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Surface-enhanced Raman scattering (SERS), electrochemistry, and generalized two-dimensional correlation analysis (G2DCA) methods were used to define neuromedin B (NMB) ordered superstructures on Ag, Au, and Cu electrode surfaces at different applied electrode potentials in an aqueous solution at physiological pH. The orientation of NMB and the adsorption mechanism were determined based on the analysis of enhancement, broadness, and shift in wavenumber of particular bands, which allow drawing some conclusions about NMB geometry and changes in this geometry upon change of the electrode type and applied electrode potential. The presented data demonstrated that NMB deposited onto the Ag, Au, and Cu electrode surfaces showed bands due to vibrations of the moieties that were in contact/close proximity to the electrode surfaces and thus were located on the same side of the polypeptide backbone. These included the Phe(9) and Trp(4) rings, the sulfur atom of Met(10), and the -CCN- and -C═O units of Asn(2). However, some subtle variations in the arrangement of these fragments upon changes in the applied electrode potential were distinguished. The Amide-III vibrations exhibited an electrochemical Stark effect (potential dependent frequencies) with Stark tuning slope sensitive to the electrode material. Potential-difference spectrum revealed that the imidazole ring of His(8) was bonded to the Cu electrode surface at relatively positive potentials.

Here, we report a systematic study showing an analogy between the activities of peptide structural component interactions with both a metal substrate and a G-protein-coupled seven-transmembrane receptor. In the present work, N-terminal fragments of human neurotensin (NT), NT(1-6), NT(1-8), and NT(1-11), and C-terminal fragments of human neurotensin, NT(8-13) and NT(9-13), as well as six specifically mutated analogues with the following modifications, Acetyl-NT(8-13), [Dab(9)]NT(8-13), [Lys(8),Lys(9)]NT(8-13), [Lys(8)-(®)-Lys(9)]NT(8-13), [Lys(9),Trp(11),Glu(12)]NT(8-13), and Boc[Lys(9),Leu(13)OMe]NT(9-13), were immobilized onto an electrochemically roughened silver electrode surface in an aqueous solution. The orientation of the adsorbed molecules and the adsorption mechanism were determined from surface-enhanced Raman scattering (SERS) spectra. A comparison was made between the structures of the mutated fragments to determine how changes in the mutation of the structure influenced the adsorption properties. The contribution of the structural components to the peptides' ability to interact with the NTR1 receptor was correlated with the SERS patterns. The SERS spectra revealed that the substitution of native amino acids in the investigated peptides slightly influenced their adsorption state on an electrochemically roughened silver surface. Thus, all of the investigated peptides, excluding [Lys(9),Trp(11),Glu(12)]NT(8-13), tended to adsorb to the surface mainly via the oxygen atom of the deprotonated phenol group, and the phenyl ring became rearranged in a slightly different edge-on manner (NT(1-8), NT(1-11), NT(8-13), Acetyl-NT(8-13), [Dab(9)]NT(8-13), [Lys(8),Lys(9)]NT(8-13), [Lys(8)-(®)-Lys(9)]NT(8-13), NT(9-13), and Boc[Lys(9), Leu(13)OMe]NT(9-13)) or in an almost horizontal manner (N(1-6)) of the tyrosine residue. Meanwhile, [Lys(9),Trp(11),Glu(12)]NT(8-13) bound to this substrate through the tilted phenyl coring of the tryptophan residue. Small changes in the enhancement of the CCNH(2), COO(-), and -CONH- group modes upon adsorption, which were consistent with the adsorption of these peptides, also occurred (with slightly different strengths) through the nitrogen and oxygen lone pair of electrons in these groups. However, for NT(1-8), a greater preferential interaction between the guanidine group of Arg(8) and the roughened silver substrate was observed in comparison to that between the guanidine moiety of the other investigated peptides and the substrate. Vibrational spectroscopy was also used to produce an extensive table of Raman and absorption infrared spectra to allow for a rapid and accurate structural determination of these biomolecules and to allow the reader to easily follow the proposed SERS assignments.

The human, pig, and frog neurotensins and four single-site mutants of human neurotensin (NT), having the following modifications, [Gln(4)]NT, [Trp(11)]NT, [D-Trp(11)]NT, and [D-Tyr(11)]NT, were immobilized onto an electrochemically roughened silver electrode surface in an aqueous solution. The orientation of adsorbed molecules was determined from surface-enhanced Raman scattering (SERS) measurements. A comparison was made between these structures to determine how the change upon the mutation of the neurotensin structure influences its adsorption properties. The SERS patterns were correlated with the contribution of the structural components of the aforementioned peptides to the ability to interact with the NTR1 G-protein receptor. Briefly, the SERS spectra revealed that the substitution of native amino acids in investigated peptides influenced slightly their adsorption state on an electrochemically roughened silver surface. Thus, human, pig, and frog neurotensins and [Gln(4)]NT and [D-Tyr(11)]NT tended to adsorb to the surface via the tyrosine ring, the oxygen atom of the deprotonated phenol group of Tyr(11), and the -CH(2)- unit(s), most probably of Tyr(11), Arg(9), and/or Leu(13). The observed changes in the enhancement of the deprotonated Tyr residue SERS signals indicated a further parallel orientation of a phenol-O bond with regard to the silver surface normal for pig NT, [Gln(4)]NT, and [D-Tyr(11)]NT, whereas the orientation was slightly tilted for human and frog NT. In the case of [Trp(11)]NT and [D-Trp(11)]NT, the formation of a peptide/Ag complex was confirmed by strong SERS bands involving the phenyl co-ring of Trp(11)/d-Trp(11) and -CH(2)- vibrations and the tilted and flat orientations of the two compounds with respect to the surface substrate. The spectral features were accompanied by a SERS signal caused by vibrations of the carboxyl group of C-terminal Leu(13) and the guanidine group of Arg(9). Reported changes in SERS spectra of L and D isomers were fully supported by generalized two-dimensional correlation analysis. Additionally, a combination of mutation-labeling and vibrational spectroscopy (Fourier-transform Raman and absorption infrared) was used to investigate the possible peptide conformations and environments of the tyrosine residues.

Neuromedin C (NMC) is a decapeptide (Gly-Asn-His-Trp-Ala-Val-Gly-His-Leu-Met-NH(2)) that acts as a growth factor in a wide range of tumors including carcinomas of the pancreas, stomach, breast, prostate, and colon. We report surface-enhanced Raman spectra (SERS) of NMC on electrochemically roughened Ag, Au, and Cu electrode surfaces over an electrode potential range varying from +0.200 to -1.200 V (depending on the electrode material). We compared the SERS spectra to the Raman spectrum of the corresponding solid species. The SERS spectra were dominated by L-tryptophan (Trp) vibrations. This indicates that Trp interacted with the metallic surfaces of the electrodes, either by binding directly to the surface or by staying in close proximity to the surface. Characteristic SERS bands showed that, in the case of the Ag electrode, the Trp residue was almost perpendicular to the surface. In contrast, the Trp residue was slightly tilted with respect to the Au electrode surface, and Trp remained some distance from the surface of the Cu electrode. These differences were due to differences in surface rheology and in the type of metal (Ag vs Au vs Cu) responsible for the observed enhancement mechanism. On the other hand, variations in the electrode potentials only had a slight influence on the SERS patterns and the observed changes were mainly due to the reorientation of the Trp ring with respect to the electrode surface. These findings were fully supported by generalized two-dimensional correlation analysis (G2DCA).

In this work, we report systematic surface-enhanced Raman spectroscopy (SERS) and generalized two-dimensional correlation analysis (G2DCA) studies of the structures of five specifically modified phenylalanine-substituted C-terminal bombesin 6-14 fragments (BN(6-14)). The fragments studied have all been tested as chemotherapeutic agents in cancer therapy, and they form amino acid sequences in bombesin: cyclo[d-Phe(6),His(7),Leu(14)]BN(6-14), [D-Phe(6),Leu-NHEt(13),des-Met(14)]BN(6-14), [D-Phe(6),Leu(13)-((R))-p-Cl-Phe(14)]BN(6-14), [D-Phe(6),beta-Ala(11),Phe(13),Nle(14)]BN(6-14), and [D-Tyr(6),beta-Ala(11),Phe(13),Nle(14)]BN(6-14). We adsorbed these fragments onto roughened Ag, Au, and Cu electrode surfaces, using a potential range from -1.200 to 0.400 V, at physiological pH. We compared the adsorption mechanism of each fragment on these substrates, as well any changes observed with varying electrode potential, to determine the relationship between adsorption strength and geometry of each of the peptides wherever it was possible. For example, we showed that none of these fragments directly interact with the Ag, Au, and Cu surfaces via residues of Phe (phenylalanine) and Trp(8) (L-tryptophane at position 8 of the BN amino acid sequence) or by an amide bond, due to a very small shift in wavenumber of their characteristic vibrations. Specific interactions were recognized from the broadening, wavenumber shift, and increase in intensity of the W18 Trp(8) mode near 759 cm(-1) and decrease in nu(12) vibration frequency of the Phe residue. In general, more intense SERS bands were observed due to the Phe ring, compared with the Trp(8) ring, which suggested a preferential adsorption of phenylalanine over tryptophane. For [D-Tyr(6),beta-Ala(11),Phe(13),Nle(14)]BN(6-14), the data also suggest some interaction of a D-Tyr(6) residue (D-tyrosine at position 6). Finally, only slight rearrangements of these moieties on the substrates are observed with changes in electrode potential.

Here, we report a systematic surface-enhanced Raman spectroscopy (SERS) study of the structures of phosphonate derivatives of the N-heterocyclic aromatic compounds imidazole (ImMeP ([hydroxy(1H-imidazol-5-yl)methyl]phosphonic acid) and (ImMe)(2)P (bis[hydroxy-(1H-imidazol-4-yl)-methyl]phosphinic acid)), thiazole (BAThMeP (butylaminothiazol-2-yl-methyl)phosphonic acid) and BzAThMeP (benzylaminothiazol-2-yl-methyl)phosphonic acid)), and pyridine ((PyMe)(2)P (bis[(hydroxypyridin-3-yl-methyl)]phosphinic acid)) adsorbed on nanometer-sized colloidal particles. We compared these structures to those on a roughened silver electrode surface to determine the relationship between the adsorption strength and the geometry. For example, we showed that all of these biomolecules interact with the colloidal surface through aromatic rings. However, for BzAThMeP, a preferential interaction between the benzene ring and the colloidal silver surface is observed more so than that between the thiazole ring and this substrate. The PC(OH)C fragment does not take part in the adsorption process, and the phosphonate moiety of ImMeP and (ImMe)(2)P, being removed from the surface, only assists in this process.

The crystal structure of the Cu(II) complex with Vitamin B(13) (orotic acid), cis-[Cu(oro)(NH(3))(2)] has revealed the presence of unusual, noncovalent pi-type interaction between the chelated Cu(II) ion and the C horizontal lineC bond of the uracilate ring [Michalska et al. Polyhedron 2007, 26, 4303]. In this work, the origin and strength of this interaction is thoroughly investigated. Comprehensive studies of the molecular structures and vibrational spectra of the title complex have been performed by using the unrestricted density functional theory methods, B3LYP, and the newly developed M05-2X functional. Calculations at the UMP2 level were also carried out for comparison. A variety of basis sets have been employed in the DFT calculations, including aug-cc-pVTZ, D95V(d,p), SDD, and LanL2DZ. The (63)Cu/(65)Cu isotope substitution technique was applied to identify the copper-ligand vibrations in the infrared spectra. The clear-cut assignment of all the bands in the FT-IR and Raman spectra of the title complex has been made on the basis of the calculated potential energy distribution, PED. It is shown that an extremely intense band at 1210 cm(-1) in the Raman spectrum of cis-[Cu(oro)(NH(3))(2)] is diagnostic for the N-1 deprotonation of the uracilate ring and coordination to the copper(II) ion. The B3LYP functional performs better than M05-2X in predicting vibrational frequencies of this complex in the solid state. Intermolecular interactions in crystal were modeled by the supramolecular system consisting of cis-[Cu(oro)(NH(3))(2)], ethylene (above), and formaldehyde (below the copper coordination plane). The stable structure of this system has been predicted only by the M05-2X and MP2 methods, which include dispersion energy, whereas the B3LYP calculations failed in geometry optimization. The distance between the Cu atom and the C horizontal lineC bond, predicted by the M05-2X method (3.00 A) is similar to the van der Waals contacts between the stacking bases in DNA. The calculated interaction energy between the chelated Cu(II) complex and ethylene amounts to -7.33 kcal mol(-1), which is similar to that determined for stacked uracil dimer. It is concluded that the London dispersion energy plays a significant role in the noncovalent interaction between the chelated Cu(II) ion and the uracilate ring in the crystal of cis-[Cu(oro)(NH(3))(2)]. Many copper enzymes in their active sites contain the chelated Cu(II) ion and the aromatic groups (Phe, Tyr and Trp) as the potential binding sites; therefore, the noncovalent copper(II)-pi interaction can be very important for the structure and functioning of these enzymes.

We used surface-enhanced Raman scattering (SERS) to characterize the adsorption behavior of bombesin (BN) and five BN-related peptides, including phyllolitorin, [Leu(8)]phyllolitorin, neuromedin C (NMC), neuromedin B (NMB), and PG-L (Pseudophryne guntheri), in a silver colloidal solution. Our experiments show that the pyrrole coring of the Trp and aromatic ring of Phe of these peptides are preferentially adsorbed on silver nanoparticles. However, the geometry of the rings and the strength of the interactions with this surface vary among peptides. Additionally, these peptides are weakly coordinated to the colloidal silver surface through the CO fragment of a peptide bond, between Gln/Leu/His and Trp residues, and CNC and SC fragments. Also, using the recently reported SERS spectra of these peptides immobilized onto an electrochemically roughened silver electrode surface, we demonstrate substrate-induced changes in the adsorption behavior of these peptides. Comparative analysis indicates that the interactions between peptides and the enhancing surfaces depend strongly on the geometry of the Trp, CONH, and SC fragments of these biomolecules etched on the surfaces.