Structural Characterization of RF‐Sputtered a‐C:N Thin Films by Raman,IR, and X‐ray Reflectometry Spectroscopies

Abstract

Amorphous carbon nitride thin films (a‐C:N) were deposited from a carbon target, at room temperature onto silicon substrates, by reactive RF sputtering in a gas mixture of argon and nitrogen. The structural properties of these films have been studied by Raman, infrared (IR), and X‐ray reflectometry spectroscopies. Both the IR and Raman spectra of the a‐C:N films reveal the presence of C–C, C?C, C?N, and C≡N bonding types. The Raman spectra analysis shows, an increase of the C≡N triple bonds content when the concentration of nitrogen C(N₂) in the gas mixture is increased. The Raman intensities ratio between the disorder (D) and graphitic (G) bands increases with C(N₂) suggesting an increased disorder with the incorporation of nitrogen in the carbon matrix. The effect of C(N₂) on the density of a‐C:N films was also investigated by X‐ray reflectometry measurement. The increase of the nitrogen concentration C(N₂) was found to have a significant effect on the density of the films: as C(N₂) increases from 0 to 100%, the density of the a‐C:N films decreases slightly from 1.81 to 1.62 g/cm³. The low values of density of the a‐C:N films were related (i) to the absence of C–N single bonds, (ii) to the increase of disorder introduced by the incorporation of nitrogen in the carbon matrix, and (iii) to the presence of the bands around 2350 cm^?1 and 3400 cm^?1 associated with the C–O bond stretching modes and the O–H vibration, respectively, suggesting a high atmospheric contamination by oxygen and water. The presence of these bands suggests the porous character of the studied samples.     

Raman and surface‐enhanced Raman studies of α‐aminophosphinic inhibitors of metalloenzymes

Here, we report the nature of new di‐α‐amino (L¹–L³) and α‐amino‐α‐hydroxyphosphinic (L⁴–L⁶) acids, which are considered potential inhibitors of the aminopeptidase N, adsorbed on a colloidal silver surface by means of surface‐enhanced Raman scattering (SERS) spectroscopy. In order to reveal the adsorption mechanism of these species from their SERS spectra, Fourier‐transform Raman (FT‐RS) spectra of these nonadsorbed molecules were measured. By examining the enhancement, shift in wavenumbers, and changes in breadth of the SERS bands due to the adsorption process, we revealed that the tilted compounds interact with the colloidal silver substrate mainly through the benzene ring, amino group, and phosphinic moiety in the following way. The benzene ring of L² and L³ is ‘standing up’ on the colloidal silver surface, and the C N bond is almost vertical to it, while the tilt angle between the O PO bond and this surface is greater than 45°. On the other hand, for L¹, L⁴, and L⁵, the aromatic ring and C N bond are arranged more or less tilted, and the tilt angle between the O PO bond and the silver substrate is smaller than 45°. The elongation of the bond to the benzene ring, the L⁶ case, produces an almost horizontal orientation of the benzene ring and the O PO bond on the silver nanoparticles. For these ligands, the complement inhibition IC₅₀ tested in vitro using porcine kidney leucine aminopeptidase was correlated mainly with the behavior of the O PO and C CH N fragments on the silver surface. Copyright © 2009 John Wiley & Sons, Ltd.     

1,1,1‐Trichloro‐3‐(1‐phenethylamino‐ethylidene)‐ pentane‐2,4‐dione—synthesis,spectroscopic, theoretical and structural elucidation

1,1,1‐Trichloro‐3‐(1‐phenethylamino‐ethylidene)‐pentane‐2,4‐dione is spectroscopically and structurally elucidated by means of linear‐polarized IR spectroscopy (IR‐LD) of oriented solids as a colloidal suspension in nematic liquid crystal. Structural information and IR‐spectroscopic assignment are supported by quantum chemical calculations at MP2 and B3LYP level of theory and 6‐311++G** basis set. The geometry is characterized with an inramolecular hydrogen bond of NH^…O?C with length of 2.526 Å and a NHO angle of 140.5(1)°. The NH? C(CH₃)C?C? C?O(CH₃) fragment is nearly flat with a maximal deviation of total planarity of 10.4°. Copyright © 2007 John Wiley & Sons, Ltd.     

Fourier transform infrared spectroscopy to detect thermal degradation of vegetable and chrome-tanned leather

Abstract

The present experimental study determined the thermal degradation stages for vegetable and chrome-tanned leathers (goat and sheep) at 90, 100, and 130?°C by using Fourier transform infrared spectroscopy (FTIR) and differential thermal analysis. Infrared spectra revealed that a temperature of 90?°C affected the adsorbed water band at 3400?cm^?1. Moreover, this temperature slightly reduced the vibrations of amide II and amid III (1340?cm^?1) confirming the preliminary decomposition of protein folds, but it is worth noting that the aliphatic side chains remained stable at this stage of aging. At 100?°C, there was a sharp rupturing in the phenolic-OH bond and side-by-side N–H vibrations decreased dramatically. The peak decomposition occurred at 130?°C, where the amide I and amide III intensities significantly increased, which can be considered indicative of protein unfolding. Those changes are substantiation of protein denaturation. Thermal analysis demonstrated that thermal aging significantly reduced the required temperature for the process of oxidation. The oxidation occurred at 217?°C in goat sample aged at 90?°C. Nevertheless, the reference sample suffered from oxidation at about 220?°C, while with increasing aging temperatures (at 100 and 130?°C), endothermic reactions were observed. Such reactions are usually associated with protein denaturation.     

NMR Studies of Crowded Diels–Alder Adducts of Phencyclone with N‐(2,6‐Dialkylphenyl)maleimides. Hindered Rotations and Magnetic Anisotropy

Abstract

Phencyclone, 1, reacted with N‐(2,6‐dimethylphenyl)maleimide, 2a; with N‐(2,6‐diethylphenyl)maleimide, 2b; and with N‐(2,6‐diisopropylphenyl)maleimide, 2c, respectively, to yield the corresponding Diels–Alder adducts, 3a–c. The adducts were extensively characterized by NMR (7 T) at ambient temperatures using one‐ and two‐dimensional (1D and 2D) proton and carbon‐13 techniques for assignments. Slow exchange limit (SEL) spectra were observed, demonstrating slow rotations on the NMR timescales, for the unsubstituted bridgehead phenyl groups [C(sp³)–C(aryl sp²) bond rotations] and for the 2,6‐dialkylphenyl groups [N(sp²)–C(aryl sp²) bond rotations]. Substantial magnetic anisotropic shifts were seen in the adducts. For example, in the N‐(2,6‐dialkylphenyl) moieties of the adducts, one of the alkyl groups is directed “into” the adduct cavity, toward the phenanthrenoid portion, and these “inner” alkyl proton NMR signals were shifted upfield. Thus, in CDCl₃, the “inner” methyl of adduct 3a exhibits a proton resonance at ?0.13 ppm, upfield of tetramethylsilane (TMS); the “inner” ethyl group signals from 3b appear at 0.026 ppm (CH₂, quartet), and ?0.21 ppm (CH₃, triplet); and the “inner” isopropyl group from 3c is seen at ?0.06 ppm (methine, approx. septet) and ?0.39 ppm (CH₃, doublet). Proton NMR of the crude N‐(2,6‐dialkylphenyl)maleamic acids (used as precursors of the maleimides, 2a–c) exhibited two sets of AB quartet signals, suggesting possible conformers from hindered rotation in the amide groups about the HN–C?O bonds.     

A theoretical conformational study on the structural parameters involved in the ring strain of exo-unsaturated four-membered heterocycles,Y = CCH2CH2X

The effect of ring-puckering angle on the structural parameters (bond lengths and angles) involved in the ring strain of a series of four-membered heterocycles (1–16) was theoretically demonstrated by using the ab initio methods MP2 and HF, and the DFT methods PBE1PBE, B3LYP, SVWN5 with 6-31+G(d,p) as basis set. The results revealed that the bonds within the ring (C–X and C–C) are the most sensitive to puckering angle changes. The variation of the C–X and C=Y bond lengths as function of puckering angle are determined by a balance between the 1,3 repulsive interactions and the electronic nature of the heteroatoms X and Y. Particularly, for azetidines and phosphetanes, the C–X and C=Y bond lengths exhibit a major increase at axial conformations. In general, the C–C bond length decreases with the puckering angle for all heterocycles. While the heteroatom–H bonds (in the ring skeleton) are very sensitive to geometric changes, exhibiting an increasing behaviour for equatorial conformations and a decreasing behaviour for axial conformations highly puckered (? > ?20°). The C–X–C angle decreases monotonically with the puckering angle, increasing the Baeyer strain on the studied molecules. Finally, all methods predicted a similar behaviour for the studied parameters as function of the puckering angle, although some smaller differences in the predictions of their respective values, especially at HF level, were observed.     

Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N–H?···?N, N–H?···?O, O–H?···?O, O–H?···?N, C–H?···?O and C–H?···?N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N–H?···?O and N–H?···?N hydrogen-bond interactions with the contraction of the N–H bond varying from 0.001 to 0.0260?Å and the corresponding blue shift of the stretching frequency by 4–291?cm^?1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N–H?···?N and N–H?···?O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X–H bond in the complexes was studied using natural bond orbital (NBO) analysis.     

Trigonally-compressed octahedral geometry of hexaamminecobalt(III) complex cation in aqueous solution investigated from the electronic spectra

Electronic spectra of hexaamminecobalt(III) complex cation in aqueous solution were analyzed to obtain spectral components. Subsequently, based on the spectral components, the coordination geometry around the cobalt(III) ion was investigated, using the reverse angular overlap model method. The result indicates that the geometry is a trigonally compressed octahedron with the polar angle of 57.9?±?1.0° under D_3d symmetry, where the polar angle is the angle between the trigonal axis and the Co–N bond. From this angle, the top and side N–Co–N bond angles are calculated as 94.4° and 85.6°, respectively. The density functional theory computation supported this trigonally compressed structure in aqueous solution.     

Magnetic brillouin zone effect on the resistivity of semimetallic-like fermi surface in USb

To probe the effect of the protein environment on the retinal chromophore of rhodopsin, we performed molecular dynamics simulations using combined quantum mechanics/molecular mechanics (QM/MM). The starting geometry of the protein is based on the 2.6Å X-ray structure of bovine rhodopsin of Okada et al. [T. Okada, et al. Proc. Natl. Acad. Sci. USA 99 5982 (2002)]. The wild-type chromophore of rhodopsin according to our calculations shows a highly twisted conformation around the central region, from C10 to C13, due to non-bonded interaction with the protein pocket. The absolute sense of twist of the C11–C12 and C12–C13 bonds is negative (?19 ± 9°) and positive (170 ± 8°), respectively. The 13-demethyl retinal chromophore, in which the methyl group at the C13 position is removed, is less distorted in this region. The C11–C12 bond is less twisted (?15 ± 10°) and the C12–C13 bond is planar (179 ± 9°) . The flattened geometry of this artificial chromophore is supported by spectroscopic evidence.     

Theoretical investigation of intramolecular π-type hydrogen bonding and internal rotation of 2-cyclopropen-1-ol, 2-cyclopropen-1-thiol and 2-cyclopropen-1-amine

ABSTRACT

Theoretical computations utilising both CCSD and MP2 methods and the cc-pVTZ basis set have been carried out to determine the structures of several conformations as well as the internal rotation potential energy functions for 2-cyclopropen-1-ol, 2-cyclopropen-1-thiol and 2-cyclopropen-1-amine. The energies and wavefunctions for these potential functions have also been computed. Each of these molecules has an energy minimum corresponding to a conformation with intramolecular π-type hydrogen bonding. The π bonding stabilisation is about 2.3?kcal/mole for the alcohol, 2.1?kcal/mole for the thiol, and about 2.5?kcal/mole for the amine. The results for the thiol demonstrate a rare example of intramolecular π-type hydrogen bonding. The calculated O–H, S–H, N–H, and C=C stretching frequencies have also been compared for the conformations with and without the π-type hydrogen bonding. The C=C stretching frequency is substantially lower in all cases for the hydrogen bonded conformers.     

Effect of protonation on individual hydrogen bonds in the 8-oxoguanine-cytosine base pair: NMR,NBO and AIM analyses

Protonation increases the total binding energy of the 8-oxoguanine-cytosine (8OG:C) base pair by 60–70% at the B3LYP/6-311++G(d,?p) level of theory. It changes the individual H-bond energies, estimated from electron charge densities at bond critical points, by 1.16 to ?16.41?kcal?mol^?1. The individual H-bond energies and the two bond X–Y spin–spin coupling constants (^2hJ_X–Y) increase with protonation where 8OG behaves as an H-bond donor; the reverse is true for the H-bonds in which the 8OG unit acts as an H-bond acceptor. Similar to ^2hJ_X–Y, the value of ^1hJ_O–H (a one-bond H?···?Y spin–spin coupling constant) is distance dependent and in linear correlation with the O?···?H distance, but the ^1hJ_N–H values are independent of the N–H distance and the PSO term is the predominant portion in it. The ¹J_X–H spin–spin coupling constant is dominated by the negative FC term for all hydrogen bonds, although the PSO term is the best to investigate the behaviour of ¹J_X–H across the X–H?·?Y H-bond.     

Structural Investigation of (5-Amino-1,3,4-thiadiazolyl-2-thionato)trimethyltin(IV): 1D Chains Generated by Hydrogen Bonding

ABSTRACT

The geometry of the four-coordinated Sn atom in the title compound, (CH₃)₃Sn(C₂H₂N₃S₂), is distorted tetrahedral with three Sn–C bonds and one Sn–S bond. Two crystallographically distinct molecules a and b within the asymmetric unit are hydrogen bonded. Intermolecular “N–H?N” hydrogen bond interactions generate infinite 1D chains consisting of alternating, centrosymmetric R2,2(8) and R4,2(10) rings.     

Computational study on structures,thermochemical properties,and bond energies of disulfide oxygen (S–S–O)‐bridged CH3SSOH and CH3SS(=O)H and radicals

Cleavage of disulfide bonds is a common method used in linking peptides to proteins in biochemical reactions. The structures, internal rotor potentials, bond energies, and thermochemical properties (Δ_fH°, S°, and Cp(T)) of the S–S bridge molecules CH₃SSOH and CH₃SS(=O)H and the radicals CH₃SS?=O and C?H₂SSOH that correspond to H‐atom loss are determined by computational chemistry. Structure and thermochemical parameters (S° and Cp(T)) are determined using density functional Becke, three‐parameter, Lee–Yang–Parr (B3LYP)/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p). The enthalpies of formation for stable species are calculated using the total energies at B3LYP/6‐31++G (d, p), B3LYP/6‐311++G (3df, 2p), and the higher level composite CBS–QB3 levels with work reactions that are close to isodesmic in most cases. The enthalpies of formation for CH₃SSOH, CH₃SS(=O)H are ?38.3 and ?16.6 kcal mol^?1, respectively, where the difference is in enthalpy RSO–H versus RS(=O)–H bonding. The C–H bond energy of CH₃SSOH is 99.2 kcal mol^?1, and the O–H bond energy is weaker at 76.9 kcal mol^?1. Cleavage of the weak O–H bond in CH₃SSOH results in an electron rearrangement upon loss of the CH₃SSO–H hydrogen atom; the radical rearranges to form the more stable CH₃SS· = O radical structure. Cleavage of the C–H bond in CH₃SS(=O)H results in an unstable [CH₂SS(=O)H]* intermediate, which decomposes exothermically to lower energy CH₂ = S + HSO. The CH₃SS(=O)–H bond energy is quite weak at 54.8 kcal mol^?1 with the H–C bond estimated at between 91 and 98 kcal mol^?1. Disulfide bond energies for CH₃S–SOH and CH3S–S(=O)H are low: 67.1 and 39.2 kcal mol^?1. Copyright © 2011 John Wiley & Sons, Ltd.     

Ionisation energy,electron affinity,and mass spectral decomposition mechanisms of RDX isomers upon electron attachment and electron ionisation

ABSTRACT

The structures, ionisation energies (IE), and electron affinities (EA) of 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) isomers upon loss and gain of an electron were calculated using density functional theory (DFT) methods. The adiabatic electron affinities (EA_ad) range from 1 to 2 eV. The vertical detachment energies are between 1.3 and 4.0 eV. The adiabatic ionisation energies (IE_ad) are in the 9.9–10.2 eV range. The vertical ionisation energies are in the 10.4–10.9 eV range. It is shown that NO₂^?/NO₂ loss would be common in anions and cations, respectively. Isomerisation and N—N bond dissociation accompany cation and anion formation, respectively. The suggested mass spectral fragmentation products for the cations along the S₀ surface are 84, 130, and 176 amu, in agreement with earlier mass spectrometry studies.     

Studies on the σ–hole bonds (halogen,chalcogen, pnicogen and carbon bonds) based on the orientation of crystal structure

ABSTRACT

The 4,7-dibromo-5,6-dinitro-2,1,3-benzothiadiazole (DDBT) crystal has two polymorphic forms [1 M.S. Pavan, A.K. Jana, S. Natarajan, and T.N. Guru Row, J. Phys. Chem. B 119, 11382 (2015).[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]], where the close contacts between two electronegative atoms are identified and studied through Hirshfeld surface analysis. Br---Br and O---O cut-off distances are addressed and analysed. The σ–hole of bromine, sulphur, oxygen atoms and π-hole of carbon and nitrogen atoms were subjected to study using molecular electrostatic potential map and 3D-deformation density map. Sixteen types of dimers from the two forms of crystal structure (6 for form I and 10 for form II) were studied using the charge transfer properties and interaction energies and made detailed analysis of halogen bond (Br---N), dihalogen bond (Br---Br), chalcogen bond (O---Br and S---Br), dichalcogen bond (S---O, O---S and O---O), pnicogen bond (N---O) and carbon bond (C---O and C---Br) interactions. The impact of orientations is discussed to define the type of interaction and its strength through charge transfer mechanism. The contribution of bond angle values for the σ-hole and π–hole bonds are discussed. Utilisation of σ–hole in smaller bond angle values (above 30°) of |θ₁ ? θ₂| existing in type II halogen–halogen bond have been examined in the two forms.     

Electron correlation and the stability of substituted alkenes

Isomerization energies for hexenes (C₆H₁₂) were evaluated with ab initio (Hartree–Fock (HF), MP2, SCS‐MP2, and CCSD(T)) and several density functional approximation (DFA) methods. CCSD(T)/6‐311+G(2d,p) energies were taken as a benchmark standard. The HF method incorrectly predicts that monosubstituted alkenes are more stable than multiply‐substituted alkenes. DFAs generally predict the correct stability trends of alkenes (mono‐, < di‐, < tri‐, < tetra‐substituted alkenes) but errors in popular functionals, such as B3LYP, can be as large as errors found for alkane hydrocarbon thermochemistries. Some of the HF error is traced back to deficiencies in modeling 1,3‐geminal and 1,4‐vicinal alkyl–alkyl group interactions, called vinylbranches, and changes in C? C and C? H bond types (sp³–sp² C? C to sp³–sp³ C? C and sp³ C? H to sp² C? H). The latter is shown to be more significant. Comparison of CCSD(T) energies of trans‐2‐butene with 2‐methylpropylene and cis‐2‐butene suggests that geminal vinylbranches are stabilizing while vicinal vinylbranches are destabilizing. B3LYP and other DFAs have much smaller errors than HF theory due to inclusion of correlation energy that better reproduces bond type changes. Copyright © 2011 John Wiley & Sons, Ltd.     

Study of near surface layer of graphite produced by nitrogen ion bombardment at high doses

To study the modified surface layers of graphites and deposited films of sputtered material, the dependences of sputtering yield Y , and ion-electron emission coefficient γ on ion incidence angle and target temperature under high dose 30 keV N⁺ ₂ ion irradiation have been measured. In the angular range θ=0-80° Y and γ increase approximately as inverse cosθ, Y of POCO-AXF-5Q are 1.5 times larger than of MPG-LT. The dependences of γ (T) manifests a step-like behaviour typical for the radiation induced phase transitions. EPR analysis shows that at near room temperatures the point electron defects are typical of carbon and the defects due to carbon atoms interacting with 14 N nuclei. At elevated temperatures (≥ 300°C) there are the defects typical of graphite-like structures. The films deposited on glass collectors shows for cold targets only the defects typical of carbon, for the heated graphites - also the defects associated with C-¹⁴N nuclei interaction.     

1H and 13C NMR Spectral Study of Some 2r-Aryl-6c-phenylthian-4-ones,Their 1-Oxides and 1,1-Dioxides

ABSTRACT

Four 2r-aryl-6c-phenylthian-4-ones 1b?1e and their 1-oxides 2b?2e and 1,1-dioxides 3b?3e have been newly synthesized. ¹H and ¹³C NMR spectra have been recorded for all these compounds and 2r,6c-diphenylthian-4-one 1-oxide 2a. ¹³C NMR spectrum has been recorded for the sulfone 3a of 1a. For selected compounds ¹H-¹H COSY, HSQC, HMBC, and NOESY spectra have been recorded. The vicinal proton–proton coupling constants suggest that in all these compounds, the heterocyclic ring adopts chair conformation with equatorial orientations of the aryl and phenyl groups. Proton and carbon chemical shifts suggest that in the sulfoxides, the S=O bond is axial and enhances the J _aa value by some special effect. The S = O bond causes a significant upfield shift even on carbons without hydrogens. Significant solvent shifts also were observed.     

Two salts and the salt cocrystal of ciprofloxacin with thiobarbituric and barbituric acids: The structure and properties

Ciprofloxacin (CfH, C₁₇H₁₈FN₃O₃) crystallizes with 2‐thiobarbituric (H₂tba) and barbituric acid (H₂ba) in the aqueous solution to yield salt CfH₂(Htba)·3H₂O ( 1 ), salt cocrystal CfH₂(Hba)(H₂ba)·3H₂O ( 2 ), and salt CfH₂(Hba)·H₂O ( 3 ). The compounds are structurally characterized by the X‐ray single‐crystal diffraction. The numerous intermolecular hydrogen bonds N–H?O and O–H?O formed by water molecules, Htba^?/Hba^? and CfH₂⁺ ions, and H₂ba molecules stabilize the crystal structures of 1 to 3 . Hydrogen bonds form a 2D plane network in the salts of 1 and 3 and a 3D network in the salt cocrystal of 2 . There are different π‐π interactions in 1 to 3 . The compounds have been characterized by powder X‐ray diffraction, thermogravimetry/differential scanning calorimetry, and Fourier transform infrared spectroscopy. The compounds dehydration ends at 130°C to 150°C, and their oxidative decomposition is observed in the range of 250°C to 275°C.     

3D processing map and hot deformation behaviour of a new type Al–Zn–Mg alloy

ABSTRACT

The thermal compression behaviour of Al–Zn–Mg alloy was studied on a thermal simulator machine at the temperature range of 380–540°C and strain rate range of 0.01–10?s^?1. The constitutive equation and 3D processing map of the alloys were established. The microstructure characteristics of the alloy were studied by metallographic observation, electron back-scatter diffraction (EBSD) analysis and transmission electron microscopy (TEM) microstructure analysis. The results show that the peak stress of high-temperature deformation of alloy decreases with the increase of deformation temperature and increases with the increase of strain rate. The dynamic recovery of the alloy occurs at the temperature range of 380–460°C and the strain rate range of 0.01–0.1?s^?1. The dynamic recrystallization of the alloy occurs at the temperature range of 460–500°C and the strain rate range of 0.01–0.1?s^?1. The alloy maintains fine and uniform recrystallized grains at a temperature range of 460–480°C and a strain rate range of 0.01–0.1?s^?1, which is suitable for hot working.