X‐ray photoelectron and carbon Kα emission measurements and calculations of O‐, CO‐, N‐, and S‐containing substances

X‐ray fluorescence measurements for O‐containing [polyethylene oxide, polyvinyl alcohol, polyvinyl methyl ether], CO‐containing [polyvinyl methyl ketone, polyethylene terephthalate], N‐containing [poly‐4‐vinylpyridine (P4VP), polyaniline oligomer (PAO)], and S‐containing [polyphenylene sulfide] substances are presented. Carbon Kα X‐ray emission spectra (XES) and X‐ray photoelectron spectra (XPS) are compared with our DFT calculations performed with the Amsterdam density functional (ADF) program. The combined analysis of valence XPS and carbon Kα XES allows us to determine the individual contributions from pσ‐ and pπ‐bonding molecular orbitals of the polymers. The ΔSCF calculations yield the accurate C1s core‐electron binding energies (CEBEs) for all carbon sites of the organic compound. We calculate all CEBEs of the model molecules using the ΔE _KS approach. Our simulated C1s photoelectron and C Kα emission spectra are in good agreement with our measurements. We also obtain WD (work function and the other energies) values for the polymers and PAO from the difference between calculated (gas‐phase) and measured (solid) CEBE values. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 162–172, 2007     

Theoretical Auger electron spectra of polymers by density functional theory calculations using model dimers

We propose a new approach for analysis of Auger electron spectra (AES) of polymers by density functional theory (DFT) calculations with the Slater's transition-state concept. Simulated AES and X-ray photoelectron spectra (XPS) of four polymers [(CH2CH2)n (PE), (CH2CH(CH3))n (PP), (CH2CH(OCH3))n (PVME), and (CH2CH(COCH3))n (PVMK)] by DFT calculations using model dimers are in a good accordance with the experimental ones. The experimental AES of the polymers can be classified in each range of 1s-2p2p, 1s-2s2p, and 1s-2s2s transitions for C KVV and O KVV spectra, and in individual contributions of the functional groups from the theoretical analysis.     

Co-adsorption NO and organic molecules on Cu sites in zeolites: Quantum chemical DFT calculations

The co-adsorption of organic molecules: acetone, formaldehyde, ethene and acetylene together with NO on the same Cu⁺ site in zeolite CuZSM-5 was investigated by DFT calculations. The aim of this study was to follow the effect of NO on activation of multiple bonds in organic molecules and the effect of organic molecules on the activation of NO bond. The extent of activation of CO, CC, CC as well as of NO bonds was characterized by the result of calculation as the elongation of the multiple bonds, decrease of bond order as the decrease of stretching frequency, while population analysis gave information on the mechanism of activation. It has been found that the presence of NO co-adsorbed on the same Cu⁺ site as organic molecule resulted in more effective activation of CO bond in acetone and formaldehyde, but resulted in a less effective activation of CC and CC bond in ethane and acetylene. On the other hand, the presence of organic molecule resulted in more effective activation of NO bond (more important bond weakening) in NO molecule. The most significant NO bond weakening took place if NO was co-adsorbed with acetone or formaldehyde. Both acetone and formaldehyde transmit the most negative charge to the Cu⁺-zeolite system if adsorbed “solo” in Cu-zeolite. This negative charge may be next transmitted to antibonding NO orbitals resulting in so important NO bond weakening.     

DFT calculations,microsynthesis and characterization of isopropyl methylphosphonoselenofluoridate [sarin-Se]

Abstract

Isopropyl methylphosphonoselenofluoridate (sarin-Se) was synthesized in order to determine its analytical data and to compare them as well as its reactivity parameters with those of sarin. After synthesis, sarin-Se was characterized using ¹ Mesilaakso, M. In: Mesilaakso, M. (Ed.), Introduction, Chemical Weapons Convention Analysis, Sample Collection, Preparation and Analytical Methods, Wiley, Chichester, 2005.[Crossref] , [Google Scholar]H, ¹³ Rayman, M. P.; Infante, H. G.; Sargent, M. Food-Chain Selenium and Human Health: spotlight on Speciation. Br. J. Nutr. 2008, 100, 238–253.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]?C and ³¹P NMR spectroscopy and high resolution mass spectrometry (HRMS). ¹ Mesilaakso, M. In: Mesilaakso, M. (Ed.), Introduction, Chemical Weapons Convention Analysis, Sample Collection, Preparation and Analytical Methods, Wiley, Chichester, 2005.[Crossref] , [Google Scholar]H and ¹³ Rayman, M. P.; Infante, H. G.; Sargent, M. Food-Chain Selenium and Human Health: spotlight on Speciation. Br. J. Nutr. 2008, 100, 238–253.[Crossref], [PubMed], [Web of Science ®] , [Google Scholar]?C NMR chemical shifts were also calculated using density functional theory (DFT) and compared with experimental data, showing a close agreement. Electrophilicity indices of sarin and sarin-Se were calculated at B3LYP/6-31++G (2d, 2p) level of theory. HOMO-LUMO analysis provides a basis to explain electrophilic nature of sarin-Se and sarin, which are almost similar. Based on calculated data, ³¹P NMR chemical shift and the reactivity of sarin-Se towards some enzymes such as acetylcholinesterase and albumin were explained.     

Complexes of dihydroxybenzenes with carbon monoxide by DFT calculations and FT-IR matrix spectroscopy

Weakly bound complexes of dihydroxybenzenes and nitrophenols with carbon monoxide were the objects of theoretical studies based on the Becke–Lee–Parr density functional. Stability and vibrational spectra of all stable bimolecular complexes were determined and the theoretical results were integrated by matrix isolation FT-IR spectroscopy measurements.     

Analysis of XPS valence band spectra of polymers using a density‐functional theory based calculation of model oligomers

XPS valence band spectra of 10 polymers (PE, PcI, PPG, PVME, PVA, PVMK, PAA, PMA, PMMA, and PGMA) were measured and simulated with the DMol ab initio molecular orbital program. We performed the calculations with model compounds such as trimers, pentamers, or hexamers of the polymers. The theoretical spectra of the oligomers show a good accordance with the experimental data. With the analysis of the calculated partial densities of states it is possible to assign the spectral features to specific atomic groups of the polymers. This gives a new detailed insight into the XPS valence band structure of the investigated polymers. The presented method could also be useful to obtain informations about the chemical structure of polymers with an unknown structure from the XPS valence band spectra. © 1999 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 37: 95–103, 1999     

A conformational study of hydroxylated isoflavones by vibrational spectroscopy coupled with DFT calculations

The conformational preferences of a series of hydroxylated isoflavones were studied by optical vibrational spectroscopy (FTIR and Raman) coupled with density functional theory (DFT) calculations. Special attention was paid to the effect of the hydroxyl substitution, due to the importance of this group in the biological activity of these systems. The isoflavones investigated – daidzein, genistein and formononetin – were shown to exist in distinct conformations in the solid state, namely regarding the orientation of the hydroxylic groups at C⁷ and within the catechol moiety, that are determinant factors for their conformational behaviour and antioxidant ability. In the light of the most stable conformers obtained for each molecule, a complete assignment of their experimental vibrational spectra was performed.     

Conformational studies of bipyrimidine-based mesogens by combination of DFT calculations and temperature-dependent infrared studies

Combination of DFT calculations and solid-state temperature-dependent infrared spectroscopy has confirmed that the central core of recently developed bipyrimidine-based mesogens is not flat, i.e. do not adopt a disc shape, inside the columnar liquid-crystalline phase. For this purpose, the intensities and the frequency shifts of the most sensitive C–N and C–C bands of the central bipyrimidine core have been studied as a function of the temperature and of the dihedral angle. The results support the reported packing model in which the molecules are interdigitated alternatively along their long axis and their short axis to form columns inside the mesophase.     

DFT calculations of 31P spin-spin coupling constants and chemical shift in dioxaphosphorinanes

One-bond heteronuclear spin-spin coupling constants (1)J(PX) (X=H, O, S, Se, C and N) between the phosphorus atom and axial and equatorial substituents in dioxaphosphorinanes are computed using density functional theory (DFT). The experimental values of these coupling constants for a variety of substituents can be applied to identify different diastereoisomers. The DFT calculations confirm the systematic trend observed in experiment, and indicate that the computed (1)J(PX) coupling constants are related to the length of the axial and equatorial bonds. A similar relation between the phosphorus chemical shift and the R(PX) bond length appears to be valid, with the exception of selenium substituents.     

Analysis of sodium adduct paeoniflorin, albiflorin and their derivatives by (+)ESI-MSn, DFT calculations and computer-aided mass spectrometry analysis program

In order to analyze paeoniflorin, albiflorin and their derivatives (PADs) in Paeonia Lactiflora rapidly and effectively, (+)ESI-MS(n) experiments were conducted, from which two diagnostic fragment patterns were acquired. Meanwhile, the dehydration ability of aglycones of PADs was obtained by calculating their activation energy using density functional theory, through which the unique dehydration phenomenon of benzoylalbiflorin, compared with benzoylpaeoniflorin, was interpreted. In addition, a computer-aided mass spectrometry analysis program was developed to facilitate the analysis of the unknown compound by suggesting the possible structure of the analyte.     

A study of the conformers of the N,N-diethyl-N-methyl-N-propylammonium ion by means of infrared spectroscopy and DFT calculations

The infrared absorption spectrum of the N,N-diethyl-N-methyl-N-propylammonium (DMPA) bis(fluorosulfonyl)imide (FSI) ionic liquid is measured as a function of temperature between 165 and 307 K. In the frequency range between 900 and 1070 cm⁻¹ only the cation gives rise to infrared bands. A conformational analysis of DMPA is performed by means of DFT calculations at the B3LYP/6-31G** level. The comparison of the experimental and calculated spectra provides evidence that the lowest energy conformers coexist in the liquid. Experimentally, we find that the energy difference between the most stable rotamer and the next energy conformers is only 1.56 ± 0.05 kJ/mol, in good agreement with the calculated value. Finally, we show that in the solid state only the most stable isomer is retained.     

Ab initio and DFT calculations for the structure and vibrational spectra of cyclopentene and its isotopomers

Ab initio calculations using the MP2/cc-pVTZ basis set do an excellent job of predicting the inversion barrier (247 vs. 232 cm⁻¹) and dihedral angle (26°) of cyclopentene. DFT calculations also do an excellent job of predicting the vibrational frequencies of the d₀, d₁, d₄, and d₈ isotopomers. They have also allowed the reassignments of several of the vibrational frequencies.     

Structures and EPR spectra of binary sulfur-nitrogen radicals from DFT calculations

The scattered electron paramagnetic resonance (EPR) spectroscopic data for binary sulfur-nitrogen (S,N) radicals have been compiled and critically assessed.Many of these are inorganic rings or cages.For each species, possible equilibrium structures in the gas phase and the EPR hyperfine coupling (hfc) constants have been calculated with DFT using the B3LYP functional and basis sets of triple-ζ (or better) quality.Good agreement is obtained between calculated and measured values for the well characterized [S₃N₂]⁺, a planar π-radical for which the s-component of the orbitals is likely to be reasonably independent of minor geometrical changes between gas-phase and condensed-phase states.The cage compounds [S₄N₄]⁻ and [S₄N₅]⁻², for which reliable experimental EPR spectra have been reported, show larger variation between calculated and measured hfc, as a consequence of the dependence of the s orbital content of the molecular orbitals on small structural changes.The very large disagreements between the DFT calculated and experimentally claimed hfc constants for [NS], [SNS] and [S₄N₄]⁻³ in condensed phases lead us to question their assignment.Among binary S,N radicals, ³³S hfc data has only been reported for [S₃N₂]⁺ (through isotopic enrichment).These values were essential for the correct identification of the EPR spectra of this important radical, which previously was misassigned to other species.Our results suggest that ³³S data will be equally important for the correct identification of the EPR spectra of other binary S,N species, many of which are cyclic systems, e.g.[S₃N₃], [S₄N₃] and[S₄N₅].     

Conformational and electronic study of N‐acetyl‐L‐isoleucine‐N‐methylamide using DFT and IPCM calculations

A conformational and electronic study on N‐acetyl‐L ‐isoleucine‐N‐methylamide was carried out. All side‐chain as well as backbone conformations were explored for this compound. Multidimensional conformational analysis predicts 81 structures in the case of N‐acetyl‐L ‐isoleucine‐N‐methylamide, 53 relaxed structures were determined at the DFT (B3LYP/6‐31G(d)) level of theory. An exhaustive electronic study employing the atoms‐in‐molecules (AIM) method was carried out. In addition, the effects of three solvents (water, acetonitrile, and chloroform) were included in the calculations using the isodensity polarizable continuum model (IPCM) method. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Benzylic coupling constants in toluene derivatives by J doubling in the frequency domain and DFT calculations

The recently modified J doubling in the frequency domain method (MJDFDM) allowed the determination of ^{4, 5, 6}J in toluene, a series of 4‐mono‐ and 3,5‐disubstituted toluene derivatives, as well as in 4‐picoline. The methyl and aromatic signals were subjected to successive deconvolution processes, which at the end led to singlet signals and afforded the corresponding coupling constant values with a high degree of accuracy. Density functional theory calculation of benzylic coupling constants by addition of the Fermi contact, the spin‐dipole, the diamagnetic spin‐orbit, and the paramagnetic spin‐orbit terms revealed good agreement between predicted and measured values when the B3LYP/aug‐cc‐pVTZ level of theory was used. Evaluation of the substituent effect over the coupling constant was made for all studied compounds and some limitations of the methodology were evidenced. Copyright © 2009 John Wiley & Sons, Ltd.     

Investigation of radionuclide 60Co(II) binding to TiO2 by batch technique, surface complexation model and DFT calculations

The interaction between radionuclides and solid/water interfaces is important to understand the physicochemical processes of radionuclides in the natural environment.Herein,the interaction of 60Co(Ⅱ) with TiO 2 in aqueous solution as a function of pH and ionic strength was studied by using batch technique combined with surface complexation model and density functional theory(DFT) calculations.The batch experimental results showed that the adsorption of 60Co(Ⅱ) was dependent on pH and independent of ionic strength,indicating the formation of inner-sphere surface complexes on TiO 2 surfaces.The results of surface complexation models and DFT calculations indicated that the surface species of 60Co(Ⅱ) adsorbed on TiO 2 followed the trend:B structure(i.e.,60Co(Ⅱ) was linked to one bridge oxygen site) was the dominant surface species at low pH,and TT structure(i.e.,60Co(Ⅱ) was linked to two terminal oxygen sites) became the important surface complex at neutral and alkaline pH values.These results demonstrated that a multi-technique approach could lead to definitive information on the structures of adsorbed 60Co(Ⅱ) at the molecular level at the TiO 2 /water interfaces,as well as realistic models to rationalize and accurately evaluate the macroscopic manifestations of radionuclide adsorption phenomena.     

FT-IR、XPS和DFT研究水杨酸钠在针铁矿或赤铁矿上的吸附机理

采用傅里叶变换红外(FT-IR)光谱、X射线光电子能谱(XPS)以及基于周期平面波的密度泛函理论(DFT)分别研究了水杨酸钠在针铁矿或赤铁矿表面上的吸附结构,并将计算得到的光电子能谱移动(CLS)和电荷转移与实验得到的XPS结果进行对比。FT-IR结果表明,水杨酸钠可能以双齿双核(V)和双齿单核(IV)的形式分别吸附于针铁矿或赤铁矿表面。由DFT计算结果可知,水杨酸钠在针铁矿(101)晶面上形成双齿双核化合物(V)的吸附能为-5.46 eV。而水杨酸钠在针铁矿(101)晶面上形成双齿单核化合物(IV)的吸附能为3.80 eV,因此水杨酸钠在针铁矿上基本不以双齿单核化合物(IV)构型存在。水杨酸钠在赤铁矿(001)晶面上形成双齿单核化合物(IV)时吸附能为-4.07 eV,说明水杨酸钠在赤铁矿(001)晶面上形成了双齿单核化合物(IV)。另外,理论计算的针铁矿(101)晶面上吸附位点铁原子的Fe 2p的CLS值(-0.68 eV)与实验观察到的Fe 2p的CLS值(-0.5 eV)吻合。理论计算的赤铁矿(001)晶面上吸附位点铁原子的Fe 2p的CLS值(-0.80 eV)与实验观察到的Fe 2p的CLS值(-0.8 eV)吻合。因此,水杨酸钠吸附在针铁矿表面时能够通过羧酸基团上一个氧原子和酚羟基上的氧原子与针铁矿(101)表面上的两个铁原子形成双齿双核(V)结构,而在赤铁矿(001)表面上,水杨酸钠中羧酸基团上一个氧原子和酚羟基上的氧原子与赤铁矿(001)表面上的一个铁原子形成了双齿单核(IV)结构。     

Synthesis, spectroscopic characterization, X-ray structure and DFT calculations of [ReOCl2(8-Sqn)(OPPh3)]

The reaction of [ReOCl₃(PPh₃)₂] with 8-quinolinethiol (8-HSqn) has been examined, and the [ReOCl₂(8-Sqn)(OPPh₃)] complex has been obtained. It was characterized by IR, UV–Vis spectroscopy and single crystal X-ray analysis. The nature of the frontier orbitals and the electronic transitions involved in the absorption spectrum have been studied by means of the density functional and time-dependent density functional methods.     

Synthesis,NMR structural characterization and molecular modeling of substituted thiosemicarbazones and semicarbazones using DFT calculations to prove the syn/anti isomer formation

Thiosemicarbazones possessing electron‐donating and electron‐withdrawing groups were prepared, and their spectral characteristics determined. In all cases, the spectra showed that one isomer was formed, allowing further functionalization to molecules of biological interest. We provide NMR data for some of the thiosemicarbazones and semicarbazones. We also provide evidence that for 2‐pyridyl thiosemicarbazone, the syn isomer slowly converts into the anti isomer in dimethyl sulfoxide solvent with first‐order kinetics. Molecular modeling and density functional theory calculations confirmed these observations. Copyright © 2014 John Wiley & Sons, Ltd.