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.     

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.     

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.     

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.     

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.     

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.     

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.     

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σ~*(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.     

Hydrogen activation on Mo-based sulfide catalysts,a periodic DFT study

Hydrogen adsorption on Mo[bond]S, Co[bond]Mo[bond]S, and Ni[bond]Mo[bond]S (10 1 macro 0) surfaces has been modeled by means of periodic DFT calculations taking into account the gaseous surrounding of these catalysts in working conditions. On the stable Mo[bond]S surface, only six-fold coordinated Mo cations are present, whereas substitution by Co or Ni leads to the creation of stable coordinatively unsaturated sites. On the stable MoS(2) surface, hydrogen dissociation is always endothermic and presents a high activation barrier. On Co[bond]Mo[bond]S surfaces, the ability to dissociate H(2) depends on the nature of the metal atom and the sulfur coordination environment. As an adsorption center, Co strongly favors molecular hydrogen activation as compared to the Mo atoms. Co also increases the ability of its sulfur atom ligands to bind hydrogen. Investigation of surface acidity using ammonia as a probe molecule confirms the crucial role of sulfur basicity on hydrogen activation on these surfaces. As a result, Co[bond]Mo[bond]S surfaces present Co[bond]S sites for which the dissociation of hydrogen is exothermic and weakly activated. On Ni[bond]Mo[bond]S surfaces, Ni[bond]S pairs are not stable and do not provide for an efficient way for hydrogen activation. These theoretical results are in good agreement with recent experimental studies of H(2)[bond]D(2) exchange reactions.     

基于2(5H)-呋喃酮的碳-杂成键反应研究进展

2(5H)-呋喃酮结构单元广泛存在于天然产物中,同时许多2(5H)-呋喃酮类化合物也是重要的有机合成中间体.因此,基于常见2(5H)-呋喃酮(1)的有机合成研究近年来引起了人们的关注.根据在有机合成反应中成键方式的不同,综述了在2(5H)-呋喃酮(1)环上形成C-O,C-N,C-S,C-P,C-Se,C-Si等碳-杂键的反应研究进展.     

Quantitative relationships between bond lengths,stretching vibrational frequencies,bond force constants,and bond orders in the hydrogen-bonded complexes involving hydrogen halides

To uncover the correlation between the bond length change and the corresponding stretching frequency shift of the proton donor D–H upon hydrogen bond formation, a series of hydrogen-bonded complexes involving HF and HCl which exhibit the characteristics of red-shifted hydrogen bond were investigated at the MP2/aug-cc-pVTZ, M062X/aug-cc-pVTZ, and B3LYP/aug-cc-pVTZ(GD3) levels of theory with CP optimizations. A statistical analysis of these complexes leads to the quantitative illustrations of the relations between bond length and stretching vibrational frequency, between bond length and bond force constant, between stretching vibrational frequency and bond force constant, between bond length and bond order for hydrohalides in a mathematical way, which would provide valuable insights into the explanation of the geometrical and spectroscopic behaviors during hydrogen bond formation.     

Some measures for making halogen bonds stronger than hydrogen bonds in H2CS-HOX (X = F, Cl, and Br) complexes

The properties and applications of halogen bonds are dependent greatly on their strength. In this paper, we suggested some measures for enhancing the strength of the halogen bond relative to the hydrogen bond in the H(2)CS-HOX (X = F, Cl, and Br) system by means of quantum chemical calculations. It has been shown that with comparison to H(2)CO, the S electron donor in H(2)CS results in a smaller difference in strength for the Cl halogen bond and the corresponding hydrogen bond, and the Br halogen bond is even stronger than the hydrogen bond. The Li atom in LiHCS and methyl group in MeHCS cause an increase in the strength of halogen bonding and hydrogen bonding, but the former makes the halogen bond stronger and the latter makes the hydrogen bond stronger. In solvents, the halogen bond in the Br system is strong enough to compete with the hydrogen bond. The interaction nature and properties in these complexes have been analyzed with the natural bond orbital theory.     

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.     

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.     

Vibrational force fields for strained hydrocarbons involving exo-double bonds. An ab initio study

Ab initio calculations of stretching force constants for the carbon-carbon double bond in a series of molecules characterized by different amounts of strain in the neighbourhood of the double bond were performed. The stretching force constants for bonds adjacent to the double bond have also been calculated as well as all relevant coupling terms. The variation in the force constant for the double bond is in agreement with the variations in bond distance predicted previously. Furthermore, it appears that the stretching force constants are linearly related to the product of s-character of the hybrids forming the bond in question, if other effects remain roughly constant. This seems to be the case in a series of studied molecules. It turns out that the strength of an exo-double bond is proportional to the amount of the angular strain inherent in the ring fragments attached to the double bond.     

An empirical scheme for evaluating in situ bond energy from MNDO data

The in situ bond energy is evaluated from the resonance integral contribution to energy with a correction term of monatomic energy obtained from MNDO calculation. The sum of the in situ bond energies in a molecule is expected to be equal to its atomization energy. Root-mean-square error of heat of formation calculated from in situ bond energy for seventy nine molecules containing hydrogen, carbon, nitrogen, oxygen, and fluorine amounts to 5.5 kcal/mol. Correlations of in situ bond energy with contributional bond energy, bond dissociation energy, isolated stretching frequency, and bond length are performed and discussed.     

Mechanism of C[bond]H bond activation/C[bond]C bond formation reaction between diazo compound and alkane catalyzed by dirhodium tetracarboxylate

The B3LYP density functional studies on the dirhodium tetracarboxylate-catalyzed C-H bond activation/C-C bond formation reaction of a diazo compound with an alkane revealed the energetics and the geometry of important intermediates and transition states in the catalytic cycle. The reaction is initiated by complexation between the rhodium catalyst and the diazo compound. Driven by the back-donation from the Rh 4d(xz) orbital to the C[bond]N sigma*-orbital, nitrogen extrusion takes place to afford a rhodium[bond]carbene complex. The carbene carbon of the complex is strongly electrophilic because of its vacant 2p orbital. The C[bond]H activation/C[bond]C formation proceeds in a single step through a three-centered hydride transfer-like transition state with a small activation energy. Only one of the two rhodium atoms works as a carbene binding site throughout the reaction, and the other rhodium atom assists the C[bond]H insertion reaction. The second Rh atom acts as a mobile ligand for the first one to enhance the electrophilicity of the carbene moiety and to facilitate the cleavage of the rhodium[bond]carbon bond. The calculations reproduce experimental data including the activation enthalpy of the nitrogen extrusion, the kinetic isotope effect of the C[bond]H insertion, and the reactivity order of the C[bond]H bond.     

硫键：从概念形成到实际应用

早期含硫键物质的合成和硫键结构的发现为硫键概念形成奠定了基础。20世纪90年代以来,对硫族原子亲电性和亲核性的探索使人们对硫键的本质有了深刻的认识,促使了硫键概念的形成。此后,化学家分别于2002年和2010年开发了硫键超分子自组装和阴离子识别功能,并开始重视硫键在固体和溶液中的应用。随着对新型分子间作用力关注度的提高,硫键会越来越受到人们的重视,其应用也会有更广阔的前景。     

Si-C bond strength in cage-like methylsilsesquioxanes and methyl-bearing metalosilsesquioxanes estimated from DFT calculations

The strength of the Si-C bond in cage-like methylsilsesquioxanes and methyl-bearing coppersilsesquioxanes was estimated from the Mulliken bond populations calculated using the B3LYP density functional method. The estimation was performed using a linear relation between Mulliken bond populations and the calculated Si-C bond strengths in a series of silanes, which is in good agreement with the published data. The introduction of Cu atoms into the silsesquioxane cage leads to a decrease in the Si-C bond strength, which can be a reason for a considerable decrease in the thermal stability of metalorganosilsesquioxanes compared to their siloxane analogs.     

键能的分子轨道理论研究 1: 理论公式

从LCAO-MO出发, 给出了一个计算键能的近似方法, 即EAB(i)-∑∑CaiSabCbiεi为第i个占据分子轨道(MO)中的一对电子对A-B键键能的贡献。对所有分子轨道求和即为该键的键能: EAB=∑EAB(i)。按该方法, 不仅可以计算各种不同分子中每两个相键连原子间的键能, 还可以从MO及AO角度分析每一具体键, 如σ, π, δ键的键能以及各AO对键能的贡献。该方法虽有别于求键焓和平衡离解能De, 但计算结果和De的实验值甚相符合。通过对键能的分析研究, 能较好地揭示原子间的相互作用关系及化学键的强弱, 从而可进一步探讨化学反应活性, 反应速率等化学性质。