Deprotecting thioacetyl-terminated terphenyldithiol for assembly on gallium arsenide

We characterize the assembly of terphenyldithiol (TPDT) on gallium arsenide (GaAs) from ethanol (EtOH) and tetrahydrofuran (THF) as a function of ammonium hydroxide (NH4OH) concentration. NH4OH facilitates the conversion of thioacetyl end groups of the TPDT precursor to thiolates in the assembly solution. The final structure of TPDT assembled on GaAs is sensitive not only to the assembly solvent but also to NH4OH concentration. In the presence of low concentrations of NH4OH (1 mM), TPDT assemblies from EtOH are oriented upright. The same assemblies are less upright when adsorption is carried out at higher NH4OH concentrations. In THF, TPDT does not adsorb significantly on GaAs at low NH4OH concentrations. The surface coverage and structural organization of these assemblies improve with increasing NH4OH concentrations, although these assemblies are never as organized as those from EtOH. The difference in the final structure of TPDT assemblies is attributed to differences in the thiolate fraction in the assembly solution at the point of substrate immersion.     

Solvent-dependent assembly of terphenyl- and quaterphenyldithiol on gold and gallium arsenide

The assembly of terphenyldithiol (TPDT) and quaterphenyldithiol (QPDT) on gold and gallium arsenide from ethanol (EtOH), tetrahydrofuran (THF), and solutions consisting of both solvents has been characterized by near-edge X-ray absorption fine structure spectroscopy. The surface coverage and the average orientation of both TPDT and QPDT on gold are solvent-independent. These molecules readily form monolayers on gold with an ensemble-average backbone tilt of 30 degrees +/- 3 degrees from the substrate normal. In sharp contrast, the assembly of TPDT and QPDT on gallium arsenide is extremely solvent-sensitive. At high ethanol fractions, both molecules form monolayers with an ensemble-average orientation that is indistinguishable from those on gold substrates. At low ethanol fractions and in pure THF, however, these molecules are disordered on gallium arsenide and the surface coverage is poor.     

Structural and orientational studies of chiral N-[4(1-pyrene)butyroyl]-phenylalanine in cast film

Cast films of chiral material N-[4(1-pyrene)butyroyl]-l-phenylalanine (Py-l-Phe) and the racemic modification (the 1:1 mixture of Py-l-Phe and Py-d-Phe) have been investigated in the present study. The microscopic structure, molecular orientation and the aggregation in the film have been studied by using ultraviolet-visible (UV-vis) and infrared (IR) spectroscopy. When a cast film is formed from the chloroform solution at room temperature, the J-aggregates of Py-l-Phe and Py-d-Phe are observed by UV-vis spectra. A comparison of Fourier transform infrared (FT-IR) transmission and reflection-absorption (RA) spectroscopy has been applied to reveal the orientation and structural characterization of the cast films. It has been found that the pyrenyl ring in the cast film of Py-l-Phe assumes a nearly vertical orientation with respect to the surface of the solid substrate. And there are two different hydrogen bonding species, cyclic dimer and linear dimer, exist in carboxyl groups in cast films. The detailed analysis of the OH and NH stretching modes of Py-l-Phe and Py-d-Phe allows us to reveal the hydrogen bonds existing in the films.     

H（Mg,Co）AlPO4—5杂原子分子筛的酸性质测定

以红外光谱和程序升温脱附法研究了H(Mg,Co)AlPO_4-5分子筛的酸性,样品红外谱图中的3820和3680cm~(-1)谱峰分别归属于v_(Al—OH)和v_(p—OH),而3660～3568cm~(-1)谱峰则分别归属于HMgAlPO_4-5和HCoAlPO_4-5分子筛的M(OH)P(M=Mg,Co)基团的振动,酸强度顺序为:Co(OH)P>Mg(OH)P>P(OH)>Al(OH),吡啶吸附的红外光谱揭示,H(Mg,Co)AlPO_4-5分子筛具有较高酸强度的B酸和L酸中心。NH_3-TPD表明分子筛的酸强度顺序为H(Co)AlPO_4-5>H(Mg)AlPO_4-5>>AlPO_4-5。     

Janus-like squaramide-based hosts: dual mode of binding and conformational transitions driven by ion-pair recognition

New tripodal squaramide-based hosts have been synthesised and structurally characterised by spectroscopic methods. In 2.5?% (v/v) [D(6)]DMSO in CDCl(3), compound 4 formed dimeric assemblies [log?K(dim)=3.68(8)] as demonstrated by (1)H?NMR spectroscopy and UV dilution experiments. AFM and SEM analyses revealed the formation of a network of bundled fibres, which indicates a preferential mechanism for aggregation. These C(3)-symmetric tripodal hosts exhibited two different and mutually exclusive modes of binding, each one easily accessible by simultaneous reorientation of the squaramide groups. In the first, a convergent disposition of the NH squaramide protons allowed the formation of an array of N-H???X(-) hydrogen bonds with anions. In the second mode, reorientation of carbonyl squaramide groups allowed multiple C=O???H interactions with ammonium cations. The titration of 4 with different tetraalkylammonium iodides persistently showed the formation of 1:1 complexes, as well as 1:2 and 1:3 complexes. The corresponding stoichiometries and binding affinities of the complexes were evaluated by multi-regression analysis. The formation of high-order complexes, supported by ROESY, NOESY and mass spectrometry experiments, has been attributed to the insertion of NR(4)I ion pairs between the carbonyl and NH protons of the squaramide groups located in adjacent arms of 4. The observed effects reflect the induction of significant conformational changes in the hosts, mainly in relation to the relative orientation of the squaramide groups adapting their geometries to incoming ion-pair complementary substrates. The results presented herein identify and fully describe two different modes of ion-pair recognition aimed at directing conformational transitions in the host, therefore establishing a base for controlling more elaborate movements of molecular devices through ion-pair recognition.     

Limitations of Linear Dichroism Spectroscopy for Elucidating Structural Issues of Light-Harvesting Aggregates in Chlorosomes

Linear dichroism (LD) spectroscopy is a widely used technique for studying the mutual orientation of the transition-dipole moments of the electronically excited states of molecular aggregates. Often the method is applied to aggregates where detailed information about the geometrical arrangement of the monomers is lacking. However, for complex molecular assemblies where the monomers are assembled hierarchically in tiers of supramolecular structural elements, the method cannot extract well-founded information about the monomer arrangement. Here we discuss this difficulty on the example of chlorosomes, which are the light-harvesting aggregates of photosynthetic green-(non) sulfur bacteria. Chlorosomes consist of hundreds of thousands of bacteriochlorophyll molecules that self-assemble into secondary structural elements of curved lamellar or cylindrical morphology. We exploit data from polarization-resolved fluorescence-excitation spectroscopy performed on single chlorosomes for reconstructing the corresponding LD spectra. This reveals that LD spectroscopy is not suited for benchmarking structural models in particular for complex hierarchically organized molecular supramolecular assemblies.     

Conformational stability, vibrational assignmenents, barriers to internal rotations and ab initio calculations of 2-aminophenol (d 0 and d3)

The Raman (3700-100 cm(-1)) and infrared (4000-400 cm(-1)) spectra of solid 2-aminophenol (2AP) have been recorded. The internal rotation of both OH and NH2 moieties produce ten conformers with either Cs or C1 symmetry. However, the calculated energies as well as the imaginary vibrational frequencies reduce rotational isomerism to five isomers. The molecular geometry has been optimized without any constraints using RHF, MP2 and B3LYP levels of theory at 6-31G(d), 6-311+G(d) and 6-31++G(d,p) basis sets. All calculations predict 1 (cis; OH is directed towards NH2) to be the most stable conformation except RHF/6-31++G(d,p) basis set. The 1 (cis) isomer is found to be more stable than 8 (trans; OH is away from the NH2 moiety and the NH bonds are out-of-plane) by 1.7 kcal/mol (598 cm(-1)) as obtained from MP2/6-31G(d) calculations. Aided by experimental and theoretical vibrational spectra, cis and trans 2AP are coexist in solution but cis isomer is more likely present in the crystalline state. Aided by MP2 and B3LYP frequency calculations, molecular force fields, simulated vibrational spectra utilizing 6-31G(d) basis set as well as normal coordinate analysis, complete vibrational assignments for HOC6H4NH2 and DOC6H4ND2 have been proposed. Furthermore, we carried out potential surface scan, to determine the barriers to internal rotations of NH2 and OH groups. All results are reported herein and compared with similar molecules when appropriate.     

A novel type of hydrogen-bonded assemblies based on the melamine.cyanuric acid motif

This paper reports the formation of novel hydrogen-bonded assemblies 1(3).CA obtained upon mixing cyanuric acid (CA) with melamine derivatives 1, in which two of the three possible H-bonding arrays have been blocked. The four components are held together by 9 hydrogen bonds and form a rigid planar structure in which a central CA (three ADA motifs: A = acceptor, D = donor) is hydrogen bonded to three peripheral melamine derivatives (DAD motif). Furthermore, the synthesis and assembly studies are described of hydrogen-bonded assemblies 2-4.CA, comprised of three melamine derivatives that are covalently connected, and CA. The overall thermodynamic stability of assemblies 2-4.CA is superior to 1(3).CA (I(Tm) = 9 vs 3.6). The presence of the 2.CA complex in chloroform was confirmed by (1)H NMR spectroscopy and MALDI-TOF mass spectrometry. Substitution of the trimelamines with chiral or fluorescent groups (R(3)) enabled the study of the assemblies by CD and fluorescence spectroscopy. Titration experiments revealed strongly enhanced stabilities even in the presence of polar solvents, such as THF and CH(3)OH. Depending on the polarity of the solvent, stacking between the planar assembly units was observed.     

Tyrosine derivatives assembled on gold

Two different tyrosine derivatives, one with the OH group free and one with the OH group phosphorylated, linked to 3-mercaptopropionic acid through an amide bond are adsorbed to gold surfaces. The adsorbates are studied by means of X-ray photoelectron spectroscopy (XPS) and infrared reflection-absorption spectroscopy (IRAS). The techniques are used to investigate the coordination to the surface and the molecular orientation of adsorbates relative to the surface. Molecular surface interactions, causing chemical shifts in the core level XPS spectra of the adsorbates on gold, are investigated using multilayer films as references. Angle-dependent XPS, XPS(theta), and IRAS are used to estimate molecular orientation relative to the surface. The tyrosine derivatives adsorb chemically to the surface through the sulfur atoms and highly organized monolayers are formed with the OH and the PO(2-)(3) exposed to the air/vacuum interface.     

Electronic and infrared spectroscopy of jet-cooled (+/-)-cis-1-amino-indan-2-ol hydrates

The role of conformational isomerism in molecular interaction has been studied using the example of jet-cooled complexes of (+/-)-cis-1-amino-indan-2-ol with water. The two formerly evidenced conformers of (+/-)-cis-1-amino-indan-2-ol easily form hydrates and dihydrates, which have been studied by means of laser-induced fluorescence and IR/UV double resonance spectroscopy, as well as ab initio calculations. All the 1 : 1 and 1 : 2 complexes with water evidenced in this work involve "ring" structures, in which the water monomer or dimer acts as an acceptor from the NH(2) and a donor to the OH groups of (+/-)-cis-1-amino-indan-2-ol. However, the water lies externally to the indan frame in the hydrates of conformer I of (+/-)-cis-1-amino-indan-2-ol, which possesses axial NH(2) and equatorial OH groups, and above it for the hydrates with the less stable conformer II, with equatorial NH(2) and axial OH groups. Consequently, the different steric constraints which exist in the two conformers result in different hydrogen bond topologies, with an additional OH[dot dot dot]pi interaction for the hydrates of conformer II.     

Steady‐State Spectroscopy of the 2‐(N‐methylacetimidoyl)‐1‐naphthol Molecule

The steady‐state spectroscopy of 2‐(N‐methylacetimidoyl)‐1‐naphthol (MAN) reveals composite absorption and emission spectra from 298 to 193 K in hexane. The ground electronic state (So) absorption can be assigned to the sum of three molecular structures: the OH normal tautomer, and two NH proton transfer tautomers. The NH‐structures are the most stable ones in equilibrium with the OH tautomer for the S₀ state. On photoexcitation of the OH tautomer the excited state intramolecular proton transfer is undergone, and the corresponding NH emission is monitored at 470 nm. On photoexcitation of the NH tautomers the previous emission is monitored in addition to another emission at 600 nm, which is ascribed to intramolecular hydrogen‐bonded (IHB) nonplanar NH structures generated from the IHB planar NH tautomers. A Jab?oński diagram is introduced which gathers all the experimental evidence as well as the theoretical calculations executed at the DFT‐B3LYP and TD‐DFT levels. The MAN molecule is compared with other analogs such as 1‐hydroxy‐2‐acetonaphthone (HAN), 2‐(1?‐hydroxy‐2?‐naphthyl)benzimidazole and methyl 1‐hydroxy‐2‐naphthoate to validate the theoretical calculations. Photoexcitation of MAN generates two emission bands at longer wavelengths than that of the emission band of HAN. The MAN molecule exhibits a great photostability in hydrocarbon solution which depends on the photophysics of the NH tautomers (keto forms).     

Infrared spectroscopy of methanol-hexane liquid mixtures. I. Free OH present in minute quantities

Methanol and hexane mixtures covering the whole solubility range are studied by Fourier transform infrared attenuated total reflectance spectroscopy in order to evaluate OH groups that are H-bond-free. The mixtures from 0 to 0.25 and from 0.75 to 1.00 mole fractions form homogeneous solutions, whereas those from 0.25 to 0.75 mole fractions are inhomogeneous, forming two phases. Factor analysis (FA) was used to find out if free OH groups were present. These were found in minute quantities at the lowest mole fraction by evaluating the OH stretch absorption. The bulk of the absorption is due to the greater than 99.9% of hydrogen-bonded methanol molecules, with a band maximum situated at 3340 cm(-1). The stretch band of the free OH groups absorbs at 3654 cm(-1), with a full width at half maximum of 35 cm(-1). The concentration is very weak but constant at less than 5 mM in the mole fraction between 0.252 and 0.067. Below this range, OH concentrations are even smaller. This represents less than 1% of the amount of methanol at the mole fraction of 0.067 (0.543M). Above 0.25 mole fraction, free methanol OH groups are not observed. Since the free OH band is very weak, almost at the noise level, we verified its presence with mixtures of hexanol in hexane. There, we found a similar free OH band with almost the same band characteristics, but with almost three times the concentrations found with methanol, which we attribute to the difference in the hydrocarbon chain length. The present study indicates clearly that solutions of methanol in hexane contain free OH groups but in minute quantities and only in the low methanol concentrations. This situation is much different from that observed in solutions of methanol in CCl(4), where free OH groups are clearly observed at all concentrations except at the concentration limits. Whereas in CCl(4), methanol is believed to form H-bonded chains, the situation is different in n-hexane: methanol in the low concentration region would form reverse micelles with the OH groups in the core and the CH(3) groups mixed with n-hexane molecules.     

Raman, infrared and XPS study of bamboo phytoliths after chemical digestion

Many phosphate containing minerals are found in the Jenolan Caves. Such minerals are formed by the reaction of bat guano and clays from the caves. Among these cave minerals is the mineral taranakite (K,NH(4))Al(3)(PO(4))(3)(OH)·9(H(2)O) which has been identified by X-ray diffraction. Jenolan Caves taranakite has been characterised by Raman spectroscopy. Raman and infrared bands are assigned to H(2)PO(4), OH and NH stretching vibrations. By using a combination of XRD and Raman spectroscopy, the existence of taranakite in the caves has been proven.     

Three-dimensional etching profiles and surface speciations (via attenuated total reflection-fourier transform infrared spectroscopy) of silicon nanowires in NH4F-buffered HF solutions: a double passivation model

A systematic study of the etching behavior, in terms of three-dimensional profiles, of one-dimensional (1-D) silicon nanowires (SiNWs) in NH(4)F-buffered hydrofluoric acid (BHF) solutions of varying concentrations and pH values and the surface speciations of the resulting etched SiNW surfaces, as characterized by attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy, is reported. It was found that SiNWs are stable only in relatively narrow pH ranges of the BHF solutions. The results are rationalized in terms of a "double passivation" model. When SiNWs are etched in BHF solutions with pH values of 1-3, the surfaces are passivated with hydrogen (inner layer) giving rise to surface moieties such as Si-H(x) species (x = 1-3); at high HF concentrations, the H-terminated Si surfaces are covered with a hydrogen bonding network of HF and related molecules (oligomers, etc.), providing an outer-layer passivation. When SiNWs are etched in BHF solutions with pH values of 11-14 (by adding a strong base such as NaOH), the surfaces are oxygen-terminated with surface moieties such as Si-(O(-))(x)() species (x = 1-3); at high NH(4)F concentrations, the negatively charged Si surfaces are stabilized by NH(4)(+) ions via ionic bonding, again providing outer-layer passivation. In BHF solutions with pH values of 3-11, the surface speciation, consisting of Si-(OH)(x)(O(-))(y) (x + y = 1-3) species, is unstable and etched away rapidly. The surface speciations of SiNWs etched in various BHF solutions were explored via ATR-FTIR spectroscopy. It was found that, while etching SiNWs with HF-rich BHF solutions with pH < 4 gave rise to Si-H(x)() surface species, no surface Si-H(x) species were observed with SiNWs etched in BHF solutions with pH >/= 4 (HF/NH(4)F /= 4 on the other. These two factors, among others, contribute to the rapid hydrolysis of the surface Si-H(x)() species (and the etching of the SiNWs), particularly in BHF solutions with low HF/NH(4)F ratios and high pH values (pH >/= 4).     

Arraying heterotypic single cells on photoactivatable cell-culturing substrates

This article describes a photochemical method for the site-selective assembly of heterotypic cells on a glass substrate modified with a silane coupling agent having a caged functional group. Silane coupling agents having a carboxyl (COOH), amino (NH 2), hydroxyl (OH), or thiol (SH) group protected by a photocleavable 2-nitrobenzyl group were synthesized to modify the surfaces of glass coverslips. The caged substrates were first coated by the adsorption of a blocking agent, bovine serum albumin (BSA), to make the entire surface non-cell-adhesive and then irradiated at 365 nm under a standard fluorescence microscope. The photocleavage reaction on the surface was followed by contact angle measurements and X-ray photoelectron spectroscopy. When COS7, NIH3T3, and HEK293 cells were seeded onto these substrates in a serum-free medium, the cells adhered selectively and efficiently to the irradiated regions on the caged NH 2 substrate, whereas the other caged COOH, SH, and OH substrates were nonphotoactivatable for cell adhesion. Qualitative and quantitative analysis of BSA adsorbed to the uncaged substrates revealed that this highly efficient photoactivation on the caged NH 2 substrate arose because of the following reasons: (i) upon photoactivation, BSA adsorbed in advance on the 2-nitrobenzyl groups was readsorbed onto the uncaged functional groups and (ii) BSA readsorbed onto the NH 2 groups became unable to passivate the surface against cell adhesion whereas BSA on the other groups still had normal passivating activity. It was also demonstrated that heterotypic single COS7, NIH3T3, and HEK293 cells were positioned at any desired arrangement on the caged NH 2 substrate by repeating the UV irradiation at optimized array spot sizes and cell seeding in optimized cell concentrations. The present method will be particularly useful in studying the dynamic processes of cell-cell interactions at a single-cell level.     

Structure of adsorbed n-dodecyl-beta-D-maltoside layers on hematite

The composition, structure, and thickness of n-dodecyl-beta-D-maltoside self-assembled layers on hematite have been evaluated using infrared external reflection spectroscopy and spectral simulation techniques. From the qualitative and quantitative analysis of the reflection spectra of the same sample recorded at different specific angles of incidence and two polarizations, the orientation of the sugar ring and hydrocarbon chain were obtained. Both of these molecular groups are positioned parallel to hematite surface, the adsorbed molecules being at low (2.2-nm-thick layer) as well as higher (11-nm) coverages. The maltoside is adsorbed through interaction of sugar ring OH groups with hematite surface hydroxyl groups. The adsorption of maltoside is not very strong and desorption takes place easily from acidic and low-basic solutions but with more difficulty from strong-basic solution.     

A hydrogen-bonding receptor that binds cationic monosaccharides with high affinity in methanol

A dicarboxylate host (1) binds cationic monosaccharides such as D-glucosamine HCl (2), D-galactosamine-HCl (3), and D-mannosamine-HCl (4) with high affinity (K1 = 8.0 x 10(4)-2.0 x 10(5) M(-1)) in methanol. In circular dichroism (CD) spectroscopy a positive exciton-coupling band was observed near 290 nm; this indicates that the saccharides are recognized by multiple point interactions. Since the corresponding neutral monosaccharides are not significantly bound, one may conclude that complex formation is primarily due to the electrostatic interaction between NH3+ in the guest and one carboxylate in the host and secondarily due to hydrogen-bonding interactions of OH groups with the other carboxylate and/or nitrogen bases. Molar ratio plots and Job plots indicate that host 1 and cationic monosaccharide guests form CD-active, pseudo-cyclic 1:1 complexes at low guest concentration followed by the formation of CD-silent, acyclic 1:2 1-saccharide complexes at high guest concentration. The possible binding modes are discussed in detail on the basis of molecular mechanics calculations and chemical shift changes in 1H NMR spectra. The results of competition experiments with several cationic reference compounds bearing fewer OH groups than 2-4 are consistent with the proposed binding model. Thus, the present study is a rare example of saccharide recognition in a protic solvent, where in general, hydrogen-bonding interactions are rarely useful because of strong solvation energy. These are apparently the strongest saccharide complexes involving noncovalent interactions between host and guest. We believe that the findings are significant as a milestone toward development of new saccharide recognition systems ultimately useful in aqueous solution.     

Supramolecular H-bonded assemblies of redox-active metallodendrimers and positive and unusual dendritic effects on the recognition of H2PO4-

The DSM polyamine dendrimers dend-DAB-(NH2)x of generations 1 (x = 4) to 4 (x = 32) form H-bonded dendritic assemblies with the phenol AB3 units p-HOC6H4C(CH2CHCH2)3 and p-HOC6H4C{(CH2)3SiCH2NHCOFc}3 (Fc = ferrocenyl), as shown by the shifts of the NH2 and OH signals giving a concentration-dependent common signal between 2.4 and 4.1 ppm in CDCl3. The supramolecular dendrimers efficiently recognize H2PO4- anions with positive and unusual dendritic effects upon electrochemical titration involving half-stoichiometry for G1, a sudden cyclovoltammetry wave change at the equivalent point, and a dramatic intensity decrease of the new wave.     

Self-assembled monolayers from biphenyldithiol derivatives: optimization of the deprotection procedure and effect of the molecular conformation

A series of biphenyl-derived dithiol (BDDT) compounds with terminal acetyl-protected sulfur groups and different structural arrangements of both phenyl rings have been synthesized and fully characterized. The different arrangements were achieved by introducing hydrocarbon substituents in the 2 and 2' positions of the biphenyl backbone. The presented model compounds enable the investigation of the correlation between the intramolecular conformation and other physical properties of interest, like, e.g., molecular assembly or electronic transport properties. Here, the ability of these model compounds to form self-assembled monolayers (SAMs) on Au(111) and Ag(111) is investigated in details. The deprotection of the target molecules was performed in situ using either NH4OH or triethylamine (TEA) deprotection agent. The fabricated films were characterized by synchrotron-based high-resolution photoelectron spectroscopy and near-edge absorption fine structure spectroscopy. Whereas the deprotection by NH4OH was found to result in the formation of multilayer films, the deprotection by TEA allowed the preparation of densely packed BDDT SAMs with a noticeably higher orientational order and smaller molecular inclination on Ag than on Au. Introduction of the alkyl bridge between the individual rings of the biphenyl backbone did not lead to a noticeable change in the structure and packing density of the BDDT SAMs as long as the molecule had a planar conformation in the respective SAM. The deviation from this conformation resulted in the deterioration of the film quality and a decrease of the orientational order.