IR/Raman spectroscopy and DFT calculations of cyclic di‐amino acid peptides. Part III: comparison of solid state and solution structures of cyclo(L‐Ser‐L‐Ser)

B3‐LYP/cc‐pVDZ calculations of the gas‐phase structure and vibrational spectra of the isolated molecule cyclo(L ‐Ser‐L ‐Ser), a cyclic di‐amino acid peptide (CDAP), were carried out by assuming C₂ symmetry. It is predicted that the minimum‐energy structure is a boat conformation for the diketopiperazine (DKP) ring with both L ‐seryl side chains being folded slightly above the ring. An additional structure of higher energy (15.16 kJ mol⁻¹) has been calculated for a DKP ring with a planar geometry, although in this case two fundamental vibrations have been calculated with imaginary wavenumbers. The reported X‐ray crystallographic structure of cyclo(L ‐Ser‐L ‐Ser), shows that the DKP ring displays a near‐planar conformation, with both the two L ‐seryl side chains being folded above the ring. It is hypothesized that the crystal packing forces constrain the DKP ring in a planar conformation and it is probable that the lower energy boat conformation may prevail in the aqueous environment. Raman scattering and Fourier‐transform infrared (FT‐IR) spectra of solid state and aqueous solution samples of cyclo(L ‐Ser‐L ‐Ser) are reported and discussed. Vibrational band assignments have been made on the basis of comparisons with the calculated vibrational spectra and band wavenumber shifts upon deuteration of labile protons. The experimental Raman and IR results for solid‐state samples show characteristic amide I vibrations which are split (Raman: 1661 and 1687 cm⁻¹, IR: 1666 and 1680 cm⁻¹), possibly due to interactions between molecules in a crystallographic unit cell. The cis amide I band is differentiated by its deuterium shift of ∼30 cm⁻¹, which is larger than that previously reported for trans amide I deuterium shifts. A cis amide II mode has been assigned to a Raman band located at 1520 cm⁻¹. The occurrence of this cis amide II mode at a wavenumber above 1500 cm⁻¹ concurs with results of previously examined CDAP molecules with low molecular weight substituents on the C^α atoms, and is also indicative of a relatively unstrained DKP ring. Copyright © 2009 John Wiley & Sons, Ltd.     

Soft X‐ray absorption spectroscopy and resonant inelastic X‐ray scattering spectroscopy below 100 eV: probing first‐row transition‐metal M‐edges in chemical complexes

X‐ray absorption and scattering spectroscopies involving the 3d transition‐metal K‐ and L‐edges have a long history in studying inorganic and bioinorganic molecules. However, there have been very few studies using the M‐edges, which are below 100 eV. Synchrotron‐based X‐ray sources can have higher energy resolution at M‐edges. M‐edge X‐ray absorption spectroscopy (XAS) and resonant inelastic X‐ray scattering (RIXS) could therefore provide complementary information to K‐ and L‐edge spectroscopies. In this study, M_2,3‐edge XAS on several Co, Ni and Cu complexes are measured and their spectral information, such as chemical shifts and covalency effects, are analyzed and discussed. In addition, M_2,3‐edge RIXS on NiO, NiF₂ and two other covalent complexes have been performed and different d–d transition patterns have been observed. Although still preliminary, this work on 3d metal complexes demonstrates the potential to use M‐edge XAS and RIXS on more complicated 3d metal complexes in the future. The potential for using high‐sensitivity and high‐resolution superconducting tunnel junction X‐ray detectors below 100 eV is also illustrated and discussed.     

Improved charge transfer multiplet method to simulate M‐ and L‐edge X‐ray absorption spectra of metal‐centered excited states

Charge transfer multiplet (CTM) theory is a computationally undemanding and highly mature method for simulating the soft X‐ray spectra of first‐row transition metal complexes. However, CTM theory has seldom been applied to the simulation of excited‐state spectra. In this article, the CTM4XAS software package is extended to simulate M_2,3‐ and L_2,3‐edge spectra for the excited states of first‐row transition metals and also interpret CTM eigenfunctions in terms of Russell–Saunders term symbols. These new programs are used to reinterpret the recently reported excited‐state M_2,3‐edge difference spectra of photogenerated ferrocenium cations and to propose alternative assignments for the electronic state of these cations responsible for the spectroscopic features. These new programs were also used to model the L_2,3‐edge spectra of Fe^II compounds during nuclear relaxation following photoinduced spin crossover and to propose spectroscopic signatures for their vibrationally hot states.     

Vibrational spectra and crystal structure of the di‐amino acid peptide cyclo(L‐Met‐L‐Met): comparison of experimental data and DFT calculations

Experimental Raman and FT‐IR spectra of solid‐state non‐deuterated and N‐deuterated samples of cyclo(L ‐Met‐L ‐Met) are reported and discussed. The Raman and FT‐IR results show characteristic amide I vibrations (Raman: 1649 cm⁻¹, infrared: 1675 cm⁻¹) for molecules exhibiting a cis amide conformation. A Raman band, assigned to the cis amide II vibrational mode, is observed at ∼1493 cm⁻¹ but no IR band is observed in this region. Cyclo(L ‐Met‐L ‐Met) crystallises in the triclinic space group P1 with one molecule per unit cell. The overall shape of the diketopiperazine (DKP) ring displays a (slightly distorted) boat conformation. The crystal packing employs two strong hydrogen bonds, which traverse the entire crystal via translational repeats. B3‐LYP/cc‐pVDZ calculations of the structure of the molecule predict a boat conformation for the DKP ring, in agreement with the experimentally determined X‐ray structure. Copyright © 2009 John Wiley & Sons, Ltd.     

Band gap and electronic structure of MgSiN2 determined using soft X‐ray spectroscopy and density functional theory

We present a study of MgSiN₂ using soft X‐ray absorption and emission spectroscopy which directly probe the partial density of states. MgSiN₂ is new as a host lattice for luminescence materials and used in phosphor‐converted light‐emitting diodes. We compare our measurements to our full potential, all electron density funtional theory calculations. We find excellent agreement between experiment and theory and the band gap of MgSiN₂ is measured to be 5.6 ± 0.2 eV in agreement with our calculated value of 5.72 eV. (© 2015 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

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.     

Tris‐amidoximate uranyl complexes via η2 binding mode coordinated in aqueous solution shown by X‐ray absorption spectroscopy and density functional theory methods

The present study sheds some light on the long‐standing debate concerning the coordination properties between uranyl ions and the amidoxime ligand, which is a key ingredient for achieving efficient extraction of uranium. Using X‐ray absorption fine structure combined with theoretical simulation methods, the binding mode and bonding nature of a uranyl–amidoxime complex in aqueous solution were determined for the first time. The results show that in a highly concentrated amidoxime solution the preferred binding mode between UO₂²⁺ and the amidoxime ligand is η² coordination with tris‐amidoximate species. In such a uranyl–amidoximate complex with η² binding motif, strong covalent interaction and orbital hybridization between U 5f/6d and (N, O) 2p should be responsible for the excellent binding ability of the amidoximate ligand to uranyl. The study was performed directly in aqueous solution to avoid the possible binding mode differences caused by crystallization of a single‐crystal sample. This work also is an example of the simultaneous study of local structure and electronic structure in solution systems using combined diagnostic tools.     

The effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer of 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone in methanol: A TD‐DFT study

Excited‐state intermolecular or intramolecular proton transfer (ESIPT) reaction has important potential applications in biological probes. In this paper, the effect of benzo‐annelation on intermolecular hydrogen bond and proton transfer reaction of the 2‐methyl‐3‐hydroxy‐4(1H)‐quinolone (MQ) dye in methanol solvent is investigated by the density functional theory and time‐dependent density functional theory approaches. Both the primary structure parameters and infrared vibrational spectra analysis of MQ and its benzo‐analogue 2‐methyl‐3‐hydroxy‐4(1H)‐benzo‐quinolone (MBQ) show that the intermolecular hydrogen bond O₁―H₂?O₃ significantly strengthens in the excited state, whereas another intermolecular hydrogen bond O₃―H₄?O₅ weakens slightly. Simulated electron absorption and fluorescence spectra are agreement with the experimental data. The noncovalent interaction analysis displays that the intermolecular hydrogen bonds of MQ are obviously stronger than that of MBQ. Additionally, the energy profile analysis via the proton transfer reaction pathway illustrates that the ESIPT reaction of MBQ is relatively harder than that of MQ. Therefore, the effect of benzo‐annelation of the MQ dye weakens the intermolecular hydrogen bond and relatively inhibits the proton transfer reaction.     

X‐ray spectroscopy for chemistry in the 2‐4 keV energy regime at the XMaS beamline: ionic liquids,Rh and Pd catalysts in gas and liquid environments,and Cl contamination in γ‐Al2O3

The 2–4 keV energy range provides a rich window into many facets of materials science and chemistry. Within this window, P, S, Cl, K and Ca K‐edges may be found along with the L‐edges of industrially important elements from Y through to Sn. Yet, compared with those that cater for energies above ca. 4–5 keV, there are relatively few resources available for X‐ray spectroscopy below these energies. In addition, in situ or operando studies become to varying degrees more challenging than at higher X‐ray energies due to restrictions imposed by the lower energies of the X‐rays upon the design and construction of appropriate sample environments. The XMaS beamline at the ESRF has recently made efforts to extend its operational energy range to include this softer end of the X‐ray spectrum. In this report the resulting performance of this resource for X‐ray spectroscopy is detailed with specific attention drawn to: understanding electrostatic and charge transfer effects at the S K‐edge in ionic liquids; quantification of dilution limits at the Cl K‐ and Rh L₃‐edges and structural equilibria in solution; in vacuum deposition and reduction of [Rh^I(CO)₂Cl]₂ to γ‐Al₂O₃; contamination of γ‐Al₂O₃ by Cl and its potential role in determining the chemical character of supported Rh catalysts; and the development of chlorinated Pd catalysts in `green' solvent systems. Sample environments thus far developed are also presented, characterized and their overall performance evaluated.     

Vibrational spectra,X‐ray and molecular structure of 1H‐ and 3H‐imidazo[4,5‐b]pyridine and their methyl derivatives: DFT quantum chemical calculations

Molecular structure, vibrational energy levels and potential energy distribution of 1H‐imidazo[4,5‐b]pyridine, 3H‐imidazo[4,5‐b]pyridine, 5‐methyl‐1H‐imidazo[4,5‐b]pyridine, 6‐methyl‐1H‐imidazo[4,5‐b]pyridine and 7‐methyl‐3H‐imidazo[4,5‐b]pyridine were determined using density functional theory (DFT) at the B3LYP/6‐31G(d,p) level. The optimised bond lengths and bond angles are in good agreement with the X‐ray data of 5‐methyl‐1H‐imidazo[4,5‐b]pyridine obtained in the present work (Pbca space group; a = 8.660(2), b = 11.078(2), c = 11.078(3) Å, Z = 8). The N⁺H group plays the role of a proton donor in a medium strong hydrogen bond of the type N H…N, linking the N‐atom of the pyridine with the adjacent molecule related by the symmetry operation: 1/2 − x, y − 1/2, z(N…N = 2.869(25) Å). The presence of hydrogen bond is confirmed by appearance in the IR spectra of a very broad and strong contour in the 2000–3100 cm⁻¹ range. The place of substitution of the methyl group at the pyridine ring influences the proton position of the NH group at the imidazole unit. Copyright © 2007 John Wiley & Sons, Ltd.     

Experimental vibrational spectra (Raman,infrared) and DFT calculations on monomeric and dimeric structures of 2‐ and 6‐bromonicotinic acid

In this work, the Fourier transform infrared and Raman spectra of 2‐bromonicotinic acid and 6‐bromonicotinic acid (abbreviated as 2‐BrNA and 6‐BrNA, C₆H₄BrNO₂) have been recorded in the region 4000–400 and 3500–50 cm⁻¹. The optimum molecular geometry, normal mode wavenumbers, infrared intensities and Raman scattering activities, corresponding vibrational assignments and intermolecular hydrogen bonds were investigated with the help of B3LYP density functional theory (DFT) method using 6‐311++G(d,p) basis set. Reliable vibrational assignments were made on the basis of total energy distribution (TED) calculated with scaled quantum mechanical (SQM) method. From the calculations, the molecules are predicted to exist predominantly as the C1 conformer. Copyright © 2009 John Wiley & Sons, Ltd.     

Vibrational spectroscopy and DFT calculations of di‐amino acid peptides: α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu in the solid state

Experimental vibrational spectroscopic studies and density functional theory (DFT) calculations of the di‐amino acid peptide derivatives α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu have been undertaken. Raman and infrared spectra have been recorded for samples in the solid state. DFT simulations were conducted using the B3‐LYP correlation functional and the cc‐pVDZ basis set to determine energy minimized/geometry optimized structures (based on a single isolated molecule in the gaseous state). Normal coordinate calculations have provided vibrational assignments for fundamental modes, including their potential energy distributions. Significant differences are observed between α‐ and β‐N‐acetyl‐L‐Asp‐L‐Glu both in the computed structures and in the vibrational spectra. The combination of experimental and calculated spectra provide an insight into the structural and vibrational spectroscopic properties of di‐amino acid peptide derivatives. Copyright © 2009 John Wiley & Sons, Ltd.     

Effects of interaction between the chelate rings and π‐conjugated systems in fused salphen complexes on UV‐Vis‐NIR spectra

Dinuclear (Zn₂, Ni₂, and NiZn) complexes of fused salphen with acene‐type annelation were synthesized from 3,7‐diformyl‐2,6‐dihydroxynaphthalene. The spectroscopic properties of these complexes were compared with those of their constitutional isomers with phene‐type annelation. The acene‐type complexes exhibited a characteristic absorption band in the near‐infrared region that showed a noticeable solvent effect. Time‐dependent density functional theory calculations suggested that the absorption arose from a π → π* transition localized at the naphthalene ring, which was perturbed by the adjoining chelate rings. Effects of the connection topology in the fused salphen complexes are discussed by comparison with those of polycyclic aromatic hydrocarbons.     

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.     

Infrared and Raman spectroscopic studies of the charge localization in one‐dimensional organic metals (DMtTTF)2X (X = ReO4, ClO4) with regular organic stacks

A novel selective synthesis of the unsymmetrically substituted tetrathiafulvalene dimethyltrimethylene‐tetrathiafulvalene (DMtTTF) is described together with its electrocrystallization to the known conducting mixed‐valence ClO₄^– and ReO₄^– salts. Infrared (IR) and Raman spectra of the two isostructural quasi‐one‐dimensional cation radical salts (DMtTTF)₂X (X = ReO₄^–, ClO₄^–) are investigated as a function of temperature (T = 5–300 K). At ambient temperature, these salts show metallic‐like properties and below T_ρ = 100–150 K, they undergo a smeared transition to semiconducting state. To study this charge localization, we measured temperature dependence of polarized IR reflectance spectra (700–16 000 cm^–1) and Raman spectra (150–3500 cm^–1, excitation λ = 632.8 nm) of single crystals. For both compounds, the Raman data and especially the bands related to the C=C stretching vibration of the DMtTTF molecule show that the charge distribution on molecules is uniform down to the lowest temperatures. Similarly, IR data confirm that down to the lowest temperatures, there is neither charge ordering nor important modification of the electronic structure. However, the temperature dependence of Raman spectra of both salts reveals a regime change at about 150 K. Additionally, using Density Functional Theory (DFT) methods, the normal vibrational modes of the neutral DMtTTF⁰ and cationic DMtTTF⁺ species and also their theoretical IR and Raman spectra were calculated. The theoretical data were compared with the experimental IR and Raman spectra of neutral DMtTTF⁰ molecule. Copyright © 2013 John Wiley & Sons, Ltd.