Hydrogen bond and halogen bond inside the carbon nanotube

The hydrogen bond and halogen bond inside the open-ended single-walled carbon nanotubes have been investigated theoretically employing the newly developed density functional M06 with the suitable basis set and the natural bond orbital analysis. Comparing with the hydrogen or halogen bond in the gas phase, we find that the strength of the hydrogen or halogen bond inside the carbon nanotube will become weaker if there is a larger intramolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom donor to the antibonding orbital of the X-H or X-Hal bond involved in the formation of the hydrogen or halogen bond and will become stronger if there is a larger intermolecular electron-density transfer from the electron-rich region of the hydrogen or halogen atom acceptor to the antibonding orbital of the X-H or X-Hal bond. According to the analysis of the molecular electrostatic potential of the carbon nanotube, the driving force for the electron-density transfer is found to be the negative electric field formed in the carbon nanotube inner phase. Our results also show that the X-H bond involved in the formation of the hydrogen bond and the X-Hal bond involved in the formation of the halogen bond are all elongated when encapsulating the hydrogen bond and halogen bond within the carbon nanotube, so the carbon nanotube confinement may change the blue-shifting hydrogen bond and the blue-shifting halogen bond into the red-shifting hydrogen bond and the red-shifting halogen bond. The possibility to replace the all electron nanotube-confined calculation by the simple polarizable continuum model is also evaluated.     

The importance of lone pair delocalizations: theoretical investigations on the stability of cis and trans isomers in 1,2-halodiazenes

The relative and thermodynamic stabilities of cis and trans isomers of 1,2-dihalodiazenes (XN=NX; X = F, Cl, or Br) were examined using high level ab initio and density functional theory (DFT) calculations. For 1,2-dihalodiazenes, it was found that the cis isomers were more stable than the corresponding trans isomers, despite the existence of several cis destabilizing mechanisms, such as steric exchange between halogen lone pairs and dipole-dipole electrostatic repulsions (Delta(trans-cis) = 3.15, 7.04, and 8.19 kcal mol(-1), respectively, at BP86/6-311++G(3df,3pd)//B3LYP /6-311++G(3df,3pd) level). Their origin of the cis-preferred difference in energy was investigated with natural bond orbital (NBO) analysis to show that the "cis effect" came mainly from antiperiplanar interactions (AP effect) between the nitrogen lone pair and the neighboring antibonding orbital of the N-X bond (n(N) --> sigma(N'X'*)). The delocalization of halogen lone-pair into the antibonding orbital of the N=N bonds (the LP effects) was also found to enhance the cis preference by 1.20 to 6.58 kcal mol(-1), depending on the substituted halogen atom. The total amount of the AP effect increased as the halogen atom became larger, and the increased AP effect promoted the triple-bond-like nature of the N=N bond (shorter N=N bond length and wider NNX angle). The greater AP effect also made the N'-X' bond easier to cleave (longer N-X bond length), and a higher energy level than that of the nitrogen lone pair was found in the N-Br bonding orbital in 1,2-dibromodiazenes, thus indicating the significant instability of this molecule. The degradability of the N-Cl bond in 1,2-dichlorodiazenes and the fair stability of the N-F bond in 1,2-fluorodiazenes were also confirmed theoretically, and were found to be consistent with the previous experimental and theoretical reports. These results clearly indicate the dominance of lone-pair-related hyperconjugations on the basic electronic structure and energetic natures of 1,2-dihalodiazene systems.     

On the origin of red and blue shifts of X-H and C-H stretching vibrations in formic acid (formate ion) and proton donor complexes.

Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.     

Electron attachment step in electron capture dissociation (ECD) and electron transfer dissociation (ETD)

We have made use of classical dynamics trajectory simultions and ab initio electronic structure calculations to estimate the cross sections with which electrons are attached (in electron capture dissociation (ECD)) or transferred (in electron transfer dissociation (ETD)) to a model system that contained both an S-S bond that is cleaved and a -NH(3)(+) positively charged site. We used a Landau-Zener-Stueckelberg curve-crossing approximation to estimate the ETD rates for electron transfer from a CH(3)(-) anion to the -NH(3)(+) Rydberg orbital or the S-S sigma* orbital. We draw conclusions about ECD from our ETD results and from known experimental electron-attachment cross sections for cations and sigma-bonds. We predict the cross section for ETD at the positive site of our model compound to be an order of magnitude larger than that for transfer to the Coulomb-stabilized S-S bond site. We also predict that, in ECD, the cross section for electron capture at the positive site will be up to 3 orders of magnitude larger than that for capture at the S-S bond site. These results seem to suggest that attachment to such positive sites should dominate in producing S-S bond cleavage in our compound. However, we also note that cleavage induced by capture at the positive site will be diminished by an amount that is related to the distance from the positive site to the S-S bond. This dimunition can render cleavage through Coulomb-assisted S-S sigma* attachment competitive for our model compound. Implications for ECD and ETD of peptides and proteins in which SS or N-C(alpha) bonds are cleaved are also discussed, and we explain that such events are most likely susceptible to Coulomb-assisted attachment, because the S-S sigma* and C=O pi* orbitals are the lowest-lying antibonding orbitals in most peptides and proteins.     

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.     

Stereoelectronic effect on one-electron reductive release of 5-fluorouracil from 5-fluoro-1-(2-oxocycloalkyl)uracils as a new class of radiation-activated antitumor prodrugs

A series of 5-fluoro-1-(2'-oxocycloalkyl)uracils (3-11) that are potentially novel radiation-activated prodrugs for the radiotherapy of hypoxic tumor cells have been synthesized to evaluate a relationship between the molecular structure and the reactivity of one-electron reductive release of antitumor 5-fluorouracil (1) in anoxic aqueous solution. All the compounds 3-11 bearing the 2'-oxo group were one-electron reduced by hydrated electrons (eaq-) and thereby underwent C(1')-N(1) bond dissociation to release 5-fluorouracil 1 in 47-96% yields upon radiolysis of anoxic aqueous solution, while control compounds (12, 13) without the 2'-oxo substituent had no reactivity toward such a reductive C(1')-N(1) bond dissociation. The decomposition of 2-oxo compounds in the radiolytic one-electron reduction was more enhanced, as the one-electron reduction potential measured by cyclic voltammetry in N,N-dimethylformamide became more positive. The efficiency of 5-fluorouracil release was strongly dependent on the structural flexibility of 2-oxo compounds. X-ray crystallographic studies of representative compounds revealed that the C(1')-N(1) bond possesses normal geometry and bond length in the ground state. MO calculations by the AM1 method demonstrated that the LUMO is primarily localized at the pi* orbital of C(5)-C(6) double bond of the 5-fluorouracil moiety, and that the LUMO + 1 is delocalized between the pi* orbital of 2'-oxo substituent and the sigma* orbital of adjacent C(1')-N(1) bond. The one-electron reductive release of 5-fluorouracil 1 in anoxic aqueous solution was presumed to occur from the LUMO + 1 of radical anion intermediates possessing a partial mixing of the antibonding C(2')=O pi* and C(1')-N(1) sigma* MO's, that may be facilitated by a dynamic conformational change to achieve higher degree of (pi* + sigma*) MO mixing.     

Halogen Bonds in Adenine-5-Bromouracil Complexes

Ab initio and density functional calculations were employed to investigate the bonding patterns in theadenine-5-bromouracil (AT+) complexes. It is shown that the Br atom in 5-bromouracil (T+) is involved in bonding both with the hydrogen atom of the amino group of adenine (A) and with N7(A) (or N1(A)). With this motif, the Br atom interacts with a nucleophile (H) in a "head-on" fashion and an electrophile(N) in a "side-on" fashion, forming both hydrogen and halogen bonds. Electrostatic attraction between the Br atom in T+ and N7 (or N1) of adenine was found via the electrostatic potential analysis. The existence of the Br···N interactions in the pairs was further conˉrmed by means of Bader's atoms in molecules theory. A bond critical point is identiˉed for the halogen bonds and the topological parameters at the bond critical point indicate the typical closed-shell interactions in the pairs. Natural bond orbital analysis suggests that the charge transfer from the lone pair of the nitrogen atom of adenine is mainly directed to the C-Br antibonding orbital. Finally, halogen bonds in the T+AT+A tetrads were also explored.     

Steric effects in electron transfer from potassium to pi-bonded oriented molecules CH3CN, CH3NC, and CCl3CN

Electron transfer from K atoms to oriented CH3CN, CH3NC, and CCl3CN is studied in crossed beams at energies near the threshold for forming an ion pair. For the methyl compounds, the dominant ions are K+ and CN-; the steric asymmetry is very small and energy-independent, characteristic of sideways attack with the electron apparently entering the pi*CN antibonding orbital. Migration of the electron to the sigma*CC orbital to break the C-C bond is greatly facilitated by interaction with the atomic donor. CH2CN- is formed in collisions preferring CH3-end attack, and the steric asymmetry becomes very large near threshold. CCl3CN mostly forms Cl- in collisions slightly favoring the CCl3 end with a small energy dependence with the electron apparently entering the sigma* LUMO. CN- is formed in much smaller yield with a slight preference for the CN end. The parent negative ion CCl3CN- is observed, and a lower limit for its electron affinity is estimated to be 0.3 eV. Fragment ions CCl2CN- and CClCN- are also observed with upper limits for the quantity bond dissociation energy - electron affinity (BDE - EA) estimated to be 0.6 and 1.0 eV, respectively.     

An ab initio and density functional theory study of the structure and bonding of sulfur ylides

Sulfur ylides are useful synthetic intermediates that are formed from the interaction between singlet carbenes and sulfur-containing molecules. Partial double-bond character frequently has been proposed as a key contributor to the stability of sulfur ylides. Calculations at the B3LYP, MP2, and CCSD(T) levels of theory employing various basis sets have been performed on the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) in order to investigate the structure and bonding of these systems. The following general properties of sulfur ylides were observed from the computational studies: C-S bond distances that are close in length to that of a typical C-S double bond, high charge transfer from the sulfide to the carbene, and large torsional rotation barriers. Analysis of the sulfur ylide charge distribution indicates that the unusually short C-S bond distance can be attributed in part to the electrostatic attraction between highly oppositely charged carbon and sulfur atoms. Furthermore, n --> sigma* stabilization arising from donation of electron density from the carbon lone pair orbital into S-H or S-C antibonding orbitals leads to larger than expected torsional barriers. Finally, natural resonance theory analysis indicates that the bond order of the sulfur ylides H(2)S-CH(2) and (CH(3))(2)S-CH(2) is 1.4-1.5, intermediate between a single and double bond.     

An electronic perspective on the reduction of an n=n double bond at a conserved dimolybdenum core

Density functional theory has been used to assess the role of the bimetallic core in supporting reductive cleavage of the N=N double bond in [Cp2Mo2(mu-SMe)3(mu-eta1:eta1-HN=NPh)]+. The HOMO of the complex, the Mo-Mo delta orbital, plays a key role as a source of high-energy electrons, available for transfer into the vacant orbitals of the N=N unit. As a result, the metal centres cycle between the Mo(III) and Mo(IV) oxidation states. The symmetry of the Mo-Mo delta "buffer" orbital has a profound influence on the reaction pathway, because significant overlap with the redox-active orbital on the N=N unit (pi* or sigma*) is required for efficient electron transfer. The orthogonality of the Mo-Mo delta and N-N sigma* orbitals in the eta1:eta1 coordination mode ensures that electron transfer into the N-N sigma bond is effectively blocked, and a rate-limiting eta1:eta1-->eta1 rearrangement is a necessary precursor to cleavage of the bond.     

Interplay between halogen bond and lithium bond in MCN-LiCN-XCCH (M = H, Li, and Na; X = Cl, Br, and I) complex: the enhancement of halogen bond by a lithium bond

Quantum chemical calculations have been performed to study the complex of MCN-LiCN-XCCH (M = H, Li, and Na; X = Cl, Br, and I). The aim is to study the cooperative effect between halogen bond and lithium bond. The alkali metal has an enhancing effect on the lithium bond, making it increased by 77 and 94% for the Li and Na, respectively. There is the cooperativity between the lithium bond and halogen bond. The former has a larger enhancing effect on the latter, being in a range of 11.7-29.4%. The effect of cooperativity on the halogen bond is dependent on the type of metal and halogen atoms. The enhancing mechanism has been analyzed in views with the orbital interaction, charge transfer, dipole moment, polarizability, atom charges, and electrostatic potentials. The results show that the electrostatic interaction plays an important role in the enhancement of halogen bond.     

Interpretation of the electronic spectra of four disilanes

Time-dependent density functional theory (TD-DFT/B3LYP(AC)/cc-pVTZ/cc-pVTZ/6-311G//MP2/cc-pVTZ/cc-pVTZ/6-31G**) has been used to compute vertical excitation energies and oscillator strengths of the six low-lying excited states of four peralkylated disilanes, hexamethyldisilane (1), hexa-tert-butyldisilane (2), 1,6-disila[4.4.4]propellane (3), and 1,7-disila[5.5.5]propellane (4). The results provide an accurate interpretation of the reported UV absorption spectra of 1-4 in solution, and for 1 also in the gas phase up to 62,000 cm(-1). The excellent agreement of the calculated with the available experimental energies and oscillator strengths, and with magnetic circular (MCD) and linear (LD) dichroism, gives us confidence that the method will be useful for dependable interpretation of the electronic spectra of longer oligosilanes. Although the disilane chromophore finds itself in quite different environments in 1-4, its fundamental characteristics remain the same, with one important exception. In all four compounds, the first valence excited state is due to an electron promotion from the sigma(1) HOMO to the pi(1)* orbital, and the second valence excited state to a promotion from the sigma(1) HOMO to the sigma(1)* orbital. Surprisingly, however, it is only in 2, which has an extraordinarily long SiSi bond, that the terminating sigma(1)* orbital is the sigma*(SiSi) antibond, as anticipated, and the sigma sigma* transition has the expected very high oscillator strength. In 1, 3, and 4, the sigma*(SiSi) antibonding orbital is high in energy and does not play any role in low-energy excitations. Instead, the terminating orbital of the sigma(1)sigma(1)* excitation is represented by Si-alkyl antibonds, combined symmetrically with respect to rotation around the SiSi axis and antisymmetrically with respect to operations that interchange the two Si atoms. The common assumption that the characteristic intense sigma sigma* transitions of longer peralkylated oligosilanes extrapolate to the lowest sigma sigma* transition in common peralkylated disilanes is incorrect, and only the weak sigma pi* transitions extrapolate simply.     

Source of Cooperativity in Halogen‐Bonded Haloamine Tetramers

Inspired by the isostructural motif in α‐bromoacetophenone oxime crystals, we investigated halogen–halogen bonding in haloamine quartets. Our Kohn–Sham molecular orbital and energy decomposition analysis reveal a synergy that can be traced to a charge‐transfer interaction in the halogen‐bonded tetramers. The halogen lone‐pair orbital on one monomer donates electrons into the unoccupied σ*_N?X orbital on the perpendicular N?X bond of the neighboring monomer. This interaction has local σ symmetry. Interestingly, we discovered a second, somewhat weaker donor–acceptor interaction of local π symmetry, which partially counteracts the aforementioned regular σ‐symmetric halogen‐bonding orbital interaction. The halogen–halogen interaction in haloamines is the first known example of a halogen bond in which back donation takes place. We also find that this cooperativity in halogen bonds results from the reduction of the donor–acceptor orbital‐energy gap that occurs every time a monomer is added to the aggregate.     

Oxidative properties of FeO2+: electronic structure and solvation effects

An electronic structure analysis is provided of the action of solvated FeO(2+), [FeO(H(2)O)(5)](2+), as a hydroxylation catalyst. It is emphasized that the oxo end of FeO(2+) does not form hydrogen bonds (as electron donor and H-bond acceptor) with H-bond donors nor with aliphatic C-H bonds, but it activates C-H bonds as an electron acceptor. It is extremely electrophilic, to the extent that it can activate even such poor electron donors as aliphatic C-H bonds, the C-H bond orbital acting as electron donor in a charge transfer type of interaction. Lower lying O-H bonding orbitals are less easily activated. The primary electron accepting orbital in a water environment is the 3sigma*alpha orbital, an antibonding combination of Fe-3d(z(2)) and O-2p(z), which is very low-lying relative to the pi*alpha compared with, for example, the sigma* orbital in O(2) relative to its pi*. This is ascribed to relatively small Fe-3d(z(2)) with O-2p(z) overlap, due to the nodal structure of the 3d(z(2)).The H-abstraction barrier is very low in the gas phase, but it is considerably enhanced in water solvent. This is shown to be due to strong screening effects of the dielectric medium, leading to relative destabilization of the levels of the charged [FeO(H(2)O)(5)](2+) species compared to those of the neutral substrate molecules, making it a less effective electron acceptor. The solvent directly affects the orbital interactions responsible for the catalytic reaction.     

On the correlation between bond-length change and vibrational frequency shift in halogen-bonded complexes

The C-Hal (Hal = Cl, Br, or I) bond-length change and the corresponding vibrational frequency shift of the C-Hal stretch upon the C-Hal···Y (Y is the electron donor) halogen bond formation have been determined by using density functional theory computations. Plots of the C-Hal bond-length change versus the corresponding vibrational frequency shift of the C-Hal stretch all give straight lines. The coefficients of determination range from 0.94366 to 0.99219, showing that the correlation between the C-Hal bond-length change and the corresponding frequency shift is very good in the halogen-bonded complexes. The possible effects of vibrational coupling, computational method, and anharmonicity on the bond-length change-frequency shift correlation are discussed in detail.     

Integration of electron density and molecular orbital techniques to reveal questionable bonds: the test case of the direct Fe-Fe bond in Fe2(CO)9

The article illustrates the advantages of partitioning the total electron density rho(rb), its Laplacian (inverted Delta)2 rho(rb), and the energy density H(rb) in terms of orbital components. By calculating the contributions of the mathematically constructed molecular orbitals to the measurable electron density, it is possible to quantify the bonding or antibonding character of each MO. This strategy is exploited to review the controversial existence of direct Fe-Fe bonding in the triply bridged Fe2(CO)9 system. Although the bond is predicted by electron counting rules, the interaction between the two pseudo-octahedral metal centers can be repulsive because of their fully occupied t(2g) sets. Moreover, previous atoms in molecules (AIM) studies failed to show a Fe-Fe bond critical point (bcp). The present electron density orbital partitioning (EDOP) analysis shows that one sigma bonding combination of the t(2g) levels is not totally overcome by the corresponding sigma* MO, which is partially delocalized over the bridging carbonyls. This suggests the existence of some, albeit weak, direct Fe-Fe bonding.     

Nature of MoH···I bonds in Cp2Mo(L)H···I‐C≡C‐R Complexes (L=H,CN, PPh2, C(CH3)3; R=NO2, Cl,Br, H,OH, CH3, NH2)

The nature of the MoH···I bond in Cp₂Mo(L)H···I‐C≡C‐R (L= H, CN, PPh₂, C(CH₃)₃; R=NO₂, Cl, Br, H, OH, CH₃, NH₂) was investigated using electrostatic potential analysis, topological analysis of the electron density, energy decomposition analysis and natural bond orbital analysis. The calculated results show that MoH···I interactions in the title complexes belong to halogen‐hydride bond, which is similar to halogen bonds, not hydrogen bonds. Different to the classical halogen bonds, the directionality of MoH···I bond is low; Although electrostatic interaction is dorminant, the orbital interactions also play important roles in this kind of halogen bond, and steric interactions are weak; the strength of H···I bond can tuned by the most positive electrostatic potential of the I atom. As the electron‐withdrawing ability of the R substituent in the alkyne increases, the electrostatic potential maximum of the I atom increases, which enhances the strength of the H···I halogen bond, as well as the electron transfer.     

Evidence for orbital-specific electron transfer to oriented haloform molecules

Beams of hyperthermal K atoms cross beams of the oriented haloforms CF(3)H, CCl(3)H, and CBr(3)H, and transfer of an electron mainly produces K(+) and the X(-) halide ion which are detected in coincidence. As expected, the steric asymmetry of CCl(3)H and CBr(3)H is very small and the halogen end is more reactive. However, even though there are three potentially reactive centers on each molecule, the F(-) ion yield in CF(3)H is strongly dependent on orientation. At energies close to the threshold for ion-pair formation ( approximately 5.5 eV), H-end attack is more reactive to form F(-). As the energy is increased, the more productive end switches, and F-end attack dominates the reactivity. In CF(3)H near threshold the electron is apparently transferred to the sigma(CH) antibonding orbital, and small signals are observed from electrons and CF(3)(-) ions, indicating "activation" of this orbital. In CCl(3)H and CBr(3)H the steric asymmetry is very small, and signals from free electrons and CX(3)(-) ions are barely detectable, indicating that the sigma(CH) antibonding orbital is not activated. The electron is apparently transferred to the sigma(CX) orbital which is believed to be the LUMO. At very low energies the proximity of the incipient ions probably determines whether salt molecules or ions are formed.     

Hydrogen bonding mediated by key orbital interactions determines hydration enthalpy differences of phosphate water clusters

Electronic structure calculations have been carried out to provide a molecular interpretation for dihydrogen phosphate stability in water relative to that of metaphosphate. Specifically, hydration enthalpies of biologically important metaphosphate and dihydrogen phosphate with one to three waters have been computed with second-order M?ller-Plesset perturbation and density functional theory (B3LYP) with up to the aug-cc-pvtz basis set and compared to experiment. The inclusion of basis set superposition error corrections and supplemental diffuse functions are necessary to predict hydration enthalpies within experimental uncertainty. Natural bond orbital analysis is used to rationalize underlying hydrogen bond configurations and key orbital interactions responsible for the experimentally reported difference in hydration enthalpies between metaphosphate and dihydrogen phosphate. In general, dihydrogen phosphate forms stronger hydrogen bonds compared to metaphosphate due to a greater charge transfer or enhanced orbital overlap between the phosphoryl oxygen lone pairs, n(O), and the antibonding O-H bond of water. Intramolecular distal lone pair repulsion with the donor n(O) orbital of dihydrogen phosphate distorts symmetric conformations, which improves n(O) and sigma*(O-H) overlap and ultimately the hydrogen bond strength. Unlike metaphosphate, water complexed to dihydrogen phosphate can serve as both a hydrogen bond donor and a hydrogen bond acceptor, which results in cooperative charge transfer and a reduction of the energy gap between n(O) and sigma*(O-H), leading to stronger hydrogen bonds. This study offers insight into how orbital interactions mediate hydrogen bond strengths with potential implications on the understanding of the kinetics and mechanism in enzymatic phosphoryl transfer reactions.