Identification of hydrogen bonds using quantum electrodynamics

A method for the identification of hydrogen bonds was investigated from the viewpoint of the stress tensor density proposed by Tachibana and following other works in this field. Hydrogen bonds are known to exhibit common features with ionic and covalent bonds. In quantum electrodynamics, the covalent bond has been demonstrated to display a spindle structure of the stress tensor density. Importantly, this spindle structure is also seen in the hydrogen bond, although the covalency is considerably weaker than in a typical covalent bond. Distinguishing it from the ionic bond is most imperative for the identification of the hydrogen bond. In the present study, the directionality of the hydrogen bond is investigated as the ionic bond is nearly isotropic, while the hydrogen bond exhibits the directionality. It was demonstrated that the hydrogen bond can be distinguished from the ionic bond using the angle dependence of the largest eigenvalue of the stress tensor density.     

Metathesis of nitrogen atoms within triple bonds involving carbon, tungsten, and molybdenum

(ButO)3Mo triple bond N and W2(OBut)6(M triple bond M) react in hydrocarbons to form Mo2(OBut)6(M triple bond M) and (ButO)3W triple bond N via the reactive intermediate MoW(OBut)6(M triple bond M). (ButO)3W triple bond N and CH3C triple bond N15 react in tetrahydrofuran (THF) at room temperature to give an equilibrium mixture involving (ButO)3W triple bond N15 and CH3C triple bond N. The (ButO)3W triple bond N compound is similarly shown to act as a catalyst for N15-atom scrambling between MeC13 triple bond N15 and PhC triple bond N to give a mixture of MeC13 triple bond N and PhC triple bond N15. From studies of degenerate scrambling of N atoms involving (ButO)3W triple bond N and MeC13 triple bond N in THF-d8 by 13C(1H) NMR spectroscopy, the reaction was found to be first order in acetonitrile and the activation parameters were estimated to be DeltaH = 13.4(7) kcal/mol and DeltaS = -32(2) eu. A similar reaction is observed for (ButO)3Mo triple bond N and CH3C triple bond N15 upon heating in THF-d8. The reaction is suppressed in pyridine solutions and not observed for the dimeric [(ButMe2SiO)3W triple bond N]2. The reaction pathway has been investigated by calculations employing density functional theory on the model compounds (MeO)3M triple bond N and CH3C triple bond N where M = Mo and W. The transition state was found to involve a product of the 2 + 2 cycloaddition of M triple bond N and C triple bond N, a planar metalladiazacyclobutadiene. This resembles the pathway calculated for alkyne metathesis involving (MeO)3W triple bond CMe, which modeled the metathesis of (ButO)3W triple bond CBut. The calculations also predict that the energy of the transition state is notably higher for M = Mo relative to M = W.     

Theoretical calculations of carbon-oxygen bond dissociation enthalpies of peroxyl radicals formed in the autoxidation of lipids

Theoretical calculations were carried out to provide a framework for understanding the free radical oxidation of unsaturated lipids. The carbon[bond]hydrogen bond dissociation enthalpies (BDEs) of organic model compounds and oxidizable lipids (R[bond]H) and the carbon[bond]oxygen bond dissociation enthalpies of peroxyl radical intermediates (R[bond]OO*) have been calculated. The carbon[bond]hydrogen BDEs correlate with the rate constant for propagation of free radical autoxidation, and the carbon[bond]oxygen BDEs of peroxyl radicals correlate with rate constants for beta-fragmentation of these intermediates. Oxygen addition to intermediate carbon radicals apparently occurs preferentially at centers having the highest spin density. The calculated spin distribution therefore provides guidance about the partitioning of oxygen to delocalized carbon radicals. Where the C[bond]H BDEs are a function of the extent of conjugation in the parent lipid and the stability of the carbon radical derived therefrom, C[bond]OO* BDEs are also affected by hyperconjugation. This gives way to different rates of beta-fragmentation of peroxyl radicals formed from oxygen addition at different sites along the same delocalized radical. We have also studied by both theory and experiment the propensity for benzylic radicals to undergo oxygen addition at their ortho and para carbons which, combined, possess an equivalent unpaired electron spin density as the benzylic position itself. We find that the intermediate peroxyl radicals in these cases have negative C[bond]OO* BDEs and, thus, have rate constants for beta-fragmentation that exceed the diffusion-controlled limit for the reaction of a carbon-centered radical with oxygen.     

Use of a novel relationship between bond length and bond order to calculate accurate bond orders for carbon–carbon bonds

An exact relationship between bond length and bond order has been derived for the first time based on the concept of electron density. This relationship allows the calculation of sufficiently accurate bond orders and also determines the number of bond-forming electrons. According to this novel relationship between bond order and bond length, the bond order of the carbon–carbon bond in ethylene is 1.75, whereas it is 2.50 in acetylene. These bond orders are readily interpreted by the fragmentation of π-bonds and a consequent decrease in bond order, which is further supported by the chemical properties of these molecules. Assuming structure-specific fragmentation of π-bonds (i.e. one structural motif always adheres to one or two types of bond fragmentation scheme), the bond orders can be predicted for molecules containing multiple carbon–carbon bonds in excellent agreement with the experimental findings.     

Investigation of the effect of drying and refining on the fiber–fiber shear bond strength measured using tensile fracture line analysis of sheets weakened by acid gas exposure

No reliable method exists for measuring the cellulose fiber–fiber shear bond strength in paper. This paper reports a simple method for measuring the fiber–fiber shear bond strength by weakening the fibers independently of the bonds in a sheet of paper, using acid vapor, until all the fibers break across the fracture line. The bond strength is then calculated from the fiber strength, as measured by the zero span test, at the point where the fibers first are weakened such that they all break. The method was used to calculate the average bond strength of handsheets made out of two different pulps. The first pulp was a never dried, 60% yield, unbleached radiata pine. The bond strength was 25.0 ± 3.3 MPa. Drying the fibers before reslushing and making sheets reduced the bond strength by up to 33%, with the reduction depending on the severity of the drying treatment. The second pulp was a bleached dried softwood kraft and was used to investigate the effect of low consistency refining on bond strength. The bond strength increased from 13.7 ± 1.0 MPa for the sheets made from the unrefined pulp to 37.0 ± 1.0 MPa, for the sheets made from the most heavily refined pulp. The bond strength measurements are considerably higher than previous literature estimates for the shear bond strength. The causes for the discrepancy include stress concentrations in tests of single fiber–fiber bonds.     

Analysis of the IGLO bond contributions to the 13C shielding tensors in the local bond frame

A new method is presented to analyze the IGLO (individual gauge for localized orbitals) bond contributions in ¹³C chemical shielding. The IGLO bond contributions calculated in the molecular frame are rotated to a local bond frame, in which one component is selected along the bond. This procedure removes the explicit angular dependence of the IGLO bond contributions and allows a comparison of the bond contributions in different molecules. The results provide a new method to study the electronic basis of shielding interactions. The problems associated with the multiple gauge origins used in the IGLO method are discussed in their relationship to the bond contribution analysis.     

Exploring the actinide-actinide bond: theoretical studies of the chemical bond in Ac2, Th2, Pa2, and U2

Multiconfigurational quantum chemical methods (CASSCF/CASPT2) have been used to study the chemical bond in the actinide diatoms Ac2, Th2, Pa2, and U2. Scalar relativistic effects and spin-orbit coupling have been included in the calculations. In the Ac2 and Th2 diatoms the atomic 6d, 7s, and 7p orbitals are the significant contributors to the bond, while for the two heavier diatoms, the 5f orbitals become increasingly important. Ac2 is characterized by a double bond with a 3Sigmag-(0g+) ground state, a bond distance of 3.64. A, and a bond energy of 1.19 eV. Th2 has quadruple bond character with a 3Dg(1g) ground state. The bond distance is 2.76 A and the bond energy (D0) 3.28 eV. Pa2 is characterized by a quintuple bond with a 3Sigmag-(0g+) ground state. The bond distance is 2.37 A and the bond energy 4.00 eV. The uranium diatom has also a quintuple bond with a 7Og (8g) ground state, a bond distance of 2.43 A, and a bond energy of 1.15 eV. It is concluded that the strongest bound actinide diatom is Pa2, characterized by a well-developed quintuple bond.     

Bond length features of linear carbon chains of finite to infinite size: Visual interpretation from Pauling bond orders

Schemes for Kekulé structure counting of linear carbon chains are suggested. Mathematical formulas, which calculate the Pauling bond order P(k, N) of a chemical bond numbered by k, are given for the carbon chain with N carbon atoms. By use of the least‐squares fitting of a linearity, relationships between Pauling bond orders and bond lengths are obtained, and such correlation of the Pauling bond order–bond length can be qualitatively extended to the excited states. The relative magnitudes of Pauling bond orders in unsaturated carbon chains dominate C–C bond lengths a well as the bond length feature with the chain size increasing. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem 94: 144–149, 2003     

The effect of hydrogen bonding on structural parameters ii. an ab initio study of the monohydrated formamide molecule

Four hydrogen-bonded formamide-water complexes have been studied by ab initio calculations, two where the amino group acts as a donor and two where the carbonyl oxygen is an acceptor. The results indicate that the effect on the conjugated NCO fragment depends on both the type and the energy of the hydrogen bond formed. Although, in all cases the formation of a hydrogen bond leads to increased conjugation, expressed as a shortening of the CN bond and a corresponding lengthening of the CO bond, there is a significant difference in the effect of the two types of hydrogen bonds. This difference may be explained by changes in the electron populations. In two of the complexes the effect of varying the hydrogen bond length has been studied in some detail. It is found that the effect on the conjugated system depends on the length of the hydrogen bond, and analytical expressions have been found for the variations of the CO and CN bond lengths with changes in the hydrogen bond length. Potential functions for the N-H β O and O-H β O hydrogen bonds have also been derived.     

Electronic basis of improper hydrogen bonding: a subtle balance of hyperconjugation and rehybridization

The X[bond]H bond length in X[bond]H...Y hydrogen bonded complexes is controlled by a balance of two main factors acting in opposite directions. "X[bond]H bond lengthening" due to n(Y)-->sigma(H[bond]X) hyperconjugative interaction is balanced by "X[bond]H bond shortening" due to increase in the s-character and polarization of the X[bond]H. When hyperconjugation dominates, X[bond]H bond elongation is reflected in a concomitant red shift of the corresponding IR stretching frequency. When the hyperconjugative interaction is weak and the X-hybrid orbital in the X[bond]H is able to undergo a sufficient change in hybridization and polarization, rehybridization dominates leading to a shortening of the X[bond]H and a blue shift in the X[bond]H stretching frequency.     

取代基对N-H…O=C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N—H…O=C氢键强度, 探讨了氢键受体分子中不同取代基对N—H…O=C氢键强度的影响. 研究表明, 不同取代基对氢键三聚体中N—H…O=C氢键强度的影响是不同的: 取代基为供电子基团, 氢键键长r(H…O)缩短, 氢键强度增强; 取代基为吸电子基团, 氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明, N—H…O=C氢键强度越强, 氢键中氢原子的正电荷越多, 氧原子的负电荷越多, 质子供体和受体分子间的电荷转移越多. 供电子基团使N—H…O=C氢键中氧原子的孤对电子n(O)对N—H的反键轨道滓*(N—H)的二阶相互作用稳定化能增加, 吸电子基团使这种二阶相互作用稳定化能减小. 取代基对与其相近的N—H…O=C氢键影响更大.     

Molecular orbital calculations of bond lengths in benzenoid hydrocarbons

The correlation between bond lengths and bond orders in benzenoid hydrocarbons has been considered. Bond orders for six molecules were obtained by means of a simple MO-LCAO-SC treatment, and a procedure is suggested for calculating accurate bond lengths from such self-consistent bond orders.     

Recent advances in simple valence-bond theory and the theory of hybrid bond orbitals

The history of important developments in the theory of hybrid bond orbitals and its application in valence-bond theory is reviewed. One of the salient points, the bond strength of a hybrid orbital, is defined as the value of the angular part of the orbital along the bond direction. Characteristic bond angles corresponding to maxima in the bond strength are presented for various basis sets. In order to alleviate computational difficulties in determining the bond strength for complex systems, an approximation to it, the pair-defect-sum approximation, is described. The results of an exhaustive test of the validity of this approximation are presented. Applicaitions of these ideas to coordinate chemistry are provided. Finally, the case is made for the continued viability of valence-bond theory in this age of omnipresent computer terminals.     

Theoretical study of the oxidation reactions of methylacrylic acid and methyl methacrylate by triplet O2

The oxidations of organic compounds and polymers by triplet O2 were called "dark oxidation" or "auto-oxidation", in contrast to their "photo-oxidation" by singlet O2. To study the relevant dark oxidation mechanism we take methylacrylic acid (MAA) and methyl methacrylate (MMA) as prototypes to study their reactions with triplet O2 by performing density functional theory calculations. Two reaction channels, the C-H bond oxidation and C=C bond oxidation, have been characterized in detail. The structures of the initial contact charge-transfer complexes, intermediates, transition states, and final oxides involved in the reactions have been localized at the UB3LYP/6-311+G(d,p) level. It is found that the C-H bond in the methyl group connected to the C=C bond presents relatively higher reactivity toward triplet O2 than the C=C bond itself. Thus, the reactions are expected to proceed via the C-H bond oxidation branch at room temperature and also via C=C bond oxidation at elevated temperature. In this sense, an effective method for preventing or retarding the dark oxidations of MAA and MMA in a natural environment is to chemically decorate or protect the C-H bond in the methyl connected to the C=C bond. The present results are expected to provide a general guide for understanding the dark oxidation mechanism of organic compounds and polymers.     

Cycloreversion of cyclobutanes

Semiempirical MO calculations with the method SINDO1 were performed to study the potential energy surface of cyclobutane and several substituted cyclobutanes with substituents F, OCH₃ and CN. The reaction pathway with the lowest activation energy leading to two ethylenic fragments is nonconcerted. One carbon bond is broken after symmetric opening of two adjacent bond angles and twisting of the carbon framework. The first transition state is asymmetric and diradicaloid. The reaction proceeds to a diradicaloid, non-zwitterionic intermediate. The second transition state is characterized by bond breaking of the inner carbon-carbon bond. For the unsubstituted case, the barrier for free rotation of the outer methylenic groups was also calculated. In comparison, the unsubstituted reaction is characterized by transition states of almost equal energy, whereas in the substituted reactions the barriers for the second bond breaking are much higher than for the first bond breaking step.     

An X-ray diffraction and MAS NMR study of the thermal expansion properties of calcined siliceous ferrierite

Powder and single-crystal X-ray diffraction, combined with MAS NMR measurements, has been used to study the thermal expansion of siliceous zeolite ferrierite as it approaches a second-order displacive phase transition from a low-symmetry (Pnnm) to a high-symmetry (Immm) structure. Below the transition temperature, ferrierite exhibits positive thermal expansivity. However, above the transition temperature a significant change in thermal behavior is seen, and ferrierite becomes a negative thermal expansion material. Accurate variable-temperature single-crystal X-ray diffraction measurements confirm the transition temperature and allow the changes in average atomic position to be followed with temperature. The results from the single-crystal X-ray diffraction study can be correlated with (29)Si MAS NMR chemical shifts for the low-temperature phase. At low temperatures the results show that the positive thermal expansivity is driven by an overall increase in Si[bond]Si distances related to an increase in Si[bond]O[bond]Si bond angles. However, in the high-temperature phase the Si[bond]O[bond]Si angles are approximately invariant with temperature, and the negative thermal expansion in this case is caused by transverse vibrations of the Si[bond]O[bond]Si units.     

Toward assessing the position-dependent contributions of backbone hydrogen bonding to beta-sheet folding thermodynamics employing amide-to-ester perturbations

An amide-to-ester backbone substitution in a protein is accomplished by replacing an alpha-amino acid residue with the corresponding alpha-hydroxy acid, preserving stereochemistry, and conformation of the backbone and the structure of the side chain. This substitution replaces the amide NH (a hydrogen bond donor) with an ester O (which is not a hydrogen bond donor) and the amide carbonyl (a strong hydrogen bond acceptor) with an ester carbonyl (a weaker hydrogen bond acceptor), thus perturbing folding energetics. Amide-to-ester perturbations were used to evaluate the thermodynamic contribution of each hydrogen bond in the PIN WW domain, a three-stranded beta-sheet protein. Our results reveal that removing a hydrogen bond donor destabilizes the native state more than weakening a hydrogen bond acceptor and that the degree of destabilization is strongly dependent on the location of the amide bond replaced. Hydrogen bonds near turns or at the ends of beta-strands are less influential than hydrogen bonds that are protected within a hydrophobic core. Beta-sheet destabilization caused by an amide-to-ester substitution cannot be directly related to hydrogen bond strength because of differences in the solvation and electrostatic interactions of amides and esters. We propose corrections for these differences to obtain approximate hydrogen bond strengths from destabilization energies. These corrections, however, do not alter the trends noted above, indicating that the destabilization energy of an amide-to-ester mutation is a good first-order approximation of the free energy of formation of a backbone amide hydrogen bond.     

Cooperative and substitution effects in enhancing strengths of halogen bonds in FCl⋯CNX complexes

In this paper, the cooperative effect of halogen bond with hydrogen bond has been used to make a halogen bond in FCl-CNH dimer vary from a chlorine-shared one to an ion-pair one. The halogen bond is strengthened in FCl-CNH-CNH trimer and its maximal interaction energy equals to -76 kJ∕mol when the number of CNH in FCl-CNH-(CNH)(n) polymer approaches infinity. Once the free H atom in FCl-CNH-CNH trimer is replaced with alkali metals, the halogen bond becomes strong enough to be an ion-pair one in FCl-CNH-CNLi and FCl-CNH-CNNa trimers. An introduction of a Lewis acid in FCl-CNH dimer has a more prominent effect on the type of halogen bond. A prominent cooperative effect is found for the halogen bond and hydrogen bond in the trimers. FH-FCl-CNH-CNH and FH-FCl-CNH-CNLi tetramers have also been studied and the interaction energy of halogen bonding in FH-FCl-CNH-CNLi tetramer is about 12 times as much as that in the FCl-CNH dimer. The atoms in molecules and natural bond orbital analyses have been carried out for these complexes to understand the nature of halogen bond and the origin of the cooperativity.     

Evidences of alkali-induced softening of the oxygen-substrate bond

The interaction of oxygen with alkalis (Na, K) on Ni(111) was studied by high-resolution electron energy loss spectroscopy. Loss measurements revealed for the first time a softening of the O-Ni bond and, simultaneously, a strengthening of the alkali-Ni bond in the alkali+O coadsorbed phase, in perfect agreement with recent theoretical calculations. The weakening of the O-Ni bond was ascribed to the alkali-induced filling of the O 2p(z) antibonding orbitals. Different physical mechanisms were discussed for explaining the strengthening of the alkali-substrate bond whenever alkalis are coadsorbed with O adatoms.     

Nature of the Hydrogen Bond Enhanced Halogen Bond

The factors responsible for the enhancement of the halogen bond by an adjacent hydrogen bond have been quantitatively explored by means of state-of-the-art computational methods. It is found that the strength of a halogen bond is enhanced by ca. 3 kcal/mol when the halogen donor simultaneously operates as a halogen bond donor and a hydrogen bond acceptor. This enhancement is the result of both stronger electrostatic and orbital interactions between the XB donor and the XB acceptor, which indicates a significant degree of covalency in these halogen bonds. In addition, the halogen bond strength can be easily tuned by modifying the electron density of the aryl group of the XB donor as well as the acidity of the hydrogen atoms responsible for the hydrogen bond.