Four New Lanthanide-Nitronyl Nitroxide (Ln(III)=Pr-III, Sm-III, Eu-III, Tm-III) Complexes and a Tb-III Complex Exhibiting Single-Molecule Magnet Behavior

Five new complexes based on rare-earth-radical [Ln(hfac)(3)(NIT-5-Br-3py)](2) (Ln=Pr (1), Sm (2), Eu (3), Tb (4), Tm (5); hfac = hexafluoroacetylacetonate; NIT-5-Br-3py = 2-(4,4,5,5-tetramethyl-3-oxylimidazoline-1-oxide)-5-bromo-3-pyridine) have been synthesized and characterized by X-ray crystal diffraction. The single-crystal structures show that these complexes have similar structures, in which a NIT-5-Br-3py molecule acts as a bridging ligand linking two Ln(III) ions through the oxygen atom of the N-O group and nitrogen atom from the pyridine ring to form a four-spin system. Both static and dynamic magnetic properties were measured for complex 4, which exhibits single-molecule magnetism behavior.

A monometallic tri-spin single-molecule magnet based on rare earth radicals

A mononuclear tri-spin single-molecule magnet based on the rare earth radical [Tb(hfac)(3)(NITPhOEt)(2)] (NITPhOEt = 4'-ethoxy-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide) has been synthesized, structurally characterized and the alternating current signals show a slow relaxation of magnetization and frequency-dependent signals.

Spectral and electrochemical detection of protonated triplex formation by a small-molecule anticancer agent

Triplex helical formation has been the focus of considerable interest because of possible applications in developing new molecular biology tools as well as therapeutic agents and the possible relevance of H-DNA structures in biology system. We report here that a small-molecule anticancer agent, coralyne, has binding preference to the less stable protonated triplex d(C+-T)(6):d(A-G)(6).d(C-T)(6) over duplex d(A-G)(6).d(C-T)(6) and shows different spectral and electrochemical characteristics when binding to triplex and duplex DNA, indicating that electrochemical technique can detect the less stable protonated triplex formation.

Small-Molecule Selectively Recognizes Human Telomeric G-Quadruplex DNA and Regulates Its Conformational Switch

Structural complexity is an inherent feature of the human telomeric sequence, and it presents a major challenge for developing ligands of pharmaceutical interest. Recent studies have pointed out that the induction of a quadruplex or change of a quadruplex conformation on binding may be the most powerful method to exert the desired biological effect. In this study, we demonstrate a quadruplex ligand that binds selectively to different forms of the human telomeric G-quadruplex structure and regulates its conformational switch. The results show that not only can oxazine750 selectively induce parallel quadruplex formation from a random coil telomeric oligonucleotide, in the absence of added cations, it also can easily surpass the energy barrier between two structures and change the G-quadruplex conformation in Na+ or K+ solution. The combination of its unique properties, including the size and shape of the G-quadruplex and the small molecule, is proposed as the predominant force for regulating the special structural formation and transitions.

Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics

We developed a coarse-grained yet microscopic detailed model to study the statistical fluctuations of single-molecule protein conformational dynamics of adenylate kinase. We explored the underlying conformational energy landscape and found that the system has two basins of attractions, open and closed conformations connected by two separate pathways. The kinetics is found to be nonexponential, consistent with single-molecule conformational dynamics experiments. Furthermore, we found that the statistical distribution of the kinetic times for the conformational transition has a long power law tail, reflecting the exponential density of state of the underlying landscape. We also studied the joint distribution of the two pathways and found memory effects.

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

Combining a single-molecule study of protein binding with a coarse grained molecular dynamics model including solvent (water molecules) effects, we find that biomolecular recognition is determined by flexibilities in addition to structures. Our single-molecule study shows that binding of CBD (a fragment of Wiskott-Aldrich syndrome protein) to Cdc42 involves bound and loosely bound states, which can be quantitatively explained in our model as a result of binding with large conformational changes. Our model identified certain key residues for binding consistent with mutational experiments. Our study reveals the role of flexibility and a new scenario of dimeric binding between the monomers: first bind and then fold.

Single molecule dynamics and statistical fluctuations of gene regulatory networks: A repressilator

The authors developed a time dependent method to study the single molecule dynamics of a simple gene regulatory network: a repressilator with three genes mutually repressing each other. They quantitatively characterize the time evolution dynamics of the repressilator. Furthermore, they study purely dynamical issues such as statistical fluctuations and noise evolution. They illustrated some important features of the biological network such as monostability, spirals, and limit cycle oscillation. Explicit time dependent Fano factors which describe noise evolution and show statistical fluctuations out of equilibrium can be significant and far from the Poisson distribution. They explore the phase space and the interrelationships among fluctuations, order, amplitude, and period of oscillations of the repressilators. The authors found that repressilators follow ordered limit cycle orbits and are more likely to appear in the lower fluctuating regions. The amplitude of the repressilators increases as the suppressing of the genes decreases and production of proteins increases. The oscillation period of the repressilators decreases as the suppressing of the genes decreases and production of proteins increases.

Probing the kinetics of single molecule protein folding

We propose an approach to integrate the theory, simulations, and experiments in protein-folding kinetics. This is realized by measuring the mean and high-order moments of the first-passage time and its associated distribution. The full kinetics is revealed in the current theoretical framework through these measurements. In the experiments, information about the statistical properties of first-passage times can be obtained from the kinetic folding trajectories of single molecule experiments ( for example, fluorescence). Theoretical/simulation and experimental approaches can be directly related. We study in particular the temperature-varying kinetics to probe the underlying structure of the folding energy landscape. At high temperatures, exponential kinetics is observed; there are multiple parallel kinetic paths leading to the native state. At intermediate temperatures, nonexponential kinetics appears, revealing the nature of the distribution of local traps on the landscape and, as a result, discrete kinetic paths emerge. At very low temperatures, exponential kinetics is again observed; the dynamics on the underlying landscape is dominated by a single barrier.

Diffusion and single molecule dynamics on biomolecular interface binding energy landscape

We propose a new approach to study the diffusion dynamics on biomolecular interface binding energy landscape. The resulting mean first passage time (MFPT) has 'U'curve dependence on the temperature. It is shown that the large specificity ratio of gap to roughness of the underlying binding energy landscape not only guarantees the thermodynamic stability and the specificity [P.A. Rejto, G.M. Verkhivker, in: Proc. Natl. Acad. Sci. 93 (1996) 8945; C.J. Tsai, S. Kumar, B. Ma, R. Nussinov, Protein Sci. 8 (1999) 1181; G.A. Papoian, P.G. Wolynes, Biopolymers 68 (2003) 333; J. Wang, G.M. Verkhivker, Phys. Rev. Lett. 90 (2003) 198101] but also the kinetic accessibility. The complex kinetics and the associated fluctuations reflecting the structures of the binding energy landscape emerge upon temperature changes. The theory suggests a way of connecting the models/simulations with single molecule experiments by analysing the kinetic trajectories.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Blue organic light-emitting diodes based on an oxadiazole-containing organic molecule exhibiting excited state intramolecular proton transfer

A blue organic light-emitting device based on an emissive layer of 2-(2-hydroxyphenyl)-5-phenyl-1,3,4-oxadiazole (HOXD), which exhibits excited state intramolecular proton transfer (ESIPT), was presented. The device had a luminance efficiency of 0.8 cd/A and a maximum brightness of 870 cd/m(2). Our studies indicate that some EL may originate from the triplet excitation state of the enol form of HOXD.

Synthesis and structural characterization of a new molecule-based complex constructed from dodecamolybdophosphoric acid and imidazole

A new compound, (CH5N2)(3)(PMo12O40CH4N23H2O)-C-.-H-. (1), was synthesized and structurally characterized by elemental analyses, IR spectra, UV spectra, NMR spectra and ESR spectra. This is, to our knowledge, the first example of an imidazole-polyoxometalate species. The compound was recrystallized from N,N-dimethylformamide (DMF), and then black block-like crystals of (C3H5N2)(4)((PMoMo11O40)-Mo-V-O-VI)(.)4C(3)H(7)NO(.) 2H(2)O (2), were obtained. It crystallizes in a triclinic space group P (1) over bar with n=12.423(3) Angstrom, b=12.666(3) Angstrom, c=13.341(3) Angstrom, alpha=70.56(3)degrees, beta=71.16(3)degrees, gamma=64.18(3)degrees, V= 1742.3(6) Angstrom(3), Z=1, R1 = 0.0585, wR2 = 0.1885. An X-ray crystallographic study showed that the crystal structure is constructed by electrostatic attractions and hydrogen bonds between a dodecamolybdophosphoric anion and an imidazole. The imidazole and DMF molecules occupy cavities in a polyoxometalate lattice ordered along a c-axis. The structure of (2) is similar to that of (1) from a comparison of both IR spectra and TGA Curves.

Applications of the method of three-dimensional projection of a molecule in quantitative structure-activity relationship of phenol derivatives

Five variables for phenol derivatives were calculated by molecular projection in three-dimensional space which were combined with eight quantum-chemical parameters and three Am indices. These variables were selected by using leaps-and-bounds regression analysis. Multiple linear regression analysis and artificial neural networks' were performed, and the results obtained by using. artificial neural networks are superior than that obtained by using multiple linear regression.