Stability of the chlorinated derivatives of the DNA/RNA nucleobases,purine and pyrimidine toward radical formation via homolytic C?Cl bond dissociation

The chlorinated derivatives of nucleobases (and nucleosides), as well as those of purine, have well‐established anticancer activity, and in some cases, are also shown to be involved in the link between chronic inflammatory conditions and the development of cancer. In this investigation, the stability of all of the isomeric forms of the chlorinated nucleobases, purine and pyrimidine are investigated from the perspective of their homolytic C? Cl bond dissociation energies (BDEs). The products of these reactions, namely chlorine atom and the corresponding carbon‐centered radicals, may be of importance in terms of potentiating biological damage. Initially, the performance of a wide range of contemporary theoretical procedures were evaluated for their ability to afford accurate C? Cl BDEs, using a recently reported set of 28 highly accurate C? Cl BDEs obtained by means of W1w theory. Subsequent to this analysis, the G3X(MP2)‐RAD procedure (which achieves a mean absolute deviation of merely 1.3 kJ mol^?1, with a maximum deviation of 5.0 kJ mol^?1) was employed to obtain accurate gas‐phase homolytic C? Cl bond dissociation energies for a wide range of chlorinated isomers of the DNA/RNA nucleobases, purine and pyrimidine.     

A dataset of highly accurate homolytic NBr bond dissociation energies obtained by Means of W2 theory

Homolytic N? Br bond dissociation constitutes the initial step of numerous reactions involving N‐brominated species. However, little is known about the strength of N? Br bonds toward homolytic cleavage. We herein report accurate bond dissociation energies (BDEs) for a set of 18 molecules using the high‐level W2 thermochemical protocol. The BDEs (at 298 K) of the species in this set range from 162.2 kJ mol^?1 (N‐bromopyrrole) to 260.6 kJ mol^?1 ((CHO)₂NBr). In order to compute BDEs of larger systems, for which W2 theory is not applicable, we have benchmarked a wide range of more economical theoretical procedures. Of these, G3‐B3 offers the best performance (root‐mean‐square deviations = 2.9 kJ mol^?1), and using this method, we have computed N? Br BDEs for four widely used N‐brominated compounds. These include (BDEs are given in parentheses): N‐bromosuccinimide (281.6), N‐bromoglutarimide (263.2), N‐bromophthalimide (274.7), and 1,3‐dibromo‐5,5‐dimethylhydantoin (218.2 and 264.8 kJ mol^?1). © 2015 Wiley Periodicals, Inc.     

Electron attachment to the DNA bases adenine and guanine and dehydrogenation of their anionic derivatives: Density functional study

Density functional theory (DFT) calculations have been used to explore electron attachment to the purines adenine and guanine and their hydrogen atom loss. Calculations show that the dehydrogenation at the N9 site in the adenine and guanine transient anions is the lowest‐cost channel of hydrogen loss, and the N9? H bond scission has Gibbs free energies of dissociation ΔG° of 8.8 kcal mol^?1 for the anionic adenine and 13.9 kcal mol^?1 for the anionic guanine. The relatively high feasibility of low‐energy electron (LEE)‐induced N9? H bond cleavage in the purine nucleobases arises from high electron affinities of their H‐deleted counterparts. Unlike adenine, other N? H bond dissociations are competitive with the N9? H bond fission in the anionic guanine. The replacement of hydrogen in the ring of purine has a significant effect on the N9? H bond fragmentation. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

A quantum chemistry study on C–H homolytic bond dissociation enthalpies of five-membered and six-membered heterocyclic compounds

The C–H homolytic bond dissociation enthalpies (BDEs) of 27 heterocyclic compounds of small systems (less than 8 non-hydrogen atoms) were evaluated by the composite ab initio methods of G4 and CBS-Q. In addition, the C–H BDEs of an extended database including 60 heterocyclic compounds were assessed by 16 DFT functionals. The correlation between the theoretical and experimental values reveals that the BMK functional provided the lowest root mean square error (RMSE) of 10.2 kJ/mol, and the correlation coefficient (R²) was 0.955. The mean deviation (MD), mean absolute deviation (MAD) of BMK are 0.1 kJ/mol and 7.9 kJ/mol separately. Therefore, we utilized BMK to research C–H BDEs together with the substituent effects of five-membered and six-membered heterocyclic compounds including large systems. The nature of C–H BDE change pattern was analyzed by the natural bond orbital (NBO).     

Benchmark approach to search of cost-effective and accurate density functional for homolytic cleavage of C─Mg bond of Grignard reagent

Grignard reactions are of importance in organic chemistry for the synthesis β-keto esters and diethyl malonate, alcohols, aldehydes or ketones, monocarboxylic acids, and other organometallic compounds. Generally, the heterolytic dissociation of C─Mg bond in Grignard reagent is the key step in these reactions. Recently, homolytic cleavage of the C─Mg bond in Grignard reagents has been reported in the preparation of stable radicals. These reactive species react with other compounds, which result in the formation of hydrocarbons and their derivatives. Therefore, the study of homolytic cleavage of C─Mg bonds is quite vital to better understand the kinetics and thermodynamics of these reactions. In the current study, a benchmark approach is adopted to find a cost-effective and accurate density functional (DF) for bond dissociation energies measurement of the C─Mg bond of Grignard reagents. Twenty-nine DFs from 13 density functional theory (DFT) classes with three types of basis sets (Pople' 6-31G(d) and 6-311G(d), Dunning's aug-cc-pVDZ, and Karlsruhe' def2-SVP basis sets) are implemented for the measurement of dissociation energies of the C─Mg bond. Theoretical dissociation energy values are compared with experimental reported values of the C─Mg bond of selected Grignard reagents. TPSSTPSS of the meta-GGA class with 6-31G (d) basis set gave accurate results, and its Pearson's correlation is 0.95. SD, root mean square deviation, and mean unsigned error of this method are 2.36 kcal mol⁻¹, 2.33 kcal mol⁻¹, and −0.46 kcal mol⁻¹, respectively. TPSSTPSS of the meta-GGA class is a one-electron, self-interaction, error-free Tao-Perdew-Staroverov-Scuseria functional that performed better with the 6-31G(d) basis set.     

CH and Chalogen bond dissociation energies for fluorinated and chlorinated methane evaluated with hybrid B3LYP density functional theory methods and their comparison with experimental data and the CBS-Q ab initio computational approach

The CH and Chalogen bond dissociation energies (BDEs) were computed with the hybrid B3LYP/6-311 + G(2d,2p) theory model for chlorinated and fluorinated methane. All computed values were substantially lower (5–10 kcal mol⁻¹) than the experimental values. To obtain better agreement, a correlation factor was introduced. When this factor was applied, excellent agreement between the B3LYP/6-311 + G(2d,2p) computed energies and the experimental BDEs was observed. On the other hand, the CBS-Q ab initio computational approach generated BDEs which are in good agreement with experimental values without a correction factor.     

Peptide cation-radicals. A computational study of the competition between peptide N-Calpha bond cleavage and loss of the side chain in the [GlyPhe-NH2 + 2H]+. cation-radical

Cation‐radicals and dications corresponding to hydrogen atom adducts to N‐terminus‐protonated N_α‐glycylphenylalanine amide (Gly‐Phe‐NH₂) are studied by combined density functional theory and Møller‐Plesset perturbational computations (B3‐MP2) as models for electron‐capture dissociation of peptide bonds and elimination of side‐chain groups in gas‐phase peptide ions. Several structures are identified as local energy minima including isomeric aminoketyl cation‐radicals, and hydrogen‐bonded ion‐radicals, and ylid‐cation‐radical complexes. The hydrogen‐bonded complexes are substantially more stable than the classical aminoketyl structures. Dissociations of the peptide N? C_α bonds in aminoketyl cation‐radicals are 18–47 kJ mol^?1 exothermic and require low activation energies to produce ion‐radical complexes as stable intermediates. Loss of the side‐chain benzyl group is calculated to be 44 kJ mol^?1 endothermic and requires 68 kJ mol^?1 activation energy. Rice‐Ramsperger‐Kassel‐Marcus (RRKM) and transition‐state theory (TST) calculations of unimolecular rate constants predict fast preferential N? C_α bond cleavage resulting in isomerization to ion‐molecule complexes, while dissociation of the C_α? CH₂C₆H₅ bond is much slower. Because of the very low activation energies, the peptide bond dissociations are predicted to be fast in peptide cation‐radicals that have thermal (298 K) energies and thus behave ergodically. Copyright © 2003 John Wiley & Sons, Ltd.     

Mechanism of the primary stages of decomposition of aliphatic nitro- and fluoronitronitramines

The primary stage of the decomposition of compounds RN(NO₂)CH₂C(NO₂)₂X is the homolytic cleavage of the C?NO₂ bond, at X=NO₂ and N?NO₂ bond at X=F. The inductive effect of substituents decreases the dissociation energies of the C?N and N?N bonds by 1–2 kcal mol^?1. Kinetic effects caused by the spatial interaction of groups and by stepwise decomposition of polyfunctional compounds are described.     

An investigation on the reaction mechanism of the F2+Cl2→2ClF using the B3LYP method

The reaction mechanism of F₂+Cl₂→2ClF has been investigated with the density functional theory at the B3LYP/6‐311G* level. Six transition states have been found for the three possible reaction paths and verified by the normal mode vibrational and IRC analyses. Ab initio MP2/6‐311G* geometry optimizations and CCSD(T)/6‐311G(2df)//MP2/6‐311G* single‐point energy calculations have been performed for comparison. It is found that when the F₂ (or Cl₂) molecule decomposes into atoms first and then the F (or Cl) atom reacts with the molecule Cl₂ (or F₂) nearly along the molecular axis, the energy barrier is very low. The calculated energy barrier of F attacking Cl₂ is zero and that of Cl attacking F₂ is only 15.57 kJ?mol^?1 at the B3LYP level. However, the calculated dissociation energies of F₂ and Cl₂ are as high as 145.40 and 192.48 kJ?mol^?1, respectively. When the reaction proceeds through a bimolecular reaction mechanism, two four‐center transition states are obtained and the lower energy barrier is 218.69 kJ?mol^?1. Therefore, the title reaction F₂+Cl₂→2ClF is most probably initiated from the atomization of the F₂ molecule and terminated by the reaction of F attacking Cl₂ nearly along the Cl? Cl bond. MP2 calculations lead to the same conclusion, but the geometry of TS and the energy barrier are somewhat different. © 2002 John Wiley & Sons, Inc. Int J Quantum Chem, 2002     

Bond dissociation enthalpies in chlorinated benzenes and phenols and enthalpies of formation of their free radicals: A Gaussian‐4 prediction

The bond dissociation enthalpies (BDEs) in chlorinated benzenes and phenols and the standard gas‐phase enthalpies of formation of chlorinated phenyl and phenoxy radicals are predicted by using Gaussian‐4 (G4) and Gaussian‐3X (G3X) model chemistries. The predicted G4 BDEs are systematically smaller than the G3X ones, with difference as much as ～15 kJ/mol for the C₆Cl₅‐Cl bond, and the G4 enthalpies of formation of the free radicals are systematically smaller than the G3X ones. The discrepancies increase gradually with the degree of chlorination; whereas for the closed‐shell species, G4 and G3X enthalpies of formation agree closely within 2 kJ/mol. The difference between G4 and G3X arises mainly from the noncanceling high‐level correction terms in G4. © 2010 Wiley Periodicals, Inc. Int J Chem Kinet 43: 62–69, 2011     

Gas-phase acidity, bond dissociation energy and enthalpy of formation of fluorine-substituted benzenes: A theoretical study

A variety of theoretical methods have been used to study the gas-phase acidity of benzene and its eleven fluorine-substituted derivatives: fluorobenzene, three isomers of difluorobenezene, three isomers of trifluorobenzene, three isomers of tetrafluorobenzene and 1,2,3,4,5-pentafluorobenzene. The high-level ab initio methods, G3//B3-LYP and CBS-QB3, are shown to reproduce experimental data to within an average of 1.9 and 1.4 kcal mol⁻¹, respectively. Of the lower-cost methods studied, M05-2X and MP2 showed the best overall performance with mean absolute deviations of just 1.2 and 1.1 kcal mol⁻¹, respectively. The effect of substitution and position on the acidity of the protons in the various compounds are studied and the structure-reactivity trends in these heterolytic C-H bond dissociation energies (BDEs) are compared with the corresponding homolytic C-H BDEs for the same species.     

Probing Reaction Mechanism of [1,5]‐Migration in Pyrrolium and Pyrrole Derivatives: Activation of a Stronger Bond in Electropositive Groups Becomes Easier

The [1,5]‐migration reaction has attracted considerable attention from experimentalists and theoreticians for decades. Although it has been extensively investigated in various systems, studies on pyrrolium derivatives are underdeveloped. Herein, a theoretical study on the reaction mechanism of [1,5]‐migration in both pyrrolium and pyrrole derivatives is presented. The results reveal lower activation barriers in [1,5]‐migration of electropositive groups (AuPMe₃ and SnH₃) in pyrrolium derivatives, although the bond dissociation energies of the Au?N bond (98.8 kcal mol^?1) and Sn?N bond (81.7 kcal mol^?1) are larger than that of the N?F bond (57.6 kcal mol^?1). The unexpectedly lower activation barriers (4.5 and 4.9 kcal mol^?1 for AuPMe₃ and SnH₃, respectively) for [1,5]‐migration of electropositive groups, in comparison with the [1,5]‐fluorine shift, can be attributed to aromaticity stabilizing the transition states, as revealed by significantly negative nucleus‐independent chemical shift (NICS) values. Further studies indicate that charge distribution and frontier molecular orbitals also play some roles in [1,5]‐migration of pyrrolium derivatives.     

Theoretical Study of the N-NO2 Bond Dissociation Energies for Energetic Materials with Density Functional Theory

The N-NO2 bond dissociation energies （BDEs） for 7 energetic materials were computed by means of accurate density functional theory （B3LYP, B3PW91 and B3P86） with 6-31G＊＊ and 6-311G＊＊ basis sets. By comparing the computed energies and experimental results, we find that the B3P86/6-311G＊＊ method can give good results of BDE, which has the mean absolute deviation of 1.30kcal/mol. In addition, substituent effects were also taken into account. It is noted that the Hammett constants of substituent groups are related to the BDEs of the N-NO2 bond and the bond dissociation energies of the energetic materials studied decrease when increasing the number of NO2 group.     

Adsorption of Proline and Glycine on the TiO2(110) Surface: A Density Functional Theory Study

The optimal adsorption modes for the amino acids glycine and proline on the ideal TiO₂(110) surface are investigated by using density functional theory (PBE) applying periodic boundary conditions. Binding modes with anionic acid moieties bridging two titanium atoms after transferring a proton to the surface are the most stable configurations for both molecules investigated—similar to previous results for carboxylic acids. In contrast to the latter compounds, amino acids can form hydrogen bonds via the amino group towards the surface‐bound proton; this provides an additional stabilisation of 15–20 kJ mol^?1. Zwitterionic binding modes are less stable (by 10–20 kJ mol^?1) and are less important for proline. Neutral modes are energetically even less favourable. Calculations of vibrational frequencies and core‐level shifts complement the adsorption study and provide guidance for future experimental investigations. Control of the computational parameters is crucial for the derivation of accurate results. The layout and thickness of the slab model used are also shown to be decisive factors. Calculations with a different GGA‐functional (PW91) provide very similar relative energies, although the absolute energies change by about 20 kJ mol^?1. Results derived with the hybrid functional PBE0 show an even greater stabilisation of the anionic binding modes with respect to the zwitterionic modes. A previously observed discrepancy between experimental and theoretical results for glycine could be solved, although the experimentally proposed free rotation of the C? C bond could not be reproduced.     

Theoretical approaches to estimating homolytic bond dissociation energies of organocopper and organosilver compounds

Although organocopper and organosilver compounds are known to decompose by homolytic pathways among others, surprisingly little is known about their bond dissociation energies (BDEs). In order to address this deficiency, the performance of the DFT functionals BLYP, B3LYP, BP86, TPSSTPSS, BHandHLYP, M06L, M06, M06-2X, B97D, and PBEPBE, along with the double hybrids, mPW2-PLYP, B2-PLYP, and the ab initio methods, MP2 and CCSD(T), have been benchmarked against the thermochemistry for the M-C homolytic BDEs (D(0)) of Cu-CH(3) and Ag-CH(3), derived from guided ion beam experiments and CBS limit calculations (D(0)(Cu-CH(3)) = 223 kJ·mol(-1); D(0)(Ag-CH(3)) = 169 kJ·mol(-1)). Of the tested methods, in terms of chemical accuracy, error margin, and computational expense, M06 and BLYP were found to perform best for homolytic dissociation of methylcopper and methylsilver, compared with the CBS limit gold standard. Thus the M06 functional was used to evaluate the M-C homolytic bond dissociation energies of Cu-R and Ag-R, R = Et, Pr, iPr, tBu, allyl, CH(2)Ph, and Ph. It was found that D(0)(Ag-R) was always lower (～50 kJ·mol(-1)) than that of D(0)(Cu-R). The trends in BDE when changing the R ligand reflected the H-R bond energy trends for the alkyl ligands, while for R = allyl, CH(2)Ph, and Ph, some differences in bond energy trends arose. These trends in homolytic bond dissociation energy help rationalize the previously reported (Rijs, N. J.; O'Hair, R. A. J. Organometallics2010, 29, 2282-2291) fragmentation pathways of the organometallate anions, [CH(3)MR](-).     

C?X⋅⋅⋅O Halogen Bonding: Interactions of Trifluoromethyl Halides with Dimethyl Ether

The formation of weakly bound molecular complexes between dimethyl ether (DME) and the trifluoromethyl halides CF₃Cl, CF₃Br and CF₃I dissolved in liquid argon and in liquid krypton is investigated, using Raman and FTIR spectroscopy. For all halides evidence is found for the formation of C? X???O halogen‐bonded 1:1 complexes. At higher concentrations of CF₃Br, a weak absorption due to a 1:2 complex is also observed. Using spectra recorded at temperatures between 87 and 125 K, the complexation enthalpies for the complexes are determined to be ?6.8(3) kJ mol^?1 (DME?CF₃Cl), ?10.2(1) kJ mol^?1 (DME?CF₃Br), ?15.5(1) kJ mol^?1 (DME?CF₃I), and ?17.8(5) kJ mol^?1 [DME(?CF₃Br)₂]. Structural and spectral information on the complexes is obtained from ab initio calculations at the MP2/ 6‐311++G(d,p) and MP2/6‐311++G(d,p)+LanL2DZ* levels. By applying Monte Carlo free energy perturbation calculations to account for the solvent influences, and statistical thermodynamics to estimate the zero‐point vibrational and thermal influences, the ab initio complexation energies are converted into complexation enthalpies for the solutions in liquid argon. The resulting values are compared with the experimental data deduced from the cryosolutions.     

Strong N−X⋅⋅⋅O−N Halogen Bonds: A Comprehensive Study on N‐Halosaccharin Pyridine N‐Oxide Complexes

A study of the strong N?X???^?O?N⁺ (X=I, Br) halogen bonding interactions reports 2×27 donor×acceptor complexes of N‐halosaccharins and pyridine N‐oxides (PyNO). DFT calculations were used to investigate the X???O halogen bond (XB) interaction energies in 54 complexes. A simplified computationally fast electrostatic model was developed for predicting the X???O XBs. The XB interaction energies vary from ?47.5 to ?120.3 kJ mol^?1; the strongest N?I???^?O?N⁺ XBs approaching those of 3‐center‐4‐electron [N?I?N]⁺ halogen‐bonded systems (ca. 160 kJ mol^?1). ¹H NMR association constants (K_XB) determined in CDCl₃ and [D₆]acetone vary from 2.0×10⁰ to >10⁸ m ^?1 and correlate well with the calculated donor×acceptor complexation enthalpies found between ?38.4 and ?77.5 kJ mol^?1. In X‐ray crystal structures, the N‐iodosaccharin‐PyNO complexes manifest short interaction ratios (R_XB) between 0.65–0.67 for the N?I???^?O?N⁺ halogen bond.     

Theoretical and Structural Analysis of Long CC Bonds in the Adducts of Polycyanoethylene and Anthracene Derivatives and Their Connection to the Reversibility of Diels–Alder Reactions

X‐ray structure determinations on four Diels–Alder adducts derived from the reactions of cyano‐ and ester‐substituted alkenes with anthracene and 9,10‐dimethylanthracene have shown the bonds formed in the adduction to be particularly long. Their lengths range from 1.58 to 1.62 Å, some of the longest known for Diels–Alder adducts. Formation of the four adducts is detectably reversible at ambient temperature and is associated with free energies of reaction ranging from ?2.5 to ?40.6 kJ mol^?1. The solution equilibria have been experimentally characterised by NMR spectroscopy. Density‐functional‐theory calculations at the MPW1K/6‐31+G(d,p) level with PCM solvation agree with experiment with average errors of 6 kJ mol^?1 in free energies of reaction and structural agreement in adduct bond lengths of 0.013 Å. To understand more fully the cause of the reversibility and its relationship to the long adduct bond lengths, natural‐bond‐orbital (NBO) analysis was applied to quantify donor–acceptor interactions within the molecules. Both electron donation into the σ*‐anti‐bonding orbital of the adduct bond and electron withdrawal from the σ‐bonding orbital are found to be responsible for this bond elongation.     

N-亚硝基吲哚系列化合物及其自由基负离子在乙腈介质中N-NO键断裂能的测定

利用滴定量热技术并结合适当的热力学循环测定了乙腈溶液中7个取代的N-亚硝基吲哚化合物中N—NO键的异裂能和均裂能, 能量范围分别为206.1~246.2 kJ/mol和119.1~124.6 kJ/mol. 表明N-亚硝基吲哚均裂释放NO自由基(NO·)比异裂释放NO正离子(NO+)要容易得多, 通过热力学循环得到的相应自由基负离子中N—NO键的异裂能和均裂能的能量范围分别为25.5~34.4和5.0~40.5 kJ/mol, 表明所研究化合物的自由基负离子在室温下很不稳定.