Isoguanine formation from adenine

Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A?C?2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A?C?2???OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG?1 or isoG?2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20?kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(?) →isoG+H(?) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG?1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.     

Ab initio reaction kinetics of hydrogen abstraction from methyl formate by hydrogen, methyl, oxygen, hydroxyl, and hydroperoxy radicals

Combustion of renewable biofuels, including energy-dense biodiesel, is expected to contribute significantly toward meeting future energy demands in the transportation sector. Elucidating detailed reaction mechanisms will be crucial to understanding biodiesel combustion, and hydrogen abstraction reactions are expected to dominate biodiesel combustion during ignition. In this work, we investigate hydrogen abstraction by the radicals H·, CH(3)·, O·, HO(2)·, and OH· from methyl formate, the simplest surrogate for complex biodiesels. We evaluate the H abstraction barrier heights and reaction enthalpies, using multireference correlated wave function methods including size-extensivity corrections and extrapolation to the complete basis set limit. The barrier heights predicted for abstraction by H·, CH(3)·, and O· are in excellent agreement with derived experimental values, with errors ≤1 kcal/mol. We also predict the reaction energetics for forming reactant complexes, transition states, and product complexes for reactions involving HO(2)· and OH·. High-pressure-limit rate constants are computed using transition state theory within the separable-hindered-rotor approximation for torsions and the harmonic oscillator approximation for other vibrational modes. The predicted rate constants differ significantly from those appearing in the latest combustion kinetics models of these reactions.     

Theoretical Study on the Dehydrogenation Reaction of H2S by VS+ (3∑-)

The dehydrogenation reaction of H2S by the 3∑- ground state of VS+: VS+ + H2S → VS2+ + H2 has been studied by using Density Functional Theory (DFT) at the B3LYP/DZVP level. It is found that the reaction proceeds along two possible pathways (A and B) yielding two isomer dehydrogenation products VS2+-1 (3B2) and VS2+-2 (3A1), respectively. For both pathways,the reaction has a two-step-reaction mechanism that involves the migration of two hydrogen atoms from S2 to V+, respectively. The migration of the second hydrogen via TS3 and that of the first via TS4 are the rate-determining steps for pathways A and B, respectively. The activation energy is 17.4 kcal/mol for pathway A and 22.8 kcal/mol for pathway B relative to the reactants. The calculated reaction heat of 9.9 kcal/mol indicates the endothermicity of pathway A and that of -11.9 kcal/mol suggests the exothermicity of pathway B.     

Kinetics of the OH + ClOOCl and OH + Cl2O reactions: experiment and theory

The rate coefficients for the reactions OH + ClOOCl --> HOCl + ClOO (eq 5) and OH + Cl2O --> HOCl + ClO (eq 6) were measured using a fast flow reactor coupled with molecular beam quadrupole mass spectrometry. OH was detected using resonance fluorescence at 309 nm. The measured Arrhenius expressions for these reactions are k5 = (6.0 +/- 3.5) x 10(-13) exp((670 +/- 230)/T) cm(3) molecule(-1) s(-1) and k6 = (5.1 +/- 1.5) x 10(-12) exp((100 +/- 92)/T) cm(3) molecule(-1) s(-1), respectively, where the uncertainties are reported at the 2sigma level. Investigation of the OH + ClOOCl potential energy surface using high level ab initio calculations indicates that the reaction occurs via a chlorine abstraction from ClOOCl by the OH radical. The lowest energy pathway is calculated to proceed through a weak ClOOCl-OH prereactive complex that is bound by 2.6 kcal mol(-1) and leads to ClOO and HOCl products. The transition state to product formation is calculated to be 0.59 kcal mol(-1) above the reactant energy level. Inclusion of the OH + ClOOCl rate data into an atmospheric model indicates that this reaction contributes more than 15% to ClOOCl loss during twilight conditions in the Arctic stratosphere. Reducing the rate of ClOOCl photolysis, as indicated by a recent re-examination of the ClOOCl UV absorption spectrum, increases the contribution of the OH + ClOOCl reaction to polar stratospheric loss of ClOOCl.     

Definitive ab initio studies of model SN2 reactions CH(3)X+F- (X=F,Cl, CN,OH, SH,NH(2), PH(2))

The energetics of the stationary points of the gas-phase reactions CH(3)X+F(-)-->CH(3)F+X(-) (X=F, Cl, CN, OH, SH, NH(2) and PH(2)) have been definitively computed using focal point analyses. These analyses entailed extrapolation to the one-particle limit for the Hartree-Fock and MP2 energies using basis sets of up to aug-cc-pV5Z quality, inclusion of higher-order electron correlation [CCSD and CCSD(T)] with basis sets of aug-cc-pVTZ quality, and addition of auxiliary terms for core correlation and scalar relativistic effects. The final net activation barriers for the forward reactions are: E (b/F,F)=-0.8, E (b/F, Cl)=-12.2, E (b/F,OH)=+13.6, E b/F,OH=+16.1, E b/F,SH=+2.8, Eb/F, NH=+32.8, and E b/F,PH =+19.7 kcal x mol(-1). For the reverse reactions E b/F,F= -0.8, Eb/Cl,F =+18.3, E b/CN,F=+12.2, E b/OH,F =-1.8, E b/SH,F =+13.2, E b/NH(2),=-1.5, and E b/PH(2) =+9.6 kcal x mol(-1). The change in energetics between the CCSD(T)/aug-cc-pVTZ reference prediction and the final extrapolated focal point value is generally 0.5-1.0 kcal mol(-1). The inclusion of a tight d function in the basis sets for second-row atoms, that is, utilizing the aug-cc-pV(X+d)Z series, appears to change the relative energies by only 0.2 kcal x mol(-1). Additionally, several decomposition schemes have been utilized to partition the ion-molecule complexation energies, namely the Morokuma-Kitaura (MK), reduced variational space (RVS), and symmetry adapted perturbation theory (SAPT) techniques. The reactant complexes fall into two groups, mostly electrostatic complexes (FCH(3).F(-) and ClCH(3).F(-)), and those with substantial covalent character (NCCH(3).F(-), CH(3)OH.F(-), CH(3)SH.F(-), CH(3)NH(2).F(-) and CH(3)PH(2).F(-)). All of the product complexes are of the form FCH(3).X(-) and are primarily electrostatic.     

A theoretical study of the mechanism for the homogeneous catalytic reversible dehydrogenation-hydrogenation of nitrogen heterocycles

A mechanism for the dehydrogenation reaction of 1,2,3,4-tetrahydroquinoline to quinoline derivatives, catalyzed by a Cp*Ir complex containing a 2-pyridonate ligand, is proposed and supported by theoretical calculations at the B3LYP level. The proposed mechanism involves two stages which are all thermodynamically unfavorable (endothermic by 36.3 kcal mol(-1) and 18.4 kcal mol(-1), respectively). The apparent activation energies of the first and second stages of the reaction are 30.8 kcal mol(-1) and 34.0 kcal mol(-1), respectively, and are considered overestimates of the entropy change of reaction. Owing to a decrease in the oxidative ability of iridium(III) coordinated to large electronegative nitrogen and chlorine, ligand promoted hydrogen abstraction is crucial at both stages of dehydrogenation, in which the oxidation state of iridium(III) does not change, and the ligand 2-pyridonate is converted to 2-hydroxypyridine. Cp*Ir(C(5)NH(4)OH)ClH, an important intermediate, releases hydrogen through an energy barrier of 23.5 kcal mol(-1).     

Noncovalent complexes between dimethyl ether and formic acid--an ab initio and matrix isolation study.

The complexes formed by noncovalent interactions between formic acid and dimethyl ether are investigated by ab initio methods and characterized by matrix isolation spectroscopy. Six complexes with binding energies between -2.26 and -7.97 kcal mol(-1) (MP2/cc-pVTZ+zero point vibrational energy+basis set superposition erros) are identified. The two strongest bound complexes are, within a range of 0.3 kcal mol(-1), isoenergetic. The binding in these six dimers can be described in terms of OH...O, C=O...H, C-O...H and CH...O interactions. Matrix isolation spectroscopy allowed to characterize the two strongest bound complexes by their infrared spectra.     

Mechanism of epoxide hydrolysis in microsolvated nucleotide bases adenine, guanine and cytosine: a DFT study

Six water molecules have been used for microsolvation to outline a hydrogen bonded network around complexes of ethylene epoxide with nucleotide bases adenine (EAw), guanine (EGw) and cytosine (ECw). These models have been developed with the MPWB1K-PCM/6-311++G(3df,2p)//MPWB1K/6-31+G(d,p) level of DFT method and calculated S(N)2 type ring opening of the epoxide due to amino group of the nucleotide bases, viz. the N6 position of adenine, N2 position of guanine and N4 position of cytosine. Activation energy (E(act)) for the ring opening was found to be 28.06, 28.64, and 28.37 kcal mol(-1) respectively for EAw, EGw and ECw. If water molecules were not used, the reactions occurred at considerably high value of E(act), viz. 53.51 kcal mol(-1) for EA, 55.76 kcal mol(-1) for EG and 56.93 kcal mol(-1) for EC. The ring opening led to accumulation of negative charge on the developing alkoxide moiety and the water molecules around the charge localized regions showed strong hydrogen bond interactions to provide stability to the intermediate systems EAw-1, EGw-1 and ECw-1. This led to an easy migration of a proton from an activated water molecule to the alkoxide moiety to generate a hydroxide. Almost simultaneously, a proton transfer chain reaction occurred through the hydrogen bonded network of water molecules and resulted in the rupture of one of the N-H bonds of the quaternized amino group. The highest value of E(act) for the proton transfer step of the reaction was 2.17 kcal mol(-1) for EAw, 2.93 kcal mol(-1) for EGw and 0.02 kcal mol(-1) for ECw. Further, the overall reaction was exothermic by 17.99, 22.49 and 13.18 kcal mol(-1) for EAw, EGw and ECw, respectively, suggesting that the reaction is irreversible. Based on geometric features of the epoxide-nucleotide base complexes and the energetics, the highest reactivity is assigned for adenine followed by cytosine and guanine. Epoxide-mediated damage of DNA is reported in the literature and the present results suggest that hydrated DNA bases become highly S(N)2 active on epoxide systems and the occurrence of such reactions can inflict permanent damage to the DNA.     

Bridging QTAIM with vibrational spectroscopy: the energy of intramolecular hydrogen bonds in DNA-related biomolecules

Physical properties of over 8000 intramolecular hydrogen bonds (iHBs), including 2901 ones of the types OH···O, OH···N, NH···O and OH···C, in 4244 conformers of the DNA-related molecules (four canonical 2'-deoxyribonucleotides, 1,2-dideoxyribose-5-phosphate, and 2-deoxy-D-ribose in its furanose, pyranose and linear forms) have been investigated using quantum theory of atoms in molecules (QTAIM) and vibrational analysis. It has been found that for all iHBs with positive red-shift of the proton donating group stretching frequency the shift value correlates with ρ(cp)-the electron charge density at the (3,-1)-type bond critical point. Combining QTAIM and spectroscopic data new relationships for estimation of OH···O, OH···N, NH···O and OH···C iHB enthalpy of formation (kcal mol(-1)) with RMS error below 0.8 kcal mol(-1) have been established: E(OH···O) = -3.09 + 239·ρ(cp), E(OH···N) = 1.72 + 142·ρ(cp), E(NH···O) = -2.03 + 225·ρ(cp), E(OH···C) = -0.29 + 288·ρ(cp), where ρ(cp) is in e a(0)(-3) (a(0)- the Bohr radius). It has been shown that XHY iHBs with red-shift values over 40 cm(-1) are characterized by the following minimal values of the XHY angle, ρ(cp) and nubla(2)ρ(cp): 112°, 0.005 e a(0)(-3) and 0.016 e a(0)(-5), respectively. New relationships have been used to reveal the strongest iHBs in canonical 2'-deoxy- and ribonucleosides and the O(5')H···N(3) H-bond in ribonucleoside guanosine was found to have the maximum energy (8.1 kcal mol(-1)).     

Activation barriers and rate constants for hydration of platinum and palladium square-planar complexes: an ab initio study

In the present work, an ab initio study on hydration (a metal-ligand replacement by water molecule or OH- group) of cis- and transplatin and their palladium analogs was performed within a neutral pseudomolecule approach (e.g., metal-complex+water as reactant complex). Subsequent replacement of the second ligand was considered. Optimizations were performed at the MP2/6-31+G(d) level with single-point energy evaluation using the CCSD(T)/6-31++G(d,p) approach. For the obtained structures of reactants, transition states (TS's), and products, both thermodynamic (reaction energies and Gibbs energies) and kinetic (rate constants) characteristics were estimated. It was found that all the hydration processes are mildly endothermic reactions-in the first step they require 8.7 and 10.2 kcal/mol for ammonium and chloride replacement in cisplatin and 13.8 and 17.8 kcal/mol in the transplatin case, respectively. Corresponding energies for cispalladium amount to 5.2 and 9.8 kcal/mol, and 11.0 and 17.7 kcal/mol for transpalladium. Based on vibrational analyses at MP2/6-31+G(d) level, transition state theory rate constants were computed for all the hydration reactions. A qualitative agreement between the predicted and known experimental data was achieved. It was also found that the close similarities in reaction thermodynamics of both Pd(II) and Pt(II) complexes (average difference for all the hydration reactions are approximately 1.8 kcal/mol) do not correspond to the TS characteristics. The TS energies for examined Pd(II) complexes are about 9.7 kcal/mol lower in comparison with the Pt analogs. This leads to 10(6) times faster reaction course in the Pd cases. This is by 1 or 2 orders of magnitude more than the results based on experimental measurements.     

Isopropylcyclopropane + OH gas phase reaction: a quantum chemistry + CVT/SCT approach

A theoretical study of the mechanism and kinetics of the OH hydrogen abstraction from isopropylcyclopropane (IPCP) is presented. Optimum geometries, frequencies and gradients have been computed at the BHandHLYP/6-311++G(d,p) level of theory for all stationary points, as well as for additional points along the minimum energy path (MEP). Energies have been improved by single-point calculations at the above geometries using CCSD(T)/6-311++G(d,p) to produce the potential energy surface. The rate coefficients are calculated for the temperature range 260-350 K by using canonical variational theory (CVT) with small-curvature tunneling (SCT) corrections. Our analysis suggests a stepwise mechanism involving the formation of a reactant complex in the entrance channel and a product complex in the exit channel, for all the modeled paths. The reactant complexes are examined in detail, because they exhibit alkene-like structure. The excellent agreement between the overall calculated and experimental rate coefficients at 298 K supports the reliability of the parameters obtained for the temperature dependence and branching ratios of the IPCP + OH reaction, proposed here for the fist time. The expression that best describes the studied reaction is k(overall) = 6.15 x 10(-13)e1747/RT cm3 x molecule(-1) x s(-1). The predicted activation energy is -0.89 kcal/mol.     

Mechanisms of the reactions of W and W+ with NOx (x=1, 2): a computational study

The mechanisms of the reactions of W and W+ with NOx (x=1, 2) were studied at the CCSD(T)/[SDD+6-311G(d)]//B3LYP/[SDD+6-31G(d)] level of theory. It was shown that the insertion pathway of the reaction W(7S)+NO2(2A1) is a multistate process, which involves several lower lying electronic states of numerous intermediates and transition states, and leads to oxidation, WO(3Sigma)+NO(2Pi), and/or nitration, WN(4Sigma)+O2(3Sigmag-), of the W-center. Oxidation products WO(3Sigma)+NO(2Pi) lie 87.6 kcal/mol below the reactants, while the nitration channel is only 31.0 kcal/mol exothermic. Furthermore, it was shown that nitration of W with NO2 is kinetically less favorable than its oxidation. The addition-dissociation pathway of the reaction W(7S)+NO2(2A1) proceeds via the octet (ground) state potential energy surface of the reaction, requires 3.3 kcal/mol barrier, and leads exclusively to oxidation products. Calculations show that oxidation of the W+ cation by NO2 is a barrierless process in the gas phase, proceeds exclusively via the insertion pathway, and is exothermic by 82.9 kcal/mol. The nitration of W+ by NO2 is only 14.1 kcal/mol exothermic and could be accessible only under high-temperature conditions. Reactions of M=W/W+ with NO are also barrierless processes in the gas phase and lead to the N-O insertion product NMO, which are 105.4 and 77.4 kcal/mol lower than the reactants for W and W+, respectively.     

Theoretical study of nucleophilic substitution at the disulfide bridge of cyclo-l-cystine

The reaction of cyclo-l-cystine with thiolate is examined at the B3LYP/6-31+G level. The two isomers of cyclo-l-cystine differ in their dihedral angle about the disulfide bond; the M isomer (with dihedral angle of -90.1 degrees) is found to be slightly lower in energy. The nucleophilic substitution reaction at sulfur follows the addition-elimination mechanism, exemplified by the hypercoordinate sulfur intermediate on the reaction surface. The reaction is exergonic (DeltaG = -6.16 kcal mol(-1)), and both the entrance and exit transition state lie below the reactant energies.     

Monomeric MnIII/II and FeIII/II complexes with terminal hydroxo and oxo ligands: probing reactivity via O-H bond dissociation energies

Non-heme manganese and iron complexes with terminal hydroxo or oxo ligands are proposed to mediate the transfer of hydrogen atoms in metalloproteins. To investigate this process in synthetic systems, the monomeric complexes [M(III/II)H(3)1(OH)](-/2-) and [M(III)H(3)1(O)](2-) have been prepared, where M(III/II) = Mn and Fe and [H(3)1](3-) is the tripodal ligand, tris[(N'-tert-butylureaylato)-N-ethyl)]aminato. These complexes have similar primary and secondary coordination spheres, which are enforced by [H(3)1](3-). The homolytic bond dissociation energies (BDEs(O-H)) for the M(III/II)-OH complexes were determined, using experimentally obtained values for the pK(a)(M-OH) and E(1/2) measured in DMSO. This thermodynamic analysis gave BDEs(O-H) of 77(4) kcal/mol for [Mn(II)H(3)1(O-H)](2-) and 66(4) kcal/mol for [Fe(II)H(3)1(O-H)](2-). For the M(III)-OH complexes, [Mn(III)H(3)1(OH)]- and [Fe(III)H(3)1(OH)]-, BDEs(O-H) of 110(4) and 115(4) kcal/mol were obtained. These BDEs(O-H) were verified with reactivity studies with substrates having known X-H bond energies (X = C, N, O). For instance, [Fe(II)H(3)1(OH)](2-) reacts with a TEMPO radical to afford [Fe(III)H(3)1(O)](2-) and TEMPO-H in isolated yields of 60 and 75%, respectively. Consistent with the BDE(O-H) values for [Mn(II)H(3)1(OH)](2-), TEMPO does not react with this complex, yet TEMPO-H (BDE(O-H) = 70 kcal/mol) reacts with [Mn(III)H(3)1(O)](2-), forming TEMPO and [Mn(II)H(3)1(OH)](2-). [Mn(III)H(3)1(O)](2-) and [Fe(III)H(3)1(O)](2-) react with other organic substrates containing C-H bonds less than 80 kcal/mol, including 9,10-dihydroanthracene and 1,4-cyclohexadiene to produce [M(II)H(3)1(OH)](2-) and the appropriate dehydrogenated product in yields of greater than 80%. Treating [Mn(III)H(3)1(O)](2-) and [Fe(III)H(3)1(O)](2-) with phenolic compounds does not yield the product expected from hydrogen atom transfer but rather the protonated complexes, [Mn(III)H(3)1(OH)]- and [Fe(III)H(3)1(OH)]-, which is ascribed to the highly basic nature of the terminal oxo group.     

Coordination environment of aqueous uranyl(VI) ion

Water dissociation from [UO2(OH2)5]2+ is studied with Car-Parrinello molecular dynamics simulations (using the BLYP density functional) in the gas phase and in aqueous solution. Free energies, DeltaA, are estimated from pointwise thermodynamic integration using one U-O(H2) distance as a reaction coordinate. While an isomeric, four-coordinate complex, [UO2(OH2)4]2+.H2O, is more stable than the five-coordinate reactant in the gas phase (DeltaA = -2.2 kcal/mol), the former is strongly disfavored in water (DeltaA = +8.7 kcal/mol).     

A direct dynamics trajectory study of F- + CH(3)OOH reactive collisions reveals a major non-IRC reaction path

A direct dynamics simulation at the B3LYP/6-311+G(d,p) level of theory was used to study the F- + CH3OOH reaction dynamics. The simulations are in excellent agreement with a previous experimental study (J. Am. Chem. Soc. 2002, 124, 3196). Two product channels, HF + CH2O + OH- and HF + CH3OO-, are observed. The former dominates and occurs via an ECO2 mechanism in which F- attacks the CH3- group, abstracting a proton. Concertedly, a carbon-oxygen double bond is formed and OH- is eliminated. Somewhat surprisingly this is not the reaction path, predicted by the intrinsic reaction coordinate (IRC), which leads to a deep potential energy minimum for the CH2(OH)2...F- complex followed by dissociation to HF + CH2(OH)O-. None of the direct dynamics trajectories followed this path, which has an energy release of -63 kcal/mol and is considerably more exothermic than the ECO2 path whose energy release is -27 kcal/mol. Other product channels not observed, and which have a lower energy than that for the ECO2 path, are F- + CO + H2 + H2O (-43 kcal/mol), F- + CH2O + H2O (-51 kcal/mol), and F- + CH2(OH)2 (-60 kcal/mol). Formation of the CH3OOH...F- complex, with randomization of its internal energy, is important, and this complex dissociates via the ECO2 mechanism. Trajectories which form HF + CH3OO- are nonstatistical events and, for the 4 ps direct dynamics simulation, are not mediated by the CH3OOH...F- complex. Dissociation of this complex to form HF + CH3OO- may occur on longer time scales.     

Interaction of adenine adducts with thymine: a computational study

The existence of DNA adducts bring the danger of carcinogenesis because of mispairing with normal DNA bases. 1,N6-ethenoadenine adducts (epsilonA) and 1,N6-ethanoadenine adducts (EA) have been considered as DNA adducts to study the interaction with thymine, as DNA base. Several different stable conformers for each type of adenine adduct with thymine, [epsilonA(1)-T(I), epsilonA(2)-T(I), epsilonA(3)-T(I) and EA(1)-T(I), EA(2)-T(I), EA(3)-T(I)] and [epsilonA(1)-T(II), epsilonA(2)-T(II), epsilonA(3)-T(II) and EA(1)-T(II), EA(2)-T(II), EA(3)-T(II)], have been considered with regard to their interactions. The differences in their geometrical structures, energetic properties, and hydrogen-bonding strengths have also been compared with Watson-Crick adenine-thymine base pair (A-T). Single-point energy calculations at MP2/6-311++G** levels on B3LYP/6-31+G* optimized geometries have also been carried out to better estimate the hydrogen-bonding strengths. The basis set superposition error corrected hydrogen-bonding strength sequence at MP2/6-311++G**//B3LYP/6-31+G* for the most stable complexes is found to be EA(2)-T(I) (15.30 kcal/mol) > EA(1)-T(II) (14.98 kcal/mol) > EA(3)-T(II) (14.68 kcal/mol) > epsilonA(2)-T(I) (14.54 kcal/mol) > epsilonA(3)-T(II) (14.22 kcal/mol) > epsilonA(3)-T(II) (13.64 kcal/mol) > A-T (13.62 kcal/mol). The calculated reaction enthalpy value for epsilonA(2)-T(I) is 10.05 kcal/mol, which is the highest among the etheno adduct-thymine complexes and about 1.55 kcal/mol more than those obtained for Watson-Crick A-T base pair and the reaction enthalpy value for EA(1)- T(II) is 10.22 kcal/mol, which is highest among the ethano addcut-thymine complexes and about 1.72 kcal/mol more than those obtained for Watson-Crick A-T base pair. The aim of this research is to provide fundamental understanding of adenine adduct and thymine interaction at the molecular level and to aid in future experimental studies toward finding the possible cause of DNA damage.     

Probing phenylalanine/adenine pi-stacking interactions in protein complexes with explicitly correlated and CCSD(T) computations

To examine the effects of pi-stacking interactions between aromatic amino acid side chains and adenine bearing ligands in crystalline protein structures, 26 toluene/(N9-methyl)adenine model configurations have been constructed from protein/ligand crystal structures. Full geometry optimizations with the MP2 method cause the 26 crystal structures to collapse to six unique structures. The complete basis set (CBS) limit of the CCSD(T) interaction energies has been determined for all 32 structures by combining explicitly correlated MP2-R12 computations with a correction for higher-order correlation effects from CCSD(T) calculations. The CCSD(T) CBS limit interaction energies of the 26 crystal structures range from -3.19 to -6.77 kcal mol (-1) and average -5.01 kcal mol (-1). The CCSD(T) CBS limit interaction energies of the optimized complexes increase by roughly 1.5 kcal mol (-1) on average to -6.54 kcal mol (-1) (ranging from -5.93 to -7.05 kcal mol (-1)). Corrections for higher-order correlation effects are extremely important for both sets of structures and are responsible for the modest increase in the interaction energy after optimization. The MP2 method overbinds the crystal structures by 2.31 kcal mol (-1) on average compared to 4.50 kcal mol (-1) for the optimized structures.