Orientation of 6-mercaptopurine SAMs at the silver electrode as studied by Raman mapping and in situ SERS

Self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) on a silver electrode in acid and alkaline media were investigated by a combination protocol of the SERS technique with Raman mapping, and it was found that the adsorption mode of 6MP SAMs changed with the pH value of the environment. Quantum calculations for the vibrational mode were performed by the BLYP/6-31G method. 6MP was adsorbed on the silver electrode with a tilted orientation via S, N1, and N7 atoms in acid medium, while the SAMs adopted head-on adsorption modes with the S atom and the N1 atom anchoring the silver surface in alkaline medium. However, 6MP SAMs turned to the same upright orientation on the electrode through the S and N7 atoms when either acid or basic solution was removed. Stability of 6MP SAMs was observed by in situ SERS spectroelectrochemical measurements. The results reveal that the desorption potentials of 6MP SAMs formed under acid and alkaline conditions from the Ag electrode were at ca. -1.3 V and -1.6 V vs SCE, respectively.     

Raman mapping and in situ SERS spectroelectrochemical studies of 6-mercaptopurine SAMs on the gold electrode

The self-assembled monolayers (SAMs) of 6-mercaptopurine (6MP) were formed at the roughened polycrystalline gold surfaces in acid and alkaline media. The time-dependent Raman mapping spectral analysis in conjunction with the quantum calculations for the vibrational modes using ab initio BLYP/6-31G method suggested that both of the resulted 6MP SAMs adopted the same adsorption mode through the S atom of pyrimidine moiety and the N7 atom of the imidazole moiety anchoring the gold surface in a vertical way. The in situ surface-enhanced Raman scattering spectroelectrochemical experiment was conducted to examine the stability of the SAMs at various bias potentials. It was found that the detaching process of the 6MP SAMs from the surface involved one electron reduction as the voltage was applied at ca. 0.7 V vs a standard calomel electrode.     

Force constants and bond polarizabilities of thiocyanate ion adsorbed on the silver electrode as interpreted from the surface enhanced Raman scattering

The surface enhanced Raman spectra of the thiocyanate ion is studied in two ways. First, normal mode analysis is employed to determine the force constants of the adsorbed thiocyanate ion. The result shows that the force constant for the CN bond becomes larger while that for the SC bond smaller in the adsorbed state. The adatom model with an effective silver mass of 0.1 m_Ag (m_Ag being the mass of the silver atom) is adequate for the analysis. This implies that the silver adatom is bound to the bulk electrode surface. The adsorption is also shown to be physical. Second, the SER intensifies are analyzed to obtain the molecular polarizability derivatives. The result shows that the polarizability derivative of the CN stretching motion is most responsive to the applied voltage. The polarizability derivative of the SC stretching motion is much smaller than that of the CN bond as compared in the solution. This conclusion is attributed to the adsorption center at the sulfur atom. In general, molecular polarizability derivatives are functions of the frequencies of the exciting lasers and the applied voltages on the electrode.     

Thiol with an unusual adsorption-desorption behavior: 6-mercaptopurine on Au(111)

A multitechnique study of 6-mercaptopurine (6MP) adsorption on Au(111) is presented. The molecule adsorbs on Au(111), originating short-range ordered domains and irregular nanosized aggregates with a total surface coverage by chemisorbed species smaller than those found for alkanethiol SAMs, as derived from scanning tunneling microscopy (STM) and electrochemical results. X-ray photoelectron spectroscopy (XPS) results show the presence of a thiolate bond, whereas density functional theory (DFT) data indicate strong chemisorption via a S-Au bond and additional binding to the surface via a N-Au bond. From DFT data, the positive charge on the Au topmost surface atoms is markedly smaller than that found for Au atoms in alkanethiolate SAMs. The adsorption of 6MP originates Au atom removal from step edges but no vacancy island formation at (111) terraces. The small coverage of Au islands after 6MP desorption strongly suggests the presence of only a small population of Au adatom-thiolate complexes. We propose that the absence of the Au-S interface reconstruction results from the lack of significant repulsive forces acting at the Au surface atoms.     

Raman spectral study of metal-cytosine complexes: a density functional theoretical (DFT) approach

The fluctuation of surface-enhanced Raman scattering (SERS) spectra has been an obstacle to the analysis of the adsorbate on the metal surface. In this paper, we aim at using the density functional theory (DFT) to study the fluctuant Raman spectra of the cytosine molecule which interacts with a coinage metal atom or cation via N1 and N3 sites. The results show that the adsorption site strongly influences the Raman spectral property of cytosine molecule, especially the relative intensity of some bands. In addition, the SERS spectra of cytosine which is adsorbed on the gold, silver, and copper electrodes are measured, and the possible orientation and adsorption site of the cytosine molecule adsorbed on metal electrodes surface are proposed with the help of DFT simulations.     

A DFT Investigation of Surface‐Enhanced Raman Scattering of Adenine and 2′‐Deoxyadenosine 5′‐Monophosphate on Ag20 Nanoclusters

We present a detailed analysis of the surface‐enhanced Raman scattering (SERS) of adenine and 2′‐deoxyadenosine 5′‐monophosphate (dAMP) adsorbed on an Ag₂₀ cluster by using density functional theory. Calculated Raman spectra show that spectral features of all complexes depend greatly on adsorption sites of adenine and dAMP. The complexes consisting of adenine adsorbed on the Ag₂₀ cluster through N3 reproduce the measured SERS spectra in silver colloids, and thus demonstrated that adenine interacts with the silver surface via N3. We also investigate the SERS spectrum of adenine at the junction between two Ag₂₀ clusters and demonstrate that adenine can bind to the clusters through N3 and the external amino group, while dAMP can be adsorbed on the cluster in an end‐on orientation with the ribose and phosphate groups near to or away from the silver cluster. In contrast to the adenine–Ag₂₀ complexes, the dAMP–Ag₂₀ complexes produce new and strong bands in the low‐ or high‐wavenumber region of the Raman spectra, due to vibrations of the ribose and phosphate groups. Furthermore, the spectrum of dAMP bound to the Ag₂₀ cluster via N7 approaches the experimental SERS spectra on silver colloids.     

Adsorption Behaviors of 4-Mercaptobenzoic Acid on Silver and Gold Films

The adsorption behaviors of 4-mercaptobenzoic acid on silver and gold nanoparticles were studied by surface-enhanced Raman scattering (SERS) and density functional theory. The silver and gold films by electrodeposition have the same excellent characteristics as SERS-active substrates. At the same, the SERS spectra indicate that 4-mercaptobenzoic acid molecules are adsorbed on the surfaces of gold nanoparticles through the S atom, and that the carboxyl group is far away from surface of gold nanoparticles, and that there is a certain angle between the plane of benzene ring and gold film. However, 4-mercaptobenzoic acid molecules are adsorbed on the surfaces of silver nanoparticles through the carboxyl group, and the S atom is far away from surface of silver nanoparticles, and there is also a certain angle between the plane of benzene ring and the surface of silver nanoparticles. Here it is demonstrated the calculated Raman frequencies are in good agreement with experimental values, and the calculated Raman frequencies are also helpful to infer the adsorption behaviors of 4-mercaptobenzoic acid molecules.     

Efficiency of post-Hartree-Fock force field for the interpretation of vibrational spectra ofN,N-dimethylnitramine

Harmonic force fields for the molecule ofN,N-dimethylnitramine were calculated in the RHF/6-31G^* and MP2/6-31G^** approximations. Scaling of the force fields obtained made it possible to reliably interpret the vibrational spectra of light and perdeuterated compounds reported in the literature. The assignment is confirmed by good reproducibility of experimental isotope shifts upon¹⁵N-amino- and¹⁵N-nitrosubstitution. The frequencies of intramolecular vibrations in far IR and Raman spectra as well as in neutron inelastic scattering spectra for the light and perdeuterated samples of solidN,N-dimethylnitramine were identified using the force field calculated with the inclusion of electron correlation (MP2). Although general structures of the force fields calculated in the RHF and MP2 approximations are similar, considerable differences in the force constants of the NO and NN stretching vibrations and especially in the constants of the NO_str/NO_str and NO_str/NN_str interactions remain even after scaling the force fields.     

4-Mercaptophenylboronic acid SAMs on gold: comparison with SAMs derived from thiophenol, 4-mercaptophenol, and 4-mercaptobenzoic acid

We report the formation and characterization of self-assembled monolayers (SAMs) derived from the adsorption of 4-mercaptophenylboronic acid (MPBA) on gold. For comparison, SAMs derived from the adsorption of thiophenol (TP), 4-mercaptophenol (MP), and 4-mercaptobenzoic acid (MBA) were also examined. The structure and properties of the SAMs were evaluated by ellipsometry, contact-angle goniometry, polarization-modulation infrared reflection-absorption spectroscopy (PM-IRRAS), and X-ray photoelectron spectroscopy (XPS). Specifically, ellipsometry was used to assess the formation of monolayer films, and contact angle measurements were used to determine the surface hydrophilicity and homogeneity. Separately, PM-IRRAS was used to evaluate the molecular composition and orientation as well as the intermolecular hydrogen bonding within the SAMs. Finally, XPS was used to evaluate the film composition and surface coverage (i.e., packing density), which was observed to increase in the following order: TP < MP < MPBA < MBA. A rationalization for the observed packing differences is presented. The XPS data indicate further that ultrahigh vacuum conditions induce the partial dehydration of MPBA SAMs with the concomitant formation of surface boronic anhydride species. Overall, the analytical data collectively show that the MPBA moieties in the SAMs exist in the acid form rather than the anhydride form under ambient laboratory conditions. Furthermore, stability studies find that MPBA SAMs are surprisingly labile in basic solution, where the terminal B-C bonds are cleaved by the attack of hydroxide ion and strongly basic amine nucleophiles. The unanticipated lability observed here should be considered by those wishing to use MPBA moieties in carbohydrate-sensing applications.     

Peculiarities of the silica surface center structure in rigid dehydroxidation conditions

A model of molecular claster and nonempirical calculation schemes MP2/6‐31G*, MP4/6‐31G*, and MP2/DZVP2 were applied to study electronic and energy characteristics of the surface centers of different SiO₂ modifications in rigid dehydroxidation conditions. It was established that depending on an angle α = Si′O′Si″ (where O′ is an oxygen atom of the nearest to the surface layer), O* atom corresponding with two surface Si atoms, could (i) form a chemical bond with one of the Si′ or Si″‐centers (an asymmetric configuration, α > 118° ÷ 120°); or (ii) be common for these centers (a symmetric configuration, α < 118° ÷ 120°). It was also established that when α > 132° ÷ 133°, the basic state was triple and at α < 132° ÷ 133°, it was single. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

An Experimental and Theoretical Approach to Investigate the Effect of Chain Length on Aminothiol Adsorption and Assembly on Gold

Despite the numerous studies on the self‐assembled monolayers (SAMs) of alkylthiols on gold, the mechanisms involved, especially the nature and influence of the thiol–gold interface are still under debate. In this work the adsorption of aminothiols on Au(111) surfaces has been studied by using surface IR and X‐ray photoelectron spectroscopy (XPS) as well as by density functional theory (DFT) modeling. Two aminothiols were used, cysteamine (CEA) and mercaptoundecylamine (MUAM), which contain two and eleven carbon atoms, respectively. By combining experimental and theoretical methods, it was possible to draw a molecular picture of the thiol–gold interface. The long‐chain aminothiol produced better ordered SAMs, but, interestingly, the XPS data showed different sulfur binding environments depending on the alkyl chain length; an additional peak at low binding energy was observed upon CEA adsorption, which indicates the presence of sulfur in a different environment. DFT modeling showed that the positions of the sulfur atoms in the SAMs on gold with similar unit cells [(2√3×2√3)R30°] depended on the length of the alkyl chain. Short‐chain alkylthiol SAMs were adsorbed more strongly than long‐chain thiol SAMs and were shown to induce surface reconstruction by extracting atoms from the surface, possibly forming adatom/vacancy combinations that lead to the additional XPS peak. In the case of short alkylthiols, the thiol–gold interface governs the layer, CEA adsorbs strongly, and the mechanism is closer to single‐molecule adsorption than self‐assembly, whereas for long chains, interactions between alkyl chains drive the system to self‐assembly, leading to a higher level of SAM organization and restricting the influence of the sulfur–gold interface.     

Rotational spectrum and inversion motions in the neon-dimethyl sulfide complex

The rotational spectra of the (20)Ne and (22)Ne isotopomers of the Ne-dimethyl sulfide (DMS) rare gas dimer have been measured by Fourier transform microwave spectroscopy. MP2/6-311++G(2d,2p) calculations, and the experimental spectroscopic data, suggest a structure of C(s) symmetry in which the Ne atom lies above the heavy atom plane of the DMS (in the sigma(v) plane which bisects the CSC angle). Experimental rotational constants are consistent with a S...Ne distance of 3.943(6) Angstroms and a (cm...S...Ne) angle of 63.2(6) degrees (where cm is the center of mass of DMS). A motion of the Ne atom from one side of the DMS to the other gives rise to inversion splittings of around 3 MHz in the c-type transitions. An ab initio potential energy surface calculation has allowed examination of several possible tunneling pathways, and suggests a barrier of between 20 and 40 cm(-1) for the inversion motion, depending on the tunneling pathway taken by the Ne. Dipole moment measurements are consistent with both the experimental and ab initio structures.     

Vibrational spectra of 1-methyluracilate complex with silver(I) and theoretical studies of the 1-MeU anion

The FT-Raman and FT-infrared spectra of (1-methyluracilato)silver, [Ag(C(5)H(5)N(2)O(2))] in the solid state have been studied. The complex is a polymer in which one silver ion is linearly bonded to two 1-MeU ligands through the deprotonated N(3) sites and another silver ion is tetrahedrally coordinated to the four 1-MeU ligands through the O2 and O4 carbonyl oxygen atoms. The harmonic vibrational frequencies, infrared intensities and Raman scattering activities of the N(3)-deprotonated 1-methyluracilate anion have been calculated using density functional (B3LYP) and ab initio (HF and MP2) methods with the 6-31G(d,p) and 6-31++G(df,pd) basis sets. The calculated potential energy distribution (PED) for the 1-MeU anion has proved to be of great help in assigning the spectra of the title complex. It can be concluded that the two strong Raman bands at 1263 and 796 cm(-1) are diagnostic for the N3-deprotonation of the 1-methyluracilate ring and complexation with silver ion. The linear N-Ag-N stretching vibrations are assigned to the bands at 448 and 362 cm(-1) (IR) and 453, 362 cm(-1) (Raman). The Ag-O stretching vibrations are assigned to the bands in the range of 280-250 cm(-1).     

A hyper-raman spectroscopy,spectrophotometry, and atomic force microscopy study of photochromism of spirocyclic compounds on nanostructured metal films

The specifics of photochromic transformations of spirocyclic molecules at the nanostructured metal surface were studied by hyper-Raman spectroscopy (HRS) and spectrophotometry. Unique nanostructured systems were prepared, and their surface morphology and optical properties were examined. Enhancement of the photochromic transformations near the nanostructured metal surface was revealed. HRS spectra for various classes of spirocyclic compounds adsorbed on nanostructured systems of different types (granular silver films, AgCl-Ag films) were measured. The bands due to in-plane vibrations have the highest intensity, thereby indicating preferred planar geometry of adsorption of the test molecules.     

Peculiarities of atomic interaction in organic molecules of 3- and 4-coordinated phosphorus using ab initio calculations and Cl NQR

The results of ab initio calculations at the MP2/6-31G(d) level of molecules of the series ClPXX′ (X, X′=C₂H₅, N(CH₃)₂, OCH₃) and ClP(M)XX′ (M=O, S; X=CH₃, ?CH₃; X′=C₂H₅, OCH₃) with total optimization of their geometry were presented. They were compared with the obtained earlier results of such calculations at the RHF/6-31G(d) level and with experimental ³⁵Cl nuclear quadrupole resonance (NQR) spectra for these compounds. MP2/6-31G(d) calculations confirm non-inductive influence of heteroatoms on the geminal Cl atom in the non-linear three-atomic Cl–P–M groups. They agree to the conclusion that the abnormal correlation of the ³⁵Cl NQR frequencies for the compounds studied at different X, X′ and M is caused, in general, by the P–Cl bond polarization under the action of the geminal atom partial charges directly through the field. The satisfactory conformity between the experimental ³⁵Cl NQR frequencies and those estimated from 3p-components of the Cl atom valence p-orbitals calculated at the MP2/6-31G(d) level was obtained.     

Raman,surface-enhanced Raman scattering and DFT study of para-nitro-aniline

Raman spectra of para-nitro-aniline (pNA), a molecule with high applicability potential in molecular electronics, were recorded in solid state and in ethanol solution. Complete assignment of the experimental spectra was made by using the B3LYP/6-31G(d) theoretical results. The calculated molecular electrostatic potential shows a high negative charge localized on the nitro group of pNA and the surface-enhanced Raman scattering (SERS) spectrum of pNA adsorbed to colloidal silver particles denote the molecule interaction with the silver surface mainly through the nitro group. However, theoretical results obtained by modeling the pNA–4Ag complex also suggest the adsorption of pNA through the amino group or a flattened orientation of pNA with respect to the silver surface.     

First-principle DFT and MP2 modeling of infrared reflection-absorption spectra of oriented helical ethylene glycol oligomers

First-principle modeling is used to obtain a comprehensive understanding of infrared reflection absorption (RA) spectra of helical oligo(ethylene glycol) (OEG) containing self-assembled monolayers (SAMs). Highly ordered SAMs of methyl-terminated 1-thiaoligo(ethylene glycols) [HS(CH2CH2O)(n)CH3, n = 5, 6] on gold recently became accessible for systematic infrared analyses [Vanderah et al., Langmuir, 2003, 19, 3752]. We utilized the quoted experimental data to validate the first-principle modeling of infrared RA spectra of HS(CH2CH2O)(5,6)CH3 obtained by (i) DFT methods with gradient corrections (using different basis sets, including 6-311++G) and (ii) HF method followed by a M?ller-Plesset (MP2) correlation energy correction. In focus are fundamental modes in the fingerprint and CH-stretching regions. The frequencies and relative intensities in the calculated spectra for a single molecule are unambiguously identified with the bands observed in the experimental RA spectra of the corresponding SAMs. In addition to confirming our earlier assignment of the dominating peak in the CH-stretching region to CH2 asymmetric stretching vibrations, all other spectral features observed in that region have received an interpretation consistent (but not in all cases coinciding) with previous investigations. The obtained results provide an improved understanding of the orientation and conformation of the molecular building blocks within OEG-containing assemblies, which, in our opinion, is crucial for being able to predict the folding and phase characteristics and interaction of OEG-SAMs with water and proteins.     

An ab initio study of van der Waals potential energy parameters for silver clusters

We employ ab initio calculations of van der Waals complexes to study the potential energy parameters (C(6) coefficients) of van der Waals interactions for modeling of the adsorption of silver clusters on the graphite surface. Electronic structure calculations of the (Ag(2))(2), Ag(2)-H(2), and Ag(2)-C(6)H(6) complexes are performed using a coupled-cluster approach that includes single, double, and perturbative triple excitations (CCSD(T)), M?ller-Plesset second-order perturbation theory (MP2), and spin-component-scaled MP2 (SCS-MP2) methods. Using the atom pair approximation, the C(6) coefficients for silver-silver, silver-hydrogen, and silver-carbon atom systems are obtained after subtracting the energies of quadrupole-quadrupole interactions from the total electronic energy.     

Surface-enhanced Raman scattering of 4,4′-bipyridine on silver by density functional theory calculations

Surface-enhanced Raman scattering (SERS) of 4,4′-bipyridine (BPy) on silver foil substrate was measured using the 488, 514.5, and 1064 nm excitation lines. Density functional theory (DFT) methods were used to calculate the structure and vibrational spectra of Ag–BPy, Ag₃–BPy and Ag₄–BPy complexes with B3LYP/6-31++G(d,p)(C,H,N)/Lanl2dz(Ag) basis set. The Raman bands of BPy were assigned on the basis of the calculation of potential energy distribution. The calculated spectra of Ag–BPy and Ag₄–BPy complexes were much closer to the experimental results of BPy adsorbed on silver surface than that of Ag₃–BPy complexes. The vibrational frequencies that are sensitive to the planar or non-planar structure of BPy and to the dihedral angle of two pyridyl rings were discussed. The DFT results showed that the angles between two pyridyl rings for Ag–BPy and Ag₄–BPy were skewed by about 38.44° and 37.1°, respectively. The energy gaps of the HOMO and LUMO from DFT were 415–912 nm for BPy–Ag complexes. The relative intensities of SERS bands changed with different excitation laser lines. Thus, a chemical enhancement mechanism should play an important role in the SERS of BPy on silver substrate.     

Comparison of the adsorption orientation for 2-mercaptobenzothiazole and 2-mercaptobenzoxazole by SERS spectroscopy

In this study, the adsorption orientation for 2-mercaptobenzothiazole (MBT) and 2-mercaptobenzoxazole (MBO) on to silver mirror and silver sol substrates have been studied by surface enhanced Raman scattering (SERS). The MBT and MBO were chemisorbed on both silver mirror and silver sol after deprotonation with a tilted orientation to the silver surfaces. The surface enhanced properties of MBT and MBO showed that the substrate of silver mirror was superior to the sliver sol. The SERS spectra of MBT and MBO revealed that both of the MBT and MBO were adsorbed on silver surfaces strongly by a common sulfur molecule and a sulfur atom from MBT and an oxygen atom from MBO. Therefore, the adsorption orientation of MBT and MBO was little tilted perpendicularly to the silver surfaces. The adsorption geometry did not undergo any significant changes in acidic and basic solutions. It showed that the adsorption orientation for MBT and MBO were stable in the both solutions.