Sigma Bonded Radical Cation Complexes: A Theoretical Study

Sulfur-centered hemi-bond radicals as active intermediates in S-DNA phosphorothioate oxidation

Phosphorothioate (PS) modifications naturally appear in bacteria and archaea genome and are widely used as antisense strategy in gene therapy. But the chemical effects of PS introduction as a redox active site into DNA (S-DNA) is still poorly understood. Herein, we perform time-resolved spectroscopy to examine the underlying mechanisms and dynamics of the PS oxidation by potent radicals in free model, in dinucleotide, and in S-oligomer. The crucial sulphur-centered hemi-bonded intermediates -P–S∴S–P- were observed and found to play critical roles leading to the stable adducts of -P–S–S–P-, which are backbone DNA lesion products. Moreover, the oxidation of the PS moiety in dinucleotides d[G_PSG], d[A_PSA], d[G_PSA], d[A_PSG] and in S-oligomers was monitored in real-time, showing that PS oxidation can compete with adenine but not with guanine. Significantly, hole transfer process from A^+• to PS and concomitant -P–S∴S–P- formation was observed, demonstrating the base-to-backbone hole transfer unique to S-DNA, which is different from the normally adopted backbone-to-base hole transfer in native DNA. These findings reveal the distinct backbone lesion pathway brought by the PS modification and also imply an alternative -P–S∴S–P-/-P–S–S–P- pathway accounting for the interesting protective role of PS as an oxidation sacrifice in bacterial genome.

Non-classical covalent bonds

The possibility of multiple bond formation between Periodic Table Group 13 – 15 elements is considered. The ways of triple bond formation between these elements are discussed; particular attention is paid to the B≡B triple bonds. New non-linear compounds with triple bonds and their molecular structures are considered. The causes are given for the formation of compounds with unusually short distances between chemically non-bonded atoms. The grounds of the theory of two-centre three-electron bonds are presented and conditions of existence of isolated square planar carbon clusters are analyzed.

The bibliography includes 181 references.

Unusual Fluorine Substitution Effect on S···Cl Bonding between Sulfides and Atomic Chlorine

A theoretical investigation on the interaction of various sulfides and their fluorinated counterparts (H₂S, HSF, F₂S, CH₃SH, CH₃SF, CH₂FSH, CH₂FSF, NH₂SH, NH₂SF) with atomic chlorine has been carried out using density functional theory (DFT) based LC-BLYP/aug-cc-pVTZ and sophisticated ab initio CCSD(T)/aug-cc-pVQZ methods. The present study is intended to discuss the influence of the substituents implanted at the sulfur atom on the bonding parameters. The optimized geometries reveal that intermolecular S···Cl distances are short and range between 2.423 and 2.561 Å. A strong contraction of the S-F bond is also predicted. Two-center-three-electron S···Cl bonds are formed; the interaction energies are large and range from -33.9 to -70.1 kJ mol^-1. Very surprisingly, the interaction energies are greater and the intermolecular distances are shorter for F-substituted sulfides than for unsubstituted ones. This is in complete contrast with the lower proton affinities and less negative electrostatic potentials of fluorinated sulfides. AIM analysis, the charge transfer from the sulfur atom to the Cl atom, and the spin densities on the Cl and S atoms are considered to explain this unusual behavior. The hyperconjugation energies from the LP(F) to the σ*(S-Cl) antibonding orbital can be considered as one of the stabilizing factors for the greater stability of the fluorinated complexes over the nonfluorinated ones.

Formal Nickelate(-I) Complexes Supported by Group 13 Ions

Formal nickelate(-I) complexes bearing Group 13 metalloligands (M=Al and Ga) were isolated. These 17 e^- complexes were synthesized by one-electron reduction of the corresponding Ni⁰ →M^III precursors, and were investigated by single-crystal X-ray diffraction, EPR spectroscopy, and quantum chemical calculations. Collectively, the experimental and computational data support: 1) the strengthening of the Ni-M bond upon one-electron reduction, and 2) the delocalization of the unpaired spin across the Ni and M atoms. An intriguing electronic configuration is revealed where three valence electrons occupy two σ-type bonding interactions: Ni(3dz2 )² →M and σ-(Ni-M)¹ . The latter is an unusual Ni-M σ-bonding molecular orbital that comprises primarily the Ni 4p_z and M np_z /ns atomic orbitals.

Pulse Radiolysis and Computational Studies on a Pyrrolidinium Dicyanamide Ionic Liquid: Detection of the Dimer Radical Anion

A pulse radiolysis study on pyrrolidinium cation based ionic liquids is presented herein. Time-resolved absorption spectra for 1-methyl-1-propylpyrrolidinium dicyanamide (DCA) at 500 ns after the electron pulse show broad absorption bands at wavelengths below 440 nm and at 640 nm. In pyrrolidinium bis(trifluoromethylsulfonyl)imide (NTf₂) and tris(perfluoroethyl)trifluorophosphate (FAP) ILs, the transient absorption below 440 nm is much weaker. The absorption at 500 ns, which increases with wavelength from 500 nm to beyond 800 nm, was assigned to the tail of the solvated electron NIR absorption spectrum, since it disappears in the presence of N₂O. In the DCA IL, the presence of a reducing species was confirmed by the formation of pyrene radical anion. The difference in the transient species in the case of the DCA IL compared to other two ILs should be due to the anion, with cations being similar. In pseudohalide ILs such as DCA, radicals are formed by direct hole trapping by the anion (X^- + h⁺ → X^•), followed by addition to the parent anion. Prediction of the UV/vis absorption spectra of the dimer radical anion by computational calculation supports the experimental results. The oxidizing efficiency of (DCA)₂^•- and its reduction potential ( E_{(DCA)2^•-/(2DCA^-)}) have been determined.

Spectroscopic observation of two-center three-electron bonded (hemi-bonded) structures of (H2S) n+ clusters in the gas phase

A two-center three-electron 2c-3e bond (hemi-bond) is a non-classical chemical bond, and its existence has been supposed in radical cation clusters with lone pairs. Though the nature of the hemi-bond and its role in the reactivity of radical cations have attracted great interest, spectroscopic observations of hemi-bonded structures have been very scarce. In the present study, the presence of a stable hemi-bonded core (H2S∴SH2)+ in (H2S) n+ (n = 3-6) in the gas phase is demonstrated by infrared spectroscopy combined with quantum chemical calculations. The spectral features of the free SH stretch of the ion core show that the hemi-bond motif of the ion core is maintained up to the completion of the first H-bonded solvation shell. All of the observed spectra are well reproduced by the minimum energy hemi-bonded isomers, and no sign of the proton-transferred ion core type H3S+-SH, which is estimated to have a much higher energy, is found. Spin density calculations show that the excess charge is almost equally delocalized over the two H2S molecules in the cluster for n = 3 to 6. This also indicates the hemi-bond nature of the (H2S∴SH2)+ ion core and the small impact of the formation of a solvation shell on the ion core.

Quantum molecular motion in the mixed ion-radical complex, [(H2O)(H2S)]. Phys Chem Chem Phys 2016;18:27450-27459. [PMID: 27711703 DOI: 10.1039/c6cp05299a]

The cation dimer of water and hydrogen sulfide, [(H₂O)(H₂S)]⁺, serves as a fundamental model for the oxidation chemistry of H₂S. The known oxidative metabolism of H₂S by biological species in sulfur-rich environments has motivated the study of the inherent properties of this benchmark complex, with possible mechanistic implications for modern water oxidation chemistry. The low-energy isomer of this open-shell ion is a proton-transferred (PT) structure, H₃O⁺SH˙. An alternative PT structure, H₃S⁺OH˙, and a hemibonded (HB) isomer, [H₂O·SH₂]⁺, are also stable isomers, placing this complex intermediate to known (H₂O)₂⁺ (PT) and (H₂S)₂⁺ (HB) limiting regimes. This intermediate character suggested the possibility of unique molecular motion, even in the vibrational ground state. Path integral molecular dynamics and anharmonic vibrational spectroscopy simulations have been performed in this study, in order to understand the inherent quantum molecular motion of this complex. The resulting structural distributions were found to deviate significantly from both classical and harmonic analyses, including the observation of large-amplitude anharmonic motion of the central proton and nearly free rotation of the terminal hydrogens. The predicted vibrational spectra are particularly unique and suggest characteristic signatures of the strong electronic interactions and anharmonic vibrational mode couplings in this radical cation.

Two-Center/Three-Electron Sigma Half-Bonds in Main Group and Transition Metal Chemistry

First proposed in a classic Linus Pauling paper, the two-center/three-electron (2c/3e) σ half-bond challenges the extremes of what may or may not be considered a chemical bond. Two electrons occupying a σ bonding orbital and one electron occupying the antibonding σ* orbital results in bond orders of ∼0.5 that are characteristic of metastable and exotic species, epitomized in the fleetingly stable He2(+) ion. In this Account, I describe the use of coordination chemistry to stabilize such fugacious three-electron bonded species at disparate ends of the periodic table. A recent emphasis in the chemistry of metal-metal bonds has been to prepare compounds with extremely short metal-metal distances and high metal-metal bond orders. But similar chemistry can be used to explore metal-metal bond orders less than one, including 2c/3e half-bonds. Bimetallic compounds in the Ni2(II,III) and Pd2(II,III) oxidation states were originally examined in the 1980s, but the evidence collected at that time suggested that they did not contain 2c/3e σ bonds. Both classes of compounds have been re-examined using EPR spectroscopy and modern computational methods that show the unpaired electron of each compound to occupy a M-M σ* orbital, consistent with 2c/3e Ni-Ni and Pd-Pd σ half-bonds. Elsewhere on the periodic table, a seemingly unrelated compound containing a trigonal bipyramidal Cu3S2 core caused a stir, leaving prominent theorists at odds with one another as to whether the compound contains a S-S bond. Due to my previous experience with 2c/3e metal-metal bonds, I suggested that the Cu3S2 compound could contain a 2c/3e S-S σ half-bond in the previously unknown oxidation state of S2(3-). By use of the Cambridge Database, a number of other known compounds were identified as potentially containing S2(3-) ligands, including a noteworthy set of cyclopentadienyl-supported compounds possessing diamond-shaped Ni2E2 units with E = S, Se, and Te. These compounds were subjected to extensive studies using X-ray absorption spectroscopy, X-ray photoelectron spectroscopy, density functional theory, and wave function-based computational methods, as well as chemical oxidation and reduction. The compounds contain E-E 2c/3e σ half-bonds and unprecedented E2(3-) "subchalcogenide" ligands, ushering in a new oxidation state paradigm for transition metal-chalcogen chemistry.

Structural and spectroscopic studies of iodine dimer radical anion hydrated clusters: an approach using a combination of stochastic and quantum chemical methods

Structures of I₂⁽⁻⁾(H₂O)₅ clusters after evaluation by simulated annealing and subsequent DFT calculation respectively.

Odd-electron-bonded sulfur radical cations: X-ray structural evidence of a sulfur-sulfur three-electron σ-bond

The one-electron oxidations of 1,8-chalcogen naphthalenes Nap(SPh)2 (1) and Nap(SPh)(SePh) (2) lead to the formation of persistent radical cations 1(•+) and 2(•+) in solution. EPR spectra, UV-vis absorptions, and DFT calculations show a three-electron σ-bond in both cations. The former cation remains stable in the solid state, while the latter dimerizes upon crystallization and returns to being radical cations upon dissolution. This work provides conclusive structural evidence of a sulfur-sulfur three-electron σ-bond (in 1(•+)) and a rare example of a persistent heteroatomic three-electron σ-bond (in 2(•+)).

Structural Investigation of Asymmetrical Dimer Radical Cation System (H2O−H2S)+: Proton-Transferred or Hemi-Bonded?

Ab initio molecular orbital and hybrid density functional methods have been employed to characterize the structure and bonding of (H2O-H2S)+, an asymmetrical dimer radical cation system. A comparison has been made between the two-center three-electron (2c-3e) hemi-bonded system and the proton-transferred hydrogen-bonded systems of (H2O-H2S)+. Geometry optimization of these systems was carried out using unrestricted Hartree Fock (HF), density functional theory with different functionals, and second-order Møller-Plesset perturbation (MP2) methods with 6-311++G(d,p) basis set. Hessian calculations have been done at the same level to check the nature of the equilibrium geometry. Energy data were further improved by calculating basis set superposition error for the structures optimized through MP2/6-311++G(d,p) calculations. The calculated results show that the dimer radical cation structure with H2O as proton acceptor is more stable than those structures in which H2O acts as a proton donor or the 2c-3e hemi-bonded (H2O thereforeSH2)+ system. This stability trend has been further confirmed by more accurate G3, G3B3, and CCSD(T) methods. On the basis of the present calculated results, the structure of H4OS+ can best be described as a hydrogen-bonded complex of H3O+ and SH with H2O as a proton acceptor. It is in contrast to the structure of neutral (H2O...H2S) dimer where H2O acts as a proton donor. The present work has been able to resolve the ambiguity in the nature of bonding between H2O and H2S in (H2O-H2S)+ asymmetrical dimer radical cation.

Structure, energy, and IR spectra of I2∙−.nH2O clusters (n=1–8): A theoretical study

The authors report theoretical results on structure, bonding, energy, and infrared spectra of iodine dimer radical anion hydrated clusters, I(2) (-).nH(2)O (n=1-8), based on a systematic study following density functional theory. Several initial guess structures are considered for each size cluster to locate minimum energy conformers with a Gaussian 6-311++G(d,p) split valence basis function (triple split valence 6-311 basis set is applied for iodine). It is observed that three different types of hydrogen bonded structures, namely, symmetrical double hydrogen bonding, single hydrogen bonding, and interwater hydrogen bonding structures, are possible in these hydrated clusters. But conformers having interwater hydrogen bonding arrangements are more stable compared to those of double or single hydrogen bonded structures. It is also noticed that up to four solvent H(2)O units can reside around the solute in interwater hydrogen bonding network. At the maximum six H(2)O units are independently linked to the dimer anion having four double hydrogen bonding and two single hydrogen bonding, suggesting the hydration number of I(2) (-) to be 6. However, conformers having H(2)O units independently linked to the iodine dimer anion are not the most stable structures. In all these hydrated clusters, the odd electron is found to be localized over two I atoms and the two atoms are bound by a three-electron hemi bond. The solvation, interaction, and vertical detachment energies are calculated for all I(2) (-).nH(2)O clusters. Energy of interaction and vertical detachment energy profiles show stepwise saturation, indicating geometrical shell closing in the hydrated clusters, but solvation energy profile fails to show such behavior. A linear correlation is observed between the calculated energy of interaction and vertical detachment energy. It is observed that formation of I(2) (-)-water cluster induces significant shifts from the normal O-H stretching modes of isolated H(2)O. However, bending mode of H(2)O remains insensitive to the successive addition of solvent H(2)O units. Weighted average energy profiles and IR spectra are reported for all the hydrated clusters based on the statistical population of individual conformers at room temperature.

Microhydration shell structure in Cl2∙−∙nH2O clusters: A theoretical study

We present the results of a detailed study on structure and electronic properties of hydrated cluster Cl2*-.nH2O (n = 1-7) based on a nonlocal density functional, namely, Becke's [J. Chem. Phys. 98, 1372 (1993)] half and half hybrid exchange-correlation functional with a split valence 6-311++G(d,p) basis function. Geometry optimizations for all the clusters are carried out with various possible initial guess structures without any symmetry restriction. Several minimum energy structures (conformers) are predicted with a small difference in total energy. There is a competition between the binding of solvent H2O units with Cl2*- dimer radical anion directly through ion-molecule interaction and forming interwater hydrogen-bonding network in Cl2*-.nH2O (n > or = 2) hydrated cluster. Structure having interwater H-bonded network is more stable over the structure where H2O units are connected to the solute dimer radical anion Cl2*- rather independently either by single or double H bonding in a particular size (n) of hydrated cluster Cl2*-.nH2O. At the maximum four solvent H2O units reside in interwater H-bonding network present in these hydrated clusters. It is observed that up to six H2O units are independently linked to the anion having four double H bondings and two single H bondings suggesting the primary hydration number of Cl2*- to be 6. In all these clusters, the odd electron is found to be mostly localized over the two Cl atoms and these two atoms are bound by a three-electron hemibond. Calculated interaction (between solute and different water clusters) and vertical detachment energy profiles show saturation at n = 6 in the hydrated cluster Cl2*-.nH2O (n = 1-7). However, calculated solvation energy increases with the increase in number of solvent H2O molecules in the cluster. Interaction energy varies linearly with vertical detachment energy for the hydrated clusters Cl2*-.nH2O (n < or = 6). Calculation of the vibration frequencies show that the formation of Cl2*(-)-water clusters induces significant shifts from the normal stretching modes of isolated water. A clear difference in the pattern of IR spectra is observed in the O-H stretching region of water from hexa- to heptahydrated cluster.

A comparative ab initio study of Br2•− and Br2 water clusters

The work presents ab initio results on structure and electronic properties of Br2*-.nH2O(n=1-10) and Br2.nH2O(n=1-8) hydrated clusters to study the effects of an excess electron on the microhydration of the halide dimer. A nonlocal density functional, namely, Becke's half-and-half hybrid exchange-correlation functional is found to perform well on the present systems with a split valence 6-31++G(d,p) basis function. Geometry optimizations for all the clusters are carried out with several initial guess structures and without imposing any symmetry restriction. Br2*-.nH2O clusters prefer to have symmetrical double hydrogen-bonding structures. Results on Br2.nH2O(n>or=2) cluster show that the O atom of one H2O is oriented towards one Br atom and the H atom of another H2O is directed to other Br atom making Br2 to exist as Br+-Br- entity in the cluster. The binding and solvation energies are calculated for the Br2*-.nH2O and Br2.nH2O clusters. Calculations of the vibrational frequencies show that the formation of Br2*- and Br2 water clusters induces significant shifts from the normal modes of isolated water. Excited-state calculations are carried out on Br2*-.nH2O clusters following configuration interaction with single electron excitation procedure and UV-VIS absorption profiles are simulated. There is an excellent agreement between the present theoretical UV-VIS spectra of Br2*-.10H2O cluster and the reported transient optical spectra for Br2*- in aqueous solution.

Structure, bonding, and spectra of cyclic dithia radical cations: a theoretical study

Ab initio molecular orbital and hybrid density functional theory methods are employed to characterize the structure, bonding and properties of several cyclic dithia radical cation systems, particularly in the context of intra molecular two-center three-electron (2c-3e) bonding between two sulfur atoms. The calculated results are able to interpret the time-resolved transient optical spectra obtained from pulse radiolysis technique for these positively charged dithia systems in aqueous solution. Visualization of the appropriate molecular orbital (MO) in the systems is able to depict the presence of a 2c-3e bond between two sulfur atoms and its sigma character. Geometry optimizations of these doublet systems are carried out at restricted open shell Becke's half-and-half (BHH) nonlocal exchange and Lee-Yang-Parr (LYP) nonlocal correlation functionals (BHHLYP) with 6-311+G(d,p) basis set including solvent effects adopting Onsager's reaction field model. Hessian calculations are done at the same level to check the nature of the equilibrium geometry. Energy data are further improved by performing MP2/6-311+G(d,p) calculations on these radical cation systems. Excited-state calculations are done following configuration interaction with single-electron excitation (CIS) method and the optical transition wavelength from the highest doubly occupied molecular orbital (HDOMO) to the lowest singly occupied molecular orbital (LSOMO) is seen to correspond and match to the position of the absorption maxima (lambda(max)) obtained from the experimental spectra for all these radical cation systems in aqueous solution. These calculations are able to resolve a long-standing ambiguity in the assignment of intra molecular 2c-3e bonding in the case of the 3-methyl-2,4-dithiapentane radical cation system and to provide new insights into bonding features of this odd electron system as well as of other cyclic dithia systems studied.