with the π−cloud to form an aromatic halogen bond, as long as the donor group is highly electron withdrawing. The Laplacian topology allows us to state that the halogen atoms can act as nucleophiles as well as electrophiles, showing clearly their dual character.     

Characteristics of beryllium bonds; a QTAIM study

The nature of beryllium bonds formed between BeX2 (X is H, F and Cl) and some Lewis bases have been investigated. The distribution of the Laplacian of electron density shows that there is a region of charge depletion around the Be atom, which, according to Laplacian complementary principal, can interact with a region of charge concentration of an atom in the base and form a beryllium bond. The molecular graphs of the investigated complexes indicate that beryllium in BeH2 and BeF2 can form “beryllium bonds” with O, N and P atoms but not with halogens. In addition, eight criteria based on QTAIM properties, including the values of electron density and its Laplacian at the BCP, penetration of beryllium and acceptor atom, charge, energy, volume and first atomic moment of beryllium atom, have been considered and compared with the corresponding ones in conventional hydrogen bonds. These bonds share many common features with very strong hydrogen bonds, however,some differences have also been observed.     

Predicting pharmacophore signals for post-coital antifertility activity of 1-trifluoromethyl-1,2,2-triphenylethylene derivatives: a statistical approximation using E-state index

Considering the worth of developing non-steroidal estrogen analogues, the present research explores the pharmacophores of 1-trifluoromethyl-1,2,2-triphenylethylenes (Fig. 1) for post-coital antifertility activity using electrotopological state atom (E-state) index. The study shows the efficacy of E-state index in developing statistically acceptable model, which explains the electronic environment and topological states of different atoms in a molecule. The exploration concluded that phenyl ring attached to an ethylenic moiety, para substitution by nucleophilic group on the phenyl ring and presence of strong electronegative group as the 4th substituent on the 1st carbon of the ethylenic moiety might be crucial for activity.     

Experimental charge density of sucrose at 20K: bond topological, atomic, and intermolecular quantitative properties

The charge density of sucrose was determined from a high-resolution X-ray data set measured at 20 K. The density distribution so obtained was analyzed quantitatively by application of Bader’s atoms in molecules (AIM) formalism, and a comparison was made with corresponding results from a B3LYP (6-311++G(3df,3pd)) calculation at the experimental geometry. Bond topological and atomic properties (volumes and charges) were derived and compared. The influence of hydrogen bonding on the experimental charge density was also studied qualitatively and quantitatively by means of topological properties. In terms of the hydrogen-bond energies, a grouping into strong, medium and very weak hydrogen bonds was made, the latter of which were involved in a bifurcated bond.     

Pheromone binding proteins of Epiphyas postvittana (Lepidoptera: Tortricidae) are encoded at a single locus

The light brown apple moth, Epiphyas postvittana (Tortricidae: Lepidoptera) uses a blend of (E)-11-tetradecenyl acetate and (E,E)-9,11-tetradecadienyl acetate as its sex pheromone. Odorant binding proteins, abundant in the antennae of male and female E. postvittana, were separated by native PAGE to reveal four major proteins with distinct mobilities. Microsequencing of their N-terminal residues showed that two were general odorant binding proteins (GOBPs) while two were pheromone binding proteins (PBPs). Full length cDNAs encoding these proteins were amplified using a combination of PCR and RACE-PCR. Sequence of the GOBPs revealed two genes (EposGOBP1, EposGOBP2), similar to orthologues in other species of Lepidoptera. Eleven cDNAs of the PBP gene were amplified, cloned and sequenced revealing two major phylogenetic clusters of PBP sequences differing by six amino acid substitutions. The position of the six amino acid differences on the protein was predicted by mapping onto the three-dimensional structure of PBP of Bombyx mori. All six substitutions were predicted to fall on the outside of the protein away from the inner pheromone binding pocket. One substitution does fall close to the putative dimerisation region of the protein (Ser63Thr). Expression of three of the cDNAs in a baculovirus expression system revealed that one class encodes an electrophoretically slow form (EposPBP1-12) while the other encodes a fast form (EposPBP1-2, EposPBP1-3). A native Western of these expressed proteins compared with antennal protein extracts demonstrated that PBP is also expressed in female antennae and that PBP may be present as a dimer as well as a monomer in E. postvittana. The fast and slow forms of EposPBP1 are allelic. Westerns on single antennal pair protein extracts and allele-specific PCR from genomic DNA both show a segregating pattern of inheritance in laboratory and wild populations. Radio labelled (E)-11-tetradecenyl acetate binds to both fast and slow PBP forms in gel assays. Taken together, the genetic and biochemical data do not support the hypothesis that these PBPs are specific for each component of the E. postvittana pheromone. However, duplication of this PBP locus in the future might allow such diversification to evolve, as observed in the other species.     

Evolution of noctuid pheromone binding proteins: identification of PBP in the black cutworm moth,Agrotis ipsilon

Male black cutworm moths (Agrotis ipsilon, Lepidoptera, Noctuoidea, Noctuidae), which are attracted by a three-component pheromone blend ((Z)-7-dodecenyl acetate, Z7-12:Ac; (Z)-9-tetradecenyl acetate, Z9-14:Ac; (Z)-11-hexadecenyl acetate, Z11-16:Ac), express diverse antennal pheromone binding proteins (PBPs). Two PBP isoforms (Aips-1 and Aips-2) that show 46% identity were cloned from antennal cDNA of male A. ipsilon. The protein Aips-1 displays a high degree of identity (70-95%) with PBPs of other noctuiids, but shows only 42-65% identity with the PBPs of more phylogenetically distant species. The other protein, Aips-2, represents a distinct group of PBP that includes proteins from Sphingidae and Yponomeutidae. These differences observed suggest that each of the two PBPs may be tuned to a specific pheromone ligand.     

Three pheromone-binding proteins in olfactory sensilla of the two silkmoth species Antheraea polyphemus and Antheraea pernyi.

Females of the sibling silkmoth species Antheraea polyphemus and A. pernyi use the same three sex pheromone components in different ratios to attract conspecific males. Accordingly, the sensory hairs on the antennae of males contain three receptor cells sensitive to each of the pheromone components. In agreement with the number of pheromones used, three different pheromone-binding proteins (PBPs) could be identified in pheromone-sensitive hairs of both species by combining biochemical and molecular cloning techniques. MALDI-TOF MS of sensillum lymph droplets from pheromone-sensitive sensilla trichodea of male A. polyphemus revealed the presence of three major peaks with m/z of 15702, 15752 and 15780 and two minor peaks of m/z 15963 and 15983. In Western blots with four antisera raised against different silkmoth odorant-binding proteins, immunoreactivity was found only with an anti-(Apol PBP) serum. Free-flow IEF, ion-exchange chromatography and Western blot analyses revealed at least three anti-(Apol PBP) immunoreactive proteins with pI values between 4.4 and 4.7. N-Terminal sequencing of these three proteins revealed two proteins (Apol PBP1a and Apol PBP1b) identical in the first 49 amino acids to the already known PBP (Apol PBP1) [Raming, K. , Krieger, J. & Breer, H. (1989) FEBS Lett. 256, 2215-2218] and a new PBP having only 57% identity with this amino-acid region. Screening of antennal cDNA libraries with an oligonucleotide probe corresponding to the N-terminal end of the new A. polyphemus PBP, led to the discovery of full length clones encoding this protein in A. polyphemus (Apol PBP3) and in A. pernyi (Aper PBP3). By screening the antennal cDNA library of A. polyphemus with a digoxigenin-labelled A. pernyi PBP2 cDNA [Krieger, J., Raming, K. & Breer, H. (1991) Biochim. Biophys. Acta 1088, 277-284] a homologous PBP (Apol PBP2) was cloned. Binding studies with the two main pheromone components of A. polyphemus and A. pernyi, the (E,Z)-6, 11-hexadecadienyl acetate (AC1) and the (E,Z)-6,11-hexadecadienal (ALD), revealed that in A. polyphemus both Apol PBP1a and the new Apol PBP3 bound the 3H-labelled acetate, whereas no binding of the 3H-labelled aldehyde was found. In A. pernyi two PBPs from sensory hair homogenates showed binding affinity for the AC1 (Aper PBP1) and the ALD (Aper PBP2), respectively.     

Structural and functional difference of pheromone binding proteins in discriminating chemicals in the gypsy moth, Lymantria dispar

Pheromone-binding proteins (PBPs) of the gypsy moth, Lymantria dispar L., play an important role in olfaction. Here structures of PBPs were first built by Homology Modeling, and each model of PBPs had seven α-helices and a large hydrophobic cavity including 25 residues for PBP1 and 30 residues for PBP2. Three potential semiochemicals were first screened by CDOCKER program based on the PBP models and chemical database. These chemicals were Palmitic acid n-butyl ester (Pal), Bis(3,4-epoxycyclohexylmethyl) adipate (Bis), L-trans-epoxysuccinyl-isoleucyl-proline methyl ester propylamide (CA-074). The analysis of chemicals docking the proteins showed one hydrogen bond was established between the residues Lys94 and (+)-Disparlure ((+)-D), and л-л interactions were present between Phe36 of PBP1 and (+)-D. The Lys94 of PBP1 formed two and three hydrogen bonds with Bis and CA-074, respectively. There was no residue of PBP2 interacting with these four chemicals except Bis forming one hydrogen bond with Lys121. After simulating the conformational changes of LdisPBPs at pH7.3 and 5.5 by constant pH molecular dynamics simulation in implicit solvent, the N-terminal sequences of PBPs was unfolded, only having five α-helices, and PBP2 had larger binding pocket at 7.3 than PBP1. To investigate the changes of α-helices at different pH, far-UV and near-UV circular dichroism showed PBPs consist of α-helices, and the tertiary structures of PBP1 and PBP2 were influenced at pH7.3 and 5.5. The fluorescence binding assay indicated that PBP1 and PBP2 have similarly binding affinity to (+)-D at pH 5.5 and 7.3, respectively. At pH 5.5, the dissociation constant of the complex between PBP1 and 2-decyl-1-oxaspiro [2.2] pentane (OXP1) was 0.68 ± 0.01 μM, for (+)-D was 5.32 ± 0.11 μM, while PBP2 with OXP1 and (+)-D were 1.88 ± 0.02 μM and 5.54 ± 0.04 μM, respectively. Three chemicals screened had higher affinity to PBP1 than (+)-D except Pal at pH5.5, and had lower affinity than (+)-D at pH7.3. To PBP2, these chemicals had lower affinity than the sex pheromone except Bis at pH 5.5 and pH 7.3. Only PBP1 had higher affinity with Sal than the sex pheromone at pH 5.5. Therefore, the structures of PBP1 and PBP2 had different changes at pH5.5 and 7.3, showing different affinity to chemicals. This study helps understanding the role of PBPs as well as in developing more efficient chemicals for pest control.     

Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: equilibrium, kinetic, and crystallographic studies.

Stringent specificity and complementarity between the receptor, a periplasmic phosphate-binding protein (PBP) with a two-domain structure, and the completely buried and dehydrated phosphate are achieved by hydrogen bonding or dipolar interactions. We recently found that the surface charge potential of the cleft between the two domains that contains the anion binding site is intensely electronegative. This novel finding prompted the study reported here of the effect of ionic strength on the equilibrium and rapid kinetics of phosphate binding. To facilitate this study, Ala197, located on the edge of the cleft, was replaced by a Trp residue (A197W PBP) to generate a fluorescence reporter group. The A197W PBP-phosphate complex retains wild-type Kd and X-ray structure beyond the replacement residue. The Kd (0.18 microM) at no salt is increased by 20-fold at greater than 0.30 M NaCl. Stopped-flow fluorescence kinetic studies indicate a two-step binding process: (1) The phosphate (L) binds, at near diffusion-controlled rate, to the open cleft form (Po) of PBP to produce an intermediate, PoL. This rate decreases with increasing ionic strength. (2) The intermediate isomerizes to the closed-conformation form, PcL. The results indicate that the high specificity, affinity, and rate of phosphate binding are not influenced by the noncomplementary electronegative surface potential of the cleft. That binding depends almost entirely on local dipolar interactions with the receptor has important ramification in electrostatic interactions in protein structures and in ligand recognition.     

Discrimination of pheromone enantiomers by two pheromone binding proteins from the gypsy moth Lymantria dispar

The gypsy moth, Lymantria dispar, uses (7R, 8S)-cis-2-methyl-7, 8-epoxyoctadecane, (+)-disparlure, as a sex pheromone. The (-) enantiomer of the pheromone is a strong behavioral antagonist. Specialized sensory hairs, sensillae, on the antennae of male moths detect the pheromone. Once the pheromone enters a sensillum, the very abundant pheromone binding protein (PBP) transports the odorant to the sensory neuron. We have expressed the two PBPs found in gypsy moth antennae, PBP1 and PBP2, and we have studied the affinity of these recombinant PBPs for the enantiomers of disparlure. To study pheromone binding under equilibrium conditions, we developed and validated a binding assay. We have addressed the two major problems with hydrophobic ligands in aqueous solution: (1) concentration-dependent adsorption of the ligand on vial surfaces and (2) separation of the protein-bound ligand from the material remaining free in solution. We used this assay to demonstrate for the first time that pheromone binding to PBP is reversible and that the two PBPs from L. dispar differ in their enantiomer binding preference. PBP1 has a higher affinity for the (-) enantiomer, while PBP2 has a higher affinity for the (+) enantiomer. The PBP from the wild silk moth, Antheraea polyphemus (Apol-3) bound the disparlure enantiomers more weakly than either of the L. dispar PBPs, but Apol-3 was also able to discriminate the enantiomers. We have observed extensive aggregation of both L. dispar PBPs and an increase in pheromone binding at high (>2 microM) PBP concentrations. We present a model of disparlure binding to the two PBPs.     

Pheromone‐binding proteins in the Asian gypsy moth females,Lymantria dispar,recognizing the sex pheromone and plant volatiles

Lepidopterans are known to have different pheromone‐binding proteins with differential expression patterns that facilitate specific signal transduction of semiochemicals. Two PBPs of the Asian gypsy moth, Lymantria dispar, were reported to express in both females and males, but their physiological functions were unknown. Results showed that LdisPBP1 and LdisPBP2 were expressed in the sensilla trichodea of males and the s. trichodea and s. basiconica of females. When LdisPBP1 gene was targeted by RNA interference (RNAi) in males, the expression of LdisPBP1 and LdisPBP2 decreased by 69 and 76%, respectively, and when LdisPBP2 gene was targeted by RNAi, they decreased by 60 and 42%, respectively. In females, after treatment with LdisPBP1 dsRNA, LdisPBP1 and LdisPBP2 levels were reduced by 26 and 69%, respectively, and LdisPBP2 dsRNA reduced the relative expression of them by 4 and 62%, respectively. The expression of LdisPBP1 and LdisPBP2 was interdependent. Electroantennogram (EAG) recordings showed that LdisPBPs participate in the recognition of the sex pheromone in males, and the sex pheromone and plant volatiles in females. The function of LdisPBPs represents the sex‐specific roles.     

Structure-Activity Relationship for Some 2′,3′-Dideoxynucleoside Anti-HIV Drugs Using Molecular Electrostatic Potential Mapping

Molecular electrostatic potential(MEP) maps of azido thymidine (AZT), some of its analogs and derivatives and certain other 2′,3′-dideoxy nucleosides having different anti-HIV activities have been studied. The optimised hybridization displacement charges (HDC) combined with MNDO Löwdin charges, continuosly distributed in three dimension spherically symmetrically as a Slater cloud at each site were used to compute the MEP maps. The negative MEP region near the O5′ sites of these molecules appears to be of primary importance from the point of view of their anti-HIV activity. The roles of the azido group in AZT and fluorine atoms substituted at different positions in the sugar moiety have been evaluated. The azido group in AZT behaves as a strongly electronegative group.     

Evidence for directional selection acting on pheromone-binding proteins in the genus Choristoneura

Patterns of nucleotide variation consistent with the action of natural selection have been discovered at a number of different gene loci. Here, pheromone-binding proteins (PBPs) are examined to determine if selection has acted to fix amino acid changes in PBPs in lineages in which pheromone changes have occurred. PBPs from five different species of moths in the genus Choristoneura were sequenced, along with the PBP of Argyrotaenia velutinana, which serves as an outgroup. Three independent major pheromone changes are represented within this group of five Choristoneura species. Two different lineages show evidence for selection based on polymorphism and divergence comparisons and comparisons of rates of replacement evolution to silent and noncoding evolution. Along one of these lineages, leading to Choristoneura fumiferana, there has been a change to an aldehyde pheromone from an acetate pheromone. The second branch does not appear to be associated with a major pheromone change. Other branches in the tree show a trend toward greater replacement fixation than expected under neutrality. This trend could reflect undetected selective events within this group of PBPs. Selection appears to have acted to fix amino acid changes in the PBP of moths from the genus Choristoneura, but it is not clear that this selection is due to pheromone changes between species.     

Topological description of the bond-breaking and bond-forming processes of the alkene protonation reaction in zeolite chemistry: an AIM study

Density functional theory and atoms in molecules theory were used to study bond breakage and bond formation in the trans-2-butene protonation reaction in an acidic zeolitic cluster. The progress of this reaction along the intrinsic reaction coordinate, in terms of several topological properties of relevant bond critical points and atomic properties of the key atoms involved in these concerted mechanisms, were analyzed in depth. At B3LYP/6-31++G(d,p)//B3LYP/6-31G(d,p) level, the results explained the electron density redistributions associated with the progressive bond breakage and bond formation of the reaction under study, as well as the profiles of the electronic flow between the different atomic basins involved in these electron reorganization processes. In addition, we found a useful set of topological indicators that are useful to show what is happening in each bond/atom involved in the reaction site as the reaction progresses.     

Comparative sex pherome biosynthesis in Thaumetopoea pityocampa and T. processionea: a rationale for the phenotypic variation in the sex pherome within the genus Thaumetopoea

The female sex pheromones of the Mediterranean processionary moths (Thaumetopoea sp.) are conjugated dienes or enynes of 16 carbon atoms with the unsaturations located at C11 and C13. To investigate the biochemical basis of this phenotypic variation, the biosynthetic pathway of T. processionea sex pheromone, a diene acetate, has been elucidated and compared to that reported for the enyne-producing species T. pityocampa. Mass labeling experiments showed that T. processionea sex pheromone is biosynthesized from palmitic acid, by subsequent (Z)-11 and (Z)-13 desaturations and final reduction and acetylation. The Pheromone Biosynthesis Activating Neuropeptide (PBAN) activates this biosynthetic pathway downstream of the dienoate intermediate. When either 11-hexadecynoic acid or (Z)-13-hexadecen-11-ynoic acid were administered to T. processionea, this species was able to produce the enyne sex pheromone of T. pityocampa upon PBAN stimulation. In contrast, T. pityocampa does not produce either 11-hexadecynyl acetate or (Z,Z)-11,13-hexadecadienyl acetate, despite having the corresponding precursors in the pheromone gland. However, both acetates are detected after administration of the corresponding alcohols. These overall results suggest that the absence of delta(11) acetylenase and the existence of an enynoate specific reductase in the diene and enyne-producing Thaumetopeae, respectively, account for the different sex pheromones produced by the two groups.     

Molecular electrostatic potentials from crystal diffraction: the neurotransmitter gamma-aminobutyric acid.

Given the electronic charge parameters obtained from a diffraction study of the charge density distribution in a crystal, a mathematical procedure is presented for deriving the electrostatic potential. The procedure allows the mapping of electrostatic potential for a molecule or group of molecules removed from the crystal structure but with each molecule retaining the effects of polarization owing to the original crystal environment. The method is applied for the neurotransmitter gamma-aminobutyric acid. The potential for a gamma-aminobutyric acid molecule is analyzed in terms of a simple model that is suitable for rapid computations concerned with Coulombic molecular interactions. Outside the molecular envelope at 1.2 A from the atomic nuclei, the total potential is well represented by a sum of spherical atom contributions with V(r) = (q/r) + exp(-beta r2). The most important aspherical component in the potential is the dipole contribution from the hydrogen atoms. This can be represented as V(r, phi) = (0.162 cos phi)/(r2 + 0.615). Here, V is in e/A, r is the distance from each nucleus in A, q is the experimentally determined net atomic charge in electron units, and phi is the angle between r and the bond X-H. We obtain beta = 1.47, 1.66, 1.83 A-2 for C, N, and O respectively. For H, no term in beta is needed.     

Pheromone binding proteins in the European and Asian corn borers: no protein change associated with pheromone differences.

Pheromone binding proteins (PBPs) are thought to play a role in the recognition of sex pheromone in male moth antennae. By binding selectively to different components of pheromone blends, these PBPs could play a role in differentiating between structurally related compounds. In this study we have characterized the pheromone binding proteins of two pheromone strains of the European corn borer (Ostrinia nubilalis) and also the closely related Asian corn borer (O. furnacalis). We have been able to detect only one PBP gene, which encodes a mature protein that is identical in amino acid sequence in individuals from different pheromone strains and different species. This result suggests that the PBP is not detecting differences between the two isomeric compounds of the European corn borer pheromone or the difference in double bond position between the pheromone molecules of the European and Asian corn borers.     

Structural investigation of selective binding dynamics for the pheromone‐binding protein 1 of the grapevine moth,Lobesia botrana

The European grapevine moth, Lobesia botrana (Denis & Schiffermüller), is a serious pest in vineyards in North and South America. Mating disruption techniques have been used to control and monitor L. botrana on the basis of its sexual communication. This needs a well‐tuned olfactory system, in which it is believed that pheromone‐binding proteins (PBPs) are key players that transport pheromones in the antennae of moths. In this study, the selectivity of a PBP, named as LbotPBP1, was tested by fluorescence binding assays against 11 sex pheromone components and 6 host plant volatiles. In addition, its binding mechanism was predicted on the basis of structural analyses by molecular docking and complex and steered molecular dynamics (SMD). Our results indicate that LbotPBP1 binds selectively to sex pheromone components over certain host plant volatiles, according to both in vitro and in silico tests. Thus, chain length (14 carbon atoms) and functional groups (i.e., alcohol and ester) appear to be key features for stable binding. Likewise, residues such as Phe12, Phe36, and Phe118 could participate in unspecific binding processes, whilst Ser9, Ser56, and Trp114 could participate in the specific recognition and stabilization of sex pheromones instead of host plant volatiles. Moreover, our SMD approach supported 11‐dodecenyl acetate as the best ligand for LbotPBP1. Overall, the dynamics simulations, contact frequency analysis and SMD shed light on the binding mechanism of LbotPBP1 and could overcome the imprecision of molecular docking, supporting the in vitro binding assays. Finally, the role of LbotPBP1 in the chemical ecology of L. botrana is discussed.