Quantum chemical investigation of the electronic spectra of the keto, enol, and keto-imine tautomers of cytosine

The low-lying excited singlet states of the keto, enol, and keto-imine tautomers of cytosine have been investigated employing a combined density functional/multireference configuration interaction (DFT/MRCI) method. Unconstrained geometry optimizations have yielded out-of-plain distorted structures of the pi --> pi and n --> pi excited states of all cytosine forms. For the keto tautomer, the DFT/MRCI adiabatic excitation energy of the pi --> pi state (4.06 eV including zero-point vibrational energy corrections) supports the resonant two-photon ionization (R2PI) spectrum (Nir et al. Phys. Chem. Chem. Phys. 2002, 5, 4780). On its S1 potential energy surface, a conical intersection between the 1pipi state and the electronic ground state has been identified. The barrier height of the reaction along a constrained minimum energy path amounts to merely 0.2 eV above the origin and explains the break-off of the R2PI spectrum. The 1pipi minimum of the enol tautomer is found at considerably higher excitation energies (4.50 eV). Because of significant geometry shifts with respect to the ground state, long vibrational progressions are expected, in accord with experimental observations. For the keto-imine tautomer, a crossing of the 1pipi potential energy surface with the ground-state surface has been found, too. Its n --> pi minimum (3.27 eV) is located well below the conical intersection between the pi --> pi and S0 states, but it will be difficult to observe because of its small transition moment. The identified conical intersections of the pi --> pi excited states of the keto cytosine tautomers are made responsible for the ultrafast decay to the electronic ground states and thus may explain their subpicoseconds lifetimes.     

Rational design of substituted N-alkoxypyridine-2(1H)thiones with increased stability against daylight

N-alkoxypyridine-2(1H)thiones serve as valuable photochemical alkoxyl radical precursors in photobiological studies, but due to a broad absorption band at about 360 nm (pi --> pi* excitation), these molecules decompose readily when exposed to daylight. The goal of the present work is to propose N-alkoxypyridine-2(1H)thiones which due to a blue shift of this band become more stable with respect to daylight and consequently are easier to handle. The shift of the pi --> pi* excitation toward shorter wave length shall be achieved by substituents introduced at the pyridine heterocycle. To study the substituent effects, excitations to the first to singlet states were calculated applying the CASPT2 approach and time dependent density functional theory (TD-DFT). The study indeed showed that electron rich substituents (like the methoxylgroup) at the positions 3, 4, and 6 of the pyridinethione heterocycle yield the desired hypsochromic shift. A free rotation of the substituent, however, is expected to quench these effects. Fluorine atoms, employed to model the influence of electron withdrawing substituents, induce also a blue shift for a substitution at the 3, 4, and 6 positions. For the multiply fluorinated molecule N-methoxy-3,4,6-trifluorinepyridine-2(1H)thione a blue shift of even 24 nm is predicted. Substituents that can conjugate with the pi electrons of the heterocycle (NO2 served as a model) only induce strong bathochromic shifts on the pi --> pi* excitation energy and therefore are not able to eliminate the daylight sensitivity of the precursor molecules.     

On the excited states involved in the luminescent probe [Ru(bpy)2dppz]2+

The nature of the excited states of [Ru(bpy)2dppz]2+ has been investigated using density functional theory with the hybrid functional B3LYP. The excitations were studied via linear response theory (TDDFT) and DeltaSCF calculations and the solvent effects were introduced by embedding the molecule in a continuum dielectric medium. It was found that the solvent effects are critical in understanding the nature of the excitations. For the molecule in ethanol, the lowest absorption predicted by TDDFT is a dark state 3pi --> pi with the electron and hole spread over the dppz ligand. Next come the excitations of 3MLCT between the ruthenium and the dppz and finally the 3MLCT excitations between the ruthenium and the bpy ligands not associated with the phenazine. Using deltaSCF calculations two low-lying excited states were identified and the geometry optimized in the presence of the continuum medium. At the optimal geometry the lowest excited state is 3MLCT (Ru --> dppz). The 3pi --> pi state is found only 0.026 eV higher.     

The invalidity of intermolecular proton transfer triggered twisted intramolecular charge transfer in excited state for 2-(4′-diethylamino-2′-hydroxyphenyl)-1H-imidazo-[4,5-b]pyridine

The excited-state dynamics of the excited-state proton transfer and intramolecular twisted charge transfer (TICT) reactions of a molecular photoswitch 2-(4′-diethylamino-2′-hydroxyphenyl)-1H-imidazo-[4,5-b]pyridine (DHP) in aprotic and alcoholic solvents have been theoretically investigated by using time-dependent density functional theory. The excited-state intramolecular proton transfer (ESIPT) reaction of DHP proceeding upon excitation in all the solvents has been confirmed, and the dual emission has been assigned to the enol and keto forms of DHP. However, for methanol and ethanol solvents within strong hydrogen-bonded capacity, the intermolecular hydrogen bonds between DHP and methanol/ethanol would promote an excited-state double proton transfer (ESDPT) along the hydrogen-bonded bridge. Importantly, the previous proposed ESDPT-triggered TICT mechanism of DHP in methanol and ethanol was not supported by our calculations. The twist motion would increase the total energy of the system for both the products of ESIPT and ESDPT. According to the calculations of the transition states, the ESDPT reaction occurs much easier in keto form generated by ESIPT. Therefore, a sequential ESIPT and ESDPT mechanism of DHP in methanol and ethanol has been reasonably proposed.     

Excited states of porphyrin macrocycles

S1 --> S(n) spectra of porphyrin, diprotonated porphyrin, and tetraoxaporphyrin dication have been measured in the energy range 2-3 eV above S1 at room temperature in solution by means of transient absorption spectroscopy exciting with femtosecond pulses. Highly excited pi pi* states not active in the conventional S0 --> S(n) spectrum have been observed. The experimental data are discussed on the basis of the time dependent density functional theory taking advantage of large scale calculations of configuration interaction between singly excited configurations (DF/SCI). The DF/SCI calculation on porphyrin has allowed to assign g states active in the S1 --> S(n) spectrum. Applying the same calculation method to tetraoxaporphyrin dication the S0 --> S(n) spectrum is reproduced relatively to the Q and B (Soret) bands as well as to the weaker E(u) bands at higher energy. According to our calculation the S1 --> S(n) transient spectrum is related to states of g symmetry mainly arising from excitations between doubly degenerate pi and pi* orbitals such as 2e(g) --> 4e(g). In the case of diprotonated porphyrin it is shown that the complex of the macrocycle with two trifluoroacetate anions plays a significant role for absorption. Charge transfer excitations from the anions to the macrocycle contribute to absorption above the Soret band, justifying the intensity enhancement of the S0 --> S(n) spectrum with respect to the other two macrocyclic systems.     

Excited state properties of 7-hydroxy-4-methylcoumarin in the gas phase and in solution. A theoretical study

TDDFT/B3LYP and RI-CC2 calculations with different basis sets have been performed for vertical and adiabatic excitations and emission properties of the lowest singlet states for the neutral (enol and keto), protonated and deprotonated forms of 7-hydroxy-4-methylcoumarin (7H4MC) in the gas phase and in solution. The effect of 7H4MC-solvent (water) interactions on the lowest excited and fluorescence states were computed using the Polarizable Continuum Method (PCM), 7H4MC-water clusters and a combination of both approaches. The calculations revealed that in aqueous solution the pi pi* energy is the lowest one for excitation and fluorescence transitions of all forms of 7H4MC studied. The calculated excitation and fluorescence energies in aqueous solution are in good agreement with experiment. It was found that, depending on the polarity of the medium, the solvent shifts vary, leading to a change in the character of the lowest excitation and fluorescence transition. The dipole-moment and electron-density changes of the excited states relative to the ground state correlate with the solvation effect on the singlet excited states and on transition energies, respectively. The calculations show that, in contrast to the ground state, the keto form has a lower energy in the pi pi* state as compared to enol, demonstrating from this point of view the energetic possibility of proton transfer from the enol to the keto form in the excited state.     

Photochemistry of flavothione and hydroxyflavothiones: mechanisms and kinetics

In this work we present a detailed study of the mechanism of photochemistry and thermal reactions, as well as of the kinetics of flavothione (FLT) in ethanol. Furthermore, we analyzed how the hydroxysubstitution pattern of FLT influenced both the kinetics and the mechanism relative to the parent FLT. We show that the primary photochemical reaction of FLT in the absence of oxygen is hydrogen (H)-atom abstraction from the solvent by way of the excited triplet state of FLT. Several products result from thermal reactions of the resulting semireduced FLTH* radical, including more than one dimer. A full mechanism is proposed, and the relevant rate constants are evaluated. On the other hand, in the presence of oxygen and a low concentration of FLT, we found that the principal photoproduct is the parent flavone (FL). The reaction leading to photoxidation is not via 1O2 attacking a thione, but instead, it is via a reaction of the FLTH* radical with ground state oxygen. The kinetic data also demonstrate that the relative values of concentrations of reactants and the rate constants of the reactions can control the dominance of one mechanism over others. We also have examined the photochemical mechanisms and kinetics for several hydroxyflavothiones (n-OHFLT) and compared them with FLT itself. We have found that the photochemical mechanism radically changes depending on the positions of substitution. These differences are directly related to the ordering of the excited states of the n-OHFLT. Specifically, FLT with lowest 3n,pi* states (FLT, 6-hydroxyflavothione, 7-hydroxyflavothione and 7,8-dihydroxyflavothione) efficiently abstract H atoms to give the semireduced radical of the thione. The radical can (1) dimerize to form two different dimers; (2) react with oxygen to produce the parent FL; and (3) recombine with the solvent radical to yield the original FLT. In contrast, FLT with lowest 3pi,pi* states (3-hydroxyflavothione, 3,6-dihydroxyflavothione and 3,7-dihydroxyflavothione) behave as photosensitizers of oxygen to form singlet oxygen, which then reacts with the ground state of the substituted FLT. Finally, when T2(pi,pi*) is above S1(n,ppi*), as for 5-hydroxyflavothione and 5,7-dihydroxyflavothione, both the S1(n,pi*) --> T1(n,pi*) intersystem crossing and photodegradation are inefficient.     

Electronic excited states of Si(100) and organic molecules adsorbed on Si(100)

The electronically excited states of the Si(100) surface and acetylene, benzene, and 9,10-phenanthrenequinone adsorbed on Si(100) are studied with time-dependent density functional theory. The computational cost of these calculations can be reduced through truncation of the single excitation space. This allows larger cluster models of the surface in conjunction with large adsorbates to be studied. On clean Si(100), the low-lying excitations correspond to transitions between the pi orbitals of the silicon-silicon dimers. These excitations are predicted to occur in the range 0.4-2 eV. When organic molecules are adsorbed on the surface, surface --> molecule, molecule --> surface, and electronic excitations localized within the adsorbate are also observed at higher energies. For acetylene and benzene, the remaining pipi* excitations are found to lie at lower energies than in the corresponding gas-phase species. Even though the aromaticity of 9,10-phenanthrenequinone is retained, significant shifts in the pipi* excitations of the aromatic rings are predicted. This is in part due to structural changes that occur upon adsorption.     

Theoretical study of the ground and excited states of 7-methyl guanine and 9-methyl guanine: comparison with experiment

The keto-enol tautomerization of 7-methyl-guanine and 9-methyl-guanine in the excited state was investigated using the time-dependent DFT (TDDFT) method. For both species, the potential energy surfaces of the ground state and two lowest singlet excited states (due to pi-->pi* and n-->pi* transitions) have been investigated and their features discussed in terms of consequences on the excited state dynamics. The findings suggest that, for both species, the state due to the n-->pi* transition, suspected to be an intermediate in the excited state deactivation, exhibits two minima with the second minimum characterized by an elongated N1-H distance. This structure, intermediate between enol and keto tautomers, might play a role in the excited state relaxation. The existence of this second well, however, is observed in both 7- and 9-methyl-guanine, which suggests that it cannot account alone for the different photophysical behavior of these species.     

Absorption spectrum and solvatochromism of the [Ru(4,4'-COOH-2,2'-bpy)2(NCS)2] molecular dye by time dependent density functional theory

We present a combined Density Functional/Time Dependent Density Functional study of the molecular structure, electronic states, and optical absorption spectrum of [Ru(4,4'-COOH-2,2'-bpy)(2)(NCS)(2)], a widely used charge-transfer sensitizer in nanocrystalline TiO(2) solar cells. Calculations have been performed both for the complex in vacuo and in ethanol and water solvents, using a continuum model to account for solute-solvent interactions. Inclusion of the solvent leads to important changes of the energies and composition of the molecular orbitals of the complex; as a consequence, whereas the computed spectrum for the Ru-complex in vacuo deviates from the experimental one in both energy and shape, the spectra calculated in the presence of the solvent are in good agreement with the experiment. The first two absorption bands are found to originate from mixed ruthenium-NCS to bipyridine-pi* transitions rather than to pure metal-to-ligand-charge-transfer (MLCT) transitions, whereas the third band arises from intraligand pi --> pi* transitions. The experimentally observed blue-shift of the spectrum in water with respect to ethanol is well reproduced by our calculations and appears to be related to a decreased dipole moment in the excited state.     

Color-tuning mechanism in firefly luminescence: theoretical studies on fluorescence of oxyluciferin in aqueous solution using time dependent density functional theory

The first singlet excited state geometries of various isomers and tautomers of firefly oxyluciferin (OxyLH2), as well as their fluorescence spectra in aqueous solution, were studied using time dependent density functional theory (TDDFT). With changing pH in aqueous solution, three fluorescence peaks, blue (450 nm), yellow-green(560 nm), and red (620 nm) correspond to neutral keto and enolic forms, the monoanionic enolic form,and the monocationic keto form respectively. A counterion, Na+, was predicted to cause a blue shift in the fluorescence of anionic OxyLH2. The contributions of a charge transfer (CT) state upon electronic excitation of the planar and twisted structures were predicted. CT was large for the twisted structures but small for the planar ones. The differences between pK and pK* of various oxyluciferin species were predicted using a Forster cycle. A new possible light emitter, namely, the monocation keto form (keto+1), was considered.     

A thermochemistry and kinetic study on the thermal decomposition of ethoxyquinoline and ethoxyisoquinoline

Quantum chemical calculations were used to study the production of ethylene and keto/enol tautomers from ethoxyquinoline (2‐EQ) and ethoxyisoquinoline (1‐EisoQ and 3‐EisoQ) in the gas phase and ethanol at the MP2/6‐311++G(2d,2p)//BMK/6‐31+G(d,p) level. The obtained data indicate that the elimination of ethylene from 1‐EisoQ and 2‐EQ is slightly more favorable than from 3‐EisoQ. Formation of quinolone and isoquinolone (2‐EQO, 1‐EisoQO, and 3‐EisoQO) is kinetically favored compared to their enols. Decomposition of 2‐EQ and 1‐EisoQ to ethylene and keto forms is thermodynamically and kinetically preferable more stable than the corresponding enols. However, the hydroxy form of 3‐EisoQ is more stable than its keto tautomer in the gas phase and ethanol. The enol tautomers cost less energy when formed from their keto forms rather than from the parent ethoxyquinolone and ethoxyisoquinoline.     

生色团连接的苯骈三氮唑衍生物的激发态分子内质子转移

用从头算和密度泛函理论研究了对硝基二苯乙烯作为生色团连接的2-(2-羟基-苯基)-苯骈三氮唑的衍生物2-羟基-5-[对硝基-二苯乙烯基-氧亚甲基]-苯基-(2H-苯骈三氮唑)(C1)和4′-硝基-3,4-二[2-羟基-(2H-苯骈三氮唑)-苄氧基]-二苯乙烯(C2)发生激发态分子内质子转移(ESIPT)的可能性.系统研究了C1和C2发生ESIPT的互变异构体的基态与激发态的性质变化,包括相关的键长、键角等结构参数,Mulliken电荷和偶极矩,前线轨道以及势能曲线.计算结果表明,对于C1来讲,酮式(keto)的基态(K)不存在稳定结构,因此发生基态分子内质子转移(GSIPT)可能性很小.酮式的激发态(K*)的氢键强度要远强于烯醇式(enol)的激发态(E*)的氢键强度.分子在光致激发后,质子供体所带负电荷减小而质子受体所带负电荷增加.在K*,HOMO→LUMO的电子跃迁导致电子密度从"酚环"向质子化杂环转移.E*→K*跃迁只需要克服较小的能垒(约41 kJ.mol-1).计算结果表明C1发生ESIPT的可能性很大.C2由于具有高能量,其具有基态的单质子转移特征的异构体EK(同时含烯醇E与酮K结构)、具有基态的双质子转移特征的异构体2K(含有双酮结构),以及具有双酮结构特征的激发态2K*均无法获得它们的稳定结构,因此,基态分子内单或双质子转移和激发态分子内双重质子转移发生的可能性极小.然而,由于双烯醇式的激发态(2E*)和EK的激发态(EK*)存在稳定结构,且2E*→EK*跃迁具有低能垒,因此C2有可能发生激发态分子内单重质子转移.本文进一步计算了两个分子的紫外-可见吸收光谱与荧光发射光谱,获得了具有较大斯托克位移的ESIPT的荧光发射峰.     

Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase,in a microhydrated environment and in aqueous solution. guanine: surprising stabilization of rare tautomers in aqueous solution

Altogether eight keto and enol tautomers of guanine were studied theoretically in the gas phase, in a microhydrated environment (1 and 2 water molecules) and in bulk water. The structures of isolated, as well as mono- and dihydrated tautomers were determined by means of the RI-MP2 method using the extended TZVPP (5s3p2d1f/3s2p1d) basis set. The relative energies of isolated tautomers included the correction to higher correlation energy terms evaluated at the CCSD(T)/aug-cc-pVDZ level. The relative enthalpies at 0 K and relative free energies at 298 K were based on the above-mentioned relative energies and zero-point vibration energies, temperature-dependent enthalpy terms and entropies evaluated at the MP2/6-31G level. The keto form having hydrogen atom at N7 is the global minimum while the canonical form having hydrogen atom at N9 represents the first local minimum at all theoretical levels in vacuo and in the presence of 1 and 2 water molecules. All three unusual rare tautomers having hydrogens at N3 and N7, at N3 and N9, and also at N9 and N7 are systematically considerably less stable and can be hardly detected in the gas phase. The theoretical predictions fully agree with existing theoretical as well as experimental results. The effect of bulk solvent on the relative stability of guanine tautomers was studied by self-consistent reaction field and molecular dynamics free energy calculations using the thermodynamic integration method. Bulk solvent, surprisingly, strongly favored these three rare tautomers over all remaining low-energy tautomers and probably only these forms can exist in water phase. The global minimum (tautomer with hydrogens at N3 and N7) is by 13 kcal/mol more stable than the canonical form (3rd local minimum). Addition of one or two water molecules does not change the relative stability order of isolated guanine tautomers but the respective trend clearly supports the surprising stabilization of three rare forms.     

2-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平上,对14种气相和水相中可能存在的2-硫代黄嘌呤互变异构体进行了几何构型全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能.Onsager反应场溶剂模型用于水相的计算.计算结果表明,2-硫代黄嘌呤在气相和水相中主要以酮式结构形式存在,与已有实验结果一致.在气相和水相中,酮式结构—N(7)(H)均比酮式结构—N(9)(H)更稳定.2-硫代黄嘌呤互变异构的熵效应小,对互变异构平衡没有显著的影响,而焓变对互变异构却产生了主要的影响.水溶剂化自由能与异构体的气相偶极矩存在相关性.另外,较详细地考察了2-硫代黄嘌呤与6-硫代黄嘌呤的相对稳定性.     

Theoretical study of the electronic spectroscopy of CO adsorbed on Pt(111)

The excited states of CO adsorbed on the Pt(111) surface are studied using a time-dependent density functional theory formalism. To reduce the computational cost, electronic excitations are computed within a reduced single excitation space. Using cluster models of the surface, excitation energies are computed for CO in the on-top, threefold, and bridge binding sites. On adsorption, there is a lowering of the 5sigma orbital energy. This leads to a large blueshift in the 5sigma- -> pi(CO*) excitation energy for all adsorption sites. The 1pi and 4sigma orbital energies are lowered to a lesser extent, and smaller shifts in the corresponding excitation energies are predicted. For the larger clusters, pi* excitations at lower energies are observed. These transitions correspond to excitations to virtual orbitals of pi* character which lie below the pi* orbitals of gas phase CO. These orbitals are associated predominantly with the metal atoms of the cluster. The excitation energies are also found to be sensitive to changes in the adsorption geometry. The electronic spectrum of CO on Pt(111) is simulated and the assignment of the bands observed in experimental electron energy loss spectroscopy discussed.     

Raman spectroscopic and density functional theory studies on a benzothiazole-2-thione derivative

The two tautomers of 7H-[1,3]dioxolo[4′,5′,4,5]benzo[1,2-d]thiazole-6-thione (DBTT) have been investigated by FT-IR and FT-Raman combined with density functional theory (DFT) calculations at the B3LYP level and 6-311+G** basis sets. On the basis of optimized structures, the harmonic force fields, vibrational frequencies and Raman intensities were calculated and scaled. The assignment of the fundamental vibrations for this molecule in its thione form was performed according to the potential energy distribution (PED) analysis. We have also discussed the adsorption behavior of DBTT on gold by means of SERS and DFT calculations at the same level. It revealed that the DBTT exhibited stable conformation of benzothiazole-2-thione (BTT) form both in solid and on gold surfaces; in addition, DBTT molecule is chemisorbed to the gold through both N and the exocyclic S atoms in its thione form and its molecular plane is perpendicular to the surface as BTT. The results show that the substituted groups in the phenyl ring have changed the characters such as the charge density in heterocyclic atoms and so on, but have little influence on the tautomeric preference of the BTT molecule and adsorption orientation on gold.     

Theoretical study on the singlet excited state of pterin and its deactivation pathway

The excited-state properties and related photophysical processes of the acidic and basic forms of pterin have been investigated by the density functional theory and ab initio methodologies. The solvent effects on the low-lying states have been estimated by the polarized continuum model and combined QM/MM calculations. Calculations reveal that the observed two strong absorptions arise from the strong pi --> pi* transitions to 1(pipi*L(a)) and 1(pipi*L(b)) in the acidic and basic forms of pterin. The first 1(pipi*L(a)) excited state is exclusively responsible for the experimental emission band. The vertical 1(n(N)pi*) state with a small oscillator strength, slightly higher in energy than the 1(pipi*L(a)) state, is less accessible by the direct electronic transition. The 1(n(N)pi*) state may be involved in the photophysical process of the excited pterin via the 1(pipi*L(a)/n(N)pi*) conical intersection. The radiationless decay of the excited PT to the ground state experiences a barrier of 13.8 kcal/mol for the acidic form to reach the (S(1)/S(0)) conical intersection. Such internal conversion can be enhanced with the increase in excitation energy, which will reduce the fluorescence intensity as observed experimentally.     

Calculations on the electronic excited states of ureas and oligoureas

We report CASPT2 calculations on the electronic excited states of several ureas. For monoureas, we find an electric dipole forbidden n --> pi* transition between 180 and 210 nm, dependent on the geometry and substituents of the urea. We find two intense pinb --> pi* transitions between 150 and 210 nm, which account for the absorptions seen in the experimental spectra. The n' --> pi* and pib --> pi* transitions are at wavelengths below 125 nm, which is below the lower limit of the experimental spectra. Parameter sets modeling the charge densities of the electronic transitions have been derived and permit calculations on larger oligoureas, using the exciton matrix method. For glycouril, a urea dimer, both the CASPT2 method and the matrix method yield similar results. Calculations of the electronic circular dichroism spectrum of an oligourea containing eight urea groups indicate that the experimental spectrum cannot be reproduced without the inclusion of electronic excitations involving the side chains. These calculations are one of the first attempts to understand the relationship between the structure and excited states of this class of macromolecule.     

Photolysis of methylcobalamin: identification of the relevant excited states involved in Co-C bond scission

The relevant excited states involved in the photolysis of methylcobalamin (MeCbl) have been examined by means of time-dependent density functional theory (TD-DFT). The low-lying singlet and triplet excited states have been calculated along the Co-C bond at the TD-DFT/BP86/6-31g(d) level of theory in order to investigate the dissociation process of MeCbl. These calculations have shown that the photodissociation is mediated by the repulsive 3(sigmaCo-C --> sigma*Co-C) triplet state. The key metastable photoproduct involved in Co-C bond photolysis was identified as an S1 state having predominantly dCo --> pi*corrin metal-ligand charge transfer (MLCT) character.