Design of Leaving Groups in Radical CC Fragmentations: Through‐Bond 2c–3e Interactions in Self‐Terminating Radical Cascades

Radical cascades terminated by β‐scission of exocyclic C?C bonds allow for the formation of aromatic products. Whereas β‐scission is common for weaker bonds, achieving this reactivity for carbon–carbon bonds requires careful design of radical leaving groups. It has now been found that the energetic penalty for breaking a strong σ‐bond can be compensated by the gain of aromaticity in the product and by the stabilizing two‐center, three‐electron “half‐bond” present in the radical fragment. Furthermore, through‐bond communication of a radical and a lone pair accelerates the fragmentation by selectively stabilizing the transition state. The stereoelectronic design of radical leaving groups leads to a new, convenient route to Sn‐functionalized aromatics.     

Ferromagnetic bonding: high spin copper clusters (n+1)Cu(n); n = 2-14) devoid of electron pairs but possessing strong bonding

Density functional theoretic studies are performed for the high-spin copper clusters (n)(+1)Cu(n) (n = 2-14), which are devoid of electron pairs shared between atoms, hence no-pair clusters (J. Phys. Chem. 1988, 92, 1352; Isr. J. Chem. 1993, 33, 455; J. Am. Chem. Soc. 1999, 121, 3165). Despite the lack of electron pairing, it is found that the bond dissociation energy per atom (BDE/n) is significant and converges (to within 1 kcal mol(-1)), around a cluster size (11)Cu(10), to a value of BDE/n = 19 kcal mol(-1). This is a very large bonding energy, much larger than has previously been obtained for no-pair clusters of lithium, BDE/n = 12 kcal mol(-1), or sodium clusters, BDE/n = 3 kcal mol(-1). This bonding, so-called ferromagnetic bonding (FM-bonding) is analyzed using a valence bond (VB) model (J. Phys. Chem. A 2002, 106, 4961; Phys. Chem. Chem. Phys. 2003, 5, 158). As such, FM-bonding in no-pair clusters is described as an ionic fluctuation, of the triplet pair, that spreads over all the close neighbors of a given atom in the clusters. Thus, if we refer to each triplet pair and its ionic fluctuations as a local FM-bond, we can regard the electronic structure of a given (n)(+1)M(n) cluster as a resonance hybrid of all the local FM-bonds between close neighbors. The model shows how a weak interaction in the diatomic triplet molecule can become a remarkably strong binding force that binds together mono-valent atoms without even a single electron pair. This is achieved because the growing number of VB structures exerts a cumulative effect of stabilization that is maximized when the cluster has a compact structure with an optimal coordination number for the atoms.     

Quantum chemical study of the hydrogen‐bonded patterns in A · T base pair of DNA: Origins of tautomeric mispairs,base flipping,and Watson–Crick ⇒ Hoogsteen conversion

The current work aims to thoroughly investigate a variety of facets of the hydrogen‐bond pattern of the Watson–Crick A · T base pair of DNA. It offers a novel mechanism of the origin of the hydrogen‐bonded mispairing in the A · T base pair based on the analysis of the lower‐energy portion of the total potential energy surface of all possible rearrangements of the hydrogen‐bond patterns in this pair, performed at the Hartree–Fock (HF), second‐order Moller–Plesset (MP2)//HF, and B3LYP computational levels in conjunction with 6‐31+G(d) basis set. The specific novelty of this mechanism is that the primary step consists of a single proton transfer along the N₃(T)–H … N₁ (A) hydrogen bond, thus leading to a transition state that is not directly related to the proton transfer. Rather, it governs the interbase shift within the A · T pair switching the hydrogen‐bonded pattern and then separating the normal A · T pair from the mispairing valley on its potential energy surface. The latter comprises three mismatched base pairs, easily converted to each other because of lower barriers (≈1 kcal/mol) of the corresponding proton transfers. It is demonstrated that, in terms of the Gibbs free energy taken at room T = 298.15 K, the most stable mispair in such valley is predicted to be less stable by 9.7 ± 2 kcal/mol than the Watson–Crick pair, thus implying that the spontaneous point mutations of this type occur as infrequently as to be characterized by an equilibrium constant of 10^?6 to 10^?9. This estimate falls into the well‐known experimental range of mutation frequency per base pair. The structure of a so‐called “base flipping” of the A · T base pair, originated from a breaking of its N₃(T)‐H … N₁ (A) hydrogen bond, is also found and reported in the current work for the first time. The transition state A · T ${}_{\text{ts}}^{\text{WC?H}}$ , which governs the conversion of the Watson–Crick pair of adenine · thymine into the Hoogsteen one and is related to a breaking of the N₆(A)–H … O₄(T), is also obtained and its energetical and geometrical features are discussed. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2003     

Hydrogen-atom abstraction from the adenine-uracil base pair

The hydrogen-abstracted radicals from the adenine-uracil (AU) base pair have been studied at the B3LYP/DZP++ level of theory. The A(N9)-U and A-U(N1) radicals, which correspond to hydrogen-atom abstraction at the adenine N9 and uracil N1 atoms, respectively, were predicted to be the two lowest-lying among the nine (AU-H) radicals studied in this study. The removal of the amino hydrogen of the adenine moiety that forms a hydrogen bond with the uracil O4 atom in the AU pair resulted in radical A(N6a)-U, which has the smallest base-pair dissociation energy, 5.9 kcal mol(-1). This radical is more likely to dissociate into the two isolated bases than to recover the hydrogen bond with the O4 atom through N6-H bond rotation along the C6-N6 bond. In general, the radicals generated by C-H bond breaking were higher in energy than those arising from N-H bond cleavage, because the unpaired electrons in the carbon-centered radicals were mainly localized on the carbon atom from which the hydrogen atom was removed. However, the highest-lying radical was found to arise from removal of the N3 hydrogen of uracil. The most remarkable structural feature of this radical is a very short C-H...O distance of 2.094 A, consistent with a substantial hydrogen bond. Although this radical lost the N1...H-N3 hydrogen bond between the two bases, its dissociation energy was predicted to be 12.9 kcal mol(-1), similar to that of the intact AU base pair. This is due to the transfer of electron density from the adenine N1 atom to the uracil N3 atom.     

Nucleophilic substitution reaction of benzyl benzenesulfonates with anilines in methanol-acetonitrile mixtures. Part 3

Kinetic studies on the nucleophilic substitution reaction of para-nitrobenzyl benzenesulfonates with anilines in methanol-acetonitrile mixtures are reported. It was found that the reaction proceeds via a dissociative S_N2 mechanism with a more product -like transition state compared to that for substrate with a less electron attracting substituent. A stronger electron withdrawing substituent in the benzyl moiety and in the leaving group is shown to enhance both bond making and bond breaking but the enhancement of bond making was found to be greater than that of bond breaking.     

Nature of the ring-closure process along the rearrangement of octa-1,3,5,7-tetraene to cycloocta-1,3,5-triene from the perspective of the electron localization function and catastrophe theory

We analyze the behavior of the energy profile of the ring‐closure process for the transformation of (3Z,5Z)‐octa‐1,3,5,7‐tetraene 5 to (1Z,3Z,5Z)‐cycloocta‐1,3,5‐triene 6 through a combination of electron localization function (ELF) and catastrophe theory (CT). From this analysis, concepts such as bond breaking/forming processes, formation/annihilation of lone pairs, and other electron pair rearrangements arise naturally through the reaction progress simply in terms of the different ways of pairing up the electrons. A relationship between the topology and the nature of the bond breaking/forming processes along this rearrangement is reported. The different domains of structural stability of the ELF occurring along the intrinsic reaction path have been identified. The reaction mechanism consists of six steps separated by fold and cusp catastrophes. The transition structure is observed in the third step, d(C1? C8) = 2.342 Å, where all bonds have topological signature of single bonds (C? C). The “new” C1? C8 single bond is not formed in transition state and respective catastrophe of the ELF field (cusp) is localized in the last step, d(C1? C8) ≈ 1.97 Å, where the two monosynaptic nonbonding basins V(C1) and V(C8) are joined into single disynaptic bonding basin V(C1,C8). The V(C1,C8) basin corresponds to classical picture of the C1? C8 bond in the Lewis formula. In cycloocta‐1,3,5‐triene 6 the single C1? C8 bond is characterized by relatively small basin population 1.72e, which is much smaller than other single bonds with 2.03 and 2.26e. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Electronic fluxes during diels‐alder reactions involving 1,2‐benzoquinones: mechanistic insights from the analysis of electron localization function and catastrophe theory

By means of the joint use of electron localization function (ELF) and Thom's catastrophe theory, a theoretical analysis of the energy profile for the hetero‐Diels‐Alder reaction of 4‐methoxy‐1,2‐benzoquinone 1 and methoxyethylene 2 has been carried out. The 12 different structural stability domains obtained by the bonding evolution theory have been identified as well as the bifurcation catastrophes (fold and cusp) responsible for the changes in the topology of the system. This analysis permits finding a relationship between the ELF topology and the evolution of the bond breaking/forming processes and electron pair rearrangements through the reaction progress in terms of the different ways of pairing up the electrons. The reaction mechanism corresponds to an asynchronous electronic flux; first, the O1? C5 bond is formed by the nucleophilic attack of the C5 carbon of the electron rich ethylene 2 on the most electrophilically activated carbonyl O1 oxygen of 1 , and once the σ bond has been completed, the formation process of the second O4? C6 bond takes place. In addition, the values of the local electrophilicity and local nucleophilcity indices in the framework of conceptual density functional theory accounts for the asychronicity of the process as well as for the observed regioselectivity. © 2012 Wiley Periodicals, Inc.     

Interaction of angelicin with DNA‐bases (III) DFT and ab initio second‐order Moeller–Plesset study

Angelicin geometry was optimized at MP2/6‐31+G(d,p) level and compared with X‐ray experimental data. The highest π‐electron density was found to be localized on C1? C2 and on C13? C14 as confirmed by the calculated bond length and bond order values. Spectrophptometric properties of angelicin were measured and compared with the computed within the TD‐DFT. Quantum chemical methods were used to study the interaction of angelicin, as a nonlinear furocoumarin, with DNA bases and base pairs. The interactions with DNA bases and base pairs were studied to shade more light on the nature of the intercalation binding forces between angelicin and DNA. Comparing computed electronic properties of angelicin with that of linear psoralens show that the former is a weaker intercalator. The geometry of complexes of angelicin with adenine, thymine, adenine–thymine base pair, cytocine, guanine as well as cytocine–guanine base pair have been optimized in two main orientations, planar and stacked, at the levels of B3LYP/cc‐pVDZ, MP2/6‐31G(d,p) and MP2/cc‐pVDZ. Effect of vertical distance and rotational angle between the stacked molecules on the interaction energy were investigated by the aforementioned methods in gas phase and water media. It was found that ab initio methods which account for the electron correlation effects are the minimum level for studying the noncovalent interactions. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

Electron pairing and chemical bonds. Electron fluctuation and pair localization in ELF domains

This article reports the numerical comparison of the quantities characterizing the extent of electron fluctuation and pair localization in the domains determined by the direct minimization of electron fluctuation with the domains resulting from the partitioning of the molecules based on the topological analysis of the so-called electron localization function (ELF). Such a comparison demonstrates that the ELF partitioning can be regarded as a feasible alternative to computationally much more demanding direct optimization of minimum fluctuation domains. This opened the possibility of the systematic scrutiny of the electron pair model of the chemical bond, and as it was demonstrated, the previous pessimistic claims about the applicability of this model are not completely justified.     

Electron localization function and electron localizability indicator applied to study the bonding in the peroxynitrous acid HOONO

The ground‐state electronic structure of peroxynitrous acid (HOONO) and its singlet biradicaloid form (HO ··· ONO) have been studied using topological analysis of the electron localization function (ELF), together with the electron localizability indicator (ELI‐D), at the DFT (B3LYP, M05, M052X, and M06), CCSD, and CASSCF levels. Three isomers of HOONO (cis‐cis, cis‐perp, and trans‐perp) have been considered. The results show that from all functionals applied, only B3LYP yields the correct geometrical structure. The ELF and ELI‐D‐topology of the O? O and central N? O bonds strongly depends on the wave function used for analysis. Calculations carried out at CAS (14,12)/aug‐cc‐pVTZ//CCSD(T)/aug‐cc‐pVTZ level reveal two bonds of the charge‐shift type: a protocovalent N? O bond with a basin population of 0.82–1.08e, and a more electron depleted O? O bond with a population of 0.66–0.71e. The most favorable dissociation channel (HOONO → HO + ONO) corresponds to breaking of the most electron‐deficient bond (O? O). In the case of cis‐ and trans‐HO ··· ONO, the ELF, ELI‐D, and electron density fields results demonstrate a closed‐shell O ··· O interaction. The α‐spin electrons are found mainly (0.64e) in the lone pairs of oxygen V_{i = 1,2} (O) from the OH group. The β‐spin electrons are delocalized over the ONO group, with the largest concentration (0.34e) on the lone pair of nitrogen V(N). © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Gas‐phase pyrolytic reactions of esters of 2‐pyridine and 8‐quinoline sulfonic acid

The rates of gas‐phase thermal elimination reaction of esters of 2‐pyridine sulfonic acid and 8‐quinoline sulfonic acid have been measured over at least 50° for each compound. The relative rates of the first‐order unimolecular decomposition at 500 K for the primary:secondary esters suggest that C O bond breaking is kinetically more significant than C H bond breaking, leading to a transition state of carbocationic character. This is consistent with the electron‐donating effect provided by the methoxy substituent in 2‐p‐methoxyphenylethyl of 2‐pyridine and 8‐quinoline sulfonate esters stabilizing the carbocation center. © 2000 John Wiley & Sons, Inc. Int J Chem Kinet 32: 771–775, 2000     

Symmetry‐Breaking Charge Transfer and Hydrogen Bonding: Toward Asymmetrical Photochemistry

Symmetry‐breaking charge transfer upon photoexcitation of a linear A‐π‐D‐π‐A molecule (D and A being electron donating and accepting groups) could be visualized using ultrafast time‐resolved infrared spectroscopy by monitoring the CN stretching modes on the A units. Whereas in apolar solvents, the S₁ state remains symmetric and quadrupolar, symmetry breaking occurs within ca. 100 fs in polar solvents as shown by the presence of two CN bands, instead of one in apolar solvents, with a splitting that increases with polarity. In protic solvents, symmetry breaking is significantly amplified by H‐bonding interactions, which are the strongest at the CN group with the highest basicity. In strongly protic solvents, the two CN bands transform in about 20 ps into new bands with a larger splitting, and the lifetime of the S₁ state is substantially reduced. This is attributed to the formation of an excited asymmetric tight H‐bond complex.     

The many flavours of halogen bonds – message from experimental electron density and Raman spectroscopy

Experimental electron‐density studies based on high‐resolution diffraction experiments allow halogen bonds between heavy halogens to be classified. The topological properties of the electron density in Cl…Cl contacts vary smoothly as a function of the interaction distance. The situation is less straightforward for halogen bonds between iodine and small electronegative nucleophiles, such as nitrogen or oxygen, where the electron density in the bond critical point does not simply increase for shorter distances. The number of successful charge–density studies involving iodine is small, but at least individual examples for three cases have been observed. (a) Very short halogen bonds between electron‐rich nucleophiles and heavy halogen atoms resemble three‐centre–four‐electron bonds, with a rather symmetric heavy halogen and without an appreciable σ hole. (b) For a narrow intermediate range of halogen bonds, the asymmetric electronic situation for the heavy halogen with a pronounced σ hole leads to rather low electron density in the (3,?1) critical point of the halogen bond; the properties of this bond critical point cannot fully describe the nature of the associated interaction. (c) For longer and presumably weaker contacts, the electron density in the halogen bond critical point is only to a minor extent reduced by the presence of the σ hole and hence may be higher than in the aforementioned case. In addition to the electron density and its derived properties, the halogen–carbon bond distance opposite to the σ hole and the Raman frequency for the associated vibration emerge as alternative criteria to gauge the halogen‐bond strength. We find exceptionally long C—I distances for tetrafluorodiiodobenzene molecules in cocrystals with short halogen bonds and a significant red shift for their Raman vibrations.     

Ionic liquids from Car-Parrinello simulations. 2. Structural diffusion leading to large anions in chloraluminate ionic liquids

We present Car-Parrinello molecular dynamics simulations of the liquid imidazolium chloride/AlCl3 by inserting one pair of [C2C1im]Cl into liquid AlCl3, forming an acidic mixture. Two different starting conditions lead to two trajectories from which we harvest structural data. For both simulations, we find large anions within the equilibrium phase: In both trajectories at longer simulation time, the anion size converges to four monomer units, i.e., to Al4Cl13-. The cluster size fluctuations indicate that Grotthus diffusion must play a role. We discuss one possible mechanism of such a reaction changing the anionic species. This process involves many steps of chlorine rattling, bond breaking, and bond forming. With the aid of the electron localization function, a probable rationale for the formation of larger anions is determined: Large anionic species are formed simply to account for the "lack of electrons" present in the acidic melt.     

Proving and Probing the Presence of the Elusive C−H⋅⋅⋅O Hydrogen Bond in Liquid Solutions at Room Temperature

Hydrogen bonds (H bonds) play a major role in defining the structure and properties of many substances, as well as phenomena and processes. Traditional H bonds are ubiquitous in nature, yet the demonstration of weak H bonds that occur between a highly polarized C?H group and an electron‐rich oxygen atom, has proven elusive. Detailed here are linear and nonlinear IR spectroscopy experiments that reveal the presence of H bonds between the chloroform C?H group and an amide carbonyl oxygen atom in solution at room temperature. Evidence is provided for an amide solvation shell featuring two clearly distinguishable chloroform arrangements that undergo chemical exchange with a time scale of about 2 ps. Furthermore, the enthalpy of breaking the hydrogen bond is found to be 6–20 kJ mol^?1. Ab‐initio computations support the findings of two distinct solvation shells formed by three chloroform molecules, where one thermally undergoes hydrogen‐bond making and breaking.     

Computational study of structures and proton transfer in hydrogen‐bonded ammonia complexes using semiempirical valence‐bond approach

In this study, the seGVB method was implemented for the N H bonding system, specifically for hydrogen‐bonded ammonia complexes, and the model well reproduces the MP2 geometries and energetics. A comparison between the ammonia dimer and water dimer is given from the viewpoint of valance‐bond structures in terms of the calculated bond energies and pair–pair interactions. The linear hydrogen bond is found to be stronger than the bent bonds in both cases, with the difference in energy between the linear and cyclic structures being comparable in both cases although the NH bonds are generally weaker. The energy decomposition clearly demonstrates that the changes in electronic energy are quite different in the two cases due to the presence of an additional lone pair on the water molecule, and it is this effect which leads to the net stabilization of the cyclic structure for the ammonia dimer. Proton‐transfer profiles for hydrogen‐bonded ammonia complexes [NH₂ H NH₂]⁻ and [NH₃ H NH₃]⁺ were calculated. The barrier for proton transfer in [NH₃ H NH₃]⁺ is larger than that in [NH₂ H NH₂]⁻, but smaller than that in the protonated water dimer. The different bonding structures substantially affect the barrier to proton transfer, even though they are isoelectronic systems. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 73: 357–367, 1999     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

Energy gap law of electron transfer in nonpolar solvents

We investigate the energy gap law of electron transfer in nonpolar solvents for charge separation and charge recombination reactions. In polar solvents, the reaction coordinate is given in terms of the electrostatic potentials from solvent permanent dipoles at solutes. In nonpolar solvents, the energy fluctuation due to solvent polarization is absent, but the energy of the ion pair state changes significantly with the distance between the ions as a result of the unscreened strong Coulomb potential. The electron transfer occurs when the final state energy coincides with the initial state energy. For charge separation reactions, the initial state is a neutral pair state, and its energy changes little with the distance between the reactants, whereas the final state is an ion pair state and its energy changes significantly with the mutual distance; for charge recombination reactions, vice versa. We show that the energy gap law of electron-transfer rates in nonpolar solvents significantly depends on the type of electron transfer.