Experimental and theoretical investigation of the electronic structure of 5-fluorouracil compounds

We present a comparison between experimental and theoretical X-ray absorption spectroscopy (XAS) and X-ray emission spectroscopy (XES) of 5-fluorouracil compounds, with an emphasis on the effects of the inclusion of nickel in the structure. By focusing on the 1s thresholds of carbon, nitrogen, oxygen, and fluorine it was possible to provide a complete picture of the occupied and unoccupied partial density of states of the 5-fluorouracil systems. Spectra calculated using density functional theory are compared to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of the compounds. All spectral features are assigned. Our results reveal that the nickel in the compound is coordinated with the nitrogen sites of the 5-fluorouracil ligands.     

Experimental and theoretical electronic charge densities in molecular crystals

Electronic charge density distribution in molecular systems has been described in terms of the topological properties. After briefly reviewing methods of obtaining charge densities from X-ray diffraction and theory, typical case studies are discussed. These studies include rings and cage systems, hydrogen bonded solids, polymorphic solids and molecular NLO materials. It is shown how combined experimental and theoretical investigations of charge densities in molecular crystals can provide useful insights into electronic structure and reactivity.     

A process for preparation of anticancer drug 9-nitro camptothecin

Camptothecin and some of its semisythetic derivatives such as topotecan, irinotecan and 9-nitrocamptothecin, have exhibited strong antitumor activity against various experimental tumor model. The water insoluble 9-nitrocamptothecin demonstrated very potent antitumor activity against many different types of human cancers and HIV. Literature procedures for preparing 9-nitrocamptothecin are direct nitration of camptothecin using a concentrated nitric/concentrated sulfuric acid system or a combin…     

Experimental and theoretical investigation of the Li is spectra of molecular lithium halides

The Li 1s absorption spectra of molecular LiF and LiCl have been studied for the first time by experimental as well as by theoretical methods. The strong absorption bands at the onset of the Li 1s excitations can qualitatively be interpreted in terms of a simple ionic model. The spectra are analyzed and assigned in more detail on the basis of SCF and Cl calculations, and also within the framework of the Z + 1 core analogy model. The limitations of this model are discussed. Li 1s ionization potentials of LiF, Li₂F₂, LiCl, and Li₂Cl₂ are derived.     

Structural photodynamics of camptothecin, an anticancer drug in aqueous solutions

Steady-state and time-resolved picosecond emission studies were carried out to study the role of the proton concentration in the acid-base properties of the anticancer drug camptothecin (CPT) in its ground and electronically first excited states. The results show that, under acidic conditions, the excited-state proton-transfer (ESPT) reaction is irreversible, in contrast to previous literature data. We found that the prototropic species are equilibrated at the excited state (pK(a)* = 1.85) only in a restricted range of pH (1.5 < pH < 3), whereas only one species, either the neutral form (τ(N) = 3.76 ns) or the protonated form (τ(C) = 2.83 ns), can be detected at pH > 3 and pH < 1.5, respectively. The proton motion from the acidic solution to the neutral form in the pH 1-2 domain is diffusion-controlled. Within the range of pH 1-2, the reaction rate constant for the formation (k(d)) of the encounter complex between the proton and the neutral form ranges from 1.17 × 10(10) to 7.33 × 10(10) M(-1) s(-1), respectively. Under more acidic conditions (pH 0.9-0.95), the protonation of CPT does not depend on the diffusive step, because of the large amount of protons. The direct proton-transfer rate constant (k(DPT)*) increases with the proton concentration (time constants change from 24 ps to ～1 ns at pH 0.9 and 2, respectively). The number of protons involved in the proton transfer changes from approximately one, for the diffusive regime, to approximately four, for the static regime. We found good agreement between the Birks model for equilibrated flourophores and the Debye-Smoluchowski equation (DSE) to accurately explain the ESPT reaction of CPT with acidic water in the reversible range. The proton motion at pH 2 (equilibrium range) exhibits diffusion-controlled behavior and can be explained using the Smoluchowski model. Our results show that the interaction of CPT with acidic water depends on the concentration of the acid, which changes the nature of both the structure and dynamics.     

Experimental and theoretical study of the electronic structure of methyl chloroformate and methyl cyanoformate

The HeI photoelectron spectra of methyl chloroformate (CH₃OC(O)Cl) and methyl cyanoformate (CH₃OC(O)CN) in the gas phase have been obtained for the first time. A complete theoretical study involving the calculation of the ionization energies using outer valence Green’s functional (OVGF) was performed, based on the calculated and previously reported energetically favorable cis-conformer (the carbonyl group eclipses the methyl group). Calculations of cationic-radical forms were carried out in order to interpret the main characters of the first six highest occupied molecular orbitals (HOMOs). The first vertical ionization potentials are 11.36 eV for CH₃OC(O)Cl and 11.65 eV for CH₃OC(O)CN, each attributed to {19a′(n_O(CO), n_Cl)}⁻¹ and {18a′(n_O(CO))}⁻¹, respectively.     

Experimental and theoretical molecular and electronic structures of the N-oxides of pyridazine,pyrimidine and pyrazine

The structures of pyridazine N-oxide, pyrimidine N-oxide and pyrazine N-oxide have been determined by X-ray diffraction for the first time. Comparison with theoretical predictions of the equilibrium structures using the B3LYP method together with a cc-pVTZ basis set, show close agreement with the structural parameters observed, and experimental dipole moments, which suggests that the charge distribution is realistic. An ‘atoms in molecules’ (AIM) analysis of the computed wave-functions shows total electron densities rather different from the classical picture of a dative bond, whereas the same wave-functions subjected to Mulliken analysis show a more conventional view of the electron distribution. This latter procedure allows a bond dipole analysis of the N-oxide charge distribution.     

Molecular structure and electronic properties of a series of oligoalkylthiophenes: A theoretical investigation

Molecular geometries and electronic properties of 3-alkylthiophenes (ATs) and their oligomers (OATs) are studied by the density functional theory (DFT). Calculations are performed on the oligomers formed by n repeating units, where n ranges from 1 to 6, using the B3LYP/6-31G** level of theory. The results obtained show that the doped oligomers have more satisfactory structural and electronic characteristics for the conducting polymers. The conjugated system in the doped oligomers has more aromaticity, with expanded and planar chains. The calculated energy gap values between the frontal orbitals and also the ionization potential values for the oligomers indicate that with increase in the oligomer chain length, the conductive band gap decreases. Furthermore, our calculations suggest that an electron-donating alkyl substituent at position 3 of the thiophene ring plays an important role in the structural and electronic properties of the polymers.     

An ab initio molecular fragment investigation of the electronic and conformational structure of formaldoxime

An ab initio molecular fragment study of formaldoxime is reported and compared with previous semiempirical and conventional ab initio studies.     

Synthesis and luminescent properties and theoretical investigation on electronic structure of nitrile-based 2-pyridone molecules

3-Cyano-4,6-dimethyl-2-pyridone and 3-cyano-4-methyl-6-phenyl-2-pyridone were synthesized effectively by the reaction of readily available 1,3-diketone and malononitrile directly and in good yield. Upon photoexcitation, 3-cyano-4-methyl-6-phenyl-2-pyridone in ethanol shows strong blue emission. The ground- and excited-state geometries, charge distributions, and excitation energies of 2-pyridone derivatives were evaluated by ab initio calculations. Organic light-emitting diodes (OLED) made using 3-cyano-4-methyl-6-phenyl-2-pyridone as dopant showed blue light emission with a maximum electroluminescence (EL) emission at around 456 nm.     

Experimental and theoretical studies of the electronic structure and the ionization and dissociation processes of trifluoromethyl peroxynitrate

In this work, we present a complete study of the ionization and dissociation processes for trifluoromethyl peroxynitrate (CF3OONO2). CF3OONO2 was generated by UV photolysis of a mixture of (CF3CO)2O, NO2, and O2. The product was detected and characterized by the photoelectron spectroscopy (PES) and photoionization mass spectroscopy (PIMS). The geometric and electronic structures of CF3OONO2 were investigated by the combination of experiments and the density functional and ab initio calculations. It is worthwhile mentioning that drastic changes occur in the geometry of CF3OONO2 after ionization. Due to the removal of one electron from the O-N sigma bond, the COON dihedral angle changes to 180 degrees and as a result, the nonplanar structure becomes planar. And the O-N single bond length increases remarkably, with the positive charge most localized on the NO2 moiety. The experimental first vertical ionization potential is 12.39 eV. Based on the calculated bond dissociation energies, the dissociation pathway was predicted. The calculated results explain the ion intensities observed in the photoionization mass spectrum. The dissociation of O-N single bond is found to be the most favored of the possible dissociation paths for CF3OONO2+.     

Investigation of the solvent effect,molecular structure,electronic properties and adsorption mechanism of Tegafur anticancer drug on Graphene nanosheet surface as drug delivery system by molecular dynamics simulation and density functional approach

To understanding the adsorption mechanism and the induced effects of an anticancer drug, Tegafur molecule, on the surface of Graphene nanosheet (GNS) as a drug delivery system, we have performed density functional theory (DFT) and molecular dynamics (MD) methods. DFT calculations give valuable information on the structure, orientation, adsorption energy and charge transfer of nanosheet-molecule in the equilibrium GNS-Tegafur complexes in the gas phase as well as in the aqueous phase, i.e., water. The optimization of GNS-Tegafur geometries shows that drug molecule tends to adsorb via its six-membered aromatic ring to the hexagonal ring of Graphene nanosheet by π–π stacking interaction at the most stable physisorption configuration. Furthermore, the calculated solvation energy (E_sol) represented by a polarizable continuum model show the significant increase in the solubility of GNS after drug adsorption on its surface in the presence of H₂O solvent which leading to the possible applications of GNS in the drug delivery systems. MD simulation is also used to determine the effect of drug concentrations on dynamic properties of Tegafur adsorption on the GNS surfaces in the solution phase. Based on the obtained MD results, it is found that by increasing drug concentration, the van der Waals (vdW) interaction energy becomes more negative and the stabilities of the simulated complexes increase.     

Experimental and theoretical electron momentum spectroscopic study of the valence electronic structure of tetrahydrofuran under pseudorotation

The most populated structure of tetrahydrofuran (THF) has been investigated in our previous study using electron momentum spectroscopy (EMS). Because of the relatively low impact energy (600 eV) and low energy resolution (DeltaE = 1.20 eV) in the previous experiment, only the highest occupied molecular orbital (HOMO) of THF was investigated. The present study reports the most recent high-resolution EMS of THF in the valence space for the first time. The binding energy spectra of THF are measured at 1200 and 2400 eV plus the binding energies, respectively, for a series of azimuthal angles. The experimentally obtained binding energy spectra and orbital momentum distributions (MDs) are employed to study the orbital responses of the pseudorotation motion of THF. The outer valence Greens function (OVGF), the OVGF/6-311++G** model, and density function theory (DFT)-based SAOP/et-pVQZ model are employed to simulate the binding energy spectra. The orbital momentum distributions (MDs) are produced using the DFT-based B3LYP/aug-cc-pVTZ model, incorporating thermodynamic population analysis. Good agreement between theory and experiment is achieved. Orbital MDs of valence orbitals exhibit only slight differences with respect to the impact energies at 1200 and 2400 eV, indicating validation of the plane wave impulse approximation (PWIA). The present study has further discovered that the orbital MDs of the HOMO in the low-momentum region (p < 0.70 a.u) change significantly with the pseudorotation angle, phi, giving a v-shaped cross section, whereas the innermost valence orbital of THF does not vary with pseudorotation, revealing a very different bonding mechanism from the HOMO. The present study explores an innovative approach to study pseudorotation of sugar puckering, which sheds a light to study other biological systems with low energy barriers among ring-puckering conformations.     

Experimental and theoretical study of the electronic spectrum of BeAl

The electronic structure of BeAl was investigated by laser induced fluorescence and resonance enhanced multiphoton ionization spectroscopy. BeAl was formed by pulsed laser ablation of a Be/Al alloy in the presence of helium carrier gas, followed by a free jet expansion into vacuum. In agreement with recent ab initio studies, the molecule was found to have a (2)Pi(1/2) ground state. Transitions to two low lying electronic states, (2)(2)Pi(1/2)(v') <-- X (2)Pi(1/2) (v' = 0) and (1)(2)Delta(v') <-- X (2)Pi(1/2) (v' = 0,1), were observed and rotationally analyzed. An additional band system, identified as (4)(2)Sigma(+)(v') <-- X (2)Pi(1/2), was found in the 28 000-30 100 cm(-1) energy range. This transition exhibited an unusual pattern of vibrational levels resulting from an avoided crossing with the (5)(2)Sigma(+) electronic state. New multi-reference configuration interaction calculations were carried out to facilitate the interpretation of the UV bands.An ionization energy of 48 124(80) cm(-1) was determined for BeAl from photoionization efficiency (PIE) measurements. Fine structure in the PIE curve was attributed to resonances with Rydberg series correlating with vibrationally excited states of the BeAl(+) ion. Analysis of this structure yielded a vibrational frequency of 240(20) cm(-1) for the cation.     

A theoretical approach to the influence of the macrocycle conformation on the molecular electronic structure in Mg-porphyrins

Nonplanar saddled (sad) ruffled (ruf) and domed (dom) conformations of the Mg-porphyrin (MgP) macrocycle in several degrees of deformation have been computed. These symmetrical distortion modes were induced in unsubstituted macrocycle using molecular definitions for calculations which permits us to achieve a systematical variation of the nonplanarity varying only a convenient geometrical parameter of the molecule. Series of nonplanar macrocycles like those synthesized in previous works employing peripheral substitutions are obtained. The procedure here used to induce deformations gives the possibility of investigating the modulator role of the out-of-plane distortions on the geometry and electronic properties of the porphyrin avoiding additional influences due to the substituents or the surrounding protein scaffolding.     

Experimental and theoretical investigation on the correlation between aqueous precursors structure and crystalline phases of zirconia

Nanometer zirconia powders were prepared by the precipitation method at different pHs and different reaction temperatures. X-ray results show that monoclinic zirconia is favored at pH 4 while tetragonal zirconia is favored at pH 9.5 at room temperature, and monoclinic zirconia is also favored at pH 9.5 and 70 °C reaction temperature, with the slow addition of alkali. Four models of zirconium complexes were applied to simulate the structural monomers in different pH solutions. Geometric parameters and Mulliken charge population were calculated by optimizing these complexes using the density functional theory (DFT/B3LYP). Theoretical analyses show that if Model I ([Zr(OH)₂(H₂O)₄]²⁺ monomers) is favored in the aqueous precursor solution, it will be preferentially polymerized into monoclinic precursor structure irrespective of slow or quick alkali addition. Contrarily, if Model IV ([Zr(OH)₇]³⁻ monomers) is major in the aqueous precursor solution, tetragonal precursor structures are favored irrespective of slow or quick alkali addition. When Model II ([Zr(OH)₄(H₂O)₂]⁰ monomers) and Model III ([Zr(OH)₆]²⁻ monomers), respectively, predominate in the aqueous precursor solution, they will be preferentially polymerized into tetragonal precursor structure at slow alkali addition, however, for quick alkali addition, they will be preferentially polymerized into monoclinic precursor structure. Our theoretical models well explain the present experimental results as well as previous experimental results, and allow building up a correlation between aqueous precursor structures and crystalline phases of zirconia.     

A theoretical study of the electronic structure of nitroethylene

The electronic ground state of nitroethylene in its planar and perpendicular conformations is studied by ab initio SCF calculations using Gaussian-lobe basis functions. The internal-rotation barrier of the nitro group has been calculated to be 6.02 kcal/mole. The dipole moment, the electric field gradient at the nitrogen and the diamagnetic contribution to the nuclear shielding for the protons have been calculated from the molecular wavefunction. Calculated and reported experimental values are in satisfactory agreement with each other. In terms of the population analysis, the electronic charge distribution has also been studied.     

Substituent effects on the energies of the electronic transitions of geminally diphenyl-substituted trimethylenemethane (TMM) radical cations. Experimental and theoretical evidence for a twisted molecular and localized electronic structure

Substituent effects on the energies (Eob) of electronic transitions of geminally diphenyl-substituted trimethylenemethane (TMM) radical cations 5a-k*+ and those of structurally related 1,1-diarylethyl cations 7a-k+ were determined experimentally by using electronic transition spectroscopy. In addition, transition energies of these radical cations were determined by using density functional theory (DFT) and time-dependent (TD)-DFT calculations. The electronic transition bands of 5a-k*+ and 7a-k+ have maxima (lambdaob) that appear at 500-432 and 472-422 nm, respectively. A Hammett treatment made by plotting the Eob values relative to that of the diphenyl-TMM radical cation 5d*+ (DeltaEob) vs the cationic substituent parameter sigma+ give a favorable correlation with a boundary point at sigma+ = 0.00 and a positive rho for sigma+ < 0 and a negative rho for sigma+ > 0. A comparison of the lambdaob and rho values for 5a-k*+ and 7a-k+ suggests that the chromophore of 5*+ is substantially the same as that of 7+. The results of TD-DFT calculations, which reproduce the experimental electronic transition spectra and relationships between DeltaEob and sigma+, and suggest that the absorption band of 5*+ is associated with the SOMO-X --> SOMO transition, while that of 7+ is due to the HOMO --> LUMO transition. Another interesting observation is that Cl and Br substituents in the diphenyl-substituted TMM radical cations and 1,1-diarylethyl cations 7a-k+ act as electron-donating groups in terms of their effect on the corresponding electronic transitions. The results show that the molecular structure of 5*+ is a considerably twisted and that 5*+ has a substantially localized electronic state in which the positive charge and odd electron are localized in the respective diarylmethyl and the allyl moieties.