Seleno-Nucleobases and Their Water-Soluble Ruthenium-Arene Half-Sandwich Complexes: Chemistry and Biological Activity

Half-sandwich organometallic ruthenium complexes of seleno-nucleobases, 3 and 4, were synthesized and characterized. The structures of both complexes were determined by X-ray crystallography and are the first crystal structures of ruthenium complexes with seleno-nucleobases. Interestingly, 3 self-assembles aided by adventitious water in DMF to give a tetranuclear square 3a center dot 6H(2)O. Complex 4 is active against Jurkat and Molt-4 cell lines but inactive against the K562 cell line, whereas 3 is completely inactive against all three cell lines. The free ligand 6-selenopurine (1) and 6-selenoguanine (2) are highly active against these cell lines. Compound 2, like its thio analogue, is unstable under UVA light, whereas 4 is stable under similar conditions, which suggests that the ruthenium complex could reduce problems associated with the instability of the free ligand, 2, under irradiation.

Synthesis and characterization of monometallic rhenium(I) complexes and their application as selective sensors for copper(II) ions

Novel imine functionalized monometallic rhenium(I) polypyridine complexes (1-4) comprising two phenol moieties attached to 2,20-bipyridine ligands L1-L4 have been synthesized and characterized. These complexes exhibit selective and sensitive detection towards copper(II) ions and this is observed through changes in UV-visible absorption, luminescence and time-resolved spectroscopic techniques. An enormous enhancement is observed in emission intensity, quantum yield and luminescence lifetime with the addition of copper(II) ions, and this can be attributed to the restriction of C=N isomerization in the Re(I) complexes. The strong binding between copper(II) ions and these complexes reveals that the binding constant values are in the range of 1.1 x 10(3)-6.0 x 103 M-1. The absorption spectral behavior of the complexes is supported by DFT calculations.

Crystal Coulomb energies: I. Organic donor-acceptor complexes--a review. II. Classical Ewald calculations of the Coulomb binding energy of four donor-acceptor crystals and Wurster's blue perchlorate. III. A rapid-convergence quantum-mechanical formalism for crystal electronic energies

Chapter I

Theories for organic donor-acceptor (DA) complexes in solution and in the solid state are reviewed, and compared with the available experimental data. As shown by McConnell et al. (Proc. Natl. Acad. Sci. U.S., 53, 46-50 (1965)), the DA crystals fall into two classes, the holoionic class with a fully or almost fully ionic ground state, and the nonionic class with little or no ionic character. If the total lattice binding energy 2ε₁ (per DA pair) gained in ionizing a DA lattice exceeds the cost 2ε_o of ionizing each DA pair, ε₁ + ε_o less than 0, then the lattice is holoionic. The charge-transfer (CT) band in crystals and in solution can be explained, following Mulliken, by a second-order mixing of states, or by any theory that makes the CT transition strongly allowed, and yet due to a small change in the ground state of the non-interacting components D and A (or D⁺ and A^-). The magnetic properties of the DA crystals are discussed.

Chapter II

A computer program, EWALD, was written to calculate by the Ewald fast-convergence method the crystal Coulomb binding energy E_C due to classical monopole-monopole interactions for crystals of any symmetry. The precision of E_C values obtained is high: the uncertainties, estimated by the effect on E_C of changing the Ewald convergence parameter η, ranged from ± 0.00002 eV to ± 0.01 eV in the worst case. The charge distribution for organic ions was idealized as fractional point charges localized at the crystallographic atomic positions: these charges were chosen from available theoretical and experimental estimates. The uncertainty in E_C due to different charge distribution models is typically ± 0.1 eV (± 3%): thus, even the simple Hückel model can give decent results.

E_C for Wurster's Blue Perchl orate is -4.1 eV/molecule: the crystal is stable under the binding provided by direct Coulomb interactions. E_C for N-Methylphenazinium Tetracyanoquino- dimethanide is 0.1 eV: exchange Coulomb interactions, which cannot be estimated classically, must provide the necessary binding.

EWALD was also used to test the McConnell classification of DA crystals. For the holoionic (1:1)-(N,N,N',N'-Tetramethyl-para- phenylenediamine: 7,7,8,8-Tetracyanoquinodimethan) E_C = -4.0 eV while 2ε_o = 4.6₅ eV: clearly, exchange forces must provide the balance. For the holoionic (1:1)-(N,N,N',N'-Tetramethyl-para- phenylenediamine:para-Chloranil) E_C = -4.4 eV, while 2ε_o = 5.0 eV: again EC falls short of 2ε₁. As a Gedankenexperiment, two nonionic crystals were assumed to be ionized: for (1:1)-(Hexamethyl- benzene:para-Chloranil) E_C = -4.5 eV, 2ε_o = 6.6 eV; for (1:1)- (Napthalene:Tetracyanoethylene) E_C = -4.3 eV, 2ε_o = 6.5 eV. Thus, exchange energies in these nonionic crystals must not exceed 1 eV.

Chapter III

A rapid-convergence quantum-mechanical formalism is derived to calculate the electronic energy of an arbitrary molecular (or molecular-ion) crystal: this provides estimates of crystal binding energies which include the exchange Coulomb inter- actions. Previously obtained LCAO-MO wavefunctions for the isolated molecule(s) ("unit cell spin-orbitals") provide the starting-point. Bloch's theorem is used to construct "crystal spin-orbitals". Overlap between the unit cell orbitals localized in different unit cells is neglected, or is eliminated by Löwdin orthogonalization. Then simple formulas for the total kinetic energy Q^(XT)_λ, nuclear attraction [λ/λ]^XT, direct Coulomb [λλ/λ'λ']^XT and exchange Coulomb [λλ'/λ'λ]^XT integrals are obtained, and direct-space brute-force expansions in atomic wavefunctions are given. Fourier series are obtained for [λ/λ]^XT, [λλ/λ'λ']^XT, and [λλ/λ'λ]^XT with the help of the convolution theorem; the Fourier coefficients require the evaluation of Silverstone's two-center Fourier transform integrals. If the short-range interactions are calculated by brute-force integrations in direct space, and the long-range effects are summed in Fourier space, then rapid convergence is possible for [λ/λ]^XT, [λλ/λ'λ']^XT and [λλ'/λ'λ]^XT. This is achieved, as in the Ewald method, by modifying each atomic wavefunction by a "Gaussian convergence acceleration factor", and evaluating separately in direct and in Fourier space appropriate portions of [λ/λ]^XT, etc., where some of the portions contain the Gaussian factor.

Electronic structure in five-coordinate complexes of nickel(II) with heavy-donor ligands

I.

Various studies designed to elucidate the electronic structure of the arsenic donor ligand, o-phenylenebisdimethylarsine (diarsine), have been carried out. The electronic spectrum of diarsine has been measured at 300 and 77˚K. Electronic spectra of the molecular complexes of various substituted organoarsines and phosphines with tetracyanoethylene have been measured and used to estimate the relative ionization potentials of these molecules.

Uv photolysis of arsines in frozen solution (96˚K) has yielded thermally labile, paramagnetic products. These include the molecular cations of the photolyzed compounds. The species (diars)⁺ exhibits hyper-fine splitting due to two equivalent ⁷⁵As(I=3/2) nuclei. Resonances due to secondary products are reported and assignments discussed.

Evidence is presented for the involvement of d-orbitals in the bonding of arsines. In (diars)⁺ there is mixing of arsenic “lone-pair” orbitals with benzene ring π-orbitals.

II.

Detailed electronic spectral measurements at 300 and 77˚K have been carried out on five-coordinate complexes of low-spin nickel(II), including complexes of both trigonal bipyramidal (TBP) and square pyramidal (SPY) geometry. TBP complexes are of the form NiLX⁺ (X=halide or cyanide,

L = Qƭ(CH₂)₃As(CH₃)₂]₃ or

P [hexagon - Q'CH₃] , Q = P, As,

Q’=S, Se).

The electronic spectra of these compounds exhibit a novel feature at low temperature. The first ligand field band, which is asymmetric in the room temperature solution spectrum, is considerably more symmetrical at 77˚K. This effect is interpreted in terms of changes in the structure of the complex.

The SPY complexes are of the form Ni(diars)₂X^z (X=CL, Br, CNS, CN, thiourea, NO₂, As). On the basis of the spectral results, the d-level ordering is concluded to be xy ˂ xz, yz ˂ z² ˂˂ x² - y². Central to this interpretation is identification of the symmetry-allowed ¹A₁ → ¹E (xz, yz → x² - y²) transition. This assignment was facilitated by the low temperature measurements.

An assignment of the charge-transfer spectra of the five-coordinate complexes is reported, and electronic spectral criteria for distinguishing the two limiting geometries are discussed.

Part I. Electric birefringence studies of deoxyribonucleic acids. Part II. Selective dissociation of nucleohistone complexes

Part I

The electric birefringence of dilute DNA solutions has been studied in considerable detail and on a large number of samples, but no new and reliable information was discovered concerning the tertiary structure of DNA. The large number of variables which effect the birefringence results is discussed and suggestions are made for further work on the subject.

The DNA molecules have been aligned in a rapidly alternating (10 to 20 kc/sec) square wave field confirming that the orientation mechanism is that of counterion polarization. A simple empirical relation between the steady state birefringence, Δn_st, and the square of the electric field, E, has been found: Δn_st = E²/(a E² + b), where a = 1/Δn_s and b = (E²/Δn_st)_E→o. Δn_s is the birefringence extrapolated to infinite field strength.

The molecules show a distribution of relaxation times from 10^-4 to 0.2 sec, which is consistent with expectations for flexible coil molecules. The birefringence and the relaxation times decrease with increasing salt concentrations. They also depend on the field strength and pulse duration in a rather non-reproducible manner, which may be due in part to changes in the composition of the solution or in the molecular structure of the DNA (other than denaturation). Further progress depends on the development of some control over these effects.

Part II

The specificity of the dissociation of reconstituted and native deoxyribonucleohistones (DNH) by monovalent salt solutions has been investigated. A novel zone ultracentrifugation method is used in which the DNH is sedimented as a zone through a preformed salt gradient, superimposed on a stabilizing D₂O (sucrose) density gradient. The results, obtained by scanning the quartz sedimentation tubes in a spectrophotometer, were verified by the conventional, preparative sedimentation technique. Procedures are discussed for the detection of microgram quantities of histones, since low concentrations must be used to prevent excessive aggregation of the DNH.

The data show that major histone fractions are selectively dissociated from DNH by increasing salt concentrations: Lysine rich histone (H I) dissociates gradually between 0.1 and 0.3 F, slightly lysine rich histone (H II) dissociates as a narrow band between 0.35 and 0.5 F, and arginine rich histone (H III, H IV) dissociates gradually above 0.5 F NaClO₄.

The activity of the partially dissociated, native DNH in sustaining RNA synthesis, their mobility and their unusual heat denaturation and renaturation behavior are described. The two-step melting behavior of the material indicates that the histones are non-randomly distributed along the DNA, but the implications are that the uncovered regions are not of gene-size length.

Proton magnetic resonance studies of ribonucleic acid complexes. I. Complexes of biological bases and oligonucleotides with RNA. II. Template recognition and the degeneracy of the genetic code

Part I. Complexes of Biological Bases and Oligonucleotides with RNA

The physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.

Previous work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T₁ measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.

The interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with uridylyl (3' → 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.

The effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D₂0 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.

Part II. Template Recognition and the Degeneracy of the Genetic Code

The interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20°C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.

Due to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the "tautomeric doublet" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.

Optical parameters and absorption of copper (II)-azo complexes thin films as optical recording media

Smooth thin films of three kinds of azo dyes of 2-(5'-tert-butyl-3'-azoxylisoxazole)-1, 3-diketones and their copper (II)-azo complexes were prepared by the spin-coating method. Absorption spectra of the thin films on a glass substrate in the 300-600 nm wavelength region were measured. Optical constants (complex refractive index N=n+ik) and thickness of the thin films prepared on single-crystal silicon substrate in the 300-600 nm wavelength region were investigated on rotating analyzer-polarizer type of scanning ellipsometer, and dielectric constants epsilon(epsilon=epsilon(1)+i epsilon(2)), absorption coefficients alpha as well as reflectance R of thin films were then calculated. In addition, one of the copper (II)-azo complex thin film prepared on glass substrate with an Ag reflective layer was also studied by atomic force microscopy (AFM) and static optical recording. AFM study shows that the copper (II)-azo complex thin film is very smooth and has a root mean square surface roughness of 1.89 nm. Static optical recording shows that the recording marks on the copper (II)-azo complex thin film are very clear and circular, and the size of the minimal recording marks can reach 200 nm. (c) 2004 Elsevier B.V. All rights reserved.

Synthesis, spectroscopic properties and thermal stability of metal(II) tetraazaporphyrin complexes with two strong wavelength absorption

Three kinds of metal(II) tetraazaporphyrin complexes with blue-violet and red light wavelength absorption were synthesized by refluxing tetraazaporphyrin ligand and different metal(II) ions, respectively. Their structures were confirmed by elemental analysis, LDI-TOF-MS, FT-IR and UV-Vis. The solubility of metal(II) tetraazaporphyrin complexes in organic solvents and absorption properties of their chloroform solution and films on K9 glass in the region 250-800 nm were measured. The influence on the difference of absorption maximum from metal(II) tetraazaporphyrin complexes to tetraazaporphyrin ligand by different metal(II) ions was studied. In addition, the thermal stability of the complexes was also evaluated. (c) 2006 Elsevier Ltd. All rights reserved.

Determination and analysis of the optical constants of thin films of nickel(II) and copper(II) hydrazone complexes by spectroscopic ellipsometry

Thin films of four nickel(II) and copper(II) hydrazone complexes, which will hopefully be used as recording layers for the next-generation of high-density recordable disks, were prepared by using the spin-coating method. Absorption spectra of the thin films on K9 optical glass substrates in the 300-700 nm wavelength region were measured. Optical constants (complex refractive indices N) and thickness d of the thin films prepared on single-crystal silicon substrates in the 275-675 nm wavelength region were investigated on a rotating analyzer-polarizer scanning ellipsometer by fitting the measured ellipsometric angles (Psi(lambda) and Delta(lambda)) with a 3-layer model (Si/dye film/air). The dielectric functions epsilon and absorption coefficients alpha as a function of the wavelength were then calculated. Additionally, a design to achieve high reflectivity and optimum dye film thickness with an appropriate reflective layer was performed with the Film Wizard software using a multilayered model (PC substrate/reflective layer/dye film/air) at 405 nm wavelength.

Optical properties of nickel(II)-azo complexes thin films for potential application as high-density recordable optical recording media

Smooth thin films of three kinds of nickel(II)-azo complexes were prepared by the spin-coating method. Absorption spectra of the thin films on K9 glass substrate in the 300-600 nn wavelength region were measured. Optical constants (complex refractive index N = n + ik) and thickness of the thin films prepared on single-crystal silicon substrate in the 300-600 nm wavelength region were investigated on rotating analyzer-polarizer type of scanning ellipsometer, and dielectric constants epsilon (epsilon = epsilon(1) + i epsilon(2)), absorption coefficients a as well as reflectance R of thin films were then calculated at 405 nm. In addition, in order to examine the possible use of nickel(II)-azo complex thin film as an optical recording medium, one of the nickel(II)-azo complex thin film prepared on K9 glass substrate with an Ag reflective layer was also studied by atomic force microscopy and static optical recording. The results show that the nickel(II)-azo complex thin film is smooth and has a root mean square surface roughness of 2.25 nm, and the recording marks on the nickel(II)-azo complex thin film are very clear and circular, and their size can reach 200 nn or less. (c) 2006 Elsevier Ltd. All rights reserved.

Synthesis, spectral, and thermal characterizations of Ni(II) and Cu(II) beta-diketone complexes with thenoyltrifluoroacetone ligand

Two kinds of nickel(II) and copper(II) P-diketone complexes derived from thenoyltrifluoroacetone ligand with blue-violet light absorption were synthesized by reacting free ligand and different metal(II) ions in sodium methoxide solution. Their structures were postulated based on elemental analysis, ESI-MS, FT-IR spectra and UV-vis electronic absorption spectra. Smooth films on K9 glass substrates were prepared using the spin-coating method. Their solubility in organic solvents, absorption properties of thin film and thermal stability of these complexes were evaluated. (c) 2006 Elsevier B.V. All rights reserved.