Cis Bonds Research Articles

One chiral fingerprint to find them all

Molecular fingerprints are indispensable tools in cheminformatics. However, stereochemistry is generally not considered, which is problematic for large molecules which are almost all chiral.Herein we report MAP4C, a chiral version of our previously reported fingerprint MAP4, which lists MinHashes computed from character strings containing the SMILES of all pairs of circular substructures up to a diameter of four bonds and the shortest topological distance between their central atoms. MAP4C includes the Cahn-Ingold-Prelog (CIP) annotation (R, S, r or s) whenever the chiral atom is the center of a circular substructure, a question mark for undefined stereocenters, and double bond cis–trans information if specified. MAP4C performs slightly better than the achiral MAP4, ECFP and AP fingerprints in non-stereoselective virtual screening benchmarks. Furthermore, MAP4C distinguishes between stereoisomers in chiral molecules from small molecule drugs to large natural products and peptides comprising thousands of diastereomers, with a degree of distinction smaller than between structural isomers and proportional to the number of chirality changes. Due to its excellent performance across diverse molecular classes and its ability to handle stereochemistry, MAP4C is recommended as a generally applicable chiral molecular fingerprint.Scientific contribution The ability of our chiral fingerprint MAP4C to handle stereoisomers from small molecules to large natural products and peptides is unprecedented and opens the way for cheminformatics to include stereochemistry as an important molecular parameter across all fields of molecular design.Graphical

Crystal structures of tri-chlorido-(4-methyl-piperidine)gold(III) and two polymorphs of tri-bromido(4-methyl-piperidine)-gold(III).

Tri-chlorido-(4-methyl-piperidine)-gold(III), [AuCl3(C6H13N)], 1, crystallizes in Pbca with Z = 8. Tri-bromido-(4-methyl-piperidine)-gold(III), [AuBr3(C6H13N)], 2, crystallizes as two polymorphs, 2a in Pnma with Z = 4 (imposed mirror symmetry) and 2b, which is isotypic to 1. The Au-N bonds trans to Cl are somewhat shorter than those trans to Br, and the Au-Cl bonds trans to N are longer than those cis to N, whereas the Au-Br bonds trans to N are slightly shorter than the cis bonds. The methyl and AuX 3 groups (X = halogen) occupy equatorial positions at the six-membered ring. The packing of all three structures involves chains of mol-ecules with offset stacking of the AuX 3 moieties associated with short Au⋯X contacts; for 1 and 2b these are reinforced by N-H⋯X hydrogen bonds, whereas for 2a there are no classical hydrogen bonds and the chains are inter-connected by Br⋯Br contacts.

Radical and Cationic Pathways in C(sp3)-H Bond Oxygenation by Dioxiranes of Bicyclic and Spirocyclic Hydrocarbons Bearing Cyclopropane Moieties.

A product and DFT computational study on the reactions of 3-ethyl-3-(trifluoromethyl)dioxirane (ETFDO) with bicyclic and spirocyclic hydrocarbons bearing cyclopropyl groups was carried out. With bicyclo[n.1.0]alkanes (n = 3-6), diastereoselective formation of the alcohol product derived from C2-H bond hydroxylation was observed, accompanied by smaller amounts of products derived from oxygenation at other sites. With 1-methylbicyclo[4.1.0]heptane, rearranged products were also observed in addition to the unrearranged products deriving from oxygenation at the most activated C2-H and C5-H bonds. With spiro[2.5]octane and 6-tert-butylspiro[2.5]octane, reaction with ETFDO occurred predominantly or exclusively at the axial C4-H to give unrearranged oxygenation products, accompanied by smaller amounts of rearranged bicyclo[4.2.0]octan-1-ols. The good to outstanding site-selectivities and diastereoselectivities are paralleled by the calculated activation free energies for the corresponding reaction pathways. Computations show that the σ* orbitals of the bicyclo[n.1.0]alkane cis or trans C2-H bonds and spiro[2.5]octanes axial C4-H bond hyperconjugatively interact with the Walsh orbitals of the cyclopropane ring, activating these bonds toward HAT to ETFDO. The detection of rearranged oxygenation products in the oxidation of 1-methylbicyclo[4.1.0]heptane, spiro[2.5]octane, and 6-tert-butylspiro[2.5]octane provides unambiguous evidence for the involvement of cationic intermediates in these reactions, representing the first examples on the operation of ET pathways in dioxirane-mediated C(sp3)-H bond oxygenations. Computations support these findings, showing that formation of cationic intermediates is associated with specific stabilizing hyperconjugative interactions between the incipient carbon radical and the cyclopropane C-C bonding orbitals that trigger ET to the incipient dioxirane derived 1,1,1-trifluoro-2-hydroxy-2-butoxyl radical.

Distance-based global analysis of consistent cis-bonds in protein backbones

Biological polypeptides are known to contain cis-linkage in their main chain as a minor but important feature. Such anomalous connection of amino acids has different structural and functional effects on proteins. Experimental evidence of cis-bonds in proteins is mainly obtained using X-ray crystallography and other methods in the field of structural biology. To date, extensive analyses have been carried out on the experimentally found cis-bonds using the Protein Data Bank (PDB) entry-wise or residue-wise; however, their consistency in each protein has not been examined on a global scale. Data accumulation and advances in computational methodology enable the use of new approaches from a proteomic point of view. Here, we sought to carry out protein-wise analysis and describe a simple procedure for the detection and confirmation of cis-bonds from a set of experimental PDB chains for a protein to discriminate this type of bond from isomerizable and/or misassigned bonds. The resulting set of consistent cis bonds (found at identical positions in multiple chains) provides unprecedented insights into the trend of “high cis content” proteins and the upper limit of consistent cis bonds per polypeptide length. Recognizing such limit would not only be important for a practical check of upcoming structures, but also for the design of novel protein folds beyond the evolutionally-acquired repertoire.

N-Heterocyclic Carbene-Coordinated M(II) (M = Yb, Sm, Ca) Bisamides: Expanding the Limits of Intermolecular Alkene Hydrophosphination.

A series of NHC-stabilized amido compounds (NHC)nM[N(SiMe3)2]2 (M = Yb(II), Sm(II), Ca(II); n = 1, 2) showed remarkable catalytic efficiency in addition of PhPH2 and PH3 to alkenes under mild conditions and low catalyst loading. The effect of σ-donor capacity of NHCs on catalytic activity in hydrophosphination of styrene with PhPH2 and PH3 was revealed. For the series of three-coordinate complexes 1-4M, a tendency to increase the catalytic activity with growth of σ-donating strength of the carbene ligand was clearly demonstrated. The complex (NHC)2Sm[N(SiMe3)2]2 (NHC = 1,3-diisopropyl-2H-imidazole-2-ylidene) (5Sm) proved to be the most efficient catalyst, which enabled hardly realizable transformations such as PhPH2 addition across internal C═C bonds of norbornene and cis- and trans-stilbenes, providing the highest reaction rate for addition of PH3 to styrene. Excellent regio- and chemoselectivities of alkylation of PH3 with styrenes allow for a selective and good-yield synthesis of desired organophosphines─either primary, secondary, or tertiary. Stepwise alkylation of PH3 with various substituted styrenes can be efficiently applied as an approach to nonsymmetric secondary phosphines. The rate equation of the addition of styrene to PH3 promoted by 5Sm was found: rate = k[styrene]1[5Sm]1.

Design and Synthesis of Sebacic Acid from Castor Oil by New Alternate Route

AbstractA simple and alternate organic synthetic route for sebacic acid, a high value ten‐carbon aliphatic dicarboxylic acid from castor oil is described in this study. Castor oil methyl esters are purified to obtain methyl ester of ricinoleic acid that is used as the starting material for the preparation of sebacic acid. The hydroxyl group of methyl ricinoleate is oxidized to corresponding 12‐oxo derivative followed by isomerization of the cis 9, 10 olefinic bond to trans 10, 11 isomer. The isomerized compound is subjected to dihydroxylation followed by oxidative cleavage and subsequent methylation to obtain dimethyl decanedioate. The dimethyl decanedioate is finally hydrolyzed to obtain sebacic acid. The intermediate compounds and final product are purified and characterized by chromatographic and spectral analysis. The final compound is analyzed by 1H and 13C‐NMR as well as high resolution mass spectrometry and compared with standard compound for the confirmation of the structure.Practical Applications: The design and preparation of sebacic acid by the novel alternate route is described.Castor oil, a renewable source, is utilized as the raw material for the preparation of sebacic acid.Isomerization of the 9, 10 cis bond to 10, 11 trans bond is the key step in the synthesis of sebacic acid.The chemical transformation of castor oil to sebacic acid by newer route is investigated.

Proline isomerization in molecular dynamics simulations of a proline-rich signaling peptide

Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the cis state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in cis, a robust methodology to accurately account for these conformations in the overall ensemble is crucial.

An Unbound Proline-Rich Signaling Peptide Frequently Samples Cis Conformations in Gaussian Accelerated Molecular Dynamics Simulations.

Disordered proline-rich motifs are common across the proteomes of many species and are often involved in protein-protein interactions. Proline is a unique amino acid due to the covalent bond between the backbone nitrogen and the proline side chain. The resulting five-membered ring allows proline to sample the cis state about its peptide bond, which other residues cannot do as readily. Because proline-rich disordered sequences exist as ensembles that likely include structures with the proline peptide bond in cis, a robust methodology to accurately account for these conformations in the overall ensemble is crucial. Observing the cis conformations of proline in a disordered sequence is challenging both experimentally and computationally. Nitrogen-hydrogen NMR spectroscopy cannot directly observe proline residues, which lack an amide bond, and computational methods struggle to overcome the large kinetic barrier between the cis and trans states, since isomerization usually occurs on the order of seconds. In the current work, Gaussian accelerated molecular dynamics was used to overcome this free energy barrier and simulate proline isomerization in a tetrapeptide (KPTP) and in the 12-residue proline-rich SH3 binding peptide, ArkA. We found that Gaussian accelerated molecular dynamics, when combined with a lowered peptide bond dihedral angle potential energy barrier (15 kcal/mol), allowed sufficient sampling of the proline cis and trans states on a microsecond timescale. All ArkA prolines spend a significant fraction of time in cis, leading to a more compact ensemble with less polyproline II helix structure than an ArkA ensemble with all peptide bonds in trans. The ensemble containing cis prolines also matches more closely to in vitro circular dichroism data than the all-trans ensemble. The ability of the ArkA prolines to isomerize likely affects the peptide’s ability to bind its partner SH3 domain, and should be studied further. This is the first molecular dynamics simulation study of proline isomerization in a biologically relevant proline-rich sequence that we know of, and a similar protocol could be applied to study multi-proline isomerization in other proline-containing proteins to improve conformational diversity and agreement with in vitro data.

Sulfur Oxidation Increases the Rate of HIRE-Type [1.4]Thiazepinone Ring Expansion and Influences the Conformation of a Medium-Sized Heterocyclic Scaffold.

The hydrated imidazoline ring expansion (HIRE-type) reaction was investigated for a series of di(hetero)arene-fused [1.4]thiazepinones in comparison with their sulfone counterparts. The sulfones were found to undergo ring expansion at a much higher rate compared to the thioethers, much in line with the current mechanistic understanding of the process. Moreover, the amide bond cis- and trans-isomers of the ring-expanded products were found, in the case of sulfones, to be stabilized through an intramolecular hydrogen bond. The latter phenomenon was studied in detail by NMR experiments and corroborated by X-ray crystallographic information.

Cadherin cis and trans interactions are mutually cooperative

Cadherin transmembrane proteins are responsible for intercellular adhesion in all biological tissues and modulate tissue morphogenesis, cell motility, force transduction, and macromolecular transport. The protein-mediated adhesions consist of adhesive trans interactions and lateral cis interactions. Although theory suggests cooperativity between cis and trans bonds, direct experimental evidence of such cooperativity has not been demonstrated. Here, the use of superresolution microscopy, in conjunction with intermolecular single-molecule Förster resonance energy transfer, demonstrated the mutual cooperativity of cis and trans interactions. Results further demonstrate the consequent assembly of large intermembrane junctions, using a biomimetic lipid bilayer cell adhesion model. Notably, the presence of cis interactions resulted in a nearly 30-fold increase in trans-binding lifetimes between epithelial-cadherin extracellular domains. In turn, the presence of trans interactions increased the lifetime of cis bonds. Importantly, comparison of trans-binding lifetimes of small and large cadherin clusters suggests that this cooperativity is primarily due to allostery. The direct quantitative demonstration of strong mutual cooperativity between cis and trans interactions at intermembrane adhesions provides insights into the long-standing controversy of how weak cis and trans interactions act in concert to create strong macroscopic cell adhesions.

Enhanced accessibility and hydrophobicity of amyloidogenic intermediates of the β2-microglobulin D76N mutant revealed by high-pressure experiments

β2-Microglobulin (β2m) is the causative protein of dialysis-related amyloidosis. Its unfolding mainly proceeds along the pathway of NC →UC ⇄ UT, whereas refolding follows the UT → IT (→NT) →NC pathway, in which N, I, and U are the native, intermediate, and unfolded states, respectively, with the Pro32 peptidyl-prolyl bond in cis or trans conformation as indicated by the subscript. It is noted that the IT state is a putative amyloidogenic precursor state. Several aggregation-prone variants of β2m have been reported to date. One of these variants is D76N β2m, which is a naturally occurring amyloidogenic mutant. To elucidate the molecular mechanisms contributing to the enhanced amyloidogenicity of the mutant, we investigated the equilibrium and kinetic transitions of pressure-induced folding/unfolding equilibria in the wild type and D76N mutant by monitoring intrinsic tryptophan and 1-anilino-8-naphthalene sulfonate fluorescence. An analysis of kinetic data revealed that the different folding/unfolding behaviors of the wild type and D76N mutant were due to differences in the activation energy between the unfolded and the intermediate states as well as stability of the native state, leading to more rapid accumulation of IT state for D76N in the refolding process. In addition, the IT state was found to assume more hydrophobic nature. These changes induced the enhanced amyloidogenicity of the D76N mutant and the distinct pathogenic symptoms of patients. Our results suggest that the stabilization of the native state will be an effective approach for suppressing amyloid fibril formation of this mutant.

Synthesis, structure, and theoretical studies of a calcium complex of a unique dianion derived from 1-methyl-pyrrolidin-2-one.

The title compound, catena-poly[[tetra-kis-(1-methyl-pyrrolidin-2-one-κO)calcium(II)]-μ-(E)-1,1'-dimethyl-2,2'-dioxo-1,1',2,2'-tetra-hydro-[3,3'-bipyrrolyl-idene]-5,5'-bis-(thiol-ato)-κ2 O:O'], [Ca(C10H8N2O2S2)(C5H9NO)4] n , 1, crystallizes in the triclinic space group P . The crystal studied was twinned by non-merohedry via two different twofold operations, about the normals to (001) and (10), giving four twin domains with refined occupancies of 0.412 (4), 0.366 (4), 0.055 (1), 0.167 (4). The Ca atoms are located on centers of inversion. Each Ca is surrounded by four 1-methyl-pyrrolidin-2-one (NMP) ligands and coordinated through one of the two O atoms to two (E)-1,1'-dimethyl-2,2'-dioxo-1,1',2,2'-tetra-hydro-[3,3'-bipyrrolyl-idene]-5,5'-bis-(thiol-ate), [C10H8N2O2S2]2-, dianions (abbreviation: DMTBT). This dianion thus facilitates the formation of a 1-D polymer, which propagates in the [011] direction. These ribbons are linked by inter-molecular C-H⋯S inter-actions. Each Ca atom is in an octa-hedral CaO6 six-coordinate environment with Ca-O bond lengths ranging from 2.308 (6) to 2.341 (6) Å, cis bond angles ranging from 88.2 (2) to 91.8 (2)° and the trans angles all 180° due to the Ca atoms being located on centers of inversion. Theoretical calculations were carried out using density functional theory (DFT) and the results showed that although the central DMTBT dianion is planar there is likely some resonance across the central bond between both aza-pentyl rings, but this is not sufficient to establish a ring current. The calculated UV-vis spectrum shows a peak at 625 nm, which accounts for the deep blue-purple color of solutions of the complex.

DFT Calculations of 1H- and 13C-NMR Chemical Shifts of Geometric Isomers of Conjugated Linoleic Acid (18:2 ω-7) and Model Compounds in Solution.

A density functional theory (DFT) study of the 1H- and 13C-NMR chemical shifts of the geometric isomers of 18:2 ω-7 conjugated linoleic acid (CLA) and nine model compounds is presented, using five functionals and two basis sets. The results are compared with available experimental data from solution high resolution nuclear magnetic resonance (NMR). The experimental 1H chemical shifts exhibit highly diagnostic resonances due to the olefinic protons of the conjugated double bonds. The “inside” olefinic protons of the conjugated double bonds are deshielded than those of the “outside” protons. Furthermore, in the cis/trans isomers, the signals of the cis bonds are more deshielded than those of the trans bonds. These regularities of the experimental 1H chemical shifts of the olefinic protons of the conjugated double bonds are reproduced very accurately for the lowest energy DFT optimized single conformer, for all functionals and basis sets used. The other low energy conformers have negligible effects on the computational 1H-NMR chemical shifts. We conclude that proton NMR chemical shifts are more discriminating than carbon, and DFT calculations can provide a valuable tool for (i) the accurate prediction of 1H-NMR chemical shifts even with less demanding functionals and basis sets; (ii) the unequivocal identification of geometric isomerism of CLAs that occur in nature, and (iii) to derive high resolution structures in solution.

Photo-Induced Ring-Opening Reaction of Flav-3-en-2-ol Monitored by Time-Resolved Infrared Spectroscopy.

Photo-induced ring-opening reaction from flav-3-en-2-ol to 2-hydroxychalcone has been studied by time-resolved infrared (TR-IR) spectroscopy and quantum chemical calculations. A vibrational band due to the C═O stretching modes for intermediate species, enol forms of 2-hydroxychalcone in the electronic ground state, was observed at 1632 cm-1 in the TR-IR spectra after photoexcitation of flav-3-en-2-ol. We also found that the C═O stretching modes of the keto forms of 2-hydroxychalcone at 1664 cm-1 appeared immediately after photoexcitation and increased in intensity in synchronization with the depletion of the 1632 cm-1 band. Because the decay of the 1632 cm-1 band and the rise of the 1664 cm-1 band were fitted with bi-exponential model functions with common rate constants 0.5 and 11 μs-1, we propose that two kinds of enol form, single bond cis- (s-cis-) and trans- (s-trans-) enols, transformed into keto forms, cis-2-hydroxychalcone (Cc) and trans-2-hydroxychalcone (Ct), respectively. Quantum chemically calculated IR spectra of related species are consistent with the proposal. The observed temporal behavior of the TR-IR spectra indicates that there were reaction paths to the photogeneration of Cc and Ct within the time resolution of the TR-IR spectrometer (∼0.1 μs) in addition to the reaction paths via the enol forms of 2-hydroxychalcone.

Structure of Monomeric Octahedral d2-Rhenium(V) Monooxo Complexes [ReO(Ltri)(Lbi)] and [ReO(Ltetra)(Lmono)] with Oxygen Atoms of Tridentate (O, O, O) and Tetradentate (O, O, O, O) Chelating Ligands

The structural features of four mononuclear octahedral d2-Re(V) monooxo complexes [ReO(Ltri)(Lbi)] and [ReO(Ltetra)(Lmono) with tridentate (O, O, O) and tetradentate (O, O, O, O) chelating ligands are discussed. It is shown that the Re–O(Ltri)trans bonds are elongated, whereas the Re–O(Ltetra)trans bonds are shortened as compared to the Re–O(L)cis bonds.

New light on an old debate: does the RCN-PtCl2 bond include any back-donation? RCN←PtCl2 backbonding vs. the IR νC[triple bond, length as m-dash]N blue-shift dichotomy in organonitriles-platinum(ii) complexes. A thorough density functional theory - energy decomposition analysis study.

For a series of organonitrile [RCN (R = Me, CF3, Ph, CH3Ph, CF3Ph)] ligands, the nature of the N-Pt bond in the related cis-/trans-(RCN)2PtCl2 complexes has been computationally investigated by Density Functional Theory. A fragment based bond analysis has been performed in the canonical Kohn-Sham molecular orbitals framework, and it has been ultimately assessed that this bond is characterized both by N→Pt σ and by N←Pt π contributions. Voronoi Deformation Density charges further confirms the occurrence of N←Pt π interactions. Moreover, the Energy Decomposition Analysis-Natural Orbital for Chemical Valence (EDA-NOCV) method shows that the strength of the N←Pt π interaction is not negligible by contributing to about 30-40% of the total orbital interaction. Finally, the well-known νC[triple bond, length as m-dash]N blue-shift occurring upon coordination to PtII, has been thoroughly investigated by exploiting the EDA-NOCV and by evaluating νC[triple bond, length as m-dash]N and force constants. The origin of the νC[triple bond, length as m-dash]N blue-shift in these systems has been discussed on the basis of the CN bond polarization. N←Pt π backbonding causes only a systematic decrease of the observed νC[triple bond, length as m-dash]N blue-shift when compared to the one calculated for RCN-X (X = H+, alkaline, Lewis acids) herein reported (X = purely σ acceptors).

Probing Proline Residues in the Prokaryotic Ligand-Gated Ion Channel, ELIC.

Erwinia ligand-gated ion channel (ELIC) is a bacterial homologue of vertebrate pentameric ligand-gated ion channels (pLGICs) and has proven to be a valuable model for understanding the structure and function of this important protein family. There is nevertheless still a question about whether molecular details can be accurately extrapolated from this protein to those found in eukaryotes. Here we explore the role of proline residues (Pros) in ELIC by creating mutant receptors, expressing them in Xenopus laevis oocytes, and using whole-cell voltage-clamp electrophysiology to monitor channel activity. In contrast to eukaryotic pLGICs, proline-to-alanine (Pro-to-Ala) substitution in ELIC mostly resulted in gain of function, and even altering highly conserved Pro residues in M1 and the M2-M3 loop did not ablate function. These substitutions also mostly resulted in ablation of the modulation by Ca2+ observed in wild-type receptors. Substitution of the Pro in the "Cys loop", however, did result in nonfunctional receptors. Probing this residue with noncanonical amino acids revealed a requirement for a substituted amine at this position, as well as a general preference for Pro analogues with greater intrinsic cis biases. We propose there is likely a cis bond at the apex of the Cys loop in this protein, which is consistent with some, but not all, findings from other pLGICs. Overall, the data show that the roles of proline residues are less critical in ELIC than in other pLGICs, supporting other studies that suggest caution must be applied in using data from this prokaryotic receptor to understand molecular details of eukaryotic pLGIC receptor function.

Effect of deodorization method on the chemical and nutritional properties of fish oil during refining

Fish oil is a health beneficial product but contains unpleasant odoriferous substances originating from the degradation of lipids and proteins. In this study, several deodorization methods including liquid-liquid extraction (LLE), green tea polyphenol (GTP) treatment, and solid-phase adsorption (SPA) with activated clay, zeolites or diatomite were studied in order to replace the industrially used molecular distillation (MD) and steam distillation (SD). These techniques were compared in terms of physicochemical characteristics, sensory properties, saturability and cis/trans configuration of fatty acids, and volatile compounds, and the results showed significant difference (p value ≤ 0.05, n = 3). The alkaline ethanol based LLE was superior in reducing acidity, peroxide, and saponification value, enriching EPA and DHA, removing unpleasant volatiles, and bleaching. Its low temperature condition can well avoid the peroxidation and degradation of lipids and geometrical isomerization of the natural cis bond. Afterwards, the method was validated and the values for intra-day repeatability (RSDs) fell within the range of 0.22–1.96%. For the inter-day repeatability, RSDs were less than 5.37% for all analytes. In conclusion, this method showed advantages with low cost, high efficient, and simplified procedure in the deodorization of crude fish oil.

Intramolecular energies of the cytotoxic protein CagA of Helicobacter pylori as a possible descriptor of strains’ pathogenicity level

The Helicobacter pylori cytotoxin-associated gene A (CagA) is known for causing gastroduodenal diseases, such as atrophic gastritis and peptic ulcerations. Furthermore Helicobacter pylori CagA positive strains has been reported as one of the main risk factors for gastric cancer (Parsonnet et al., 1997). Structural variations in the CagA structure can alter its affinity with the host proteins, inducing differences in the pathogenicity of H. pylori. CagA N-terminal region is characterized for be conserved among all H. pylori strains since the C-terminal region is characterized by an intrinsically disorder behavior. We generated complete structural models of CagA using different conformations of the C-terminal region for two H. pylori strains. These models contain the same EPIYA (ABC1C2) motifs but different level of pathogenicity: gastric cancer and duodenal ulcer. Using these structural models we evaluated the pathogenicity level of the H. pylori strain, based on the affinity of the interaction with SHP-2 and Grb2 receptors and on the number of interactions with the EPIYA motif. We found that the main differences in the interaction was due to the contributions of certain types of energies from each strain and not from the total energy of the molecule. Specifically, the electrostatic energy, helix dipole energy, Wander Waals clashes, torsional clash, backbone clash and cis bond energy allowed a separation between severe and mild pathology for the interaction of only CagA with SHP2.

Structural transformations of 3-fluoro and 3-fluoro-4-methoxy benzaldehydes under cryogenic conditions: A computational and low temperature infrared spectroscopy investigation

Structural transformations of 3-fluorobenzaldehyde (C7H5FO; 3FBA) and 3-fluoro-4-methoxybenzaldehyde (C8H7FO2; 3F4MBA), taking place in different solid phase environments and at low temperature, were investigated by infrared spectroscopy, complemented by quantum chemistry calculations undertaken at the DFT(B3LYP)/6–311++G(d,p) level of approximation. The studied compounds were isolated from gas phase into cryogenic inert matrices (Ar, Xe), allowing to characterize their equilibrium conformational composition in gas-phase at room temperature. In both cases, two conformers differing by the orientation of the aldehyde moiety (with the carbonyl aldehyde bond cis or trans in relation to the aromatic ring fluorine substituent) were found to coexist, with the cis conformer being slightly more populated than the trans form. In situ narrowband UV irradiation of the as-deposited matrices led either to preferential isomerization of the cis conformer into the trans form or decarbonylation of both conformers, depending on the used excitation wavelength. Deposition of the vapours of 3F4MBA only, onto the cold (15 K) substrate, produced an amorphous solid containing also both the cis and trans conformers of the compound. Subsequent heating of the amorphous phase up to 268 K led to crystallization of the compound, which is accompanied by conformational selection, the cis form being the single species present in the crystal. The experimentally observed transformations of the studied compounds, together with the structural and vibrational results obtained from the performed quantum chemical calculations, allowed a detailed structural and vibrational characterization of the individual conformers.