Electronic structure of the pyrimidine and purine components of nucleic acids in their ground and lower excited singlet and triplet states

Quantum-chemical calculation of the energies of the electronic transitions and the electronic structures of the neutral and ionic species of the nucleic acids components in their ground and lower excited singlet and triplet ππ* and nπ* states has been carried out in the all-valence-electron approximation CNDO /S . The results of the calculation allow one to identify the most photoreactive sites of the molecules and to consider the dependence of the location of these sites on the ionic state of the molecules. The calculated data are compared with our previous results obtained in a π-electron approximation. The individual absorption spectra of various ionic and tautomeric species of the nucleic acids components obtained by us earlier have been decomposed into bands corresponding to separate electronic transitions. As a rule, there is a good agreement between the calculated data in the two approximations and the experimental results.     

Identification of ionic and tautomeric species of uracil by second derivative UV absorption spectroscopy.

The individual UV absorption spectra of ionic and tautomeric species of uracil and eight derivatives have been determined by second derivative spectroscopy. Second derivative bands have been ascribed to different species by taking into account the proportion of each molecular species at each pH value and the tautomer fixed for derivatives. Theoretical results in the literature are in good agreement with the observed λ_Min(D^2nd) positions of both N(1)- and N(3)- uracil monoanion and dianion. Neutral uracil species (diketo form) presents six second derivative bands (two in normal spectra). For the three higher electronic transition energies, the discrepancy between calculated and experimental values does not exceed 0.05 e V. Literature assignment from normal spectra for the N(3)- anion are ππ* transitions but our results show that n π* are possible too.     

Solvent and pH Effects on the Electronic Spectra of Some Azo Benzimidazoles

The spectral behaviour of some new azobenzimidazoles in pure and mixed organic solvents and buffer solutions of varying pH have been studied. The observed bands are assigned to the possible electronic transition. The shoulder appearing in the visible region in the spectra of P‐NO₂ derivatives is ascribed to the existence of these compounds in azo‐hydrazone tautomeric equilibrium. The possibility of the formation of an intermolecular H‐bonded solvated complex between the molecules of p‐NO₂ derivatives and the proton acceptor solvents DMSO and DMF were studied. The pK values of these compounds were determined and explained on the basis of the relative contribution of acidic and basic character of respective species.     

Calculation of Raman spectra and structure elucidation of guanine in the polycrystalline state and in aqueous solution

The frequencies and relative intensities of lines in the Raman spectra of the condensed states of guanine and its deutero substituted analog have been calculated. The effect of hydrogen bonding on the Raman spectrum has been studied. Guanine exists in different tautomeric forms (G-N₉H and G-N₇H) at different pH in aqueous solution (for acidic and alkaline media, respectively).     

Ab initio prediction of the structure and vibration‐rotation spectroscopic properties of Na2OH and K2OH

The equilibrium structures and potential energy surfaces of the Na₂OH and K₂OH radicals and the corresponding cations in their electronic ground states have been determined from accurate ab initio calculations. The vibration‐rotation energy levels and spectroscopic constants of various isotopic species were calculated by a perturbational approach. The predicted spectroscopic constants may serve as a useful guide for detecting these species by vibration‐rotation spectroscopy and for assigning their spectra. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Computational Investigation of the Effect of pH on the Color of Firefly Bioluminescence by DFT

In spite of recent advances towards understanding the mechanism of firefly bioluminescence, there is no consensus about which oxyluciferin (OxyLH₂) species are the red and yellow‐green emitters. The crystal structure of Luciola cruciata luciferase (LcLuc) revealed different conformations for the various steps of the bioluminescence reaction, with different degrees of polarity and rigidity of the active‐site microenvironment. In this study, these different conformations of luciferase (Luc) are simulated and their effects on the different chemical equilibria of OxyLH₂ are investigated as a function of pH by means of density functional theory with the PBE0 functional. In particular, the thermodynamic properties and the absorption spectra of each species, as well as their relative stabilities in the ground and excited states, were computed in the different conformations of Luc. From the calculations it is possible to derive the acid dissociation and tautomeric constants, and the corresponding distribution diagrams. It is observed that the anionic keto form of OxyLH₂ is both the red and the yellow‐green emitter. Consequently, the effect of Luc conformations on the structural and electronic properties of the Keto‐(?1) form are studied. Finally, insights into the Luc‐catalyzed light‐emitting reaction are derived from the calculations. The multicolor bioluminescence can be explained by interactions of the emitter with active‐site molecules, the effects of which on light emission are modulated by the internal dielectric constant of the different conformations. These interactions can suffer also from rearrangement due to entry of external solvent and changes in the protonation state of some amino acid residues and adenosine monophosphate (AMP).     

Author index to volume 59

Expansion of tetracene vapour with excess argon carrier gas through a nozzle of a supersonic jet apparatus permits the controlled formation of (C₁₈H₁₂)Ar_n molecules. These have been studied by laser fluorescence techniques in the 450 nm region of the spectrum corresponding to excitation of the parent tetracene molecules to the ¹B_1u electronic state. We have been able to observe up to the n = 10 complex and have identified three different binding sites on the tetracene framework. From the resolved fluorescence spectra of these species one obtains an upper limit of the van der Waals binding energy of 314 cm^?1 in the upper electronic states and 274 cm^?1 in the ground state. These resolved spectra also exhibit features identified as due to the tetracene-argon stretching vibration giving a value of 36.5 ± 2 cm^?1 for the lowest transition in the ground state of (C₁₈H₁₂)Ar.     

Spectroscopic structural studies of salicylic acid,salicylamide and aspirin

The electronic absorption spectra of the salicylic acid and the salicylamide molecules have been studied using SCF—CL calculations. The singlet and the triplet electronic transition energies have been calculated. The state functions of eight excited states for these molecules have been calculated in addition to the oscillator strengths, charge densities, ionization potentials and electron affinities. Our calculations lead to the presence of salicylic acid and salicylamide in the β-forms in which the carboxylic hydroxyl group or the amino group is directed toward the enolic hydroxyl group. The salicylic acid and the salicylamide molecules have the C_s point group symmetry, but the aspirin molecule has the C₁ point group symmetry, in which the acetyl group does not lie in the plane of the salicylic acid molecule.     

Quantum-chemical and correlation study of deprotonation and complexation of 1-amino-4-hydroxyanthraquinone

Existing views on the deprotonation and complexation of 1-amino-4-hydroxyanthraquinone are wrong. This compound, its anions, and complexes with metals are not individual substances, but they form a dynamic equilibrium mixture of keto-enol (keto-oxide) and amino-imine tautomers. Different samples of the same compound differ by the tautomeric composition, the respective information is contained in their electron absorption spectra. In weak alkaline solutions the deprotonation occurs exclusively at the hydroxy group. Most typical structure of 1-amino-4-hydroxyanthraquinone anions is 1,10-quinoid, its metal complexes have 9,10-and 1,10-quinoid structures. The ground states of molecules are more responsible for the tautomeric transformations than the excited states. Quantum-chemical calculations of tautomeric anthraquinones by semiempirical PPP methods are more reliable than modern ab initio calculations.     

Ab initio calculation of the potential surfaces and the electronic transition moments for the valence and Rydberg doublet electronic states of BH2

The bending and symmetric stretching potential curves for the low-lying doublet electronic states of the BH₂ radical are calculated by means of the configuration interaction method. Special attention is paid to consideration of the interaction between valence and Rydberg-type species. The dissociation of BH₂ in its various electronic states into H + B + H is studied. The results of calculations predict a complicated structure of both, the absorption and emission spectra caused by a number of avoided crossings between the excited states of the same symmetry in the geometry region close to the equilibrium geometry of the ground state.     

Tautomerism and the spectroscopic properties of some 4,6-disubstituted pyrimedines

Tautomerism of some 4,6-disubstituted pyrimidines (with the electron-donor groups such as OH, SH and NH₂) is discussed with regard to their electronic absorption spectra. The spectra of different tautomeric forms of the molecules are satisfactorily interpreted by means of the Pariser—Parr—Pople type of calculations.     

DFT assessment of the spectroscopic constants and absorption spectra of neutral and charged diatomic species of group 11 and 14 elements

The spectroscopic constants and absorption spectra of neutral and charged diatomic molecules of group 11 and 14 elements formulated as [M₂]^+/0/? (M = Cu, Ag, Au), and [E₂]^+/0/? (E = C, Si, Ge, Sn, Pb) have been calculated at the PBE0/Def2‐QZVPP level of theory. The electronic and bonding properties of the diatomics have been analyzed by natural bond orbital analysis approach and topology analysis by the atoms in molecules method. Particular emphasis was given on the absorption spectra of the diatomic species, which were simulated by time‐dependent density functional theory calculations employing the hybrid Coulomb‐attenuating CAM‐B3LYP density functional. The simulated absorption spectra of the [M₂]^+/0/? (M = Cu, Ag, Au) and [E₂]^+/0/? (E = C, Si, Ge, Sn, Pb) species are in close resemblance with the experimentally observed spectra whenever available. The neutral M₂ and E₂ diatomics strongly absorb in the ultraviolet region, given rise to UVC, UVA and in a few cases UVB absorptions. In a few cases, weak absorbion bands also occur in the visible region. The absorption bands have thoroughly been analyzed and assignments of the contributing principal electronic transitions associated to individual excitations have been made. © 2014 Wiley Periodicals, Inc.     

Electronic absorption spectra of 5- and 6- fluoroindoles

The electronic absorption spectra of 5-and 6-fluoroindoles, corresponding to the λ2850 Å system of indole, have been recorded in the vapour phase and analysed, assuming C_s symmetry for the molecules. The observed band system in both the molecules which lies in the region λ3100–2680 Å has been identified as a π* ← π transition corresponding to a ¹A′ ← ¹A′ transition. The i.r. spectra of these molecules have also been recorded and analysed and the results are used in the analyses of the electronic spectra. These show that there is not much change in the shape and very little change in size of either of these molecules in the excited electronic states.     

Similarities in the Intensities of Analogous Rydberg–Rydberg Transitions in the Molecular Series CF x Cl y (x=3, 2, 1; y=1, 2, 3)

In this work, the photoabsorption behaviour of the molecular series CF₃Cl, CF₂Cl₂ and CFCl₃, involving their ground state and two different Rydberg series, has been studied. The discrepancies or similarities in the intensities of homologous transitions in the three CF _x Cl _y molecules have been analysed on account of their electronic structure. Absorption oscillator strengths have been calculated with the Molecular quantum defect orbital (MQDO) approach. Electronic transitions between states belonging to two different unperturbed Rydberg series of the same molecule have been calculated by us for the first time. The quality of the achieved oscillator strengths has been assessed by comparison with, to our knowledge, scarce experimental data available in the literature, through analysis of the discrepancies or similarities in the intensities of homologous transitions in the molecular series CF _x Cl _y when states of different type are involved, and by testing the compliance of regularities by the Rydberg series object of our study.Article for the special issue dedicated to J.-P. Malrieu     

Tautomeric forms of Oxy- and Oxo-derivatives of 1,3,5-Triazine. Part VI. Isomerization mechanism and thermal stability of the methyl esters of cyanuric acid

Previous investigations of the kinetics and the mechanism of the thermal isomerization C₃N₃(OMe)₃ → C₃(NMe)₃O₃ have been continued with a study of the isomerization mechanism of the mixed O,O,N- and O,N,N-trimethyl esters of cyanuric acid. A full discussion of the overall process is given, in which it is assumed that the above mixed esters are intermediates. It is shown that the tautomeric transformation occurs as the consequence of the attack of Me⁺ cations on the ring nitrogen of the neutral molecules. The presence of such cations in the melt was established by ionic exchange with the H⁺ of the molten acids. It is also shown that the tautomeric transformation in solution proceeds with the same mechanism. An explanation is proposed for the thermal instability of the mixed esters (which isomerize even in the solid state, more than 20° below their melting point), which is based on the high polarity of these molecules. This property is discussed in terms of electronic structure calculations carried out with the Pariser-Parr-Pople approximation of the A.S.M.O., S.C.F., method.     

Theoretical electronic structure of the molecule ScI

Theoretical investigation of the 18 lowest electronic states of the molecule ScI in the representation ^2S+1Λ^(±) has been performed via CASSCF and MRCI (single and double excitation with Davidson correction) calculations. To the best of our knowledge these calculated electronic states are the first ones from ab initio methods. Thirteen electronic states between 4,500 cm^?1 and 21,000 cm^?1 have been studied for the first time and have not yet been observed experimentally. The harmonic frequency ω_e, the internuclear distance R_e, the electronic transition energy with respect to the ground state T_e, and the rotational constant B_e have been calculated for the considered electronic states. By using the canonical functions approach the eigenvalues E_υ and the rotational constants B_υ have also been calculated for the six lowest‐lying electronic states. The comparison of these results with the theoretical and the experimental data available in the literature shows a good agreement. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

In situ monitoring of pH titration by Raman spectroscopy

Molecular speciation of organic compounds in solution is essential for the understanding of ionic complexation. The Raman technique was chosen because it allows the identification of compounds in different states, and it can give information about the molecular geometry from the analysis of the vibrational spectra. The effect of pH on organic compounds can give information about the ionisation of molecule species. In this study the ionisation steps of salicylic acid and paracetamol have been studied by means of potentiometry coupled with Raman spectroscopy at 30.0 °C in a solution of ionic strength 0.96 mol dm^?3 (KNO₃) and 0.04 mol dm^?3 (HNO₃). The protonation and deprotonation behaviour of the molecules were studied in different pH regions. The abundance of the three different species in the Raman spectra of aqueous salicylic acid have been identified satisfactorily, characterised, and determined by numeric treatment of the data using a multiwavelength curve-fitting program and confirmed with the observed spectral information.     

Electronic Substitution Effect on the Ground and Excited State Properties of Indole Chromophore: A Computational Study**

Indole, being the main chromophore of amino acid tryptophan and several other biologically relevant molecules like serotonin, melatonin, has prompted considerable theoretical and experimental interest. The current work focuses on the investigation of substitution effect on the ground and excited electronic states of indole using computational quantum chemistry. Having three close-lying excited electronic states, the vibronic coupling effect becomes extremely important yet challenging for the photophysics and photochemistry of indole. Here, we have evaluated the performance of time-dependent density functional theory against available experimental and ab initio results from the literature. The electronic effects on the excited states of indole and indole derivatives e. g. tryptophan, serotonin and melatonin are reported. A bathochromic shift has been observed in the absorption spectrum for the L_a state. The absorption wavelength increases in the order of indole<tryptophan <serotonin <melatonin. While the contribution of the in-plane small adjacent groups increases the electron density of the indole ring, the out-of-plane long substituent groups have minor effect. The absorption spectra calculated including the vibronic coupling are in good agreement with experiments. These results can be used to estimate the error in photophysical observables of indole derivatives calculated considering indole as a prototypical system.     

Ion-molecule chemistry of C+2: Evidence for the production of excited state dicarbon cation

Ion-molecule reactions of C⁺₂ with several neutral partners have been studied using Fourier transform mass spectrometry. The reactant ion was formed by electron impact of various neutral precursors and the internal energy content of the ion estimated using charge transfer/energy-bracketing reactions. These reactions indicate the production of a long-lived excited state ion when C⁺₂ is formed from C₂N₂ and the production of a mixture of states when formed from small hydrocarbon molecules. The observed reactions and energetics are consistent with the calculated electronic structure of this ion.     

Character of the electronic ground state and of charge-transfer excited states in ionic solids: An ab initio cluster model approach

The electronic structure of the ground electronic state and of some special charge-transfer excited states in ionic solids is examined from the ab initio cluster model approach. Different ab initio wave functions, including a frozen orbital approach, the Hartree–Fock self-consistent field, and multireference configuration interaction wave functions, are considered and analyzed using different theoretical techniques. We explicitly consider some alkaline–earth oxides such as CaO, a more difficult case such as A1₂O₃, a transition-metal oxide such as NiO, and a system with a more complicated structure such as KNiF₃. Analysis of ab initio wave functions in terms of valence bond components shows that all these compounds are largely ionic, thus supporting the simple picture arising from the ionic model. However, the nature of the excited states is more complex. Alkaline–earth oxides lowest excited states are essentially described as charge-transfer excitations dominated by a single resonant valence bond structure and the calculated energy difference is comparable to the experimental optical gap. In the case of A1₂O₃, the electronic spectra presents excitonic features and the local charge-transfer excitation excited states provide a reasonable representation of these phenomena. Finally, several different valence bond structures are present in the lowest electronic states of KNiF₃. © 1994 John Wiley & Sons, Inc.