Bond Pattern Research Articles

Interfaces of affectivity and interpersonal bonds building in the mental health of mothers and daughters victims of sexual abuse

The objective was to investigate the affection in the bond mother and daughter victims of sexual abuse, understanding the affective logics of conduct, and to investigate transgenerational issues and mental health. Three families from an assistance program to victims of sexual abuse participated in this study conducted by means of home visits, semi-structured interviews with parents, genograms for viewing the families’ life cycle. The analysis of the results used the constructive-interpretative method of González Rey, resulting in four areas of meaning which revealed: 1) transgenerational abuse issues in learning about protection, 2) development of links patterns, 3) affective logics of conduct built on the experiences of the roles and 4) aggressiveness as a interpersonal bond pattern in victims of violence. We perceived the the importance of welcoming families with their pains, opening a safe space to identify and express themselves, trying to break patterns transgenerational lack of protection, avoiding revictimization, and trying to promote family mental health.

Study on H-bond patterns in phosphoric triamides having a P(O)NHC(O) skeleton, a gauche orientation of P(O) vs C(O) in new compounds

The crystal and packing structures of new phosphoric triamides, in a rare gauche orientation of P(O) versus C(O), with the formula (CCl 2HC(O)NH)X 2P(O), X = NC 4H 8 ( 1), N(C 2H 5) 2 ( 2), N(CH 3)(C 6H 11) ( 3) and (CCl 2HC(O)NH)(Y)P(O), Y = NHCH 2C(CH 3) 2CH 2NH ( 4) have been investigated. This article also reviews 91 similar structures deposited in the CSD aiming to classify hydrogen bond patterns in this category of phosphorus compounds. The present X-ray structural analysis shows that the H-bond pattern in the studied structures strongly depends on the conformation in the P(O)NHC(O) skeleton and the kind of amide linked to the P atom. The spectroscopic features ( 31P{ 1H}, 1H and 13C NMR, IR) of the new compounds have been investigated.

Ethyl Anomaly in the Nucleophilic Substitution at a Series of β-Methylated Alkyl RCH2Z and Carbonyl RCOZ Carbon Centers for R = Me, Et, i-Pr, t-Bu, and Z = LG.

We have carried out DFT studies to explore the cause of anomalously fast reaction rates of ethyl group (R = Et) in the gas-phase S(N)2 reactions of RCH(2)Cl+Cl(-) and RCH(CN)Cl+Cl(-), and also for those in the cationic forms of RCH(2)(+) and RCH(CN)(+) with R = Me, Et, i-Pr, and t-Bu. The TS stabilization by hyperconjugative donor-acceptor vicinal charge transfers (CTs) from R to the major NBOs at the reaction center carbon in the S(N)2 TSs were estimated using natural bond orbital (NBO) analyses. In all cases the hyperconjugative CT stabilization increases in the order R = t-Bu < i-Pr < Me < Et in agreement with the experimental as well as theoretical rate orders, exhibiting an ethyl anomaly. We have also determined the reorganization energies and hyperconjugative CTs from R to the two major NBOs, C-O(-) and C-N(+), in the tetrahedral intermediate formed with five water molecules, T(5w), by transformation of sp(2) to sp(3) centers in the reactions of RC(═O)OC(6)H(5) with NH(3). The reorganization energy is the lowest and CT stabilization is the strongest with R = Et in line with the fastest experimental rate. We conclude that C-H is a better donor than C-C bond orbital and hyperconjugative vicinal σ chain extension leads to a stronger CT stabilization in the TS. The stronger CT stabilization for R = Et rather than Me is achieved by enhanced hyperconjugative CT to the reaction center in the TS as a result of narrower energy gap and greater overlap brought about by long-range orbital mixing as the C-H σ-chain is extended from n = 2 for Me to n = 3 for Et. We find that CT properties of the all-trans vicinal hyprconjugative C-H σ-chains are closely analogous to the corresponding conjugative polyene π-chains although skeletal patterns of bridge bonds are different and the stabilization energy gained by extension of the σ-chain is much weaker than that gained by the π-chain.

Study of Hydrogen Bonding Patterns of a Pharmaceutically Active Drug Molecule Paraldehyde: a Raman and DFT Study

Abstract Raman spectra of neat paraldehyde (prldh) and its binary mixtures with methanol (M) with varying mole fractions of prldh from 0.1 to 0.8 were recorded in order to explore the hydrogen bonding patterns of prldh and their influence on spectral features of some selected vibrational bands of prldh in the region 400–1200 cm−1. Only few vibrational bands of paraldehyde show a significant change in their peak position in going from neat prldh to the complexes. One peculiar feature in this study is that the solvent band which occurs at ∼1034 cm−1 shows significant red shift of &gt;4 cm−1 at higher mole fractions of prldh. This red shift is caused due to the hydrogen bonding between the O atom of the prldh ring and H atom of the methanol molecules. The Raman band at ∼1097 cm−1 band shows a blue shift of ∼5 cm−1 upon dilution and its linewidth also shows an increase of ∼5 cm−1 in going from neat prldh to extreme dilution. The line broadening upon dilution clearly indicates that the diffusion mechanism plays a dominant role in the dephasing of this vibrational mode. Density functional theoretic (DFT) calculations were performed employing B3LYP functional and high level basis set, 6-311++G(d,p) to obtain the ground state geometry of neat prldh and its hydrogen bonded complexes with methanol in gas phase. Basis set superimpose error (BSSE) correction was also introduced using the counterpoise method. In order to realize a condition quite close to the experiment, the polarizable continuum model (PCM, specific plus bulk solvation) calculations were also performed. For a detailed vibrational assignment of the normal modes, potential energy distribution (PED) calculation was also performed.

Effect of electrostatic interaction on the mechanism of dehalogenation catalyzed by haloalkane dehalogenase

AbstractTheoretical calculation has been carried out for the nucleophilic displacement reaction of 1,2‐dichloroethane catalyzed by haloalkane dehalogenase. The results indicate that different hydrogen bond patterns of the oxyanion hole and the halide‐stabilizing residues play an important role in the dehalogenation reaction. They cause concertedly an earlier transition state (TS) with the activation barrier of 16.60 kcal/mol. The stabilization effect of Trp125 and Trp175 on chlorine atom in the TS is larger than that of the reactant complex by 15.67 kcal/mol so that, they make contribution to the stabilization of the TS. Moreover, the reaction shows the enzymatic action can be attributed to a combination of reactant‐state destabilization and transition‐state electrostatic stabilization. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011

Hydrogen Bonding Patterns of the Co-Crystal Containing the Pharmaceutically Active Ingredient Isoniazid and Terephthalic Acid

AbstractThe title co-crystal (terephthalic acid)·(isonicotinic acid hydrazide) 2 was prepared by solution methods and solvent-assisted grinding. The crystal belongs to the monoclinic space group P2 1 /c with a = 6.2395(4), b = 3.7705(3), c = 41.220(3) A and β = 94.494(6)°. X-ray single crystal structure analysis reveals that the carboxylic acid···pyridine heterosynthon is utilized to co-crystallize the anti-tubercolosis drug isoniazid with the co-crystal former terephthalic acid. The co-crystal crystallizes out as needles, and the homosynthons associated with the isoniazid and the π stacking of the terephthalic acid produce fastest crystal growth in the direction of the needle axis, corresponding to the short (~3.7 A) b crystallographic axis.Index AbstractThe crystal structure of the co-crystal (terephthalic acid)·(isonicotinic acid hydrazide) 2 was determined and reveals that the carboxylic acid···pyridine heterosynthon is utilized to co-crystallize the two molecules. Homosynthons associated with the isoniazid and the π stacking of the terephthalic acid produce fastest crystal growth in one direction to give needle-shaped co-crystals.[IMAGE]

Site-selective assembly between 1,8-diiodoperfluorooctane and 4,7,8,11-tetraazahelicene driven by halogen bonding

The X-ray diffraction analysis on single crystals obtained from the self-assembly of 1,8-diiodoperfluorooctane 1 with the tetraazahelicene derivative 2 revealed a site-selective pattern of halogen bonds (XBs) in the solid state. Indeed, two non-equivalent XBs drive the formation of an indefinitely repeating pentameric (1)3·(2)2 unit. Interestingly, the N…I–C bonding formation occurred selectively on the pyridazinic/cinnolinic nitrogen atoms of the tetraazahelicene unit, which were preferred over the pyridinic/quinolinic ones. On the basis of molecular electrostatic potential and molecular orbital analyses, DFT calculations predicted and explained well this site-selective XB formation, thus demonstrating to be efficient tools for the prediction of the XB site selectivity in similar polynitrogen systems.

From a Simple Pyrazole‐Derived 1,2‐Amino Alcohol to Mono‐ and Multinuclear Complexes by Tailoring Hydrogen Bond Patterns

AbstractStarting from easily accessible ethyl‐5(3)‐methylpyrazole‐3(5)‐carboxylate, 2‐[(1,5‐dimethyl)pyrazol‐3‐yl]propan‐2‐ol (3) can be obtained in good yields in just two steps. The latter compound undergoes coordination to a series of transition metal ions; the resulting complexes were characterized by means of spectroscopy and magnetic measurements.

An efficient algorithmic approach for mass spectrometry-based disulfide connectivity determination using multi-ion analysis

BackgroundDetermining the disulfide (S-S) bond pattern in a protein is often crucial for understanding its structure and function. In recent research, mass spectrometry (MS) based analysis has been applied to this problem following protein digestion under both partial reduction and non-reduction conditions. However, this paradigm still awaits solutions to certain algorithmic problems fundamental amongst which is the efficient matching of an exponentially growing set of putative S-S bonded structural alternatives to the large amounts of experimental spectrometric data. Current methods circumvent this challenge primarily through simplifications, such as by assuming only the occurrence of certain ion-types (b-ions and y-ions) that predominate in the more popular dissociation methods, such as collision-induced dissociation (CID). Unfortunately, this can adversely impact the quality of results.MethodWe present an algorithmic approach to this problem that can, with high computational efficiency, analyze multiple ions types (a, b, bo, b*, c, x, y, yo, y*, and z) and deal with complex bonding topologies, such as inter/intra bonding involving more than two peptides. The proposed approach combines an approximation algorithm-based search formulation with data driven parameter estimation. This formulation considers only those regions of the search space where the correct solution resides with a high likelihood. Putative disulfide bonds thus obtained are finally combined in a globally consistent pattern to yield the overall disulfide bonding topology of the molecule. Additionally, each bond is associated with a confidence score, which aids in interpretation and assimilation of the results.ResultsThe method was tested on nine different eukaryotic Glycosyltransferases possessing disulfide bonding topologies of varying complexity. Its performance was found to be characterized by high efficiency (in terms of time and the fraction of search space considered), sensitivity, specificity, and accuracy. The method was also compared with other techniques at the state-of-the-art. It was found to perform as well or better than the competing techniques. An implementation is available at: http://tintin.sfsu.edu/~whemurad/disulfidebond.ConclusionsThis research addresses some of the significant challenges in MS-based disulfide bond determination. To the best of our knowledge, this is the first algorithmic work that can consider multiple ion types in this problem setting while simultaneously ensuring polynomial time complexity and high accuracy of results.

Inactive extracellular superoxide dismutase disrupts secretion and function of active extracellular superoxide dismutase

Extracellular superoxide dismutase (EC-SOD) is an antioxidant enzyme that protects cells and tissues from extracellular damage by eliminating superoxide anion radicals produced during metabolism. Two different forms of EC-SOD exist, and their different enzyme activities are a result of different disulfide bond patterns. Although only two folding variants have been discovered so far, five folding variants are theoretically possible. Therefore, we constructed five different mutant EC-SOD expression vectors by substituting cysteine residues with serine residues and evaluated their expression levels and enzyme activities. The mutant EC-SODs were expressed at lower levels than that of wild-type EC-SOD, and all of the mutants exhibited inhibited extracellular secretion, except for C195S ECSOD. Finally, we demonstrated that co-expression of wild-type EC-SOD and any one of the mutant EC-SODs resulted in reduced secretion of wild-type EC-SOD. We speculate that mutant EC-SOD causes malfunctions in systems such as antioxidant systems and sensitizes tissues to ROS-mediated diseases.

Edge effects, electronic arrangement, and aromaticity patterns on finite-length carbon nanotubes

Previous investigations have revealed that even long carbon nanotubes (CNTs) retain bond patterns that are characterized by the localization of Clar rings. Even for CNTs with 10 nm length, an alternated, oscillating structure of Clar and Kekulé patterning was also found, indicating that these arrangements may possibly persist for even longer nanotubes, given that they are finite. In the present work, we perform a detailed and comprehensive theoretical study of this phenomenon, in order to find the causes that give rise to these patterns. A complete set of CNTs with different chiralities, diameters (up to 2 nm), lengths (up to 10 nm) and endings (capped, uncapped, and tailored endings) was considered for such purposes. The results indicate that the Clar patterning appears not only on armchair CNTs, but also on those with chiral angle values close to 30°, and this results in a stabilization of the structure, when compared with the uniform, zigzag CNTs. This stabilizing effect points to the causes that underlie the three Nakamura CNT types, resulting as the superposition of structures with a maximal number of Clar rings. Although there is a strict dependence on the border shape, the main cause of the bond patterning in long tubes is to be found in the intrinsic wrapping of each CNT, because the type and number of oscillations present in the longest structures do not depend on the particular length. Nevertheless, the three Nakamura types of armchair tubes appear to subsist beyond the appearance of oscillations, because each of these sets evolves in a different manner, and energy properties that link them together. Apart from the geometry, Clar patterning was investigated through NICS (Nucleus Independent Chemical Shifts) measures, which reveal a connection between the Clar rings and a local concentration of aromaticity.

Structural and dynamic effects of changing the pattern of disulfide bonds in the vascular endothelial growth factor

Structural and dynamic effects of changing the pattern of disulfide bonds in the vascular endothelial growth factor

Affinity of Avr2 for tomato cysteine protease Rcr3 correlates with the Avr2‐triggered Cf‐2‐mediated hypersensitive response

The Cladosporium fulvum Avr2 effector is a novel type of cysteine protease inhibitor with eight cysteine residues that are all involved in disulphide bonds. We have produced wild-type Avr2 protein in Pichia pastoris and determined its disulphide bond pattern. By site-directed mutagenesis of all eight cysteine residues, we show that three of the four disulphide bonds are required for Avr2 stability. The six C-terminal amino acid residues of Avr2 contain one disulphide bond that is not embedded in its overall structure. Avr2 is not processed by the tomato cysteine protease Rcr3 and is an uncompetitive inhibitor of Rcr3. We also produced mutant Avr2 proteins in which selected amino acid residues were individually replaced by alanine, and, in one mutant, all six C-terminal amino acid residues were deleted. We determined the inhibitory constant (K(i) ) of these mutants for Rcr3 and their ability to trigger a Cf-2-mediated hypersensitive response (HR) in tomato. We found that the two C-terminal cysteine residues and the six amino acid C-terminal tail of Avr2 are required for both Rcr3 inhibitory activity and the ability to trigger a Cf-2-mediated HR. Individual replacement of the lysine-17, lysine-20 or tyrosine-21 residue by alanine did not affect significantly the biological activity of Avr2. Overall, our data suggest that the affinity of the Avr2 mutants for Rcr3 correlates with their ability to trigger a Cf-2-mediated HR.

Analysis of the stabilities of hexameric amyloid-β(1–42) models using discrete molecular dynamics simulations

Amyloid-β (Aβ) oligomers appear to play a pivotal role in Alzheimer's disease. A 42 residue long alloform, Aβ42, is closely related to etiology of the disease. In vitro results show evidences of hexamers; however structures of these hexamers have not been resolved experimentally. Here, we use discrete molecular dynamics (DMD) to analyze long duration stabilities of Aβ42 hexamer models developed previously in our lab. The hydrophobic core of these models is a six-stranded β-barrel with 3-fold radial symmetry formed by residues 30–40. This core is shielded from water by residues 1–28. The nine models we analyzed differ by the relative positions of the core β-strands, and whether the other segments surrounding the core contain α helices or β-strands. A model of an annular protofibril composed of 36 Aβ peptides was also simulated. Results of these model simulations were compared with results of aggregation simulations that started from six well separated random coils of Aβ42 and with simulations of two known β-barrel structures. These results can be categorized into three groups: stable models with properties similar or superior to those of experimentally determined β-barrel proteins, aggregation-prone models, and an amorphous aggregate from random coils. Conformations at the end of the simulation for aggregation-prone models have exposed hydrophobic core with dangling β-strands on the surface. Hydrogen bond patterns within the β-barrel were a critical factor for stability of the β-barrel models. Aggregation-prone conformations imply that the association of these hexamers may be possible, which could lead to the formation of larger assemblies.

Electron Density Based Characterization of π Bonds in Planar Molecules

A new method has been developed to detect and analyze molecular π systems. The concept of bonding critical point is generalized to electronic π systems, and it is shown how a π bond can be characterized via the corresponding bond critical point (BCP) in planar molecules. In this context, charge density and its Laplacian at the BCP(π) of a strongly delocalized π system can be distinguished from that of a localized one. The presented formalism is applied to three types of nanoconductors as conjugated polyenes, which revealed the alternative pattern of the double bonds. Also, several cyclic conjugated molecules are considered to explore their π electronic structure and aromaticity.

Conformational characterization of disulfide bonds: A tool for protein classification

Background Throughout evolution, mutations in particular regions of some protein structures have resulted in extra covalent bonds that increase the overall robustness of the fold: disulfide bonds. The two strategically placed cysteines can also have a more direct role in protein function, either by assisting thiol or disulfide exchange, or through allosteric effects. In this work, we verified how the structural similarities between disulfides can reflect functional and evolutionary relationships between different proteins. We analyzed the conformational patterns of the disulfide bonds in a set of disulfide-rich proteins that included twelve SCOP superfamilies: thioredoxin-like and eleven superfamilies containing small disulfide-rich proteins (SDP). Results The twenty conformations considered in the present study were characterized by both structural and energetic parameters. The corresponding frequencies present diverse patterns for the different superfamilies. The least-strained conformations are more abundant for the SDP superfamilies, while the “catalytic” +/−RHook is dominant for the thioredoxin-like superfamily. The “allosteric” –RHSaple is moderately abundant for BBI, Crisp and Thioredoxin-like superfamilies and less frequent for the remaining superfamilies. Using a hierarchical clustering analysis we found that the twelve superfamilies were grouped in biologically significant clusters. Conclusions In this work, we carried out an extensive statistical analysis of the conformational motifs for the disulfide bonds present in a set of disulfide-rich proteins. We show that the conformational patterns observed in disulfide bonds are sufficient to group proteins that share both functional and structural patterns and can therefore be used as a criterion for protein classification.

The Protein-disulfide Isomerase DsbC Cooperates with SurA and DsbA in the Assembly of the Essential β-Barrel Protein LptD

The assembly of the β-barrel proteins present in the outer membrane (OM) of Gram-negative bacteria is poorly characterized. After translocation across the inner membrane, unfolded β-barrel proteins are escorted across the periplasm by chaperones that reside within this compartment. Two partially redundant chaperones, SurA and Skp, are considered to transport the bulk mass of β-barrel proteins. We found that the periplasmic disulfide isomerase DsbC cooperates with SurA and the thiol oxidase DsbA in the folding of the essential β-barrel protein LptD. LptD inserts lipopolysaccharides in the OM. It is also the only β-barrel protein with more than two cysteine residues. We found that surAdsbC mutants, but not skpdsbC mutants, exhibit a synthetic phenotype. They have a decreased OM integrity, which is due to the lack of the isomerase activity of DsbC. We also isolated DsbC in a mixed disulfide complex with LptD. As such, LptD is identified as the first substrate of DsbC that is localized in the OM. Thus, electrons flowing from the cytoplasmic thioredoxin system maintain the integrity of the OM by assisting the folding of one of the most important β-barrel proteins.

A Novel Disulfide Pattern in Laminin-Type Epidermal Growth Factor-like (LE) Modules of Laminin β1 and γ1 Chains

In-depth mass spectrometric analysis of disulfide bond patterns in recombinant mouse laminin β1 and γ1 chain N-terminal fragments comprising the laminin N-terminal (LN) domain and the first four laminin epidermal growth factor-like (LE) domains revealed a novel disulfide pattern for LE domains. This showed a (2-3, 4-5, 6-7, 8-1) connectivity with the last cysteine of one LE domain being connected to the first cysteine of the following LE domain. The same pattern was also found in E4, the N-terminal β1 chain fragment derived by elastase digestion of mouse EHS tumor laminin-111, showing that this pattern occurs in native laminin. The strictly linear pattern with an interdomain disulfide has not been described previously for EGF domains. The N-terminal portions of laminin short arms, consisting of the LN domain and LE domains 1-4, are essential for laminin-laminin self-interactions, whereas the internal LE domains 7-9 in the laminin γ1 chain harbor the nidogen binding site and have a conventional disulfide pattern. This suggests that LE domains differing in function also differ in their disulfide patterns.

On the crystal structures and hydrogen bond patterns in proline pseudopolymorphs

Amino acids often cocrystallize with water molecules, which make them pseudopolymorphs of their anhydrous forms. In this work, we discuss in detail the hydrogen bond patterns in anhydrous L-proline and DL-proline and its pseudopolymorphic forms: L-proline monohydrate and DL-proline monohydrate. For this propose, the crystal structure of L-proline anhydrous was determined from synchrotron X-ray powder diffraction data and refined using the Rietveld method. Special emphasis is given to the role played by the water molecule in the hydrogen bond network observed in the crystalline structures.

Molecular Complexes of Alprazolam with Carboxylic Acids, Boric Acid, Boronic Acids, and Phenols. Evaluation of Supramolecular Heterosynthons Mediated by a Triazole Ring

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O--H...N hydrogen bonds with the triazole ring.