Σ-electron System Research Articles

Hydrogen bond types which do not fit accepted definitions.

There are various interactions that either partially fit or do not fit the currently accepted definitions of the hydrogen bond. However, they possess characteristics of this interaction. It seems that it is partly connected to the fact that these definitions are not precise. The typical 3c-4e (three centres - four electrons) A-H⋯B hydrogen bond is characterized by the single-atom A and B centres that are highly electronegative. On the other hand, non-typical interactions that do not fit the hydrogen bond definitions well are characterised by uncommon proton donors and/or proton acceptors. The cases of multi-centre proton acceptors, π-electron or σ-electron systems are well known - such interactions are designated as A-H⋯π and A-H⋯σ hydrogen bonds, respectively. However, the cases of interactions with the multi-centre proton donors and proton acceptors do not fit the majority of definitions of hydrogen bond. The π⋯H+⋯π system in the proton-bound homodimer of acetylene is an example. This system can be classified as a hydrogen bond according to the two-sites hydrogen bond, 2sHB, definition. There are various types of interactions discussed in this review; among them, those that are undoubtedly unclassified as hydrogen bonds, i.e., hydride bonds, and charge inverted hydrogen bonds, CIHBs. Special emphasis is also put here on the proton sponges and other systems such as the [FHF]- anion or [NgHNg]+ cation (Ng is the noble gas centre).

Substituent Effect in the Cation Radicals of Monosubstituted Benzenes.

In 30 monosubstituted benzene cation radicals, studied at the ωB97XD/aug-cc-pVTZ level, the phenyl rings usually adopt a compressed form, but a differently compressed form—equivalent to an elongated one—may coexist. The computational and literature ionization potentials are well correlated. The geometrical and magnetic aromaticity, estimated using HOMA and NICS indices, show the systems to be structurally aromatic but magnetically antiaromatic or only weakly aromatic. The partial charge is split between the substituent and ring and varies the most at C(ipso). In the ring, the spin is 70%, concentrated equally at the C(ipso) and C(p) atoms. The sEDA(D) and pEDA(D) descriptors of the substituent effect in cation radicals, respectively, were determined. In cation radicals, the substituent effect on the σ-electron system is like that in the ground state. The effect on the π-electron systems is long-range, and its propagation in the radical quinone-like ring is unlike that in the neutral molecules. The pEDA(D) descriptor correlates well with the partial spin at C(ipso) and C(p) and weakly with the HOMA(D) index. The correlation of the spin at the ring π-electron system and the pEDA(D) descriptor shows that the electron charge supplied to the ring π-electron system and the spin flow oppositely.

On the nonadditivity of the substituent effect in homo-disubstituted pyridines

The substituent effect in mono- and disubstituted pyridines was studied by means of the sEDA and pEDA substituent effect descriptors expressing the substituent effect on the σ- and π-electron systems of the ring, respectively. The sEDA descriptors calculated for mono- or disubstituted pyridines can be presented as perfectly linear functions of either benzene or monosubstituted pyridine sEDA descriptors, respectively. For the pEDA descriptors, there are substantial deviations from linearity observed for both mono- and disubstituted systems. For the disubstituted systems, the nonadditivity of the pEDA descriptors is strongly pronounced for the substituents in the ortho- and para-positions to each other while it is only weak for the meta-located groups. For both mono- and disubstituted systems, there are correlations between charge at the nitrogen lone electron pair and the σ- and π-electron withdrawing and donating properties of the substituent. In general, the electron charge increases with the increase of the σ-electron donating ability but decreases with the increase of π-electron donating ability of substituents. Again, the effects are more significant for substituents in the ortho- and para-positions than in the meta-position. The influence of the π-electron properties of the substituent on the lone pair, belonging to σ-electron system of pyridines, shows the presence of hyperconjugation effects in the substituted pyridines. The hyperconjugation can be also clearly observed in cross-dependencies of the sEDA and pEDA descriptors.

The Role of Aromaticity, Hybridization, Electrostatics, and Covalency in Resonance-Assisted Hydrogen Bonds of Adenine-Thymine (AT) Base Pairs and Their Mimics.

Hydrogen bonds play a crucial role in many biochemical processes and in supramolecular chemistry. In this study, we show quantum chemically that neither aromaticity nor other forms of π assistance are responsible for the enhanced stability of the hydrogen bonds in adenine–thymine (AT) DNA base pairs. This follows from extensive bonding analyses of AT and smaller analogs thereof, based on dispersion-corrected density functional theory (DFT). Removing the aromatic rings of either A or T has no effect on the Watson–Crick bond strength. Only when the smaller mimics become saturated, that is, when the hydrogen-bond acceptor and donor groups go from sp2 to sp3, does the stability of the resulting model complexes suddenly drop. Bonding analyses based on quantitative Kohn–Sham molecular orbital theory and corresponding energy decomposition analyses (EDA) show that the stronger hydrogen bonds in the unsaturated model complexes and in AT stem from stronger electrostatic interactions as well as enhanced donor–acceptor interactions in the σ-electron system, with the covalency being responsible for shortening the hydrogen bonds in these dimers.

DFT investigation on hydrogen bonding in cyclohexane-1,2,3,4,5-pentol crystal structure

The cyclohexane-1,2,3,4,5-pentol,C6H12O5 is a natural product extracted from Adiscanthus fusciflorus (Rutaceae). It crystallizes in the non-centrosymmetric space group P21 with one molecule in the asymmetric unit and it has been postulated to have at least ten strong O-H…O intermolecular interactions, two per each OH group of one molecule, producing a three-dimensional network. The crystal packing is defined by O-H…O hydrogen bonds. Due to the crucial role of the hydrogen bonds in defining the crystal structure, theoretical investigations in the gas phase have been carried out in order to explore the hydrogenbonding mechanism through a quantitative Kohn-Sham molecular orbital and corresponding energy decomposition analyses. The existence of a covalent component in hydrogen bonds has been proved which originates from donor-acceptor orbital interactions in the σ-electron system. Our analyses show that the stability of the crystal structure is enhanced by the formation of two hydrogen bonds with two vicinal molecules for each OH group in C6H12O5 molecule with respect to the formation of one or two hydrogen bonds with only one vicinal molecule, thus confirming the proposed existence of ten strong O-H…O intermolecular interactions for each molecule in the asymmetric unit. The presence of a cooperativity effect is observed which originates from a charge separation induced by the two vicinal molecules hydrogenbonded to an OH group in C6H12O5 molecule.

Photoinduced charge transport over branched conjugation pathways: donor–acceptor substituted 1,1-diphenylethene and 2,3-diphenylbutadiene

Photoinduced charge transport in 1,1-diphenylethene and 2,3-diphenylbutadiene functionalized with an electron donating dimethylamino group and an electron accepting cyano group is reported. UV-spectroscopy reveals that in these compounds, which incorporate a cross-conjugated spacer, a direct charge transfer transition is possible. It is shown by application of the generalized Mulliken-Hush approach that introduction of an additional branching point in the π-electron spacer (i.e., when going from the 1,1-diphenylethene to the 2,3-diphenylbutadiene) leads to only a moderate reduction (68-92%) of the electronic coupling between the ground and the charge separated state. The σ-electron system is however likely to be dominant in the photoinduced charge separation process.

Telomere Structure and Stability: Covalency in Hydrogen Bonds, Not Resonance Assistance, Causes Cooperativity in Guanine Quartets

We show that the cooperative reinforcement between hydrogen bonds in guanine quartets is not caused by resonance-assisted hydrogen bonding (RAHB). This follows from extensive computational analyses of guanine quartets (G(4)) and xanthine quartets (X(4)) based on dispersion-corrected density functional theory (DFT-D). Our investigations cover the situation of quartets in the gas phase, in aqueous solution as well as in telomere-like stacks. A new mechanism for cooperativity between hydrogen bonds in guanine quartets emerges from our quantitative Kohn-Sham molecular orbital (MO) and corresponding energy decomposition analyses (EDA). Our analyses reveal that the intriguing cooperativity originates from the charge separation that goes with donor-acceptor orbital interactions in the σ-electron system, and not from the strengthening caused by resonance in the π-electron system. The cooperativity mechanism proposed here is argued to apply, beyond the present model systems, also to other hydrogen bonds that show cooperativity effects.

The application of the density matrix method for the investigation of thetrans-effect of heteroatom in ?-electron systems

The dependence of the intramolecular charge transfer through the σ-electron systems of substituted hydrocarbons on the spatial arrangement of the X(SINGLE BOND)Cα and Cβ(SINGLE BOND)Cγ bonds has been studied using the perturbation theory for the one-electron density matrix (DM). Analytical expressions for the populations of the orbitals pertinent to the cis- and trans-bonds with respect to the X(SINGLE BOND)Cα bond have been obtained and analyzed. The Hamiltonian matrix elements determining the predominant direction of the above-defined charge transfer (cis or trans) have been revealed. The electron-accepting and electron-donating substituents (X) have been considered separately and the dependence of the resulting charge-transfer direction on the properties of substituent has been established. © 1996 John Wiley & Sons, Inc.

Electronic and geometric structures of oligothiophenes

The semi-empirical MNDO (modified neglect of diatomic overlap) method was applied to investigate ultraviolet photoelectron spectra (UPS) and molecular geometries of some oligothiophenes: α 7, which is an α-linked septithiophene, α 3βα 3, in which the middle thiophene ring of septithiophene has β-linkages, and α 3Vα 3, in which the fourth thiophene ring of α 7 is replaced by a vinyl group. The reliability of the MNDO calculation was carefully investigated by a comparison with the observed molecular geometries and the observed UPS spectra of thiophene and 2,2′-bithiophene. The results of the MNDO calculations were also compared with those of the ab initio HF/STO-3G calculations. The observed UPS spectra of oligothiophenes were well reproduced by using Koopmans' theorem ionization energies with a Gaussian function of width of δ=0.6 eV. The β-linkage and the vinyl group act as an impurity in the polythiophene system. In the molecular geometry of α 3βα 3 optimized by MNDO, where a β-linked ring is perpendicular to the plane of normal α-linked parts (α 3), the π-band spectrum of α 3βα 3 could be reproduced by the superposition of the spectra of two α 3s and thiophene. Therefore, it is confirmed that the β-linkage prohibits the delocalization of π-electrons and divides the polymer chain into short π-segments. In the case of α 3Vα 3, in which two α 3s are connected by a vinyl having a trans double bond conformation, the molecular geometry according to the MNDO calculation was almost planar and the UPS spectrum was almost the same as that of normal α 7. The mixing of the vinyl group into the polythiophene system does not cause any drastic change in the π-electron system but changes its σ-electron system. Simulated UPS spectra accurately reproduced the difference between α 3Vα 3 and α 7. Since these molecules are good models for polythiophene (α n), the features of the UPS spectra and the molecular geometry proposed by the theoretical calculation can explain several experimental observations on polythiophene. Further, it is suggested that the method of polymerization strongly affects the electronic and electric properties of polythiophene, and the control of the polymerization process is very important for achieving good conductivity.

Photoelectron and Penning ionization electron spectroscopic investigation of some silazanes

Penning ionization electron spectroscopy and CNDO/S calculations have been successfully applied to the analyses of the UV photoelectron spectra of some silazanes. The relative intensities of the lone pair bands are enhanced in the Penning spectra compared with those in the UV photoelectron spectra. The intensity differences between the two spectra give useful informations for the investigation of the σ-electron systems.

Molecular model potentials: Combination of atomic boxes

A new Combination of Atomic Boxes (CAB) molecular orbital model is introduced, having the following characteristics: The model is tested on a large variety of π-electron systems containing atoms of four rows of the periodic system. Branched and cyclic molecules are also treated. The comparison of the calculated first and higher ionization and first excitation energies with the observed data gives the mean deviations 0.540 eV and 0.388 eV resp. The common physical basis of the CAB and the model-pseudopotential methods is discussed. The constant potential within the box is a consequence of the partial cancellation of the electrostatic potential by a repulsive term representing the Pauli principle. It is shown that CAB is not restricted to π-electrons but can be extended to σ-electron systems as well.

Radiation damage to proteins--an e.s.r. study of a single crystal of glycyl-glycine at low temperatures.

SummaryThe electron paramagnetic spectra from a single crystal of glycyl-glycine have been analysed in the temperature range between 77 and 300 k, after the crystal had been irradiated at 77 k and then gradually heated. At 77 k a decarboxylation product remains stabilized within the crystal lattice, as well as, most probably, the product of a deamination process. At about 140 k, the finally stable radical appears, although the decarboxylation product dissappears, simultaneously. The finally stable radical is due to a hydrogen abstraction at the carbon-6 position. Two other radical species also arise, one of which is reported to originate from a hydrogen abstraction from the carbon-1 position, whereas the other is thought to stem from a fragmentation process at the peptide nitrogen. Both these radicals convert, upon further heating, into the finally stable radical. The entire spectrum also contains some other resonances, which are interpreted to originate from odd σ-electron systems.

Chromium and manganese carbonyl π-complexes of 2-benzylpyrrole and 2-phenylpyrrole. Spectra and electronic effects

Cr(CO) 3 and Mn(CO) 3 complexes of 2-benzylpyrrole and 2-phenylpyrrole and the complexes in which both a Cr(CO) 3 and an Mn(CO) 3 group are attached to complex of 2-phenylpyrrole, have been isolated. In each case the Cr(CO) 3 group is π-bonded to the phenyl ring and the Mn(CO) 3 group to the pyrrolyl ring. The NMR spectra can be interpreted in terms of electronic effects transmitted through the σ-electron system and in ring current effects. The IR carbonyl stretching frequencies show little effect of one M(CO) 3 group on the other.

Applications of the group function method

By application of the formulae derived in I, a general formula for proton-proton coupling constants is derived which is independent of the function used for the separated π and σ-electron systems. ...

Conformational dependence of the proton contact shifts for σ-electron systems: a 220 MHz nuclear magnetic resonance study

The conformation dependence of the contact shifts for various protons in piperdine derivatives has been determined by 220 MHz n.m.r., and is discussed in relation to the modes of electron spin distribution through the σ-skeleton.

Semiempirical quantum-chemical methods for examining ?-electron systems and calculation of ?-electron radicals

The field of semiempirical quantum-chemical calculations of σ-electron systems has undergone vigorous development in the investigations of the last ten years. One of the first formulated was the EHT method in which overlap was taken into account in explicit form. This was no accident since for a long time the opinion prevailed that disregarding overlap in calculations of σ-electron systems is an unjustifiably daring approximation. However, the general opinion with respect to this problem began to change after practical successes of a number of semiempirical computational schemes which disregard overlap. The results of such calculations with appropriate selection of parameters agree with experiment at least not worse than the results of calculations in which overlap is taken into account in explicit form. In the second section of this review, this was illustrated in the case of the HFI constants in σ-electron radicals. This is also valid with respect to many other molecular properties: energies, dipole moments, ionization potentials, etc. In our opinion, one of the reasons for the success of the methods which “disregard” overlap consists in the fact that overlap is partially taken into account by the effective selection of parameters (see the discussion of the hybrid-basis method). In this connection, the path for constructing huge computational schemes which explicitly take overlap into account is less valid. It should also be emphasized that familiarization with rather complex and laborious methods is not necessary in semiempirical calculations which disregard overlap since simpler and more obvious schemes often turn out to be just as effective and lead to results which are no worse, and sometimes better, than the results of more complex methods.

Studies on the paramagnetic shifts for σ-electron systems. Conformational dependency of13C contact shifts

13 C Contact shifts for piperidine derivatives and quinuclidine induced by complexation with nickel acetylacetonate observed using the proton-decoupled 13C n.m.r. technique are discussed in terms of their conformational dependency and the delocalized nature of the lone-pair electrons.

The Calculation of directly bonded 13C-H and 13C-13C coupling constants using delocalized molecular orbital theory

The Pople-Santry theory of coupling in σ-electron systems lias been applied to directly bonded CH and CC coupling constants. Calculations on normal hydrocarbons, e.g. CH4, C2H6, C2H4, C2H2, show that the theory can give a satisfactory explanation of such coupling constants, although the values are sensitive to the parameters used in the calculation. The theory has been applied with varying success to the larger hydrocarbons methylacetylene, butadiene and benzene, and to the strained molecules cyclopropane and ferrocene. No difficulty arises in applying the theory to hetero-atomic systems (pyridine and pyrimidine) and the results are quite satisfactory.

Electronic Structures and Spectra of Some Nitrogen-Oxygen Compounds

The electronic structures and spectra of nitrite ion, nitrosomethane, nitrosamine, and nitrate ion have been calculated by a semiempirical method, which includes both the π-electron system and, in a more limited manner, the σ-electron system. The calculated transition energies and intensities for the first three compounds above agree fairly satisfactorily with experiment. For nitrate ion, however, it seems possible that the lowest observed transition may be a very low energy n→σ* transition, σ* being an antibonding σ orbital, rather than one of the n→π* transitions considered in the present work.

Electronic Structures and Spectra of Nitromethane and Nitrogen Dioxide

The electronic structures and spectra of nitromethane and nitrogen dioxide have been calculated by a semiempirical method. The self-consistent molecular orbitals and energies of the π-electron system have been calculated; however, for the nonbonding σ-electron system Hückel-type molecular orbitals are used. The nonbonding 2p oxygen orbitals of nitromethane are very slightly modified by mixing with the σ-electron system; in nitrogen dioxide, on the other hand, the totally symmetric combination of 2p oxygen orbitals and the sp2 nonbonding nitrogen orbital mix strongly to form slightly bonding and slightly antibonding molecular orbitals. The calculated transition energies of nitromethane are in reasonable agreement with experiment. For nitrogen dioxide a series of transition energies are obtained which may illuminate experimental results; the complexity of the empirical data, however, and the multitude of calculated low-energy excited states, preclude definite assignment of the observed band systems at this stage.