Nonplanar Form Research Articles

Conformational analysis of carboxylic acid anhydrides: A microwave and computational study

The microwave spectra of four carboxylic acid anhydrides, RCOOCOR′, (R,R′) = (CH3,CF3), (C(CH3)3,CF3), (C6H5, CF3) and (CH3, C(CH3)3), have been observed in a supersonic jet. Calculations at the M06-2X/6-311++G(d,p) and MP2/6-311++G(d,p) levels of theory predict the lowest energy conformations for all four species to be nonplanar cis structures, i.e., conformations in which the C=O groups point in approximately the same direction, but are twisted out of a coplanar orientation. The observed spectra are consistent with these predictions. In addition, for all but the (R,R′) = (CH3, C(CH3)3) species, higher energy nonplanar trans conformers are also predicted, typically within 1–2 kcal/mole the nonplanar cis form. For (R,R′)= (C(CH3)3, CF3), extensive isotopic substitution has enabled a determination of most of the (non-fluorine) heavy atom structural parameters. Excellent agreement with the DFT and MP2 structures was obtained, thus validating the theoretical methods used. A strong correlation is found between the calculated O=C⋯C=O dihedral angle and the average of the vapor phase C=O stretching frequencies of RCOOH and R′COOH.

Non-planar form factors of generic local operators via on-shell unitarity and color-kinematics duality

Form factors, as quantities involving both local operators and asymptotic particle states, contain information of both the spectrum of operators and the on-shell amplitudes. So far the studies of form factors have been mostly focused on the large Nc planar limit, with a few exceptions of Sudakov form factors. In this paper, we discuss the systematical construction of full color dependent form factors with generic local operators. We study the color decomposition for form factors and discuss the general strategy of using on-shell unitarity cut method. As concrete applications, we compute the full two-loop non-planar minimal form factors for both half-BPS operators and non-BPS operators in the SU(2) sector in mathcal{N} = 4 SYM. Another important aspect is to investigate the color-kinematics (CK) duality for form factors of high-length operators. Explicit CK dual representation is found for the two-loop half-BPS minimal form factors with arbitrary number of external legs. The full-color two-loop form factor result provides an independent check of the infrared dipole formula for two-loop n-point amplitudes. By extracting the UV divergences, we also reproduce the known non-planar SU(2) dilatation operator at two loops. As for the finite remainder function, interestingly, the non-planar part is found to contain a new maximally transcendental part beyond the known planar result.

DFT Study on Conformation of 1-Alkyl-3-methylimidazolium with Ethyl, Propyl, Butyl, Pentyl, and Hexyl Group

Abstract Comprehensive conformational analyses of 1-alkyl-3-methylimidazolium cations ([Cnmim]+ where n = 2–6) were performed by DFT calculations with dispersion correction in the gas phase. The energy difference (ΔE) of each conformer from the non-planar and all-trans (t) form was calculated. The planar forms have 2–3 kJ mol−1 higher energy than the corresponding non-planar form. A significant difference between these two forms is that unlike the non-planar form, the planar form cannot take gauche (g) or gauche′ (g′) in the second dihedral angle of the alkyl group. The conformational behavior for the alkyl group somewhat resembles that of alkane while interactions between the alkyl group and the imidazolium ring play an important role for [Cnmim]+ in both attractive and repulsive ways. For example, when the conformers contain g/g′ in the inner dihedral position, they tend to provide low ΔE due to the attractive interaction. Meanwhile, the strong repulsive interactions coming from steric hindrance do not allow some non-planar forms to stably exist. Instead, such a conformer takes the planar form that experiences less steric hindrance. The calculated results were compared with those from the Cambridge Structural Database, and Raman bands of the calculated cations were displayed and discussed.

Unique Features of Metformin: A Combined Experimental, Theoretical, and Simulation Study of Its Structure, Dynamics, and Interaction Energetics with DNA Grooves.

There are certain small molecules that exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as an antidiabetic drug for type-two diabetes. Recent lines of evidence of its role in antitumor activities and increasing the survival rates of cancer patients (namely, colorectal, breast, pancreas, and prostate cancer) are emerging. However, theoretical studies of the structure and dynamics of metformin have not yet been fully explored. In this work, we investigate the characteristic structural and dynamical features of three monoprotonated forms of metformin hydrochloride with the help of experiments, quantum chemical calculations, and atomistic molecular dynamics simulations. We validate our force field by comparing simulation results to those of the experimental findings. Energetics of proton transfer between two planar monoprotonated forms reveals a low energy barrier, which leads us to speculate a possible coexistence of them. Nevertheless, among the protonation states, we find that the nonplanar tautomeric form is the most stable. Our calculated values of the self-diffusion coefficient agree quantitatively with NMR results. Metformin forms strong hydrogen bonds with surrounding water molecules, and its solvation dynamics shows unique features. Because of an extended positive charge distribution, metformin possesses features of being a permanent cationic partner toward several targets. We study its interaction and binding ability with DNA using UV spectroscopy, circular dichroism, fluorimetry, and metadynamics simulation. We find a nonintercalative mode of interaction. Metformin feasibly forms a minor/major groove-bound state within a few tens of nanoseconds, preferably with AT-rich domains. A significant decrease in the free energy of binding is observed when it binds to a minor groove of DNA.

Shield Optimization and Formulation of Regression Equations for Split-Ring Resonator

Microwave resonators are widely used for numerous applications including communication, biomedical and chemical applications, material testing, and food grading. Split-ring resonators in both planar and nonplanar forms are a simple structure which has been in use for several decades. This type of resonator is characterized with low cost, ease of fabrication, moderate quality factor, low external noise interference, high stability, and so forth. Due to these attractive features and ease in handling, nonplanar form of structure has been utilized for material characterization in 1–5 GHz range. Resonant frequency and quality factor are two important parameters for determination of material properties utilizing perturbation theory. Shield made of conducting material is utilized to enclose split-ring resonator which enhances quality factor. This work presents a novel technique to develop shield around a predesigned nonplanar split-ring resonator to yield optimized quality factor. Based on this technique and statistical analysis regression equations have also been formulated for resonant frequency and quality factor which is a major outcome of this work. These equations quantify dependence of output parameters on various factors of shield made of different materials. Such analysis is instrumental in development of devices/designs where improved/optimum result is required.

Analysis, simulation, and experimental verification of split‐ring resonator

ABSTRACTSplit‐ring resonator (SRR) finds its utility in various applications where moderate quality factor is required. Application areas for this type of microwave resonator include communication, biomedical, chemical, material testing, and food grading. Design is usually based for a particular band of frequency, dictated by its intended utility/application. A metallic cylindrical shield or cavity is used to enclose resonator for controlling environmental effects. Quality factor determines resonator's figure of merit. Resonant frequency, quality factor, and other output parameters are dependent mainly on critical dimensions and materials used to fabricate resonator and shield. Numerous models have been formulated to predict output parameters. In this study, variations in quality factor and resonant frequency have been analyzed for nonplanar form of SRR structure model based on parametric changes. Simulated and calculated results were analyzed for model validity. Sensitivity analysis was performed to determine sensitivity of output parameters over SRR dimensions. Output parameters of SRR structure fabricated to operate at 3 GHz, was measured for experimental verification of simulated and calculated results. © 2015 Wiley Periodicals, Inc. Microwave Opt Technol Lett 57:2358–2363, 2015

A New Class of Thin Composite Parts for Small Batch Productions

During the manufacturing process of polymeric composite materials, geometric unconformities may arise due to the onset of residual stresses, that are due to the chemical shrinkage of the matrix, to the polymerization process and to the difference in value between the CTE of matrix and that of fibres during cooling. The behaviour of thin non-planar form laminates (L, T, U shapes) is not the same of flat ones: even if the laminate presents a symmetrical and balanced structure, the condition of stresses and deformations is more complex and causes geometric deviations. The solution currently used to solve this problem is the equipment compensation. In this paper a new class of thin composite parts is presented. It consists of prepreg laminate stratified around an aluminium core, which serves as mould. In this way a new L-shape laminate may be developed for example. Experimental tests were carried out to produce the new class of composite parts. The obtained results demonstrated that the new class of thin composite parts is characterized by reduced geometrical unconformities. Moreover, it does not require an external forming mould, that is geometrically very complex, but an internal one, that is an aluminium core. The aluminium core is cheap, but it remains inside the part; therefore, the new class of parts is not adapt to large batch production. Finally, the new class presents a thermo-mechanical behaviour so simple that it is possible to foresee it numerically.

Trans- and cis-stilbene isolated in cryogenic argon and xenon matrices

Monomers of trans- (TS) and cis-stilbene (CS) were isolated in cryogenic argon and xenon matrices, and their infrared (IR) spectra were fully assigned and interpreted. The interpretation of the vibrational spectra received support from theoretical calculations undertaken at the DFT(B3LYP)/6-311++G(d,p) level of theory. In situ broadband UV irradiation of the matrix-isolated CS led to its isomerization to TS, which appeared in the photolysed matrices in both non-planar and planar configurations. The non-planar species was found to convert into the more stable planar form upon subsequent annealing of the matrices at higher temperature. TS was found to be photostable under the used experimental conditions. The structure of the non-planar TS form was assigned based on the comparison of its observed IR spectrum with those theoretically predicted for different conformations of TS. Chemometrics was used to make this assignment. Additional reasoning on the structure of the studied stilbenes is presented taking as basis results of the Natural Bond Orbital analysis.

Encapsulation and isomerization of curcumin with cyclodextrins characterized by electronic and vibrational spectroscopy

FT-Raman and UV–visible adsorption spectroscopy are applied for the first time in the structural study of the antioxidant, antitumoral polyphenol curcumin and its complexation with β- and γ-cyclodextrin. Additionally, high performance liquid chromatography linked to UV spectroscopy was employed to monitor the encapsulation yield of curcumin. These techniques indicate that the effectiveness of the encapsulation is higher in the case of γ-cyclodextrin (γ-CD) likely due to the better fit of the polyphenol size with the dimensions of the γ-CD cavity. Raman spectra provided specific structural information from the ligand which indicates that the encapsulation takes place at the level of the aromatic rings, through H-bonds, and that a tautomerization from the planar keto enol form to the non-planar diketo form of curcumin also occurs. These changes may lead to an increase of the chemical stability, the bioavailability and the biological activity of curcumin.

Excited-state intramolecular proton transfer and charge transfer in 2-(2′-hydroxyphenyl)benzimidazole crystals studied by polymorphs-selected electronic spectroscopy

Crystal structures of polymorphs of 2-(2'-hydroxyphenyl)benzimidazole (HPBI), Forms α and β, are analyzed by X-ray crystallography. The fluorescence excitation (FE) and fluorescence spectra of the polymorphs are separately observed at temperatures 77-298 K. It has been found that the electronic spectra of the two crystal forms are significantly different from each other. Photo-excitation of the enol forms in Forms α and β induces the excited-state intramolecular proton transfer (ESIPT) to produce the S(1) state of the keto forms. In the FE spectra of Forms α and β, the S(1) ← S(0) (ππ*) transition of the keto form is observed in the 360-420 nm region in addition to that of the enol form in the 250-420 nm region. In the FE spectrum of Form β a new band peaking at 305 nm is observed, which is assigned to the S(1) ← S(0) transition of a non-planar enol form based on the observation of dual fluorescence in the UV and visible regions and quantum chemical calculation on the transition energy against the twisted angle between the benzimidazole and hydroxyphenyl rings. The fluorescence quantum yield (φ(T)) for the keto form is remarkably dependent on polymorphs at room temperature; φ(T) = 0.53 for Form α is much larger than φ(T) ≤ 0.23 for Form β. At 77 K the φ(T) values for Forms α and β increase to 0.67 and ≤0.57, respectively. The changes in the φ(T) values are associated with the intramolecular charge transfer (ICT) state. The potential barrier height between the S(1)-keto and S(1)-ICT states is significantly lower for Form β than for Form α. At 77 K the S(1)-keto → S(1)-ICT process followed by S(1)-ICT → S(0)-keto internal conversion is significantly suppressed in Form β. We compare difference in the dynamics between Forms α and β in the electronic ground and excited states.

Microwave Spectrum and Conformational Composition of 1-Vinylimidazole

The microwave spectrum of 1-vinylimidazole has been investigated in the 21-80 GHz spectral region. The spectra of two conformers have been assigned. One of these forms is planar, while the other is nonplanar with the imidazole ring and the vinyl group forming an angle of 15(4)° from coplanarity. The planar form is found to be 5.7(7) kJ/mol more stable than the nonplanar rotamer by relative intensity measurements. The spectra of 10 vibrationally excited states of the planar form and one excited-state spectrum of the nonplanar form were assigned. The vibrational frequencies of several of these states were determined by relative intensity measurements. The microwave work has been augmented by quantum chemical calculations at the CCSD/cc-pVTZ, MP2/cc-pVTZ, and B3LYP/cc-pVTZ levels of theory. The B3LYP calculations predict erroneously that both forms of 1-vinylimidazole are planar, whereas the MP2 and CCSD calculations correctly predict the existence of a planar and a nonplanar conformer of this compound.

IgM and its receptors: Structural and functional aspects

This review combines the data obtained before the beginning of the 1990s with results published during the last two decades. The predominant form of the IgM molecule is a closed ring composed of five 7S subunits and a J chain. The new model of spatial structure of the pentamer postulates nonplanar mushroom-shaped form of the molecule with the plane formed by a radially-directed Fab regions and central protruding portion consisting of Cµ4 domains. Up to the year 2000 the only known Fc-receptor for IgM was pIgR. Interaction of IgM with pIgR results in secretory IgM formation, whose functions are poorly studied. The receptor designated as Fcα/µR is able to bind IgM and IgA. It is expressed on lymphocytes, follicular dendritic cells, and macrophages. A receptor binding IgM only named FcµR has also been described. It is expressed on T- and B-lymphocytes. The discovery of new Fc-receptors for IgM requires revision of notions that interactions between humoral reactions involving IgM and the cells of the immune system are mediated exclusively by complement receptors. In the whole organism, apart from IgM induced by immunization, natural antibodies (NA) are present and comprise in adults a considerable part of the circulating IgM. NA are polyreactive, germ-line-encoded, and emerge during embryogenesis without apparent antigenic stimuli. They demonstrate a broad spectrum of antibacterial activity and serve as first line of defense against microbial and viral infections. NA may be regarded as a transitional molecular form from invariable receptors of innate immunity to highly diverse receptors of adaptive immunity. By means of interaction with autoantigens, NA participate in maintenance of immunological tolerance and in clearance of dying cells. At the same time, NA may act as a pathogenic factor in atherosclerotic lesion formation and in development of tissue damage due to ischemia/reperfusion.

Comparative study between the X-ray, DFT and Møller–Plesset structure of solid phenoxyacetohydrazide

The structure of phenoxyacetohydrazide was investigated at the B3LYP/6-311G **, MP2/6-311G ** and MP4(SDQ)/6-311G ** levels of theory and compared to the corresponding structure obtained from the X-ray study. At the DFT-B3LYP level, the planar Ttcp conformation of phenoxyacetohydrazide was predicted to be about 0.7 kcal/mol lower in energy than the non-planar Tgcnp structure. At the MP2 and the MP4(SDQ) levels, a reverse conformational behavior was reported where the planar form was predicted to be about 1.3 and 0.5 kcal/mol lower in energy than the non-planar form, respectively. A drastic difference in the COCC torsional angle of about 90° was predicted between the X-ray and the computed ground state structure. The X-ray structure (near-planar Ttcnp) of the molecule was then optimized at the three levels of theory. At the DFT-B3LYP level, the near-planar Ttcnp structure was predicted to turn into the planar Ttcp structure. At the two Møller–Plesset levels the Ttcnp structure was found to be in excellent agreement with the X-ray structure but being 0.5–1.3 kcal/mol higher in energy than the computed lowest energy Tgcnp form. The computed vibrational frequencies of the near-planar structure at the B3LYP/6-311G ** level of calculation were combined with experimental infrared and Raman data to provide tentative vibrational assignments of the molecule.

Does 2-Methylacetophenone Comply with Steric Inhibition of Resonance? A Direct Experimental Proof of Its Nonplanar Conformation from a Joint Ab Initio/Electron Diffraction Analysis

The structure and conformations of 2-methylacetophenone (1) have been investigated by ab initio calculations carried out at the MP2(full)/6-311++G** level and by gas electron diffraction (GED). According to both methods, 1 exists predominantly as a form with the C=O bond synclinal with respect to the C(ar)-C(O) bond (1B), with a torsional angle [C(6)-C(1)-C=O] of 32.7(24) degrees as determined by GED and 26.0 degrees from MP2(full)/6-311++G**. Calculations also predict the presence of a second conformer, the anticlinal structure (1C), with phi = 140.0 degrees, with an abundance of less than 6%, an amount hardly detectable by GED. Different DFT computational protocols both support a nonplanar form of the predominant conformer (B2PLYP) and are in contradiction (B3LYP, M052x, B98, B97-D) with this experimental finding. The GED results, supported by the calculations that involve long-range correlation, are in a good agreement with (13)C NMR spectroscopic investigations, UV spectra, and dipole moment studies. However, previous claims that assumed steric inhibition of resonance caused by a significantly nonplanar conformation with phi close to 90 degrees have been disproved. Steric crowding is evident from the geometrical parameters, particularly from the C(1)-C(2) bond length and from the C(1)-C(2)-C(H(3)) and C(2)-C(1)-C(O) bond angles. It is concluded that any explanation of reactivity by steric inhibition of resonance and by other steric factors must be supported by experimental and/or theoretical investigation of the actual molecular shape.

Organic Electronics at the Interface with Biology

AbstractThe emergence of organic electronics represents one of the most dramatic technological developments of the past two decades. Perhaps the most important frontier of this field involves the interface with biology. The “soft” nature of organics offers better mechanical compatibility with tissue than traditional electronic materials, while their natural compatibility with mechanically flexible substrates suits the nonplanar form factors often required for implants. More importantly, the ability of organics to conduct ions in addition to electrons and holes opens up a new communication channel with biology. In this article, we consider a few examples that illustrate the coupling between organic electronics and biology and highlight new directions of research.

Dechlorination of chlorobenzene in subcritical water with Fe/ZrO2, Ni/ZrO2 and Cu/ZrO2

To obtain information about dechlorination of organochlorine compounds in subcritical water catalyzed by metals assisted with ZrO(2), dechlorination of chlorobenzene has been investigated in the presence of Fe/ZrO(2), Ni/ZrO(2) and Cu/ZrO(2) catalysts. The dechlorination efficiency was increased with increasing residence time, temperature and pressure. The order of effectiveness of the catalysts was Cu/ZrO(2) < Ni/ZrO(2) < Fe/ZrO(2). The dechlorination of chlorobenze obeyed pseudo-first-order kinetics models. The rate constants in subcritical water were much greater than that in ambient-temperature water; the activation energies were obtained. ZrO(2) in the catalyst had the power to absorb chlorobenzene onto the catalyst surface and promoted the dechlorination ability of the metal. The primary mechanism for dechlorinaton of chlorobenzene involved the reduction of chlorobenzene by reaction with nascent hydrogen. The nascent hydrogen reacted with the chlorobenzene, which adsorbed on the catalyst in non-planar and co-planar form, and formed benzene and chloride ions.

CCSD(T) and MRCI studies on the ground and excited states of BrOClO and ClOBrO

AbstractIn this work, three forms (cis, trans and nonplanar) of ClOBrO and BrOClO were optimized at CCSD(T)/cc‐pVTZ level of theory. At the most stable forms (nonplanar form) of ClOBrO and BrOClO, the vertical excitation energies for the lowest six singlet states and two triplet states were calculated at the multireference internally contracted configuration interaction (MRCI) level of theory using cc‐pVDZ, Aug‐cc‐pVDZ, cc‐pVTZ, and Aug‐cc‐pVTZ basis sets. The scalar relativistic effect on the excited states of BrOClO and ClOBrO were estimated. In addition, the potential energy curves of the lowest six singlet states and two triplet states of BrOClO and ClOBrO, as well as BrOOCl were calculated at both MCSCF (complete active space self‐consistent field) and MRCI levels of theory using Aug‐cc‐pVDZ basis set on the active space (18e,12o) along the distances of BrOClO, ClOBrO, and BrOOCl. The results were compared among BrOOCl, ClOBrO, and BrOClO. The first singlet excited state of BrOOCl is 1.12 eV higher than that of BrOClO and 1.36 eV higher than that of ClOBrO at MRCI/cc‐pVTZ level of theory. The first triplet excited state of BrOOCl is 0.77 eV higher than that of BrOClO and 0.86 eV higher than that of ClOBrO at MRCI/cc‐pVTZ level of theory. Most of the excited states of BrOClO studied in this work are unbound states; but most of the ClOBrO and BrOOCl excited states studied in this work are weakly bound states at MRCI level of theory. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009

From planar to nonplanar cyclotriphosphazenes

A possible existence of planar (PNX 2) 3 cyclotriphosphazene, where X = H, F, Cl and Br, or nonplanar (PXNX) 3 was studied at the B3LYP/6-311++G ∗∗ and MP2/6-311++G ∗∗ level of calculations. A linear correlation of total electronic energy difference (Δ E = E nonplanar − E planar) on electronegativity of the X substituent was observed. The more stable nonplanar form was predicted (Δ E = −43.49 kcal/mol) only in case of X = H. The remaining planar halogenocyclotriphosphazenes are more stable, in agreement with a few available experimental data.

Ab Initio Static and Molecular Dynamics Study of 4‐Styrylpyridine

We report an in-depth theoretical study of 4-styrylpyridine in its singlet S(0) ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree-Fock (HF), second-order Møller-Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post-HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis=trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car-Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within approximately 1 ps during the simulation carried out at 150 K on this isomer.

Molecular mechanics parameters for the FapydG DNA lesion

FapydG is a common oxidative DNA lesion involving opening of the imidazole ring. It shares the same precursor as 8-oxodG and can be excised by the same enzymes as 8-oxodG. However, the loss of the aromatic imidazole in FapydG results in a reduction of the double bond character between C5 and N7, with an accompanying increase in conformational flexibility. Experimental characterization of FapydG is hampered by high reactivity, and thus it is desirable to investigate structural details through computer simulation. We show that the existing Amber force field parameters for FapydG do not reproduce X-ray structural data. We employed quantum mechanics energy profile calculations to derive new molecular mechanics parameters for the rotation of the dihedral angles in the eximidazole moiety. Using these parameters, all-atom simulations in explicit water reproduce the nonplanar conformation of cFapydG in the crystal structure of the complex with L. lactis glycosylase Fpg. We note that the nonplanar structure is stabilized by an acidic residue that is not present in most Fpg sequences. Simulations of the E-->S mutant, as present in E. coli, resulted in a more planar conformation, suggesting that the highly nonplanar form observed in the crystal structure may not have direct biological relevance for FapydG.