Bond Angle Strain Research Articles

Molecular structure analysis and biological properties investigation on antiseptic drug; 2-amino-1-phenyl-1-propanol using spectroscopic and computational research analysis

The inducement of physical, chemical, structural and biological properties to entice of pharmaceutical property was analyzed by Vibrational spectroscopic, biological and theoretical tools. The structural arrangement for describing structure activity was investigated by injecting ligand groups in internal coordinate system by molecular tools (FT adopted IR, Raman, and NMR). Bond length and bond angle strain was pronounced much due to the chemical equivalent forces extension due to the injection of substitutional groups on base compound and thus non-Centro symmetry was processed. The molecular charge depletion profile was thoroughly studied to persuade protonic and electronic delocalization setup for arranging the drug potential. The chemi-equivalent potential exchange was monitored among different parts of the molecule for obtaining drug mechanism. The biological profile was keenly observed to look at the biological ambiance of the present molecule to fabricate advanced drug. The Lipinski five rule parameters; MV = 137.18, LogP = 0.27, HBD = 2, HBA = 2 and TPSA = 46.2 A2 showed the enhancement of additive drug quality. The exchange of oscillating chemical energy in the core and allied carbons of the base skeleton was keenly noted to find the prearranged chemical environment for successful drug mechanism. The non bonded transitions between Lewis acid and base of bonded molecular system were observed to determine the restoring potential to customize drug potential. The drug assistance for enantiomer characteristics of chirality sequence was displayed to expose the toxicity effect of the molecule. The active molecular bondings on different sites of molecule were measured by estimating polarizability and associated biological inhibition was validated.

Structure and dynamics of succinic, methylsuccinic and itaconic anhydrides in the gas phase

The pure rotational spectra of succinic, itaconic, and methylsuccinic anhydrides were collected in the region of 7–18 GHz using Fourier transform microwave spectroscopy. Each molecule shows varying degrees of puckering, demonstrating the effects of substitution on torsional and bond angle strain. The spectra of all three molecules exhibit perturbations consistent with internal motion; succinic and itaconic anhydride display pseudorotational motion (ΔE = 0.1 cm−1 and 0.2 cm−1, respectively), while methylsuccinic anhydride shows two uncoupled vibrations (ΔE01 = 0.4 cm−1 and ΔE02 = 1.2 cm−1). Analyses of similar five-membered rings demonstrate the relationship between the planarity of the ring and the barrier to pseudorotation.

Influence of co-substitution driven property tailoring in lanthanum orthoferrites (LaFeO3)

Abstract In this paper, effect of partial co-substitution (La by Li at A-site and Fe by Mn at B-site) on structural, electrical, optical and magnetic properties of perovskite type LaFeO 3 is reported. Polycrystalline La 1−x Li x Fe 1−y Mn y O 3 (x = y = 0–0.2) has been prepared by modified Pechini route. X-ray diffraction (XRD) results confirmed single phase polycrystalline powder. Effect of co-substitution on structural property has been noted in terms of changes in Fe/Mn-O-Fe/Mn bond angle and lattice strain on Rietveld refinement. The co-substitution driven structural changes have also been corroborated by fourier transform infrared (FTIR) spectrum in terms of upward shift of Fe/Mn-O stretching mode and downward shift of Fe/Mn-O-Fe/Mn bending mode of vibrations. Surface morphology of the materials indicated typical nanocrystalline microstructure with visible change in grain size with change in substituent concentration. Structural changes on co-substitution has significant effect on magnetic property tailoring arising due to deviation in Fe/Mn-O-Fe/Mn bond angle and/or indirect exchange interactions between two magnetic sub lattices Fe/Mn via intervening oxygen ion. The dielectric spectrum exhibited typical non-Debye type response as confirmed by modulus spectrum which shows peak at specific frequency for all concentration accompanied by shift of peak position towards higher frequency side with increasing concentration. Estimated relaxation time and electrical conductivity shows thermally activated Arrhenius type response with a maximum conductivity ~ 5.37 × 10 −4 S cm −1 at 423 K for 20% co-substitution. This is attributed to combined effect of grain and grain boundary contribution.

Change of local structures for 0.5Li2MnO3–0.5LiMn1/3Ni1/3Co1/3O2 in first charge process of different rates

An investigation was carried out into the charging rate dependence of local structural changes in a layered 0.5Li2MnO3–0.5LiMn1/3Ni1/3Co1/3O2 solid solution during the initial charging cycle. To clarify the mechanism involved in local atomic rearrangement, a pair distribution function (PDF) analysis was performed using the results of powder neutron diffraction and synchrotron X-ray total scattering measurements. First-principles calculations (VASP code) were used to determine the initial structure when performing the PDF analysis. The bond-length strain (λ) and the bond-angle strain (σ 2) for the optimized model were calculated following the PDF analysis in order to clarify the effect of the charging rate on the crystal structure distortion. Before charging, the distortion was small for MnO6 octahedra compared to that for NiO6 and CoO6 octahedra. During charging at a rate of 1C, the MnO6 octahedra experienced increasing distortion, whereas at 3C the CoO6 octahedra became more distorted. In addition, when charging at 3C, the values of λ and σ 2 increased for NiO6 octahedra that had entered the Li layer as a result of cation mixing. This appeared to be related to whether the localized atom was Mn or Co within the average structure during charge process. It is thought that distortion occurs in MO6 octahedra containing whichever element becomes localized, and this depends on the charging rate. This leads to the possibility that decreasing the fractional composition of the element that becomes localized may lead to reduced distortion and improved the cyclability.

Sign-tunable Poisson's ratio in semi-fluorinated graphene.

Poisson's ratio is a fundamental property of a material which reflects the transverse strain response to the applied axial strain. Negative Poisson's ratio is allowed theoretically, but is rare in nature. Besides the discovery and tailoring of bulk auxetic materials, recent studies have also found a negative Poisson's ratio in nanomaterials, while their negative Poisson's ratio is mainly based on conventional rigid mechanical models as bulk auxetic materials. In this work, we report the existence of in-plane negative Poisson's ratio in a two-dimensional convex structure of newly synthesized semi-fluorinated graphene by using first-principles calculations. In addition, the sign of the Poisson's ratio can be tuned by the applied strain. Interestingly, we find that this unconventional negative Poisson's ratio cannot be explained by conventional rigid mechanical models but originates from the enhanced bond angle strain over the bond strain due to chemical functionalization. This new mechanism of auxetics extends the scope of auxetic nanomaterials and can serve as design principles for future discovery and design of new auxetic materials.

Effect of co-substitution on structural, optical, dielectric and magnetic behavior of LaFeO3

Effect of co-substitution by Na at La site and Mn at Fe site of perovskite type LaFeO3 on its structural, optical, dielectric and magnetic properties at room temperature have been studied. Single phase nanocrystalline La1−xNaxFe1−yMnyO3 (x = y = 0–0.2) have been prepared by modified Pechini route. Substantial effect of substitution on structural property has been observed, which is clearly visible in view of changes in Fe/MnOFe/Mn bond angle and lattice strain. The substitution concentration dependent structural changes have also been confirmed by Fourier transform infrared (FTIR) spectrum in terms of upward shift of stretching mode (Fe/MnO) and downward shift of bending mode of vibrations (Fe/MnOFe/Mn). Typical nanocrystalline surface morphology has been observed with visible change in grain size on changes in concentration, which is also confirmed by X-ray diffraction (XRD). These changes have profound effect on magnetic property tailoring and appear to be correlated with Fe/MnOFe/Mn bond angle deviation and indirect exchange interactions between Fe and Mn ions via intervening Oxygen ion. Dielectric response (εr ∼ 103) at room temperature was observed on Na and Mn co-substituted LaFeO3. The dielectric spectrum shows typical non Debye type behavior. Modulus spectrum reveals shift of peak position toward higher frequency side with increasing concentration i.e. concentration dependent relaxation time. Electrical conductivity shows thermally activated Arrhenius type response with a maximum of ∼2.5 × 10−4 S cm−1 at 450 K for La0.85Na0.15Fe0.85Mn0.15O3. Both grain and grain boundary contribution to conduction mechanism has been observed.

Carbon-Bridged Oligo(phenylenevinylene)s: Stable π-Systems with High Responsiveness to Doping and Excitation

The high responsiveness of π-conjugated materials to external stimuli, such as electrons and photons, accounts for both their utility in optoelectronic applications and their chemical instability. Extensive studies on heteroatom-stabilized π-conjugated systems notwithstanding, it is still difficult to combine high performance and stability. We report here that carbon-bridged oligo(p-phenylenevinylene)s (COPV-n) are not only more responsive to doping and photoexcitation but also more stable than the conventional p-phenylenevinylenes and poly(3-hexylthiophene), surviving photolysis very well in air, suggesting that they could serve as building blocks for optoelectronic applications. Activation of the ground state by installation of bond angle strain toward the doped or photoexcited state and the flat, rigid, and hindered structure endows COPVs with stimuli-responsiveness and stability without recourse to heteroatoms. For example, COPV-6 can be doped with an extremely small reorganization energy and form a bipolaron delocalized over the entire π-conjugated system. Applications to bulk and molecular optoelectronic devices are foreseen.

Relaxation and derelaxation of pure and hydrogenated amorphous silicon during thermal annealing experiments

The structural relaxation of pure amorphous silicon (a-Si) and hydrogenated amorphous silicon (a-Si:H) materials, that occurs during thermal annealing experiments, has been analyzed by Raman spectroscopy and differential scanning calorimetry. Unlike a-Si, the heat evolved from a-Si:H cannot be explained by relaxation of the Si–Si network strain but it reveals a derelaxation of the bond angle strain. Since the state of relaxation after annealing is very similar for pure and hydrogenated materials, our results give strong experimental support to the predicted configurational gap between a-Si and crystalline silicon.

Acid catalyzed intramolecular attack of β‐phenylthioureido group on amide function. Parallel formation of thiodihydrouracil and 4‐iminothiodihydrouracil. Different pathways in the Edman degradation reaction in the formation of six‐ versus five‐membered cyclic intermediates

AbstractContrary to the cleavage of α‐phenylthioureido peptides 1 proceeding through intermediate 2‐anilinothiazolinone 2, the b‐analog cis‐2‐(3‐phenylthioureido)cyclopentane‐carboxamide 5 forms transiently 4‐imino‐2‐thioxopyrimidine 6. Monitoring amide cyclization and hydrolysis of iminopyrimidine 6 in acid by UV showed that an equilibrium between 5 and 6 was reached followed by slower conversion of both compounds into 2‐oxo‐4‐thioxopyrimidine 7. Both processes were characterized by isosbestic points, the first due to parallel conversion of 5 into 6 and 7 (or 6 into 5 and 7) at a constant ratio while the second identical for both reactants – to conversion of equilibrated 5 and 6 into 7. The special isosbestic points allowed the determination of the individual constants of Scheme 2. Further confirmation was obtained from NMR product analysis and following the cyclization of amide 5 in DMSO:DCl. Product 2‐oxo‐4‐ thioxopyrimidine 7 hydrolyzed reversibly to thioureido acid 8. The cyclization rate of 8 allowed the participation of 6‐oxothiazine 10 formed by sulfur attack to be excluded. The absence of sulfur attack in the six‐membered case is explained by the longer CS bond bringing about greater bond angle strain at the tetrahedral ring atoms due to the geometrical characteristics of five‐ and six‐membered rings with planar segments. The cyclizations of amide 5 to iminopyrimidine 6 and to thiodihydrouracil 7 are first order in [H+], while the reactions of protonated imine 6H+ are zero order to amide and −1 to thiodihydrouracil. The reaction orders can be reconciled by assuming a rate determining proton transfer from the tetrahedral intermediate in amide cyclization. Copyright © 2007 John Wiley & Sons, Ltd.

Thermally induced stress hysteresis and co-efficient of thermal expansion changes in nanoporous SiO2

The thermomechanical response of electron beam deposited nanoporous silicon dioxide is examined using substrate curvature measurements and nanoindentation. Analysis of the thin film bond angle strain distributions versus temperature indicates that low temperature (T < 100 °C) stress hysteresis and tensioning are primarily attributed to hydrogen bonded water desorption. However, at higher temperatures, the absence of water desorption suggests that the thermomechanical behaviour is related to thermally induced bond angle strain redistributions towards the local bonding environment of quartz and thermally grown silicon dioxide. This is supported by the co-efficient of thermal expansion data that trend lower with higher annealing temperatures. The re-absorption of water into the thin film accounts for the reproducibility of the open-loop stress hysteresis and tensioning observations.

Palladium Pincer Complexes with Reduced Bond Angle Strain: Efficient Catalysts for the Heck Reaction

Palladium pincer complexes composed of six-membered fused metallacycles have been synthesized directly from 1,3-bis(2-pyridyloxy)benzene. The pincer complexes show remarkably high turnover numbers and frequencies in the Heck reaction.

The theoretical study on interaction of hydrogen with single-walled boron nitride nanotubes. I. The reactive force field ReaxFFHBN development

We present a new reactive force field ReaxFF(HBN) derived to accurately model large molecular and condensed phase systems of H, B, and N atoms. ReaxFF(HBN) has been tested against quantum calculation data for B-H, B-B, and B-N bond dissociations and for H-B-H, B-N-B, and N-B-N bond angle strain energies of various molecular clusters. The accuracy of the developed ReaxFF(HBN) for B-N-H systems is also tested for (i) H-B and H-B bond energies as a function of out of plane in H-B(NH2)3 and H-N(BH2)3, respectively, (ii) the reaction energy for the B3N3H6+H2-->B3N3H8, and (iii) crystal properties such as lattice parameters and equations of states for the hexagonal type (h-BN) with a graphite structure and for the cubic type (c-BN) with a zinc-blende structure. For all these systems, ReaxFF(HBN) gives reliable results consistent with those from quantum calculations as it describes well bond breaking and formation in chemical processes and physical properties. Consequently, the molecular-dynamics simulation based on ReaxFF(HBN) is expected to give a good description of large systems (>2000 atoms even on the one-CPU machine) with hydrogen, boron, and nitrogen atoms.

Synthesis and Ring-Opening Metathesis Polymerization of Aryl-Substituted 1,1‘-(1,3-Butadienylene)ferrocenes

The unsaturated aryl-substituted ferrocenophanes 1,1‘-(1-phenylbuta-1,3-diene-1,4-diyl)ferrocene and 1,1‘-(1-mesitylbuta-1,3-diene-1,4-diyl)ferrocene were synthesized and used to prepare high molecular weight conjugated polymers by ring-opening metathesis polymerization. X-ray crystal structures of the phenyl- and mesityl-substituted monomers showed substantial bond angle strain in the butadiene bridge. The monomers were readily polymerized upon exposure to a tungsten-based initiator to give high molecular weight polymers that were soluble in common organic solvents. UV/vis spectral analysis indicated that the aryl moieties gave rise to enhanced conjugation when compared to related alkyl-substituted ferrocene-containing polymers. The enhanced conjugation was further supported by electrochemical analysis. The thermal stability of the new ferrocene-containing polymers was similar to that of oligomeric poly(ferrocenylene), and the conductivities upon doping were on the order of 10-5 S cm-1.

Bond angle versus torsional deformation in an overcrowded alkene: 9-(2,2,2-triphenylethylidene)fluorene.

Competition between bond angle and torsional strain in sterically crowded alkenes generally causes twisting in tetrasubstituted alkenes, while most structurally characterized trisubstituted alkenes are planar. To investigate structural effects of steric repulsion between a planar aromatic ring and a vicinal triphenylmethyl (trityl) group, 9-(2,2,2-triphenylethylidene)fluorene (1 a) was synthesized by reaction of 9-bromomethylenefluorene with triphenylmethyllithium. For comparison with a less strained analogue, 9-ethylidenefluorene (1 b) was prepared by reaction of fluorenone with ethylmagnesium bromide. The X-ray crystal structures show that the difference between bond angles at the 9-fluorenyl carbon atom is much larger for 1 a (12.9 degrees) than 1 b (2.6 degrees). Bond angle and torsional deformations were compared theoretically (HF/6-31+G*) with the tert-butyl analogue (1 c), 1,2,2-tri-tert-butylethene (7), and 2,4,4-trimethyl-2-pentene (8) and crystallographically with six known 1,1-diaryl-2-tert-alkylethenes (2). The trisubstituted alkenes formed three groups with 1) large angle distortion with moderate twisting (1 a, 1 b, and 7), 2) moderate bending with a large range of torsional angles (2), and 3) little bending or twisting (1 b and 8). For the entire series, there appears to be a delicate balance between angle and torsional deformation, but twisting appears to produce smaller relief from steric strain than angle bending. In the crystallographically characterized trisubstituted alkenes, the choice between the two is mainly determined by more subtle packing forces.

Microscopic nature of Staebler-Wronski defect formation in amorphous silicon

Light-induced metastable defects in a-Si:H are proposed to be silicon dangling bonds accompanied by pairs of hydrogen atoms breaking a silicon bond, forming a complex with two Si-H bonds. This supports the model of Branz. These defects are the analog of the H2* defect in c-Si and their energy correlates with the bond-angle strain. Several features of the annealing are well described by this defect complex.

Microscopic Nature of Nature Light Induced Defects

ABSTRACTMolecular dynamics simulations find light-induced metastable defects to be silicon dangling bonds accompanied by (Si-H)2 defect complexes that have two Si-H bonds. These complexes are formed by pairs of hydrogen breaking a silicon bond. This supports the model of Branz. These defects are the analogue of the H2* defect in c-Si and their energy correlates with the bond-angle strain. Several features of annealing including E-field induced effects are well accounted for by the (Si-H)2 defect.

A Remarkable Effect of C-O-C Bond Angle Strain on the Regioselective Double Nucleophilic Substitution of the Acetal Group of Tetraacetal Tetraoxa-Cages and a Novel Hydride Rearrangement of Tetraoxa-Cages.

A remarkable effect of C-O-C bond angle strain on the regioselective double nucleophilic substitution of the acetal group of tetraacetal tetraoxa-cages and a novel regioselective and stereoselective hydride rearrangement of tetraoxa-cages are reported. Reaction of the tetraacetal tetraoxa-cages 1 with 3 equiv of triethylsilane (at -78 degrees C), cyanotrimethylsilane (at 25 degrees C), and allyltrimethylsilane (at -78 degrees C) in dichloromethane in the presence of TiCl(4) gave the double nucleophilic substitution products 2, 6, and 7 in 85-90% yields, respectively. No detectable amount of other regioisomers was obtained. Reaction of 1a with (methylthio)trimethylsilane and (phenylthio)trimethylsilane in dichloromethane in the presence of TiCl(4) at -78 degrees C gave the symmetric products 10a,b and the unsymmetric products 11a,b in ratios of 8-10:1. The stereochemistry of the symmetric substitution products was proven by X-ray analysis of the crystalline compound 10a. The mechanism of the double nucleophilic substitution of the tetraoxa-cages 1 are discussed. Treatment of the tetraoxa-cages 1a,c and 22a-c with 2 equiv of TiCl(4) or MeSO(3)H in dichloromethane at 25 degrees C for 3 h regioselectively and stereoselectively gave the novel hydride rearrangement products 16a,b and 23a-c respectively. No detectable amount of other regioisomers was observed. The stereochemistry of the hydride rearrangement was proven by DIBAL-H reduction of 16 and 23 and X-ray analysis of the reduction product 24a. We attribute the high regioselectivity of the double nucleophilic substitution and the hydride rearrangement of the tetraoxa-cages 1 to the bond angle strain of the unusually large bond angle of C(3)-O(4)-C(5) of the tetraoxa-cages.

X-ray Crystal Structures and ab Initio Calculations on the Photochemically Formed Dewar Isomers of the 4(3H)-Pyrimidinone Derivatives

The structures of the 5-oxo-2,6-diazabicyclo[2.2.0]hex-2-enes (imine Dewar pyrimidinones) 2a-h have been studied by X-ray diffraction analysis and ab initio calculations at the HF/6-31G(d,p) and MP2/6-31G(d,p) levels of theory. The crystal structures of 1-alkyl-3-tert-butyl-6-methyl imine Dewar pyrimidinones 2a-c have been determined at low temperature. The X-ray diffraction studies revealed that both the 2-azetidinone and dihydroazete rings are almost planar, and their eight bond angles are nearly 90 degrees (81-100 degrees ). The C1-N2(=C3) bond distance in the dihydroazete ring is longer due to the bond angle strain by ca. 0.06 Å than that of a typical straight-chain imine molecule. Full geometry optimizations on the imine Dewar isomers (2a and 2d-h) show deviations between the HF and MP2 geometries. The MP2 structure of the 3-tert-butyl-1,6-dimethyl imine Dewar pyrimidinone 2a is compared with those of the X-ray diffraction. The results of the calculations are found to be in good agreement with the X-ray diffraction data. The full geometry optimizations are necessary with the inclusion of electron correlation for the highly strained molecules. The ab initio calculations of the 2-azetidinone 9, 3,4-dihydroazete 11, and N-ethylidenemethylamine 12 have been carried out at the HF and MP2/6-31G(d,p) levels of theory to compare with the structures, orbital hybridization, bond orders, and charge distributions of the Dewar pyrimidinones 2. The theoretical results reveal that the MP2 C1-N2 bond distance of the Dewar pyrimidinone 2a is consistent with the abnormally elongated X-ray C1-N2 bond distance. The electronegative N2 and N6 atoms in the Dewar pyrimidinones 2 give the great positive charge on the C1 atom. The smaller bond angles (ca. 90 degrees ) in the Dewars 2 than typical sp(2) and sp(3) bond angles (ca. 120 and 109 degrees ) increase p character in the endocyclic bonds and decrease p character in the exocyclic bonds.

Proton Exchange and Inversion at Coordinatedsec-Amine Centers. Particularly Rapid Inversion at Sterically Strained “Planar” N in Some [Co(cyclen)(S-AlaO)]2+and [Co(Mecyclen)(S-AlaO)]2+Complexes1

It is shown that the syn(N),syn(O)- isomer (3) is the intermediate on the reaction path for interconversion between the syn(N),anti(O)- (1) and syn(O),anti(N)- (2) diastereomers of syn(Me)-[Co(Mecyclen)(S-AlaO)]2+ and [Co(cyclen)(S-AlaO)]2+. 1H-exchange rate constants for the various NH protons are reported (kH/M-1 s-1, 25 °C, D2O) and are correlated with the derived isomerization rate constants (kN/M-1 s-1, 25 °C, H2O). At equilibrium (25 °C, I ∼ 0.1 M) the [1]:[2]:[3] ratios are 73:21:6 and 63:32:5, respectively, for the two complexes. Ratios of kH/kN show that the two “planar” sec-N centers of the coordinated cyclen ligand are particularly susceptible to inversion, with estimated k2 values for lone pair inversion being between 5 × 106 and 2 × 108 s-1 at 25 °C. The effects of long-range electronegative substituents (trans carboxylate-O, trans amine-N) and CNC bond angle strain on inversion at metal-coordinated amines is discussed.

A mechanism-mediated model for carcinogenicity: model content and prediction of the outcome of rodent carcinogenicity bioassays currently being conducted on 25 organic chemicals.

A hierarchical model consisting of quantitative structure-activity relationships based mainly on chemical reactivity was developed to predict the carcinogenicity of organic chemicals to rodents. The model is comprised of quantitative structure-activity relationships, QSARs based on hypothesized mechanisms of action, metabolism, and partitioning. Predictors included octanol/water partition coefficient, molecular size, atomic partial charge, bond angle strain, atomic acceptor delocalizibility, atomic radical superdelocalizibility, the lowest unoccupied molecular orbital (LUMO) energy of hypothesized intermediate nitrenium ion of primary aromatic amines, difference in charge of ionized and unionized carbon-chlorine bonds, substituent size and pattern on polynuclear aromatic hydrocarbons, the distance between lone electron pairs over a rigid structure, and the presence of functionalities such as nitroso and hydrazine. The model correctly classified 96% of the carcinogens in the training set of 306 chemicals, and 90% of the carcinogens in the test set of 301 chemicals. The test set by chance contained 84% of the positive thio-containing chemicals. A QSAR for these chemicals was developed. This posttest set modified model correctly predicted 94% of the carcinogens in the test set. This model was used to predict the carcinogenicity of the 25 organic chemicals the U.S. National Toxicology Program was testing at the writing of this article.