Correlation of electronic structures of three cyclic dipeptides with their photoemission spectra

We have investigated the electronic structure of three cyclic dipeptides: cyclo(Glycyl-Glycyl) (cGG), cyclo(Leucyl-Prolyl) (cLP), and cyclo(Phenylalanyl-Prolyl) (cPP). These compounds are biologically active and cLP and cPP are derived from cGG (also known as diketopiperazine), by the addition of the respective functional groups of the amino acids, namely, phenyl, alkyl or a fused pyrrolidine ring (proline). Experimental valence and core level spectra have been interpreted in the light of theoretical calculations to identify the basic chemical properties associated with the central ring, and with the additional functional groups in cLP and cPP. The theoretically simulated spectra of all three cyclic dipeptides in both valence and core spaces agreed reasonably well with the experimental spectra. The three molecules displayed similarities in their core spectra, suggesting that the diketopiperazine structure plays an important role in determining the inner shell spectrum. The experimental C 1s spectra of cLP and cPP are analogous but differ from cGG due to the side chains attached to the diketopiperazine structure. Single spectral peaks in the N 1s (and O 1s) spectra of the dipeptides indicate that the chemical environment of the nitrogen atoms (and oxygen atoms) are very similar, although they show a small splitting in the simulated spectra of cPL and cPP, due to the reduction of their point group symmetry. Valence band spectra of the three dipeptides in the frontier orbital region of 9-11 eV exhibit similarities; however theoretical analysis shows that significant changes occur due to the involvement of the side chain in the frontier orbitals of cPP, while lesser changes are found for cLP.     

Theoretical UV circular dichroism of aliphatic cyclic dipeptides

Four cyclic dipeptides (piperazine-2,5-diones), cyclo(L-Pro-Gly), cyclo(L-Pro-L-Leu), cyclo(L-Ala-L-Ala), and cyclo(L-Pro-L-Ala), were modeled from crystal structure data. Conformations resulting from energy minimization using molecular mechanics were compared with traditional ab initio and density functional theory geometric optimizations for each dipeptide. In all computational cases, the gas phase was assumed. The pi-pi transition feature of the UV circular dichroic (CD) spectra was predicted for each peptide structure via the classical dipole interaction model. The dipole interaction model predicted CD spectra that qualitatively agreed with experiment when MP2 or DFT geometries were used. By coupling MP2 or DFT geometric optimizations with the classical physics method of the dipole interaction model, significantly better CD spectra were calculated than those using geometries obtained by molecular mechanics. Thus, one can couple quantum mechanical geometries with a classical physics model for calculation of circular dichroism.     

Quantification of cyclic dipeptides from cultures of Lactobacillus brevis R2Δ by HRGC/MS using stable isotope dilution assay

Lactic acid bacteria (LAB) play an important role as natural preservatives in fermented food and beverage systems, reducing the application of chemical additives. Thus, investigating their antifungal compounds, such as cyclic dipeptides, has gained prominence. Previous research has primarily focussed on isolation of these compounds. However, their precise quantification will provide further information regarding their antifungal performance in a complex system. To address this, deuterated labelled standards of the cyclic dipeptides cyclo(Leu-Pro), cyclo(Pro-Pro), cyclo(Met-Pro) and cyclo(Phe-Pro) were synthesized, and stable isotope dilution assays were developed, enabling an accurate quantification of cyclo(Leu-Pro), cyclo(Pro-Pro), cyclo(Met-Pro) and cyclo(Phe-Pro) in MRS-broth and wort. Quantitative results showed that, in the Lactobacillus brevis R2Δ fermented MRS-broth, the concentrations of cyclo(Leu-Pro), cyclo(Pro-Pro) and cyclo(Phe-Pro) were significantly higher (P?<?0.05), than in wort for cyclo (Leu-Pro) when compared with their controls. This indicates that the formation of these three cyclic dipeptides is related to L. brevis R2Δ metabolism. Furthermore, this represents the first report of cyclic dipeptides quantification using stable isotope dilution assays in LAB cultures both in vitro and in a food system.     

Synthesis,Conformation, and Interactions with Small Molecules of Bis (Cyclic Dipeptides)

Bis (cyclic dipeptides), cyclo and S, S ′-bis(cyclo(hemiCys-Pro)), were synthesized. These bis (cyclic dipeptides) very efficiently formed complexes with Ba²⁺ and Na⁺ owing to intramolecular cooperation of two cyclicdipeptide moieties, the bis-effect. Cyclo stacked sodium 8-anilino-1-naphthalensulfonate in aqueous solution. These properties of complexation were controlled by the nature of the bridge connecting two cyclic dipeptide moieties. The geometry of the complex between S, S′-bis (cyclo (hemiCys-Pro)) and metal ion was investigated with the help of circular dichroism, nuclear magnetic resonance, and Raman spectroscopy.     

Cyclic beta-tetra- and pentapeptides: synthesis through on-resin cyclization and conformational studies by X-ray, NMR and CD spectroscopy and theoretical calculations

The solution-phase synthesis of the simplest cyclic beta-tetrapeptide, cyclo(beta-Ala)4 (4), as well as the solid-phase syntheses through side chain anchoring and on-resin cyclization of the cyclic beta3-tetrapeptide cyclo(-beta3hPhe-beta3hLeu-beta3hLys-beta3hGln-) (14) and the first cyclic beta3-pentapeptide cyclo(-beta3hVal-beta3hPhe-beta3hLeu-beta3hLys-beta3hLys-) (19) are reported. Extensive computational as well as spectroscopic studies, including X-ray and NMR spectroscopy, were undertaken to determine the preferred conformations of these unnatural oligomers in solution and in the solid state. cyclo(beta-Ala)4 (4) with no chiral side chains is shown to exist as a mixture of rapidly interchanging conformers in solution, whereas inclusion of chiral side chains in the cyclo-beta3-tetrapeptide causes stabilization of one dominating conformer. The cyclic beta3-pentapeptide on the other hand shows larger conformational freedom. The X-ray structure of achiral cyclo(beta-Ala)4 (4) displays a Ci-symmetrical 16-membered ring with adjacent C=O and N-H atoms pointing pair wise up and down with respect to the ring plane. CD spectroscopic examinations of all cyclic beta-peptides were undertaken and revealed results valuable as starting point for further structural investigations of these entities.     

Experimental and Theoretical Electronic Structure Investigations on alpha-Nb(3)Cl(8) and the Intercalated Phase beta'-NaNb(3)Cl(8)

The electronic structures of the cluster compound alpha-Nb(3)Cl(8) and the intercalated phase beta'-NaNb(3)Cl(8) have been studied by core level and valence band X-ray and ultraviolet photoelectron spectroscopy (XPS and UPS), diffuse reflectance spectroscopy, and charge-self-consistent molecular orbital (CSC-EH) and band structure (CSC-EH-TB) calculations. The crystal structures of the two compounds consist of layers of interconnected Nb(3)Cl(13) units. XP and UP valence band spectra as well as the band structure calculations show well separated sets of Cl 3p levels at lower energy (higher binding energy) and Nb 4d levels at higher energy (lower binding energy), indicative of mainly ionic Nb-Cl bonding. The UP spectra of alpha-Nb(3)Cl(8) reveal a triple-peak structure for the Nb 4d levels, corresponding to the 1a(1), 1e, and 2a(1) metal-metal bonding orbitals of a seven-electron Nb(3) cluster as suggested by theory. The valence band shapes are in good agreement with the theoretical density-of-states curve. The relative intensities in the XP valence band spectra of beta'-NaNb(3)Cl(8) evidence an additional electron in the Nb 4d orbitals. The better resolved UP spectra, however, show a broad pattern for the Nb 4d levels which is neither expected from a single cluster model nor given by the theoretical density-of-states curve. Possible origins for this discrepancy between experiment and theory are discussed. Electrostatic interactions between Na(+) and Cl(-) ions in beta'-NaNb(3)Cl(8) lead to a narrowing of the Cl 2p core level and Cl 3p valence band signals, the former being shifted to higher binding energy in comparison to alpha-Nb(3)Cl(8). Two rather narrow absorptions in the optical spectra of alpha-Nb(3)Cl(8) are assigned to the transitions from the 1a(1) and 1e levels into the singly occupied 2a(1) orbital. These absorptions are missing in the optical spectra of beta'-NaNb(3)Cl(8), in agreement with the theoretical expectations for an eight electron Nb(3) cluster.     

Fragmentation of deprotonated cyclic dipeptides by electrospray ionization mass spectrometry

The fragmentation pathways of deprotonated cyclic dipeptides have been studied by electrospray ionization multi‐stage mass spectrometry (ESI‐MSⁿ) in negative mode. The results showed that the fragmentation pathways of deprotonated cyclic dipeptides depended significantly on the different substituents, the side chains of amino acid residues at the diketopiperazine ring. In the spectra of deprotonated cyclic dipeptides, the ion [M? H? substituent radical]^? was firstly observed in the ESI mode. The characteristic fragment ions [M? H? substituent radical]^? and [M? H? (substituent? H)]^? could be used as the symbols of particular cyclic dipeptides. The hydrogen/deuterium (H/D) exchange experiment, the high‐resolution mass spectrometry (Q‐TOF) and theoretical calculations were used to rationalize the proposed fragmentation pathways and to verify the differences between the fragmentation pathways. The relative Gibbs free energies (ΔG) of the product ions and possible fragmentation pathways were estimated using the B3LYP/6–31++G(d, p) model. The results have some potential applications in the structural elucidation and interpretation of the mass spectra of homologous compounds and will enrich the gas‐phase ESI‐MS ion chemistry of cyclic dipeptides. Copyright © 2009 John Wiley & Sons, Ltd.     

Electronic structure, spectra, and magnetic circular dichroism of cyclohexa-, cyclohepta-, and cyclooctapyrrole

Three recently obtained expanded porphyrins represent nice examples of compounds for which the electronic and spectral properties can be predicted from symmetry considerations alone. Perimeter-model-based theoretical analysis of the electronic structure of doubly protonated cyclo[6], cyclo[7], and cyclo[8]pyrrole leads to the anticipation of qualitatively the same electronic absorption and magnetic circular dichroism patterns for all three compounds. These predictions are fully confirmed by experiments, as well as DFT and INDO/S calculations. Due to a characteristic pattern of frontier molecular orbitals, a degenerate HOMO and a strongly split LUMO pair, the three cyclopyrroles show comparable absorption intensity in the Q and Soret regions. Magnetic circular dichroism spectra reveal both A and B Faraday terms, of which the signs and magnitudes are in remarkably good agreement with theoretical expectations. The values of the magnetic moments of the two lowest degenerate excited states have also been obtained.     

Analytical pyrolysis of dipeptides containing proline and amino acids with polar side chains. Novel 2,5-diketopiperazine markers in the pyrolysates of proteins

The formation of cyclic dipeptides (DKPs, 2,5-diketopiperazines) from dipeptides having proline (Pro) as the fixed N-terminal amino acid was investigated by analytical pyrolysis with a heated platinum filament coil. Glutamic acid (Glu), aspartic acid (Asp), glutamine (Gln), lysine (Lys) or arginine (Arg) was the terminal amino acid. Products evolved from off-line pyrolysis at 500 °C were analysed by GC–MS as such or after trimethylsilylation. The structure of a novel DKP from the pyrolysis of Pro-Glu, namely hexahydrodipyrrolo[1,2-a:1′,2′-d]pyrazine-3,5,10(10aH)-trione, was established by ESI-MS/MS and extensive NMR analysis. This DKP could be identified in the pyrolysates of dipeptide Pro-Gln, tripeptide Pro-Glu-Leu, collagen and bovine serum albumin (BSA). Pyrolysis of Pro-Lys and Lys-Pro-Leu afforded the cyclo(Pro-Lys) tentatively identified by interpretation of its trimethylsilyl (TMS) derivative mass spectra and the DKPs resulting from the deamination of the lateral chain. The dipeptide Pro-Asp yielded isomeric cyclo(Pro-Asp) revealed as TMS derivatives and cyclo(Pro-Ala) from the decarboxylation of the side chain. Analytical pyrolysis of the above peptides as well as of Pro-Tyr, collagen and BSA enabled the compilation of GC (retention times relative to an internal standard) and MS data (characteristic ions) of over eighty DKPs including their TMS derivatives, the latter ones useful in the identification of thermal degradation products of proteinaceous materials in several matrices.     

Geometry of simple molecules: nonbonded interactions, not bonding orbitals, and primarily determine observed geometries.

The forces responsible for the observed geometries of the YX(3) (Y = N or P; X = H, F, or Cl) molecules were studied through ab initio computations at the HF-SCF/6-31G level. The calculated molecular orbitals were grouped as contributing primarily to (a) the covalent bonds, (b) the terminal atom nonbonding electrons (for X = F or Cl), and (c) the central atom nonbonding electrons. This grouping was accomplished through 3-D plotting and an atomic population analysis of the molecular orbitals. The molecules were then moved through a X-Y-X angular range from 90 degrees to 119 degrees, in four or five degree increments. Single-point calculations were done at each increment, so as to quantify the energy changes in the molecular orbital groups as a function of geometry. These calculations show that the nonbonding electrons are much more sensitive to geometry change than are the bonding orbitals, particularly in the trihalide compounds. The molecular orbitals representing the nonbonding electrons on the terminal atoms (both valence and core electrons) contribute to the spreading forces, as they favor a wider X-Y-X angle. The contracting forces, which favor a smaller X-Y-X angle, consist of the orbitals comprising the nonbonding electrons on the central atom (again, both valence and core electrons). The observed geometry is seen as the balance point between these two sets of forces. A simple interaction-distance model of spreading and contracting forces supports this hypothesis. Highly linear trends are obtained for both the nitrogen trihalides (R(2) = 0.981) and phosphorus trihalides (R(2) = 0.992) when the opposing forces are plotted against each other. These results suggest that a revision of the popular conceptual models (hybridization and VSEPR) of molecular geometry might be appropriate.     

Photoelectron spectra of some antibiotic building blocks: 2-azetidinone and thiazolidine-carboxylic Acid

X-ray photoelectron spectra of the core and valence levels of the fundamental building blocks of β-lactam antibiotics have been investigated and compared with theoretical calculations. The spectra of the compounds 2-azetidinone and the 2- and 4-isomers of thiazolidine-carboxylic acid are interpreted in the light of theoretical calculations. The spectra of the two isomers of thiazolidine-carboxylic acid are rather similar, as expected, but show clear effects due to isomerization. Both isomers are analogues of proline, which is well-known to populate several low energy conformers in the gas phase. We have investigated the low energy conformers of thiazolidine-4-carboxylic acid theoretically in more detail and find some spectroscopic evidence that multiple conformers may be present. The measured valence levels are assigned for all three compounds, and the character of the frontier orbitals is identified and analyzed.     

Antibacterial activity of cyclo(L-Pro-L-Tyr) and cyclo(D-Pro-L-Tyr) from Streptomyces sp. strain 22-4 against phytopathogenic bacteria

Two bioactive cyclic dipeptides, cyclo(L-Pro-L-Tyr) and cyclo(D-Pro-L-Tyr), were isolated from the culture broth of Streptomyces sp. strain 22-4 and tested against three economically important plant pathogens, Xanthomonas axonopodis pv. citri, Ralstonia solanacearum and Clavibacter michiganensis. Both cyclic dipeptides were active against X. axonopodis pv. citri and R. Solanacearum with MIC of 31.25 μg/mL. No activity could be observed against C. michiganensis.     

Electronic structure of copper phthalocyanine: an experimental and theoretical study of occupied and unoccupied levels

An experimental and theoretical study of the electronic structure of copper phthalocyanine (CuPc) molecule is presented. We performed x-ray photoemission spectroscopy (XPS) and photoabsorption [x-ray absorption near-edge structure (XANES)] gas phase experiments and we compared the results with self-consistent field, density functional theory (DFT), and static-exchange theoretical calculations. In addition, ultraviolet photoelectron spectra (UPS) allowed disentangling several outer molecular orbitals. A detailed study of the two highest occupied orbitals (having a(1u) and b(1g) symmetries) is presented: the high energy resolution available for UPS measurements allowed resolving an extra feature assigned to vibrational stretching in the pyrrole rings. This observation, together with the computed DFT electron density distributions of the outer valence orbitals, suggests that the a(1u) orbital (the highest occupied molecular orbital) is mainly localized on the carbon atoms of pyrrole rings and it is doubly occupied, while the b(1g) orbital, singly occupied, is mainly localized on the Cu atom. Ab initio calculations of XPS and XANES spectra at carbon K edge of CuPc are also presented. The comparison between experiment and theory revealed that, in spite of being formally not equivalent, carbon atoms of the benzene rings experience a similar electronic environment. Carbon K-edge absorption spectra were interpreted in terms of different contributions coming from chemically shifted C 1s orbitals of the nonequivalent carbon atoms on the inner ring of the molecule formed by the sequence of CN bonds and on the benzene rings, respectively, and also in terms of different electronic distributions of the excited lowest unoccupied molecular orbital (LUMO) and LUMO+1. In particular, the degenerate LUMO appears to be mostly localized on the inner pyrrole ring.     

Investigation of the amino acids glycine, proline, and methionine by photoemission spectroscopy

The valence and core level photoelectron spectra of glycine, proline, and methionine in the gas phase have been investigated by VUV and soft X-ray radiation. The outer valence band photoemission spectra are similar to previously reported He I spectra, although relative peak intensities are different due to the different photon energy. We extended the spectral range to include the inner valence region. The carbon, nitrogen, and oxygen 1s as well as the sulfur 2p core level spectra of these amino acids have been measured and the states identified. Valence band spectra of proline have been recorded as a function of temperature, and they provide information about the relative populations of the lowest energy conformers.     

Variable-energy photoelectron spectroscopy of substituted rhenium and manganese pentacarbonyls: molecular orbital assignments and the interatomic resonant effect

High-resolution variable-energy photoelectron spectra of M(CO)5X [M = Re, X = Re(CO)5, Cl, Br, and I; and M = Mn, X = Mn(CO)5 and Br] are reported. Tunable synchrotron radiation is used to distinguish the Re 5d and Br 4p orbital based peaks for the controversial Re(CO)5Br. Our results provide firm molecular orbital assignments for all of these molecules. The valence orbital in the ordering of ionization energies for M(CO)5Cl (M = Mn and Re) and Mn(CO)5Br is a 1(M-X) > e(X) > b2(M) > e(M); but for M(CO)5I (M = Mn and Re) and Re(CO)5Br the ordering is a1(M-X) > e(M) > b2(M) > e(X). The crossover of the HOMO in the Re molecules due to the change in the halogen electronegativities occurs at Re(CO)5Br. The metal np-->nd resonance is observed for all of these molecules. For molecules like M2(CO)10 (M = Re and Mn) and Mn(CO)5Br, the observation of this np-->nd resonance is useful in assigning the metal nd based orbitals in their valence level spectra. However, for molecules like Re(CO)5X (X = Br and Cl), a np-->nd type resonance is observed on bands arising from both Re 5d and halogen mp based orbitals. This new resonant effect on the ligand-based orbitals is shown to be mainly due to the interatomic resonant effect. The core and valence level chemical shifts of these compounds are treated using Jolly's approach to confirm the assignments for the valence level spectra of some of these molecules. The high-resolution inner valence and core level spectra of these compounds are reported. Broadening of Re 4f, Br 3d, and I 4d core level spectra is discussed. The Auger peaks are observed in the high-resolution, high-intensity Br 3d of Re(CO)5Br and I 4d of Re(CO)5I spectra.     

Unambiguous Stereochemical Assignment of Cyclo(Phe-Pro), Cyclo(Leu-Pro), and Cyclo(Val-Pro) by Electronic Circular Dichroic Spectroscopy

2,5-diketopiperazines (DKPs) are cyclic dipeptides ubiquitously found in nature. In particular, cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) are frequently detected in many microbial cultures. Each of these DKPs has four possible stereoisomers due to the presence of two chirality centers. However, absolute configurations of natural DKPs are often ambiguous due to the lack of a simple, sensitive, and reproducible method for stereochemical assignment. This is an important problem because stereochemistry is a key determinant of biological activity. Here, we report a synthetic DKP library containing all stereoisomers of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro). The library was subjected to spectroscopic characterization using mass spectrometry, NMR, and electronic circular dichroism (ECD). It turned out that ECD can clearly differentiate DKP stereoisomers. Thus, our ECD dataset can serve as a reference for unambiguous stereochemical assignment of cyclo(Phe-Pro), cyclo(Leu-Pro), and cyclo(Val-Pro) samples from natural sources. The DKP library was also subjected to a biological screening using assays for E. coli growth and biofilm formation, which revealed distinct biological effects of cyclo(D-Phe-L-Pro).     

Multielectron coincidence spectroscopy for core-valence doubly ionized states of CO

Double photoionization into states which have holes in one core and one valence orbitals has been observed in CO using a state-of-the-art multielectron coincidence method. The core-valence CO2+ structures exhibited on the electron coincidence spectra are assigned by comparison with the available calculation [H. Schulte et al., J. Chem. Phys. 105, 11108 (1996)]. Features of the spectrum confirm that the properties of the CO2+ states are characterized by the interaction between the localized valence holes and the core holes.     

Thermodynamic characterization of the osmolyte effect on protein stability and the effect of GdnHCl on the protein denatured state

To understand the biomolecular interactions of osmolytes or guanidine hydrochloride (GdnHCl) with protein functional groups, we have determined the apparent transfer free energies (Delta'(tr)) of a homologous series of cyclic dipeptides (CDs) from water to aqueous solutions of osmolytes or GdnHCl through solubility measurements, as a function of osmolyte or GdnHCl concentration at 25 degrees C under atmospheric pressure. The materials investigated in the present study included the CDs of cyclo(Gly-Gly), cyclo(Ala-Gly), cyclo(Ala-Ala), cyclo(Leu-Ala), and cyclo(Val-Val), the osmolytes of trimethylamine N-oxide (TMAO), sarcosine, betaine, proline, and sucrose, and the denaturant of GdnHCl. We observed positive values of (Delta'(tr)) for CDs from water to osmolyte, indicating that interactions between osmolytes and CDs are unfavorable. In contrast, negative (Delta'(tr)) contributions were observed for CDs from water to GdnHCl, revealing that favorable interactions are predominant. The experimental results were further used to estimate the transfer free energies (Delta'(tr)) of the peptide bond (-CONH-), the peptide backbone unit (-CH2C=ONH-), and various functional groups from water to aqueous solutions of osmolyte or GdnHCl.