Trans-hydrogen-bond (h2)J(NN) and (h1)J(NH) couplings in the DNA A-T base pair: natural bond orbital analysis

Natural bond orbital (NBO) analysis described here demonstrates that trans-hydrogen-bond (trans-H-bond) NMR J couplings in the DNA A-T base pair, h2JNN and h1JNH, are determined largely by three terms: two Lewis-type contributions (the single-orbital contribution from the adenine lone pair and the contribution from the sigmaN3H3 natural bond orbital of the thymine ring) and one contribution from pairwise delocalization of spin density (between the lone pair in adenine and the sigma* antibonding orbital linking N3 and H3 of thymine). For h2JNN coupling, all three contributions are positive, whereas for h1JNH coupling, the delocalization term is negative, and the other two terms are positive, resulting in a small net positive coupling constant. This result rationalizes the experimental findings that the two-bond coupling (h2JNN approximately 9 Hz) is larger than the one-bond coupling (h1JNH approximately 3 Hz) and demonstrates that the same hyperconjugative and steric mechanisms that stabilize the H-bond are involved in the transmission of J coupling information. The N1...H3-N3 H-bond of the DNA A-T base pair is found to exhibit significant covalent character, but steric effects contribute almost equally to the trans-H-bond coupling.     

Decomposition of nuclear magnetic resonance spin-spin coupling constants into active and passive orbital contributions

The theory of the J-OC-PSP (decomposition of J into orbital contributions using orbital currents and partial spin polarization) method is derived to distinguish between the role of active, passive, and frozen orbitals on the nuclear magnetic resonance (NMR) spin-spin coupling mechanism. Application of J-OC-PSP to the NMR spin-spin coupling constants of ethylene, which are calculated using coupled perturbed density functional theory in connection with the B3LYP hybrid functional and a [7s,6p,2d/4s,2p] basis set, reveal that the well-known pi mechanism for Fermi contact (FC) spin coupling is based on passive pi orbital contributions. The pi orbitals contribute to the spin polarization of the sigma orbitals at the coupling nuclei by mediating spin information between sigma orbitals (spin-transport mechanism) or by increasing the spin information of a sigma orbital by an echo effect. The calculated FC(pi) value of the SSCC (1)J(CC) of ethylene is 4.5 Hz and by this clearly smaller than previously assumed.     

Lone-pair orbital interactions in polythiaadamantanes

The electronic structures of a series of polythiaadamantanes from thiaadamantane through 2,4,6,8,9,10-hexathiaadamantane (HTA) have been analyzed using density functional theory calculations in conjunction with Hückel and natural bond orbital analysis. The effects of multiple sulfur p-type lone-pair orbital interactions on ionization potentials, hole mobilities, and electronic coupling have been determined. An overall increase in the average energy of the lone-pair orbitals as the number of sulfur atoms increases is predicted, with the exact positioning of the HOMO depending on specific lone-pair interactions. Separation of through-bond (TB) and through-space (TS) interactions between intramolecular sulfur atoms has been performed using localized molecular orbitals and model systems based on interacting hydrogen sulfide molecules. TB interations were found to reduce orbital splitting, while TS interactions were found to increase orbital splitting. TS interactions were more or less constant from one polythiaadamantane to the next, and the contributions of TB effects to individual orbital energies vary depending on the relative orientation of sulfur atoms as determined by the sigma molecular framework. Electronic coupling between intermolecular sulfur lone-pair orbitals was determined by investigating unique dimer pairs observed in the crystal structure of HTA. Electronic coupling is not as strong as expected given the short intermolecular S-S distances observed in the crystal structure. In general, B3LYP/6-31G(d) and B3LYP/6-311+G(d,p) give very similar orbital energies and splittings.     

One-electron versus electron-electron interaction contributions to the spin-spin coupling mechanism in nuclear magnetic resonance spectroscopy: analysis of basic electronic effects

For the first time, the nuclear magnetic resonance (NMR) spin-spin coupling mechanism is decomposed into one-electron and electron-electron interaction contributions to demonstrate that spin-information transport between different orbitals is not exclusively an electron-exchange phenomenon. This is done using coupled perturbed density-functional theory in conjunction with the recently developed J-OC-PSP [=J-OC-OC-PSP: Decomposition of J into orbital contributions using orbital currents and partial spin polarization)] method. One-orbital contributions comprise Ramsey response and self-exchange effects and the two-orbital contributions describe first-order delocalization and steric exchange. The two-orbital effects can be characterized as external orbital, echo, and spin transport contributions. A relationship of these electronic effects to zeroth-order orbital theory is demonstrated and their sign and magnitude predicted using simple models and graphical representations of first order orbitals. In the case of methane the two NMR spin-spin coupling constants result from totally different Fermi contact coupling mechanisms. (1)J(C,H) is the result of the Ramsey response and the self-exchange of the bond orbital diminished by external first-order delocalization external one-orbital effects whereas (2)J(H,H) spin-spin coupling is almost exclusively mitigated by a two-orbital steric exchange effect. From this analysis, a series of prediction can be made how geometrical deformations, electron lone pairs, and substituent effects lead to a change in the values of (1)J(C,H) and (2)J(H,H), respectively, for hydrocarbons.     

The effect of carbonyl group in the asymmetry of 3,4JCH coupling constants in norbornanones

A rationalization of the known difference between the 3,4JC4H1 and 3,4JC1H4 couplings transmitted mainly through the 7-bridge in norbornanone is presented in terms of the effects of hyperconjugative interactions involving the carbonyl group. Theoretical and experimental studies of 3,4JCH couplings were carried out in 3-endo- and 3-exo-X-2-norbornanone derivatives (X = Cl, Br) and in exo- and endo-2-noborneol compounds. Hyperconjugative interactions were studied with the natural bond orbital (NBO) method. Hyperconjugative interactions involving the carbonyl pi*(C2=O) and sigma*(C2=O) antibonding orbitals produce a decrease of three-bond contribution to both 3,4JC4H1 and 3,4JC1H4 couplings. However, the latter antibonding orbital also undergoes a strong sigmaC3--C4 --> sigma*(C2=O) interaction, which defines an additional coupling pathway for 3,4JC4H1 but not for 3,4JC1H4. This pathway is similar to that known for homoallylic couplings, the only difference being the nature of the intermediate antibonding orbital; i.e. for 3,4JC4H1 it is of sigma*-type, while in homoallylic couplings it is of pi*-type.     

Analyzing molecular properties calculated with two-component relativistic methods using spin-free natural bond orbitals: NMR spin-spin coupling constants

An analysis method for static linear response properties employing two-component (spin-orbit) relativistic density functional theory along with scalar relativistic "natural localized molecular orbitals" (NLMOs) and "natural bond orbitals" (NBOs) has been developed. The spin-orbit NLMO/NBO analysis has been applied to study the indirect spin-spin coupling (J-coupling) constants in Tl-I, PbH(4), and a dinuclear Pt-Tl bonded complex with a very large Pt-Tl coupling constant (expt.: 146.8 kHz). For Tl-I it is shown that the analysis scheme based on scalar relativistic NLMOs is applicable even if spin-orbit coupling is responsible for most of the coupling's magnitude. For PbH(4) it is shown that electron delocalization plays a much larger role for the Pb-H coupling than it is the case for the C-H coupling in methane. For the Pt-Tl complex the analysis clearly demonstrates the strong influence of the ligands on the Pt-Tl coupling constant and quantifies the effect of the delocalization of the Pt-Tl bond on the Pt-Tl coupling constant.     

Analysis of electron correlation effects and contributions of NMR J-couplings from occupied localized molecular orbitals

NMR J-coupling calculations at the second-order of polarization propagator approach, SOPPA, are among the most reliable. They include a high percentage of the total electron correlation effects in saturated and unsaturated molecular systems. Furthermore, J-couplings are quite sensitive to the whole electronic molecular framework. We present in this article the first study of all three response mechanisms, Fermi contact, FC, spin-dipolar, SD and paramagnetic spin-orbital, PSO, for J-couplings with occupied localized molecular orbitals at the SOPPA level of approach. Even though SOPPA results are not invariant under unitary transformations, the difference between results obtained with canonical and localized molecular orbitals, LMOs, are small enough to permit its application with confidence. The following small-size saturated and unsaturated compounds were analyzed: CH(4), CH(3)F, C(2)H(6), NH(3), C(2)H(4), CH(2)NH, H(2)C═CHF, and FHC═CHF. The local character of the FC mechanism that appears in J-couplings of these molecular models is shown through the analysis of contributions from LMOs. The importance of including the electron correlation on the engaged bonding orbitals for one-bond couplings is emphasized. Almost all electron correlation effects are included in such orbitals. Interesting findings were the large contributions by s-type LMOs to the C-H and C-C J-couplings; they are responsible for the variation of (1)J(C-C) when going from ethane to ethene and to 1,2-difluoroethene. The previously proposed hyperconjugative transfer mechanism has been tested. Among other tests we found the difference anti-syn of one-bond (1)J(C-H) in imine as due to both the corresponding σ(C-H) and the lone-pair, LP, contribution. Geminal and vicinal J-couplings were also analyzed. Our findings are in accord with a previous work by Pople and Bothner-by, who considered results taken from calculations or empirical data. For all geminal couplings the pattern of J-couplings, like the change of sign, is originated in the main bondings that participate in the coupling pathways. The finding of asymmetric contributions of LP to vicinal H-H couplings in imine is highlighted. The analysis of J-couplings by contributions from LMOs to the noncontact mechanisms, SD and PSO, show that the π electronic framework makes both terms grow in the specific case of the model compounds studied here. The PSO mechanism is more efficient when a σ bond is vicinal to a π bond. We found in this way an efficient and powerful scheme to get a deeper insight on the electronic molecular framework on which J-couplings are transmitted.     

Evidence for d orbital aromaticity in square planar coinage metal clusters

Quantitative evidence for the existence of aromaticity involving the d orbitals of transition metals is provided for the first time. The doubly bridged square planar (D(4)(h)()) coinage metal clusters (M(4)Li(2), M = Cu (1), Ag (2), and Au (3)) are characterized as aromatic by their substantial nucleus independent chemical shifts (NICS) values in the centers (-14.5, -14.1, and -18.6, respectively). Nevertheless, the participation of p orbitals in the bonding (and cyclic electron delocalization) of 1-3 is negligible. Instead, these clusters benefit strongly from the delocalization of d and to some extent s orbitals. The same conclusion applies to Tsipis and Tsipis' H-bridged D(4)(h)() Cu(4)H(4) ring (4). Canonical MO-NICS analysis of structures 1-3 shows the total diatropic d orbital contributions to the total NICS to be substantial, although the individual contributions of the five sets of filled d orbitals vary. The d orbital aromaticity of Cu(4)Li(2) also is indicated by its atomization energy, 243.2 kcal/mol, which is larger than Boldyrev's doubly (sigma and pi) aromatic Al(4)Li(2) (215.9 kcal/mol).     

Effect of Coulomb interactions on the vibronic couplings in C60(-)

Vibronic couplings in C(60)(-) anion are discussed on the basis of the concept of the vibronic coupling density (VCD) [T. Sato, K. Tokunaga, and K. Tanaka, J. Chem. Phys. 124, 024314 (2006); K. Tokunaga, T. Sato, and K. Tanaka, J. Chem. Phys. 124, 154303 (2006); and T. Sato, K. Tokunaga, and K. Tanaka, J. Phys. Chem. A 112, 758 (2008)]. The VCD analysis clearly reveals that the coupling to the bending h(g)(2) mode is weaker than the coupling to the stretching h(g)(7) and h(g)(8) modes. For the vibronic couplings with the stretching modes, polarizations of the electron density difference on the bonds play a crucial role in the vibronic couplings. Such a polarized electron density difference appears as a result of the Coulomb interactions between the electrons in the lowest unoccupied molecular orbital and relevant doubly-occupied orbitals.     

Pathway analysis of super-exchange electronic couplings in electron transfer reactions using a multi-configuration self-consistent field method

We present a novel pathway analysis of super-exchange electronic couplings in electron transfer reactions using localized molecular orbitals from multi-configuration self-consistent field (MCSCF) calculations. In our analysis, the electronic coupling and the tunneling pathways can be calculated in terms of the configuration interaction (CI) Hamiltonian matrix obtained from the localized MCSCF wave function. Making use of the occupation restricted multiple active spaces (ORMAS) method can effectively produce the donor, acceptor, and intermediate configuration state functions (CSFs) and CIs among these CSFs. In order to express the electronic coupling as a sum of individual tunneling pathways contributions, we employed two perturbative methods: L?wdin projection-iteration method and higher-order super-exchange method. We applied them to anion couplings of butane-1,4-diyl and pentane-1,5-diyl. The results were (1) the electronic couplings calculated from the two perturbative methods were in reasonable agreement with those from a non-perturbative method (one-half value of the energy difference between the ground and first excited states), (2) the main tunneling pathways consisted of a small number of lower-order super-exchange pathways where bonding, anti-bonding, or extra-valence-shell orbitals were used once or twice, and (3) the interference among a huge number of higher-order super-exchange pathways significantly contributed to the overall electronic coupling, whereas each of them contributed only fractionally. Our method can adequately take into account both effects of non-dynamical electron correlation and orbital relaxation. Comparing with the analyses based on the Koopmans' theorem (ignoring both effects) and the ORMAS-CIs from frozen localized reference orbitals (ignoring the effect of orbital relaxation), we discuss these effects.     

Bond orbital approach for optical rotatory strength calculations

Directly determined localized approximate molecular Orbitals are used in excitation energy and optical rotatory strength calculations within the CNDO/2 scheme. Using strictly localized bond orbitals one obtains qualitatively good excitation energies, but quantitative agreement can be found only by considering delocalization effects, which have been proved to be crucial in determining the optical rotatory strength. The delocalization interactions are classified as through space and through bond ones and even the latter is found to have significant contributions. The chiroptical properties of the lowest lying transitions in the twisted glyoxal molecule are analysed in terms of localized molecular orbital contributions.     

DFT studies of the conformational/structural dependencies of geminal 1H,1H scalar coupling 2J(H,H') in substituted methanes

A study is presented of the structural dependencies for scalar, interproton J-coupling across two bonds in a series of substituted methanes. The coupled perturbed, density functional theory method with a B3PW91 functional and aug-cc-pVTZ-J basis sets is used to examine coupling between geminal protons (2)J(H,H') in methane and a series of substituted compounds CH(3)X (X = CH3, CH(2)CH(3), CH=CH2, CH=O, and NH2) as functions of the dihedral angle phi measured about the C1-X2 bonds. All four contributions are obtained but all conformational effects are dominated by the Fermi contact term. Simple linear combination of atomic orbitals (LCAO)-molecular orbital (MO) sum-over-states methods are used to examine the relationships of the coupling constants with dihedral angles as well as internal H-C-H and H-C1-X2 angles. This study explores some novel aspects of geminal H-H coupling including an analysis of the asymmetry in the conformational dependencies arising from non-next-nearest neighbor interactions. For each of the substituted methanes, explicit trigonometric/exponential expressions are given and these accurately reproduce the (2)J(H,H') structural dependencies with standard deviations usually less than 0.03 Hz. The molecular structures for representative bicyclic molecules were fully optimized, and DFT results for (2)J(H,H') reproduce all the trends in the experimental data. A discussion is given on the applicability of the equations for H--H coupling in the substituted methanes to coupling in the bicyclic molecules.     

Experimental and theoretical study of hyperconjugative interaction effects on NMR 1J(CH) scalar couplings

Hyperconjugative and electrostatic interactions effects on 1J(CH) spin-spin coupling constants (SSCCs) are critically studied from both theoretical and experimental points of view. A qualitative model is used to predict how the former affect such SSCCs, while electrostatic interactions are modeled with a point charge placed in the vicinity of the corresponding sigma(CH) bond. Hyperconjugative interactions are calculated using the "natural bond orbital" approach, and using the point-charge model, it is shown how intertwined are both types of interactions. Several members of the series 1-X-bicyclo[1.1.1]pentane and 1-X-3-methylbicyclo[1.1.1]pentane are chosen as model compounds for measuring 1J(CH) SSCCs; in some of them were performed also DFT-SSCC calculations. The strained cage substrate in these series defines strong sigma-hyperconjugative interactions, making these compounds excellent examples to verify the qualitative model presented in this work. It is verified that (a) hyperconjugative interactions from the sigma(CH) bond or into the sigma(CH) antibond containing the coupling nuclei yield a decrease of the corresponding 1J(CH) SSCC and (b) hyperconjugative interactions from other bonds involving the coupling C nucleus yield an increase of that 1J(CH) SSCC.     

A graphical tool for the prediction of vicinal proton-proton 3J(HH) coupling constants

The easy to use and free available graphical tool MestRe-J, developed for Win-32 platforms, calculates the vicinal proton-proton coupling constants 3J(HH) from the torsion angle phi between the coupled protons for the two kinds of generalized Karplus equations developed by Altona's group as well as for equations from other authors. Besides the classical Haasnoot-de Leeuw-Altona equations, including individual substituent effects that depend on their relative Huggins's electronegativities Deltachi, the program incorporates the more recent and precise Díez-Altona-Donders equations. The substituent effects in these equations, that include effects of interactions between substituents, depend on substituent parameters lambda optimized from the 3J(HH) couplings to methyl groups. Weighted time-averaged couplings can be calculated. The equations for 3J(HH) can be solved to provide the torsion angles phi.     

Through-space spin-spin coupling in van der Waals dimers and CH/pi interacting systems. An ab initio and DFT study

The through-space J(HH) and J(CH) spin-spin coupling constants of model van der Waals dimers (involving methane, ethylene, and benzene), and of selected compounds showing the CH/pi interaction, have been investigated by means of DFT and ab initio calculations. In the range of intermolecular separations for which the interaction is stabilizing, weak couplings (0.1-0.3 Hz) are predicted for J(CH), while the corresponding J(HH) couplings are much smaller. The relative contributions (Fermi-contact, spin-orbit, and spin-dipole) are strongly dependent on the geometry of the dimers and on the distance; the non-negligible values of J(CH) for pi systems stem largely from an incomplete cancellation of spin-orbit terms. The results obtained for the larger molecules, that is, acetonitrile@calix[4]arene 5, the imine 6, and the aryl ester 7 are consistent with those on the model dimers. For 7, the occurrence of a through-space mechanism for the transmission of coupling is established by examining trends in the magnitude of couplings as a function of the number of intervening covalent bonds.     

Probing the electronic structure of peptide bonds using methyl groups

The observed V3 torsional barriers measured by microwave spectroscopy for nine methyl groups attached alpha to peptide bond linkages in five gas-phase biomimetics have been found to differ considerably from one molecule to the next and even depend on the position of substitution, being sensitive to structural changes at the other end of the peptide bond. In the search for an explanation for these results, ab initio calculations have been performed at the HF/6-311++G(d,p) level of theory and interpreted in terms of the natural bond orbitals and resonance structures of the peptide bond. These calculations reveal that resonance delocalization in peptide bonds is influenced by methyl conformation through the coupling of vicinal sigma to sigma* orbital interactions with the n to pi*. Thus, CN double-bond character increases (and CO double-bond character decreases) as the methyl group is rotated from the syn to the anti position. A quasilinear correlation exists between the barriers to internal rotation of attached methyl groups and the relative importance of the two principal resonance structures that contribute to the peptide bond.     

Extended charge decomposition analysis and its application for the investigation of electronic relaxation

A general and comprehensive molecular orbital method for the investigation of the electronic relaxation contribution to redox processes is presented. This method is based on the population analysis of the molecular orbitals of the final electronic state in terms of the occupied and unoccupied molecular orbitals of the Koopmans’ state. The DFT calculations for oxidation and reduction of transition-metal species indicate a dramatic magnitude of electronic relaxation in these systems. The passive molecular orbitals play a more significant role in electronic relaxation than the redox-active molecular orbital that directly participates in the redox process. The mechanism of electronic relaxation in the oxidation of Fe^II and Cu^I species varies from the ligand to metal 3d charge transfer (LMCT) interactions to the ligand to metal 4s,4p LMCT. For systems with significant electronic delocalization, electronic relaxation becomes smaller leading to much smaller contributions to the redox processes. Dedication: This contribution is to celebrate Philip Stephen’s seminal contributions to theory and experiment. An erratum to this article can be found at     

Magnetic studies of a syn-anti triatomic carboxylate-bridging chainlike copper(II) complex exhibiting ferromagnetic exchange

The magnetic properties of triatomic syn-anti carboxylate bridging copper(II) complex, {[Cu(2,2'-bipydine)(maleate)].2H2O}infinity (complex 1), were investigated experimentally and theoretically, suggesting weak ferromagnetic intrachain interaction. The magnetic data were analyzed and interpreted in terms of Heisenberg chain model corrected by a mean molecular field. Fitting parameters obtained for J, g, and zJ' are 3.14 cm(-1), 2.08, and -0.13, respectively. Density functional theory with generalized gradient approximation was applied to calculate the electronic structure and spin distribution of the present complex. The structural and electronic factors controlling the magnetic interactions were also determined. Ferromagnetic intrachain interactions through triatomic syn-anti carboxylate bridge result from nonplanarity of the bridging network, the exchange pathway involving both the sigma and pi orbitals of the carboxylate bridge and the spin delocalization of each magnetic orbital on the atoms of the carboxylate bridge from the copper(II) centers.