C12: The building block of hexagonal diamond

The crystalline structure of diamond may consist of C8, C10 or C12 building units. C8 was regarded as the building block of the hexagonal diamond also known as Lonsdaleite. Adamantane (C₁₀H₁₆) alicyclic hydrocarbon has the same arrangement of carbon atoms as the basic C10 unit of the cubic diamond lattice. C12 has five rings of mixed type, three of them in boat, two in chair conformation. Model building revealed that the C8 unit containing exclusively three rings in boat conformation does not exist. Further addition of carbon atoms to C8: a) results in C12 unit, b) allows the multiplication of C12 units, and c) by reducing the boat-to-chair ratio explains the hardness of the hexagonal diamond Lonsdaleite. The Lonsdaleite nucleus can be grown to special diamond grains with the outer atoms of the C12 building units replaced by different elements. This recognition can be utilized in the production of synthetic diamonds under high-pressure high-temperature conditions or in the chemical vapor deposition growth technique.      

Direct electrochemistry of cytochrome C at nanocrystalline boron-doped diamond

Direct electron transfer of horse heart cytochrome c is measured at a nanocrystalline boron-doped diamond thin-film electrode. A quasi-reversible, diffusion-controlled cyclic voltammetric response is observed for untreated diamond. The peak currents change linearly with the concentration, and importantly, there is no electrode fouling. The results, observed for a hydrogen-terminated and uncharged surface, (i.e., no ionizable carbon-oxygen functional groups), raise interesting questions about the necessary surface interactions of cytochrome c for relatively rapid electrode kinetics.     

Multifunctional transition metal complexes: Information transfer at the molecular level

Recent investigations from our laboratory have described compelling experimental evidence to the effect that polyacetylenes operate as extremely effective molecular-scale wires for conducting electronic charge between redox-active terminals. The unusually low electronic resistivity of polyacetylenic bridges is derived from their relatively accessible HOMOs and LUMOs, which facilitate electron and hole tunnelling over long distances, and because of the excellent electronic coupling that occurs between adjacent carbon atoms, these being in very close proximity. In order to prevent direct participation of the acetylenic bridge in triplet energy-transfer processes or in light-induced electron-transfer reactions, it is prudent to restrict the conjugation length of the bridge to less than five ethynylene groups. We now consider various synthetic strategies for the engineering of such molecular systems that retain the favorable electronic properties of a polyacetylenic bridge but that include a relay or insulator in the bridging moiety. A convenient way to construct such systems is to use a Pt^II bis-acetylide as the spacer that separates terminal metal oligopyridine complexes. In this case, the central Pt^II complex becomes an insulator. By careful design of the system, this insulatory behavior can be exploited as a means by which to introduce directionality and selectivity into the system, and we demonstrate such effects by using polycyclic hydrocarbons and metalloporphyrins as the photoactive terminals. Similar effects can be obtained with polycyclic hydrocarbons built into the acetylenic wire and, in such cases, the energetics of the bridge can be tuned over an inordinately wide range by varying the extent of conjugation inherent to the aromatic nucleus. A special case is identified in which the polycycle itself possesses vacant coordination sites since the energy of the bridge can be further tuned by external complexation of adventitious cations. In order to provide for an energy gradient along the molecular axis, we have devised a versatile synthetic strategy for attaching different types of ligand to the terminals. This approach also facilitates both extension of the molecular axis and alteration of the molecular shape. The photophysical and electrochemical properties have been recorded for all the molecular systems reported herein and used as a simple experimental means by which to quantify the extent of electronic communication along the molecular axis. For mixed-metal or mixed-ligand systems, rates of intramolecular energy or electron transfer have been measured. In most cases, these rates are extremely fast and testify to the remarkable electronic coupling properties of this family of compounds. Finally, some consideration is given to the preparation of third-generation systems.     

Cytosine-5 methylation-directed construction of a Au nanoparticle-based nanosensor for simultaneous detection of multiple DNA methyltransferases at the single-molecule level

DNA methylation at cytosine/guanine dinucleotide islands (CpGIs) is the most prominent epigenetic modification in prokaryotic and eukaryotic genomes. DNA methyltransferases (MTases) are responsible for genomic methylation, and their aberrant activities are closely associated with various diseases including cancers. However, the specific and sensitive detection of multiple DNA MTases has remained a great challenge due to the specificity of the methylase substrate and the rareness of methylation-sensitive restriction endonuclease species. Here, we demonstrate for the first time the cytosine-5 methylation-directed construction of a Au nanoparticle (AuNP)-based nanosensor for simultaneous detection of multiple DNA MTases at the single-molecule level. We used the methyl-directed endonuclease GlaI to cleave the site-specific 5-methylcytosine (5-mC). In the presence of CpG and GpC MTases (i.e., M.SssI and M.CviPI), their hairpin substrates are methylated at cytosine-5 to form the catalytic substrates for GlaI, respectively, followed by simultaneous cleavage by GlaI to yield two capture probes. These two capture probes can hybridize with the Cy5/Cy3–signal probes which are assembled on the AuNPs, respectively, to form the double-stranded DNAs (dsDNAs). Each dsDNA with a guanine ribonucleotide can act as the catalytic substrate for ribonuclease (RNase HII), inducing recycling cleavage of signal probes to liberate large numbers of Cy5 and Cy3 molecules from the AuNPs. The released Cy5 and Cy3 molecules can be simply quantified by total internal reflection fluorescence (TIRF)-based single-molecule imaging for simultaneous measurement of M.SssI and M.CviPI MTase activities. This method exhibits good specificity and high sensitivity with a detection limit of 2.01 × 10⁻³ U mL⁻¹ for M.SssI MTase and 3.39 × 10⁻³ U mL⁻¹ for M.CviPI MTase, and it can be further applied for discriminating different kinds of DNA MTases, screening potential inhibitors, and measuring DNA MTase activities in human serum and cell lysate samples, holding great potential in biomedical research, clinical diagnosis, drug discovery and cancer therapeutics.

Cytosine-5 methylation-directed construction of Au nanoparticle-based nanosensors enables specific and sensitive detection of multiple DNA methyltransferases.     

Boolean and fuzzy logic implemented at the molecular level

In this work, it is shown how to implement both hard and soft computing by means of two structurally related heterocyclic compounds: flindersine (FL) and 6(5H)-phenanthridinone (PH). Since FL and PH have a carbonyl group in their molecular skeletons, they exhibit Proximity Effects in their photophysics. In other words, they have an emission power that can be modulated through external inputs such as temperature (T) and hydrogen-bonding donation (HBD) ability of solvents. This phenomenology can be exploited to implement both crisp and fuzzy logic. Fuzzy Logic Systems (FLSs) wherein the antecedents of the rules are connected through the AND operator, are built by both the Mamdani’s and Sugeno’s models. Finally, they are adopted as approximators of the proximity effect phenomenon and tested for their prediction capabilities. Moreover, FL as photochromic compound is also a multiply configurable crisp logic molecular element.     

Hydration of mineral surfaces probed at the molecular level

By employing the nonlinear optical, interface selective experiment of sum frequency spectroscopy together with independent ab initio and density functional theory calculations, we determine the functional species of a corundum (001) surface: doubly coordinated OH groups which differ in their bond tilt angles. The interaction of the functional species with the adjacent water molecules is also observed. In a large pH range around the point of zero charge, the interaction is not controlled electrostatically but by hydrogen bonding. The functional species' tilt angles are crucial parameters, determining whether the species act as hydrogen bond donors or acceptors.     

Surface transfer doping of hydrogen-terminated diamond by C60F48: energy level scheme and doping efficiency

Surface sensitive C1s core level photoelectron spectroscopy was used to examine the electronic properties of C(60)F(48) molecules on the C(100):H surface. An upward band bending of 0.74 eV in response to surface transfer doping by fluorofullerene molecules is measured. Two distinct molecular charge states of C(60)F(48) are identified and their relative concentration determined as a function of coverage. One corresponds to ionized molecules that participate in surface charge transfer and the other to neutral molecules that do not. The position of the lowest unoccupied molecular orbital of neutral C(60)F(48) which is the relevant acceptor level for transfer doping lies initially 0.6 eV below the valence band maximum and shifts upwards in the course of transfer doping by up to 0.43 eV due to a doping induced surface dipole. This upward shift in conjunction with the band bending determines the occupation of the acceptor level and limits the ultimately achievable hole concentration with C(60)F(48) as a surface acceptor to values close to 10(13) cm(-2) as reported in the literature.     

Low-temperature specific heat of the cluster compound Au55 (P(C6H5)3)12Cl6

Specific-heat measurements on the cluster compound Au₅₅(P(C₆H₅)₃)₁₂Cl₆ at temperatures 0.06 K ≤T≤3 K and in magnetic fields 0≤B≤6 T are reported. While above 0.6 K the specific heatC is dominated by the inter-cluster vibrational contribution observed previously, an anomalous increase ofC towards lowT is observed below 0.3 K, withC ～T ^?2. This contribution develops into a Schottky-like anomaly forB≥0.4 T, indicating that it might be attributed to local moments which are also observed in ESR measurements. From the height of the anomaly one can infer that approximately one tenth of the Au₅₅ clusters carry a magnetic moment. For 0.6 K≤T≤1 K andB=0 our data indicate the absence of a linear electronic specific-heat contribution expected for bulk Au. This possibly constitutes the first direct observation of the quantum-size effect on electronic energy levels in the specific heat.     

Benzene on Au[111] at 4 K: monolayer growth and tip-induced molecular cascades

Low-temperature scanning tunneling microscopy has been used to characterize the various structures of submonolayer and near-monolayer coverages of benzene (C6H6) on Au[111] at 4 K. At low coverage, benzene is found to adsorb preferentially at the top of the Au monatomic steps and is weakly adsorbed on the terraces. At near-monolayer coverage, benzene was found to form several long-range commensurate overlayer structures that depend on the regions of the reconstructed Au[111] surface, namely a (radical 52 x radical 52)R13.9 degrees structure over the hcp regions and a (radical 133 x radical 133)R17.5 degrees "pinwheel" structure over the fcc regions. Time-lapse imaging revealed concerted cascade motion of the benzene molecules in the (radical 133 x radical 133)R17.5 degrees pinwheel overlayer. We demonstrate that the observed cascade motion is a result of concerted molecular motion and not independent random motion.     

Syntheses of molecular wires containing redox center： Reversible redox property and good energy level matching with Au electrode

Molecular wires with tetrathiafulvalene （TTF） as redox center were synthesized and characterized. UV-vis spectra and cyclic voltammetry showed these wires had good reversible redox behavior under ambient conditions and their HOMO energy levels （--5.0 eV） matched well with the Fermi level of Au （--5.1 eV）.     

Cyclic alumosiloxanes and alumosilicates: exemplifying the Loewenstein rule at the molecular level

The cyclic alumosiloxane [{LAl(μ-O)(Ph(2)Si)(μ-O)}(2)] (3) and alumosilicate [{LAl(μ-O){((t)BuO)(2)Si}(μ-O)}(2)] (4) were obtained by reaction of the appropriate R(2)Si(OH)(2) precursor (R = Ph, O(t)Bu) with [{LAl(H)}(2)(μ-O)] (1), providing a nice illustration of the Loewenstein rule at work at the molecular level.     

Monitoring molecular beacon DNA probe hybridization at the single-molecule level

We have monitored the reaction dynamics of the DNA hybridization process on a liquid/solid interface at the single-molecule level by using a hairpin-type molecular beacon DNA probe. Fluorescence images of single DNA probes were recorded by using total internal reflection fluorescence microscopy. The fluorescence signal of single DNA probes during the hybridization to individual complementary DNA probes was monitored over time. Among 400 molecular beacon DNA probes that we tracked, 349 molecular beacons (87.5 %) were hybridized quickly and showed an abrupt fluorescence increase, while 51 probes (12.5 %) reacted slowly, resulting in a gradual fluorescence increase. This ratio stayed about the same when varying the concentrations of cDNA in MB hybridization on the liquid/surface interface. Statistical data of the 51 single-molecule hybridization images showed that there was a multistep hybridization process. Our results also showed that photostability for the dye molecules associated with the double-stranded hybrids was better than that for those with the single-stranded molecular beacon DNA probes. Our results demonstrate the ability to obtain a better understanding of DNA hybridization processes using single-molecule techniques, which will improve biosensor and biochip development where surface-immobilized molecular beacon DNA probes provide unique advantages in signal transduction.     

Biomimetically constructing a hypoxia-activated programmable phototheranostics at the molecular level

The hypoxic microenvironment is considered the preponderant initiator to trigger a cascade of progression and metastasis of tumors, also being the major obstacle for oxygen consumption therapeutics, including photodynamic therapy (PDT). In this work, we report a programmable strategy at the molecular level to modulate the reciprocal interplay between tumor hypoxia, angiogenesis, and PDT outcomes by reinforcing synergistic action between a H₂O₂ scavenger, O₂ generator and photosensitizer. The modular combination of a catalase biomimetic (tri-manganese cryptand, 1) and a photosensitizer (Ce6) allowed the rational design of a cascade reaction beginning with dismutation of H₂O₂ to O₂ under hypoxic conditions to enhance photosensitization and finally photooxidation. Concurrently, this led to the decreased expression of the vascular endothelial growth factor (VEGF) and effectively reduced unwanted growth of blood vessels observed in the chick chorioallantois membrane (CAM). Notably, the proof-of-principle experiments using the tumor-bearing models proved successful in enhancing PDT efficacy, prolonging their life cycles, and improving immunity, which could be monitored by magnetic resonance imaging (MRI).

A programmable strategy at the molecular level to modulate the ratio of a catalyst and photosensitizer to maximize the collaborative efficiency of anti-angiogenesis and PDT.