β‐Elimination of an aziridine to an allylic amine: a mechanistic study

The base‐induced rearrangement of aziridines has been examined using a combination of calculations and experiment. The calculations show that the substituent on nitrogen is a critical feature that greatly affects the favorability of both α‐deprotonation, and β‐elimination to form an allylic amine. Experiments were carried out to determine whether E2‐like rearrangement to the allylic amine with lithium diisopropyl amide (LDA) is possible. N‐tosyl aziridines were found to deprotonate on the tosyl group, preventing further reaction. A variety of N‐benzenesulfonyl aziridines having both α‐ and β‐protons decomposed when treated with LDA in either tetrahydrofuran or hexamethylphosphoramide. However, when α‐protons were not present, allylic amine was formed, presumably via β‐elimination. Copyright © 2011 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and crystal structure analysis of two polymorphs of the di‐amino acid peptide cyclo(L‐Glu‐L‐Glu)

Cyclo(L ‐Glu‐L ‐Glu) has been crystallised in two different polymorphic forms. Both polymorphs are monoclinic, but form 1 is in space group P2₁ and form 2 is in space group C2. Raman scattering and FT‐IR spectroscopic studies have been conducted for the N,O‐protonated and deuterated derivatives. Raman spectra of orientated single crystals, solid‐state and aqueous solution samples have also been recorded. The different hydrogen‐bonding patterns for the two polymorphs have the greatest effect on vibrational modes with N H and CO stretching character. DFT (B3‐LYP/cc‐pVDZ) calculations of the isolated cyclo(L ‐Glu‐L ‐Glu) molecule predict that the minimum energy structure, assuming C₂ symmetry, has a boat conformation for the diketopiperazine ring with the two L ‐Glu side chains being folded above the ring. The calculated geometry is in good agreement with the X‐ray crystallographic structures for both polymorphs. Normal coordinate analysis has facilitated the band assignments for the experimental vibrational spectra. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and DFT calculations of di‐amino acid cyclic peptides. Part I: cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) in the solid state and in aqueous solution

Investigations of the vibrational spectra of cyclo(Gly‐Gly), cyclo(L‐Ala‐L ‐Ala) and cyclo(L ‐Ala‐Gly) are reported. Raman scattering and Fourier transform infrared (FTIR) spectra of solid‐state and aqueous protonated samples, as well as their corresponding N‐deuterated isotopomers, have been examined. In addition, density functional theory (DFT) (B3‐LYP/cc‐pVDZ) calculations of molecular structures and their associated vibrational modes were carried out. In each case, the calculated structures of lowest energy for the isolated gas‐phase molecules have boat conformations. Assignments have been made for the observed Raman and FTIR vibrational bands of the cyclic di‐amino acid peptides (CDAPs) examined. Raman polarization studies of aqueous phase samples are consistent with C₂ and C₁ symmetries for the six‐membered rings of cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly), respectively. There is a good correlation between experimental and calculated vibrational bands for the three CDAPs. These data are in keeping with boat conformations for cyclo(L‐Ala‐L‐Ala) and cyclo(L‐Ala‐Gly) molecules, predicted by the ab initio calculations, in both the solid and aqueous solution states. However, Raman spectroscopic results might infer that cyclo(L‐Ala‐Gly) deviates only slightly from planarity in the solid state. The potential energy distributions of the amide I and II modes of a cis‐peptide linkage are shown to be significantly different from those of the trans‐peptides. For example, deuterium shifts have shown that the cis‐amide I vibrations found in cyclo(Gly‐Gly), cyclo(L‐Ala‐L‐Ala), and cyclo(L‐Ala‐Gly) have larger N‐H contributions compared to their trans‐amide counterparts. Compared to trans‐amide II vibrations, cis‐amide II vibrations show a considerable decrease in N H character. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopic studies of the structure of di‐amino acid peptides. Part II: cyclo(L‐Asp‐L‐Asp) in the solid state and in aqueous solution

Solid‐state protonated and N,O‐deuterated Fourier transform infrared (IR) and Raman scattering spectra together with the protonated and deuterated Raman spectra in aqueous solution of the cyclic di‐amino acid peptide cyclo(L ‐Asp‐L ‐Asp) are reported. Vibrational band assignments have been made on the basis of comparisons with previously cited literature values for diketopiperazine (DKP) derivatives and normal coordinate analyses for both the protonated and deuterated species based upon DFT calculations at the B3‐LYP/cc‐pVDZ level of the isolated molecule in the gas phase. The calculated minimum energy structure for cyclo(L ‐Asp‐L ‐Asp), assuming C₂ symmetry, predicts a boat conformation for the DKP ring with both the two L ‐aspartyl side chains being folded slightly above the ring. The CO stretching vibrations have been assigned for the side‐chain carboxylic acid group (e.g. at 1693 and 1670 cm⁻¹ in the Raman spectrum) and the cis amide I bands (e.g. at 1660 cm⁻¹ in the Raman spectrum). The presence of two bands for the carboxylic acid CO stretching modes in the solid‐state Raman spectrum can be accounted for by factor group splitting of the two nonequivalent molecules in a crystallographic unit cell. The cis amide II band is observed at 1489 cm⁻¹ in the solid‐state Raman spectrum, which is in agreement with results for cyclic di‐amino acid peptide molecules examined previously in the solid state, where the DKP ring adopts a boat conformation. Additionally, it also appears that as the molecular mass of the substituent on the C^α atom is increased, the amide II band wavenumber decreases to below 1500 cm⁻¹; this may be a consequence of increased strain on the DKP ring. The cis amide II Raman band is characterized by its relatively small deuterium shift (29 cm⁻¹), which indicates that this band has a smaller N H bending contribution than the trans amide II vibrational band observed for linear peptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Interaction of water‐soluble triphenylphosphines with β‐cyclodextrin: a quantum chemistry study

The interaction of β‐cyclodextrin (β‐CD) with meta‐trisulfonated triphenylphosphine derivatives bearing one or two methyl (or methoxy) groups on the aromatic rings has been investigated by PM3 calculations. The results show that phosphine molecules interact with β‐CD having either an unsubstituted sulfophenyl group or a substituted sulfophenyl group at the para and/or meta‐position. The presence of one methyl or methoxy group in the ortho‐position on each aromatic ring prevents the formation of an inclusion complex between meta‐trisulfonated triphenylphosphine derivatives and β‐CD. The deeply included phosphines in the β‐CD cavity show significant van der Waals interactions with β‐CD. These interactions are at the origin of the high association constants between these molecules and β‐CD. Phosphines exhibiting small association constants interact with β‐CD by forming H‐bonds and weak (or null) van der Waals interactions. Copyright © 2011 John Wiley & Sons, Ltd.     

Synthesis and Raman spectroscopic investigation of a new self‐assembly monolayer material 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid for organic light‐emitting devices

We have synthesized 4‐[N‐phenyl‐N‐(3‐methylphenyl)‐amino]‐benzoic acid (4‐[PBA]) and investigated its molecular vibrations by infrared and Raman spectroscopies as well as by calculations based on the density functional theory (DFT) approach. The Fourier transform (FT) Raman, dispersive Raman and FT‐IR spectra of 4‐[PBA] were recorded in the solid phase. We analyzed the optimized geometric structure and energies of 4‐[PBA] in the ground state. Stability of the molecule arising from hyperconjugative interactions and charge delocalization was studied using natural bond orbital analysis. The results show that change in electron density in the σ* and π* antibonding orbitals and E₂ energies confirm the occurrence of intramolecular charge transfer within the molecule. Theoretical calculations were performed at the DFT level using the Gaussian 09 program. Selected experimental bands were assigned and characterized on the basis of the scaled theoretical wavenumbers by their total energy distribution. The good agreement between the experimental and theoretical spectra allowed positive assignment of the observed vibrational absorption bands. Finally, the calculation results were applied to simulate the Raman and IR spectra of the title compound, which show agreement with the observed spectra. Copyright © 2011 John Wiley & Sons, Ltd.     

Ultraviolet resonance Raman spectroscopy of a β‐sheet peptide: a model for membrane protein folding

The partitioning of a hydrophobic hexapeptide, N‐acetyl‐tryptophan‐pentaleucine (AcWL5), into self‐associated β‐sheets within a vesicle membrane was studied as a model for integral membrane protein folding and insertion via vibrational and electronic spectroscopy. Ultraviolet resonance Raman spectroscopy allows selective examination of the structures of amino acid side chains and the peptide backbone and provides information about local environment and molecular conformation. The secondary structure of AcWL5 within a vesicle membrane was investigated using 207.5‐nm excitation and found to consist of β‐sheets, in agreement with previous studies. The β‐sheet peptide shows enhanced Raman scattering cross‐sections for all amide modes as well as extensive hydrogen‐bonding networks. Tryptophan vibrational structure was probed using 230‐nm excitation. Increases in Raman cross‐sections of tryptophan modes W1, W3, W7, W10, W16, W17, and W18 of membrane‐incorporated AcWL5 are primarily attributed to greater resonance enhancement with the B_b electronic transition. The W17 mode, however, undergoes a much greater enhancement than is expected for a simple resonance effect, and this observation is discussed in terms of hydrogen bonding of the indole ring in a hydrophobic environment. The observed tryptophan mode frequencies and intensities overall support a hydrophobic environment for the indole ring within a vesicle, and these results have implications for the location of tryptophan in membrane protein systems. Copyright © 2009 John Wiley & Sons, Ltd.     

Relative stabilities and molecular structures of the isomeric enol ethers and carboxylic esters derived from α‐acetyl‐γ‐butyrolactone and α‐acetyl‐δ‐valerolactone

Recently recorded ¹⁷O NMR spectra of compounds studied in a previous work (Taskinen E. Acta Chem. Scand. 1985; B39 : 489–494) dealing with the thermodynamics of isomerization of the enol ethers of α‐acetyl‐γ‐butyrolactone reveal an error in compound identification, caused by an unexpected isomerization reaction during the synthetic procedure. Thus, acid‐catalyzed treatment of the lactone with HC(OR)₃ in the respective alcohol ROH is shown to lead initially to the desired enol ethers which, however, are gradually isomerized to a mixture of the enol ethers and an ester of 2‐methyl‐4,5‐dihydrofuran‐3‐carboxylic acid. As a result, only one of the two isomeric compounds detected in the previous equilibration study was the expected enol ether (the thermodynamically more stable E isomer) of α‐acetyl‐γ‐butyrolactone, while the other, dominating species was the respective carboxylic ester. In the present work, the evidence provided by the ¹⁷O NMR spectra is presented, and the relative stabilities of the isomeric compounds are discussed on the basis of computational enthalpy data. The treatment is also extended to the respective isomeric compounds derived from α‐acetyl‐δ‐valerolactone. Copyright © 2007 John Wiley & Sons, Ltd.     

Polarized Raman scattering in helimagnetic β‐MnO2

A rutile β‐MnO₂ film was grown on MgO substrate using plasma‐assisted molecular beam epitaxy (PAMBE) monitored by reflection high‐energy electron diffraction (RHEED). Polarized Raman spectra at various temperatures were obtained to investigate the influence of the helimagnetic structure on the vibrational modes of β‐MnO₂. A red shift of E_g modes indicates a gradual formation of spin angles between neighboring Mn⁴⁺ ions. The intensities of the E_g and A_1g modes with y‐polarized incidence increase remarkably below the Néel temperature. A new view as vibrational mode projection (VMP) indicates the interactions between the magnetic component of incident light and the helimagnetic structure. Copyright © 2008 John Wiley & Sons, Ltd.     

Solvatochromism of 2‐(N,N‐dimethylamino)‐7‐nitrofluorene and the natural dye β‐carotene: application for the determination of solvent dipolarity and polarizability

The effects of solvents on chemical phenomena (rate and equilibrium constants, spectroscopic transitions, etc.) are conveniently described by solvation free‐energy relationships that take into account solvent acidity, basicity and dipolarity/polarizability. The latter can be separated into its components by manipulating the UV–vis spectra of two solvatochromic probes, 2‐(N,N‐dimethylamino)‐7‐nitrofluorene (DMANF) and a di‐(tert‐butyl)‐tetramethyl docosanonaen probe (ttbP9) whose synthesis is laborious and expensive. Recently, we have shown that the natural dye β‐carotene can be conveniently employed instead of ttbP9 for the determination of solvent polarizability (SP) of 76 molecular solvents and four ionic liquids. In the present work, we report the polarizabilities of further 24 solvents. Based on the solvatochromism of β‐carotene and DMANF, we have calculated solvent dipolarity (SD) for 103 protic and aprotic molecular solvents, and ionic liquids. The dependence of SD and SP on the number of carbon atoms in the acyl‐ or alkyl group of several homologous series (alcohols; 2‐alkoxyethanols; carboxylic acid‐ anhydrides, and esters, ionic liquids) is calculated and briefly discussed. Copyright © 2013 John Wiley & Sons, Ltd.     

DFT study the interaction of β‐cyclodextrin with benzyl azide and phenyl acetylene in synthesis of 1,2,3‐triazoles

The phenyl acetylene and benzyl azide cycloaddition reaction in water in the presence of β‐cyclodextrin (β‐CD) as a phase transfer catalyst (PTC) can get a better yield in a shorter time. The interaction between β‐CD and phenyl acetylene or benzyl azide plays an important role in this reaction. This paper studies the complexes of β‐CD with phenyl acetylene and benzyl azide using density functional theory (DFT) method. In order to find out the orientations of guests in the cavity of β‐CD, binding energy and deformation energy are investigated, and the calculated results are confirmed by ¹H nuclear magnetic resonance (¹HNMR). The data from single point energy indicate that the inclusion complexes can improve the solubilities of phenyl acetylene and benzyl azide in water. The ¹³C and ¹⁵N spectra show that the most obvious variation concentrates on C₆ and C₈ of phenyl acetylene and N₁₅ of benzyl azide in complexes. Mulliken charge and frontier orbital are employed for revealing the charge distribution. The effect of β‐CD is discussed in terms of the calculated parameters. Copyright © 2014 John Wiley & Sons, Ltd.     

The Raman spectrum of the γ′‐V2O5 polymorph: a combined experimental and DFT study

Structure and vibrational dynamics of γ′‐V₂O₅ synthesized from a pristine γ‐LiV₂O₅ sample via a chemical oxidation route was studied by means of Raman spectroscopy and quantum‐chemical calculations. The calculations based on density functional theory reliably reproduce the experimental structure of the γ′‐V₂O₅ lattice. The calculated Raman spectrum agrees remarkably well with the experimental one. Making use of the agreement, a complete assignment of Raman bands to vibrations of particular structural units is proposed. The comparison of Raman spectra and structural features of α‐V₂O₅ and γ′‐V₂O₅ polymorphs allowed establishing reliable ‘structure–spectrum’ correlations and identifying Raman peaks characteristic for different structural units. Copyright © 2015 John Wiley & Sons, Ltd.     

SERS spectrum of the peptide thymosin‐β4 obtained with Ag nanorod substrate

Thymosin‐β4 is a peptide found at high concentrations in a wide range of mammalian cells. It has been shown to be elevated in metastatic cells. In this study, the surface‐enhanced Raman spectrum of thymosin‐β4 was obtained using a silver nanorod array surface‐enhanced Raman scattering substrate. Significant Raman peaks were found, and the corresponding vibrational modes were assigned based on previously published literature, with amide A–B, amide I, and amide III modes all identified. The majority of the remaining peaks were assigned modes based on the spectra of lysine and glutamic acid, the two most abundant amino acids in the thymosin‐β4 sequence. A standard Raman spectrum of thymosin‐β4 was also obtained and analyzed for comparison. Because thymosin‐β4 plays a significant role in regulating the formation of cellular cytoskeleton and other several biological processes, its Raman spectrum will be of use to researchers. Copyright © 2014 John Wiley & Sons, Ltd.     

Structural and vibrational study of 2‐(2′‐ furyl)‐4,5‐1H‐dihydroimidazole

In this study 2‐(2′‐furyl)‐4,5‐1H‐dihydroimidazole (1) was prepared and then characterized by infrared, Raman, and multidimensional nuclear magnetic resonance (NMR) spectroscopies. The crystal and molecular structures of 1 were determined by X‐ray diffraction methods. The density functional theory (DFT) and second‐order Møller–Plesset theory (MP2) with Pople's basis set show that there are two conformers for the title molecule that have been theoretically determined in the gas phase, and that only one of them, conformer I, is present in the solid phase. NMR spectra observed for 1 were successfully compared with the calculated chemical shifts at the B3LYP/6‐311++G** level theorized for this conformer. The harmonic vibrational frequencies for the optimized geometry of the latter conformer were calculated at the B3LYP/6‐311++G** level in the approximation of the isolated molecule. For a complete assignment of the IR and Raman spectra in the solid phase of 1 , DFT calculations were combined with Pulay´s scaled quantum mechanics force field (SQMFF) methodology to fit the theoretical frequency values to the experimental ones. Copyright © 2009 John Wiley & Sons, Ltd.     

DFT simulations and vibrational analysis of FTIR and FT‐Raman spectra of 2‐amino‐4,6‐dihydroxypyrimidine

This work deals with the vibrational spectroscopy of 2‐amino‐4,6‐dihydroxy pyrimidine (ADHP) by means of quantum chemical calculations. The mid‐ and far FTIR and FT‐Raman spectra were measured in the condensed state. The fundamental vibrational wavenumbers and intensity of vibrational bands were evaluated using density functional theory (DFT) with the standard B3LYP/6‐311 + G** methods and basis set combinations, and were scaled using various scale factors, which yielded good agreement between the observed and calculated wavenumbers. The vibrational spectra were interpreted with the aid of normal coordinate analysis based on the scaled density functional force field. The results of the calculations were applied to simulate the infrared and Raman spectra of the title compound, which showed excellent agreement with the observed spectra. Copyright © 2008 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and DFT calculations of N,N′‐dicyclohexylcarbodiimide

Infrared (IR) and Raman spectra were obtained for N,N′‐dicyclohexylcarbodiimide (DCC) in the solid state and in CHCl₃ solution. Structures and vibrational spectra of isolated, gas‐phase DCC molecules with C₂ and C_i symmetries, computed at the B3‐LYP/cc‐pVTZ level, show that the IR and Raman spectra provide convincing evidence for a C₂ structure in both the solid state and in CHCl₃ solution. Using a scaled quantum‐chemical force field, these density functional theory calculations have provided detailed assignments of the observed IR and Raman bands in terms of potential energy distributions. Comparison of solid‐state and solution spectra, together with a Raman study of the melting behaviour of DCC, revealed that no solid‐state effects were evident in the spectra. Copyright © 2010 John Wiley & Sons, Ltd.     

Raman spectroscopic study of serum albumins: an effect of proton‐ and γ‐irradiation

Raman spectroscopy was applied to analyse structural changes in serum albumins (bovine serum albumin, BSA; human serum albumin, HSA) following proton and γ‐irradiation (0.5, 5 and 50 Gy). Characteristic Raman bands of both polypeptide backbone and amino acid residues were sensitive to irradiation. Significant damage of HSA/BSA was observed only at the highest dose (50 Gy). Raman spectra confirmed radiation‐induced denaturation, destruction of helical structures and aggregation of serum albumins. The differences in the dose‐dependent effects of proton and γ‐radiation on studied proteins are discussed. Copyright © 2007 John Wiley & Sons, Ltd.     

Raman scattering of L‐tryptophan enhanced by surface plasmon of silver nanoparticles: vibrational assignment and structural determination

Vibrational bands of L ‐tryptophan which was adsorbed on Ag nanoparticles (∼10 nm in diameter) have been investigated in the spectral range of 200–1700 cm⁻¹ using surface‐enhanced Raman scattering (SERS) spectroscopy. Compared with the normal Raman scattering (NRS) of L ‐tryptophan in either 0.5 M aqueous solution (NRS‐AS) or solid powder (NRS‐SP), the intensified signals by SERS have made the SERS investigation at a lower molecular concentration (5 × 10⁻⁴ M ) possible. Ab initio calculations at the B3LYP/6‐311G level have been carried out to predict the optimal structure and vibrational wavenumbers for the zwitterionic form of L ‐tryptophan. Facilitated with the theoretical prediction, the observed vibrational modes of L ‐tryptophan in the NRS‐AS, NRS‐SP, and SERS spectra have been analyzed. In the spectroscopic observations, there are no significant changes for the vibrational bands of the indole ring in either NRS‐AS, NRS‐SP, or SERS. In contrast, spectral intensities involving the vibrations of carboxylate and amino groups are weak in NRS‐AS and NRS‐SP, but strong in SERS. The intensity enhancement in the SERS spectrum can reach 10³–10⁴‐fold magnification. On the basis of spectroscopic analysis, the carboxylate and amino groups of L ‐tryptophan are determined to be the preferential terminal groups to attach onto the surfaces of Ag nanoparticles in the SERS measurement. Copyright © 2008 John Wiley & Sons, Ltd.     

UV resonance Raman study of TrpZip2 and related peptides: π‐π interactions of tryptophan

Aromatic interactions are important stabilizing forces in proteins but are difficult to detect in the absence of high‐resolution structures. Ultraviolet resonance Raman spectroscopy is used to probe the vibrational signatures of aromatic interactions in TrpZip2, a synthetic β‐hairpin peptide that is stabilized by edge‐to‐face and face‐to‐face tryptophan π‐π interactions. The vibrational markers of isolated edge‐to‐face π‐π interactions are investigated in the related β‐hairpin peptide W2W11. The bands that comprise the Fermi doublet exhibit systematic shifts in position and intensity for TrpZip2 and W2W11 relative to the model peptide, W2W9, which does not form aromatic interactions. Additionally, hypochromism of the B_b absorption band of tryptophan in TrpZip2 leads to a decrease in the relative Raman cross‐sections of B_b‐coupled Raman bands. These results reveal spectral markers for stabilizing tryptophan π‐π interactions and indicate that ultraviolet resonance Raman may be an important tool for the characterization of these biological forces. Copyright © 2012 John Wiley & Sons, Ltd.     

Analysis of vibrational spectra of 2‐fluoro‐6‐nitrotoluene based on density functional theory calculations

The conformational behavior and structural stability of 2‐fluoro‐6‐nitrotoluene (FNT) were investigated by utilizing density functional theory (DFT) with the standard B3LYP/6‐311 + G** method and basis set combinations. The vibrational wavenumbers of FNT were computed at DFT levels and complete vibrational assignments were made on the basis of normal coordinate calculations. Normal coordinate analysis (NCA) has been carried out to support the vibrational analysis. The results were compared with the experimental values. The observed Fourier transform infrared (FTIR) and Fourier transform (FT) Raman vibrational wavenumbers were analyzed and compared with the theoretically predicted vibrational spectra. The results of vibrational spectra of FNT were also compared with the vibrational spectra of some toluene derivatives. The assignments of bands to various normal modes of the molecules were also carried out. Copyright © 2008 John Wiley & Sons, Ltd.