SCF?CI and SCF open-shell studies of the base components of the nucleic acids

The π-electron structure of adenine, guanine, cytosine, thymine and uracil in their ground, ionized, singlet and triplet excited states are investigated by means of the SCF ? CI and SCF open-shell methods. The calculations for singlets fit the maxima of the absorption bands well. The energy difference between the first and the second singlet states of adenine is found to be very small. The open-shell method leads to the same relative ionization potential as does the SCF (with the integrals empirically corrected). The calculated energies of the triplet states almost coincide in the SCF open-shell and the SCF ? CI approximation. The calculated transition energies to the first triplet state of the pyrimidines are higher than in the case of the purines. The value of the singlet–triplet separation energy of purines is in agreement with experimental data.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

Thermodynamics of α-Cyclodextrin Complexation with Bases of Nucleic Acids and Their Derivatives

The interactions of -cyclodextrin with adenine, thymine, uracil, cytosine, and caffeine in water at 298.15 K have been studied by the calorimetric method. -Cyclodextrin is found to interact selectively with nucleic bases and their derivatives to form complexes with uracil, cytosine, and caffeine only. The influence of the structure and solvation of the reactants on the thermodynamic characteristics of their complexation in a solution has been examined.     

Activation barriers for DNA alkylation by carcinogenic methane diazonium ions

Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 A shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine.     

Theoretical study of electronic spectra of the DNA bases

Excited π-electronic states of cytosine and uracil are calculated by the CI method. The effects of a transition from the single-excited configuration set to the set involving all double-excited configurations are considered. The set expansion is shown to affect essentially the transition energies and oscillator strengths, in particular, an additional electron transition related to the first absorption band occurs in the singlet uracil spectrum. When doubly excitations are taken into account the triplet transition energies considerably increase and become practically insensitive to repulsion integral parametrization.     

Photochemical Reaction Between 1,2‐Naphthoquinone and Adenine in Binary Water‐Acetonitrile Solutions

The photochemical reaction between 1,2‐naphthoquinone (NQ ) and adenine was investigated using nanosecond time‐resolved laser flash photolysis. With photolysis at 355 nm, the lowest triplet state T₁ of NQ was produced via intersystem crossing from its singlet excited state. The triplet‐triplet absorption of the state contributes three bands of transient spectra at 374, 596 and 650 nm, respectively, in pure acetonitrile and binary water‐acetonitrile solutions. In the presence of adenine, the observation of ⁺ (at 363 nm) and radical (at 343 and 485 nm) indicates a multistep mechanism of electron transfer process followed by a proton transfer between ³NQ * and adenine. By fitting with the Stern‐Volmer relationship, the quenching rate constant k _q of ³NQ * by adenine in binary water‐acetonitrile solutions (4/1, volume ratio, v/v) is determined as 1.66 × 10⁹ m ⁻¹ s⁻¹. Additionally, no spectral evidence confirms the existence of electron transfer between ³NQ * with thymine, cytosine and uracil.     

Stacking of the mutagenic DNA base analog 5-bromouracil

The potential energy surface of the stacked 5-bromouracil/uracil (BrU/U) dimer has been investigated in the gas phase and in solution (water and 1,4-dioxane), modeled by a continuum solvent using the polarizable continuum model. Minima and transition states were optimized using DFT (the M06-2X density functional and the 6-31+G(d) basis set). Six stacked gas-phase BrU/U minima were located: four in the face-to-back orientation and two face-to-face. The global minimum in the gas phase is a face-to-face structure with a twist angle of 60° and a zero-point energy-corrected interaction energy of ?10.7 kcal/mol. The BrU/U potential energy surface is geometrically and energetically similar to that of U/U (Hunter and Van Mourik in J Comput Chem 33:2161, 2012). Energy calculations were also performed on experimental geometries of stacked dimers (47 containing BrU stacking with either adenine, cytosine, guanine or thymine and 51 containing thymine also stacking with one of those four bases) taken from DNA structures in the Protein Data Bank. Single-point interaction energies were computed at different levels of theory including MP2, CCSD(T) and DFT using the mPW2PLYP-D double-hybrid functional augmented with an empirical dispersion term, using basis sets ranging from aug-cc-pVDZ to aug-cc-pVQZ. No strong evidence was found for the suggestion that the mutagenicity of BrU is due to enhanced stacking of BrU compared to the corresponding stacked dimers involving thymine.     

Excitation Energies of Canonical Nucleobases Computed by Multiconfigurational Perturbation Theories

In this computational work, we assessed the performance of ab initio multireference (MR) methods for the calculation of vertical excitation energies of five nucleobases: adenine, guanine, cytosine, thymine and uracil. In total, we have studied 38 singlet and 30 triplet excited states. Where possible we used the multireference configuration interaction (MRCI) method as a reference for various flavors of multireference perturbation theory to second order. In particular, we have benchmarked CASPT2, NEVPT2 and XMCQDPT2. For CASPT2, we have analyzed the single‐state, multistate (MS) and extended MS variants. In addition, we have assessed the effect of the ionization potential electron affinity (IPEA) shift. For NEVPT2, we have used the partially and the strongly contracted variants. Further, we have tested the commonly used RI‐CC2, RI‐ADC2 and EOM‐CCSD methods. Generally, we observe the following trends for singlet excited states: NEVPT2 is the closest MR method to MRCISD+Q, closely followed by CASPT2 with the default IPEA shift. The same trend is observed for triplet states, although NEVPT2 and CASPT2‐IPEA are getting closer. Interestingly, the n, π* singlet excited states were described more accurately than π, π* excited states, while for triplet states the trend is inverted except for NEVPT2. This work is an important benchmark for future photochemical investigations.     

Excited state dipole moments and geometries of the bases of nucleic acids

CNDO/s-CI and VE-PPP methods have been employed to calculate the dipole moments of the bases of nucleic acids in the ground and excited states. A component analysis in terms of μ_hyb^(σ), μ_ch and μ_π has been done using the CNDO/s-CI method and these results have been compared with those obtained by the CNDO/2 and IEHT methods. It is observed that while the CNDO/2 and CNDO/s-CI methods give almost the same total dipole moments, component-wise their predictions are very different.Dipole moments of the molecules have also been studied for the lowest excited singlet and triplet π^* ← π states. It is observed that the conventional method of calculating dipole moments using changes of only the net charges in the excited state does not give correct results for uracil and thymine, for which experimental results are available. Considering deformed non-planar excited state geometries for these molecules, the observed excited state dipole moments have been explained. A method has been suggested to include the effects of non-planarity while calculating the properties of a complex molecule in a π^* ← π excited state. For adenine, guanine and cytosine, the excited state dipole moments are found to be smaller than the ground state values.     

Triplet states via intermediate neglect of differential overlap: Benzene,pyridine and the diazines

The intermediate neglect of differential overlap technique is modified and applied to the calculation of excited triplet states. The resulting method generally reproduces the transition energies of the better-classified observations within a rms error of 1000 cm^–1. Trends are well reproduced, and the calculated orders ofn-* and -* triplet states are in good accord with the experimental information to date.The method is applied to benzene and the azines. The lowest four triplet states of benzene are calculated in good accord with experiment. Pyridine is calculated to have an-* triplet nearly degenerate with the lowest lying -* triplet, corroborating suggestions of Japar and Ramsay based on experimental information. A detailed analysis is made of the diazines, and assignments are suggested for the higher lying triplet states not yet classified or not yet observed.     

TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach

A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of pisigma* type Rydberg transition was found near the lowest singlet pipi* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases.     

Electron attachment to DNA and RNA nucleobases: An EOMCC investigation

We report a benchmark theoretical investigation of both vertical and adiabatic electron affinities of DNA and RNA nucleobases: adenine, guanine, cytosine, thymine, and uracil using equation of motion coupled cluster method. The vertical electron affinity (VEA) values of the first five states of the DNA and RNA nucleobases are computed. It is observed that the first electron attached state is energetically accessible in gas phase. Furthermore, an analysis of the natural orbitals exhibits that the first electron attached states of uracil and thymine are valence‐bound in nature and undergo significant structural changes on attachment of an extra electron, which reflects in the deviation of the adiabatic electron affinity (AEA) than that of the vertical ones. Conversely, the first electron attached states of cytosine, adenine, and guanine are in the category of dipole‐bound anions. Their structure, by and large, remain unaffected on attachment of an extra electron, which is evident from the observed small difference between the AEA and VEA values. VEA and AEA values of all the DNA and RNA nucleobases are found to be negative, which implies that the first electron attached states are not stable rather quasi bound. The results of all previous theoretical calculations are out of track and shows large deviation with respect to the experimentally measured values, whereas, our results are found to be in good agreement. Therefore, our computed values can be used as a reliable standard to calibrate new theoretical methods. © 2015 Wiley Periodicals, Inc.     

A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.     

The first excited triplet states of the nucleotide bases calculated with different semiempirical SCF schemes

The π-electron distributions, spin densities, and energies of the first triplets of the nucleotide bases, uracil, thymine, cytosine, adenine, and guanine, were investigated in various semiempirical approximations. Results are presented for calculations using the semiempirical form of the closed-shell SCF configuration interaction method, of the different orbitals for different spins (unrestricted Hartree–Fock) treatment, with and without spin projection, and of the Roothaan's open-shell procedure.     

Gas-phase theoretical prediction of the metal affinity of copper(I) ion for DNA and RNA bases

The most stable tautomeric forms of free DNA and RNA bases were considered as substrates for the interaction of Cu(+) ion. Several suitable attachment sites were selected that involved mono- and bi-coordination of the cation. B3LYP/6-311 + G(2df,2p) bond energies showed that copper ion has the major affinity for guanine and cytosine bases. The proposed values of Cu(+) ion affinity are 59.9, 60.0, 80.2, 88.0 and 69.0 kcal mol(-1) for uracil, thymine, cytosine, guanine and adenine, respectively. The preference for the mono- or bi-coordination depends on the particular tautomer for each base.     

Transport Selectivity of a Diethylene Glycol Dimethacrylate- Based Thymine-imprinted Polymeric Membrane over a Cellulose Support for Nucleic Acid Bases

The binding mechanism between 9-vinyladenine and pyrimidine base thymine in methanol was studied with UV-visible spectrophotometric method. Based on this study, using thymine as a template molecule, 9-vinyladenine as a novel functional monomer and diethylene glycol dimethacrylate as a new cross-linker, a specific diethylene glycol dimethacrylate-based molecularly imprinted polymeric membrane was prepared over a cellulose support. Then, the resultantly polymeric membrane morphologies were visualized with scanning electron microscopy and its permselectivity was examined using thymine, uracil, cytosine, adenine and guanine as substrates. This result showed that the imprinting polymeric membrane prepared with diethylene glycol dimethacrylate exhibited higher transport capacity for the template molecule thymine and its optimal analog uracil than other nucleic acid bases. The membrane also took on higher permselectivity than the imprinted membrane made with ethylene glycol dimethacrylate as a cross-linker. When a mixture including five nucleic acid bases thymine, uracil, cytosine, adenine and guanine passed through the diethylene glycol dimethacrylate-based thymine-imprinted polymeric membrane, recognition of the membrane for the template molecule thymine and its optimal analog uracil was demonstrated. It was predicted that the molecularly imprinted membrane prepared with diethylene glycol dimethacrylate as cross-linker might be applicable to thymine assay of absolute hydrolysates of DNA or uracil assay of absolute hydrolysates of RNA in biological samples because of its high selectivity for the template molecule thymine and its optimal analog uracil.     

Optimum geometries and relative energies for cytosine,thymine, uracil,the imino tautomer of cytosine,the enol tautomer of thymine,and the enol tautomer of uracil by the MINDO/2 SCF MO method

A MINDO /2 SCF MO geometry optimization of cytosine (C), thymine (T), uracil (U), the imino tautomer of cytosine (C*), the enol tautomer of thymine (T*), and the enol tautomer of uracil (U*)was made. The optimized geometries for cytosine, thymine, and uracil agree well with crystallographic data. The optimized geometries for the tautomers show the correct trends in bond lengthening and bond angle except for the C4—O4 length and C4—O4—H angle of T* and U*. The energies of tautomerization were found to be 10.3, ?9.0, and ?14.2 kcal/mol for C?C*, T?T*, and U?U*, respectively, when optimized geometries are used. The overestimation of the C4—O4—H angle is speculated to arise because of an inadequacy in the parametrization of the one-center integrals in MINDO /2.     

Na+, Mg2+, and Zn2+ binding to all tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine: a correlated ab initio quantum chemical study

Interactions of adenine, cytosine, guanine, and thymine with Na(+), Mg(2+), and Zn(2+) cations were studied using an approximate resolution of identity correlated second-order MP2 (RI-MP2) method with the TZVPP ([5s3p2d1f/3s2p1d]) basis set. All existing tautomers of adenine, cytosine, and thymine and the eight most stable keto/enol tautomers of guanine were considered. Cations bind mostly in a bidentate manner, and stabilization energies of these complexes are larger than those in the case when cations bind in a unidentate manner. The cation...Y (Y equal to N or O) distances for divalent metals are shorter than those for Na(+) and for Zn(2+) are mostly shorter than the Mg(2+)...Y distance. The intermolecular distances between the cation and the base for complexes containing adenine and cytosine are systematically shorter than those for complexes containing guanine and thymine. Only for cytosine the canonical keto/amino tautomer structure with ions represents the global minimum. For guanine, the metalated canonical form is again the most stable, but its stabilization energy is within less than 5% of the stabilization energies of the two other rare tautomers, which indicates that the canonical form and these two rare tautomers could coexist. The canonical structures of adenine and thymine in the presence of ions are considerably less stable (by more than 10%) than the complexes of the rare tautomers. It can be concluded that the interaction of Na(+), Mg(2+), and Zn(2+) cations with cytosine in the gas phase will not induce the change of the canonical form to the rare tautomeric form. In the case of isolated guanine, the equilibrium of the canonical form with rare tautomers can be found. For isolated adenine and thymine the presence of rare tautomers is highly probable.     

PHOTOCHEMISTRY AND PHOTOPHYSICS OF GUANINE-CONTAINING DINUCLEOSIDES

Abstract— Yields and action spectra are reported for photochemistry. fluorescence. and total lumincscence at 405 nm due to UV excitation (240–300 nm) or dilutc (-0.1 mM ) solutions or guanosine 5–monophosphate (GMP) and the dinucleosides linking guanine with adenine (ApG and GpA). cytosine (CpG) and uracil (GpU) in neutral ethylene glycol-water (7:3) glasses at 140–165 K. Phosphorescence lifetimes were determined at 140 K. Less complete data are presented for GpC, UpG and dpGpT. Quantum yields for all three processes were usually found to increase as the excitation wavelength increases. Although intramolecular exciplex formation was not dominant under these conditions interactions were strong enough to frustrate attempts at interpretation of results within the Forster very weak coupling framework. There is evidence that the GMP photochemistry proceeds from the triplet state. Surprisingly, this photochemistry is not quenched in ApG, GpA, and dpGpT at 163 K although the adenine (A) and thymine (T) moieties are known to have lower triplet states. At 140 K the phosphorescence from ApG and GpA was entirely characteristic of A but both G and T components were observed from dpGpT.     

Excited states of the benzyl radical

The CI method is used in the -electron approximation with orbitals for closed and open shells to calculate the properties of excited doublet states with allowance for all singly excited configurations and some doubly excited ones, and also for the first quartet and sextet states, which are calculated in the one-configuration approximation via the open-shell theory. The energies and transition moments agree satisfactorily with the available experimental evidence. A classification and assignment is given for the excited terms. Truncation of the complete set of singly excited configurations greatly distorts the calculated spectrum. Inclusion of doubly excited configurations in the CI also produces a substantial change in the spectrum; in some cases it alters the order of adjacent terms. Conversion in CI from basis closed-shell orbitals to open-shell ones produces a considerable lowering of all terms in the spectrum. As in the case of triplet terms for molecules, weakening of electron interaction brings the lowest excited term of the radical closer to the ground-state term. The electron-density and spin-density distributions are calculated for the excited states.