Self-assembly and molecular recognition of adenine- and thymine-functionalized nucleolipids in the mixed monolayers and thymine-functionalized nucleolipids on aqueous melamine at the air-water interface

Self-assembly and molecular recognition of the monolayers composed of an equimolar mixture of adenine- and thymine-functionalized nucleolipids at the air-water interface have been investigated in detail using surface pressure-molecular area isotherms and in situ infrared reflection absorption spectroscopy (IRRAS). Prior to molecular recognition, the adenine moieties in the monolayer were almost oriented on an end-on mode through π-stacking and hydrogen bonding interactions, and the C-C-C planes of the alkyl chains were preferentially oriented perpendicular to the water surface, while the thymine moieties in the monolayer were involved in hydrogen bonding almost with a flat-on orientation. On aqueous subphases containing complementary bases, no significant molecular recognition was observed for the monolayers of individual nucleolipids. In the monolayer of equimolar mixture, molecular recognition occurred between the adenine and thymine moieties through hydrogen bonding probably with the development of cyclic structures of adenine-thymine-adenine-thymine quartets. Although molecular recognition between the monolayer of thymine-functionalized nucleolipids and aqueous melamine took place through triple hydrogen bonds, no melamine binding to the monolayer of equimolar mixture was observed, which reflects the formation of the quartets in the mixed monolayers at the air-water interface. FTIR and small-angle X-ray diffraction (XRD) results of the corresponding Langmuir-Blodgett films support the hydrogen bonding recognition and molecular orientation.     

间苯二甲酰腙分子钳的合成及阴离子识别研究

设计合成了3种新型间苯二甲酰腙类化合物,利用UV-Vis及¹H NMR考察了其与F^-、Cl^-、Br^-、I^-、CH₃COO^-、HSO₄^-、H₂PO4-、ClO4-阴离子的相互作用。结果表明,主体分子4a(双对硝基苯并呋喃甲醛间苯二甲酰腙)在DMSO溶液中对F-和CH₃COO-有显著识别效果,溶液颜色由黄色变为深黄色和棕红色。通过¹H NMR滴定及质子溶剂效应进一步证明,主体分子与阴离子之间是以氢键作用方式相结合。Job曲线表明,主客体间形成1：1型氢键络合物。基于实验结果,探讨了主客体间形状和大小匹配对识别能力的影响以及主客体之间的识别模式。     

Intra- and intermolecular interactions in the series of acyclic and macrocyclic compounds containing nucleotide bases and their derivatives

Intra-and intermolecular interactions in acyclic compounds containing nucleotide base (uracil and thymine) derivatives and their macrocyclic analogs (pyrimidinophanes) were studied by IR, UV, luminescence, and NMR spectroscopy. Molecules of these compounds include one or two N³-methylsubstituted or N³-unsubstituted uracil fragment or two adenine fragments linked through a hexamethylene spacer to an uracil, 5,5′-methylenediuracil or diphenylmethane fragment. The examined compounds almost all are characterized by π-π interactions and intramolecular hydrogen bonding between the terminal uracil or adenine fragments. Intramolecular association constants were determined and factors affecting them were discussed. Complex formation of acyclic and macrocyclic ligands with adenine and thymine derivatives was studied. The low values of the association constants were interpreted in terms of a competition between intra-and intermolecular bonding and very labile ligand structure.     

Highly selective recognition of adenine nucleobases by synthetic hosts with a linked five-six-five-membered triheteroaromatic structure and the application to potentiometric sensing of the adenine nucleotide

A new structure for an adenine-selective host molecule, featuring the pertinent link of five-six-five-membered heteroaromatic rings and two carbamoyl NH sites, was developed. This structure provides a correctly oriented array of complementary hydrogen bonding sites for the adenine nucleobase, which exploits both Watson-Crick and Hoogsteen-type interactions. The complexation with adenine nucleobases by multiple hydrogen bonding was supported by (1)H NMR spectroscopy. This type of host displayed high selectivity in complexation, with an accompanying fluorescent response to lipophilized adenosine in CHCl(3). Furthermore, a remarkably selective potentiometric response was attained for adenosine 5'-monophosphate over 5'-GMP, 5'-CMP, and 5'-UMP by using an ion-selective electrode with a PVC-supported solvent polymeric membrane. This indicates recognition of water-soluble nucleotide guests through the membrane-water interface. These findings are expected to form a reliable basis for the development of artificial sensing systems for mononucleotides in biological systems.     

Effect of hydrogen bonding on the structure and vibrational spectra of the complementary pairs of nucleic acid bases. II. adenine-thymine

The vibrational spectra of an isolated complementary adenine-thymine pair are calculated in the B3LYP/6-311++G(d,p) approximation and analyzed. The effect of hydrogen bonds on the structure is shown along with the position of frequencies and intensities of normal vibrations of the pair in comparison with the spectra of isolated thymine and adenine molecules. A comparative analysis of the hydrogen bonding effect on the IR and Raman spectra of thymine and adenine is performed     

Formation of organic monolayers on silicon via gas-phase photochemical reactions

A new method for the formation of molecular monolayers on silicon surfaces utilizing gas-phase photochemical reactions is reported. Hydrogen-terminated Si(111) surfaces were exposed to various gas-phase molecules (hexene, benzaldehyde, and allylamine) and irradiated with ultraviolet light from a mercury lamp. The surfaces were studied with in situ Fourier transform infrared spectroscopy, high-resolution electron energy loss spectroscopy, and scanning tunneling microscopy. The generation of gas-phase radicals was found to be the initiator for organic monolayer formation via the abstraction of hydrogen from the H/Si(111) surface. Monolayer growth can occur through either a radical chain reaction mechanism or through direct radical attachment to the silicon dangling bonds.     

紫铜表面3-巯丙基三乙氧基硅烷薄膜的制备与耐蚀性能

利用傅里叶变换红外(FTIR)光谱分析了3-巯丙基三乙氧基硅烷分别在酸性和碱性的醇-水溶液中水解后以及在紫铜表面成膜后的结构特征. 利用极化曲线、电化学阻抗谱(EIS)和盐水浸泡实验测试了硅烷膜的耐腐蚀性能. 结果表明: 3-巯丙基三乙氧基硅烷在酸性溶液中能够发生一定程度的水解并生成Si―OH结构, 且当该溶液在自然状态下晾干后, 其水解程度进一步增大. 在碱性溶液中该硅烷只发生少量的水解, 溶液中含有较多SiOCH₂CH₃结构, 且在溶液自然晾干后水解程度也没有明显增大. 由酸性硅烷溶液制得的薄膜中硅烷分子以Si―O―Si 键相互交联的程度比由碱性硅烷溶液制得的薄膜高. 硅烷膜降低了紫铜电极的腐蚀电流密度, 其保护效率分别为90.3%(酸性)和79.2%(碱性). 在3.5% (w) NaCl溶液中浸泡24 h后, 由酸性溶液制得的薄膜表现出更高的阻抗值, 而由碱性溶液制得的薄膜则基本失去了对基底的保护能力.     

A “plug and play” polymer through biocomplementary hydrogen bonding

This article describes a DNA‐like polymer that exhibits the ability to self‐assemble through hydrogen bonding. We synthesized poly[1‐(4‐vinylbenzyl)thymine] (PVBT) and 9‐hexadecyladenine (A‐C16) through an atom transfer radical polymerization (ATRP) and alkylation, respectively. Biocomplementary PVBT/A‐C16 hierarchical supramolecular complexes formed in dilute DMSO solution through nucleobase recognition, that is, hydrogen bonding interactions between the thymine (T) groups of PVBT and the adenine (A) group of A‐C16; evidence for this molecular recognition was also gained from dynamic light scattering studies. ¹H NMR titration studies in CDCl₃ showed that T–A complexes formed rapidly on the NMR time scale with high association constants (up to 534 M^?1). Moreover, FTIR spectroscopic, differential scanning calorimetry, wide‐angle X‐ray diffraction, and small‐angle X‐ray scattering analyses provided further details into the nature of the self‐assembly of these systems. In the bulk state, these complexes self‐assemble into well‐ordered lamellar structures; the changing d‐spacing distance (ranging from 4.98 to 2.32 nm) at different A‐C16 loadings reveals that the molecular structures of the PVBT/A‐C16 complexes are readily tailored. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 6416–6424, 2008     

Surface modification of ZnO using triethoxysilane-based molecules

Zinc oxide (ZnO) is an important material for hybrid inorganic-organic devices in which the characteristics of the interface can dominate both the structural and electronic properties of the system. These characteristics can be modified through chemical functionalization of the ZnO surface. One of the possible strategies involves covalent bonding of the modifier using silane chemistry. Whereas a significant body of work has been published regarding silane attachments to glass and SiO2, there is less information about the efficacy of this method for controlling the surface of metal oxides. Here we report our investigation of molecular layers attached to polycrystalline ZnO through silane bonding, controlled by an amine catalyst. The catalyst enables us to use triethoxysilane precursors and thereby avoid undesirable multilayer formation. The polycrystalline surface is a practical material, grown by sol-gel processing, that is under active exploration for device applications. Our study included terminations with alkyl and phenyl groups. We used water contact angles, infrared spectroscopy, and X-ray photoemission spectroscopy to evaluate the modified surfaces. Alkyltriethoxysilane functionalization of ZnO produced molecular layers with submonolayer coverage and evidence of disorder. Nevertheless, a very stable hydrophobic surface with contact angles approaching 106 degrees resulted. Phenyltriethoxysilane was found to deposit in a similar manner. The resulting surface, however, exhibited significantly different wetting as a result of the nature of the end group. Molecular layers of this type, with a variety of surface terminations that use the same molecular attachment scheme, should enable interface engineering that optimizes the chemical selectivity of ZnO biosensors or the charge-transfer properties of ZnO-polymer interfaces found in oxide-organic electronics.     

Adsorption/desorption of mono- and diblock copolymers on surfaces using specific hydrogen bonding interactions

Diblock copolymers containing recognition units designed to participate in specific three-point hydrogen bonding were adsorbed onto modified gold surfaces. Self-assembled monolayers (SAMs) containing complementary recognition units were used to direct the adsorption process. The polymer-modified surfaces obtained were characterized using X-ray photoelectron spectroscopy, water contact angle, and ellipsometry. The role of individual block lengths on the adsorption process was followed by observing frequency changes of thymine-SAM-modified quartz crystal microbalance chips during adsorption of diamidopyridine-functionalized polymers from a nonpolar solvent. The renewable nature of these recognition unit functionalized surfaces was demonstrated by reversible binding of polymers. Adsorption onto fresh surfaces, followed by desorption and subsequent readsorption of monoblock and diblock copolymers was also investigated.     

Combined study of anion recognition by a carbazole-based neutral tripodal receptor in a competitive environment

Anion recognition studies have been carried out on a series of neutral synthetic receptors in which carbazole-2-carboxamide has been used as building block. Different ligands which include one to three carbazole units in their structure have been prepared. Binding experiments have been performed under competitive conditions in DMSO and DMSO-water solutions. The tripodal receptor offered a better host-guest association due to the synergistic effect of a well arranged set of hydrogen bonds. A selective response towards the biologically important pyrophosphate anion has been achieved. This selectivity is enhanced when studies are carried out with an increasing water content, which gets as high as 20% (v/v) in NMR experiments. The significance of this result lies in the use of a neutral receptor which exclusively interacts with the anionic guest through hydrogen bonding. The influence of multiple equilibria in the studied system has been analysed. Several techniques ((1)H NMR, (31)P NMR, mass spectrometry, diffusion-NMR, ITC, absorption and emission spectroscopy) have been employed to get a better understanding of the different processes taking place in solution for the evaluated receptors.     

Salicylaldehyde-indole-2-acylhydrazone: a simple,colorimetric and absorption ratiometric chemosensor for acetate ion

A simple anion receptor (i.e. salicylaldehyde-indole-2-acylhydrazone) was synthesised and its recognition properties were investigated by naked-eye observation, UV–vis titration spectra, ¹H NMR spectroscopy and DFT calculations. The obtained results indicated that this receptor could realise the selective colorimetric sensing and absorption ratiometric response towards AcO^?  in CH₃CN–DMSO medium, by virtue of threefold intermolecular hydrogen bonding interactions formed with phenolic OH, indole NH and amide NH.     

Probing proteins on functionalized silicon surfaces using matrix-assisted laser desorption/ionization mass spectrometry

Flat H-terminated Si(111) substrates modified with alkyl monolayers terminated with hydrophobic and hydrophilic functional groups were prepared using known surface functionalization methods and characterized by FTIR, X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The surfaces were then used for the study of non-specific binding of proteins from complex mixtures (using standard mixture of proteins with average molecular weight approximately 6-66 kDa) by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). Protein adsorption on these surfaces (following on-probe fractionation of the mixture) was found to be dependent on the nature of surface functional groups, and nature and pH of rinsing solutions used. The results obtained in this work demonstrate that simple silicon-based surface modifications can be effective for direct analysis of complex mixtures by MALDI-MS. Preliminary results obtained using similarly functionalized porous silicon substrates proved that such substrates are (due to their increased surface areas) better performing than flat silicon.     

Stability of monomolecular films of archaebacterial tetraether lipids on silicon wafers: a comparison of physisorbed and chemisorbed monolayers

The monomolecular organisation of symmetric, chemically modified tetraether lipids caldarchaeol-PO(4) was studied using Langmuir film balance, ellipsometry, and atomic force microscopy (AFM). Solid silicon wafer substrates were modified to hydrophobic, hydrophilic, and amino-silanised surfaces; and Langmuir-Blodgett (LB)-films were transferred onto each. LB-caldarchaeol-PO(4) films were subjected to further rinsing with organic solvent and additional physical treatments, to compare their resistance and stability on chemisorbed (amino-silanised) and physisorbed (hydrophobic and hydrophilic) surfaces. The resistance and stability of these monolayer films was characterized by ellipsometry and AFM, and film thickness was determined using ellipsometry. AFM was also employed to observe surface morphology. Monolayer films on hydrophobic surfaces were found to be more resistant to rinsing with organic solvent and additional physical treatments than monolayer films on either amino-silanised or hydrophilic surfaces. The hydrophobic effect with hydrophobic surfaces appears to support the formation of stronger caldarchaeol-PO(4) films on silicon wafer substrates, with increased resistance and stability.     

Surface bonding on silicon surfaces as probed by tip-enhanced Raman spectroscopy

Tip-enhanced Raman spectroscopy (TERS) has been used to obtain the Raman signal of surface species on silicon single crystal surfaces without the necessity for surface enhancement by addition of Ag nanoparticles. By illuminating the hydrogen terminated silicon surface covered with a droplet of 4-vinylpyridine with UV light, a 4-ethylpyridine modified silicon surface can be easily obtained. By bringing a scanning tunneling microscope (STM) Au tip with a nanoscale tip apex to a distance of ca. 1 nm from the m...     

Study of the reaction between 1,5-naphtalene diisocyanate and polycaprolactone in different solvents

The reaction between polycaprolactone and 1,5-naphtalene diisocyanate has been investigated in solvents with different dielectric constants and hydrogen bonding powers (toluene, ethyl acetate, ethyl methyl ketone), and in the same solvents with the addition of a catalytic amount of dimethyl sulfoxide (DMSO). The reaction was considered to proceed over two steps, the reaction of the first NCO group being faster. The course of the reaction was measured by titration of the unreacted NCO groups, ¹H- and ¹³C-NMR spectroscopy, and size exclusion chromatography. By titration only the overall reaction order and reaction rate constants could be determined. DMSO accelerated the reaction in all three solvents, which was explained by the stabilization of the activation complex by DMSO. Both steps of the reaction could be specified by NMR spectroscopy. The ratio between the reaction rate constants for the first and the second step decreased with the increased hydrogen bonding strength of the solvent and with DMSO. By SEC only the reaction of the first NCO group could be determined due to the low resolution for higher molar mass reaction products with a broad distribution. The values obtained for the first step reaction rate constants were in good agreement with NMR values. © 1995 John Wiley & Sons, Inc.     

Synthesis, physicochemical properties, and hydrogen bonding of 4(5)-substituted 1-H-imidazole-2-carboxamide, a potential universal reader for DNA sequencing by recognition tunneling

We have developed a chemical reagent that recognizes all naturally occurring DNA bases, a so called universal reader, for DNA sequencing by recognition tunneling in nanopores.1 The primary requirements for this type of molecules are the ability to form non-covalent complexes with individual DNA bases and to generate recognizable electronic signatures under an electrical bias. 1-H-imidazole-2-carboxamide was designed as such a recognition moiety to interact with the DNA bases through hydrogen bonding. In the present study, we first furnished a synthetic route to 1-H-imidazole-2-carboxamide containing a short ω-functionalized alkyl chain at its 4(5)?position for its attachment to metal and carbon electrodes. The acid dissociation constants of the imidazole-2-carboxamide were then determined by UV spectroscopy. The data show that the 1-H-imidazole-2-carboxamide exists in a neutral form between pH?6-10. Density functional theory (DFT) and NMR studies indicate that the imidazole ring exists in prototropic tautomers. We propose an intramolecular mechanism for tautomerization of 1-H-imidazole-2-carboxamide. In addition, the imidazole-2-carboxamide can self-associate to form hydrogen bonded dimers. NMR titration found that naturally occurring nucleosides interacted with 1-H-imidazole-2-carboxamide through hydrogen bonding in a tendency of dG>dC?dT>dA. These studies are indispensable to assisting us in understanding the molecular recognition that takes place in the nanopore where routinely used analytical tools such as NMR and FTIR cannot be conveniently applied.     

Density functional study toward understanding dehydrogenation of the adenine-thymine base pair and its anion

The dehydrogenated radicals and anions of Watson-Crick adenine-thymine (A-T) base pair have been investigated by the B3LYP/DZP++ approach. Calculations show that the dehydrogenated radicals and anions have relatively high stabilities compared with the single base adenine and thymine. The electron attachment to the A-T base pair and its derivatives significantly modifies the hydrogen bond interactions and results in remarkable structural changes. As for the dehydrogenated A-T radicals, they have relatively high electron affinities and different dehydrogenation properties with respect to their constituent elements. The relatively low-cost hydrogen eliminations correspond to the (N9)-H (adenine) and (N1)-H (thymine) bonds cleavage. Both dehydrogenation processes have Gibbs free energies of reaction DeltaG degrees of 13.4 and 17.2 kcal mol-1, respectively. The solvent water exhibits significant effect on electron attachment and dehydrogenation properties of the A-T base pair and its derivatives. In the dehydrogenating process, the anionic A-T fragment gradually changes its electronic configuration from pi* to sigma* state, like the single bases adenine and thymine.     

Hydrogen bonding configuration and thermal stability of ambient exposed and in situ hydrogenated polycrystalline diamond surfaces studied by high resolution electron energy loss spectroscopy

In this work we report on an investigation of hydrogen bonding and thermal stability on the surface of poly-crystalline diamond by high resolution electron energy loss spectroscopy (HR-EELS). Diamond films were grown on silicon substrates from CH(4)/H(2) as well as from CD(4)/D(2) gas mixtures by hot filament chemical vapor deposition (HF-CVD). The impact of ex situ ambient exposure on hydrogen bonding and its thermal stability was examined for: (i) as deposited films from a CH(4)/H(2) gas mixture; (ii) the same sample treated ex situ in micro-wave activated hydrogen plasma; and (iii) as deposited films from a CD(4)/D(2) gas mixture. In order to clarify the changes in the hydrogen bonding configuration detected on the different surfaces as a function of thermal annealing in situ hydrogenation by thermally activated atomic hydrogen was performed and examined. This study provides direct evidence that the exposure to ambient conditions and low temperature vacuum annealing have a pronounced effect on the hydrogen-carbon bonding configuration onto the poly-crystalline diamond surfaces.     

Potentialities of silane-modified silicas to regulate palladium nanoparticles sizes

A promising approach to control palladium nanoparticle sizes by application of silane modified silicas was suggested. The combination of reductive properties of silicon hydride groups and hydrophobic properties of alkylsilyl groups which act as agglomeration limiters for metal nanoparticles gives an opportunity to synthesize uniformly distributed particles with a specified size. Silicas modified with triethoxysilane (TES) and diisopropylchlorosilane (DIPCS), as well as, the combination of hexamethyldisilazane (HMDS) and triethoxysilane were applied for formation of such bifunctional matrices. Properties of the silane-modified silica samples and changes occurred during the formation of palladium nanoparticles were studied by IR spectroscopy. Thermal stability of surface chemical compounds was investigated by thermogravimetric analysis (TGA); low-temperature nitrogen adsorption was used to study structural properties of the applied materials. With the use of transmission electron microscopy (TEM) the dependence of palladium nanoparticle size on the nature of support surface layer was found.