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1.
Metal-thiolate active sites play major roles in bioinorganic chemistry. The M--S(thiolate) bonds can be very covalent, and involve different orbital interactions. Spectroscopic features of these active sites (intense, low-energy charge transfer transitions) reflect the high covalency of the M--S(thiolate) bonds. The energy of the metal-thiolate bond is fairly insensitive to its ionic/covalent and pi/sigma nature as increasing M--S covalency reduces the charge distribution, hence the ionic term, and these contributions can compensate. Thus, trends observed in stability constants (i.e., the Irving-Williams series) mostly reflect the dominantly ionic contribution to bonding of the innocent ligand being replaced by the thiolate. Due to high effective nuclear charges of the Cu(II) and Fe(III) ions, the cupric- and ferric-thiolate bonds are very covalent, with the former having strong pi and the latter having more sigma character. For the blue copper site, the high pi covalency couples the metal ion into the protein for rapid directional long range electron transfer. For rubredoxins, because the redox active molecular orbital is pi in nature, electron transfer tends to be more localized in the vicinity of the active site. Although the energy of hydrogen bonding of the protein environment to the thiolate ligands tends to be fairly small, H-bonding can significantly affect the covalency of the metal-thiolate bond and contribute to redox tuning by the protein environment.  相似文献   

2.
The reaction of the bifunctional organic molecule 1-(dimethylamino)-2-propyne (DMAP) on the Si(100) surface has been investigated by density functional calculations employing a two-dimer cluster model. We found that, once in the physisorbed dative bonded well (-20.0 kcal mol(-1)), DMAP can proceed via a number of pathways, involving the formation of Si-C sigma bonds, which lead to thermodynamically more stable configurations. We first considered the cycloaddition of the CC triple bond, leading to a Si-C di-sigma bonded product (-58.7 kcal mol(-1)), for which we computed an energy barrier of only 12.5 kcal mol(-1), consistently with the observed switching of DMAP adsorption linkage at 300 K. We also explored the dissociative pathway involving the methylene C-H bond cleavage on the dative bonded DMAP, leading to three adsorption products with one (-57.3 kcal mol(-1)) and three Si-C sigma bonds (-58.7 and -60.6 kcal mol(-1)). The energy barrier for this pathway is computed 24.7 kcal mol(-1) and may therefore compete at temperature above 300 K with the reaction pathway involving the addition of the alkyne unit.  相似文献   

3.
本文详细研究了络阴离子{Nd[SSCN(C_2H_5)_2]_4}~-的简化模型[Nd(SSCNH_2)_4]~-的电子结构和化学键合情况。从对键能的贡献看, 钕和硫原子之间的结合主要是离子性的, 但从电荷的重新分布看,应该认为共价结合对成键有一定贡献。σ键起主要作用, 对Nd—S和Nd—S′键来说, π键级只有σ键级的1/5~1/6。根据计算结果分析了为什么至今只合成了很少几种有机硫配位镧系络合物而存在大量稳定无机复合镧系硫化物的原因。建议了几种合成稳定的有机硫配位镧系络合物的可能途径。  相似文献   

4.
5.
A cationic hydrogen-substituted iridium silylene complex [(PNP)(H)Ir Si(Mes)H][B(C6F5)4] (2) was synthesized via hydride abstraction from the corresponding neutral iridium silyl hydride complex. DFT calculations for 2 indicate that the cationic charge is localized at the silicon center and depict a LUMO with predominant silicon p-orbital character. Notably, complex 2 reacts rapidly with unhindered alkenes at ambient temperatures to afford disubstituted silylene complexes via Si-C bond formation. Complex 2 is also the catalyst for alkene hydrosilation of primary silanes with a high degree of anti-Markovnikov selectivity.  相似文献   

6.
Ab initio studies carried out at the MP2(full)/6-311+G(2df) and MP2(full)/aug-cc-pVTZ-PP computational levels reveals that dinitrogen (N(2)) and cuprous halides (CuX, X = F, Cl, Br) form three types of systems with the side-on and end-on coordination of N(2): N[triple bond]N-CuX (C(infinity v)), N(2)-CuX (C(2v)) stabilized by the donor-acceptor bonds and weak van der Waals complexes N(2)...XCu (C(2v)) with dominant dispersive forces. An electron density transfer between the N(2) and CuX depends on type of the N(2) coordination and a comparison of the NPA charges yields the [N[triple bond]N](delta+)-[CuX](delta-) and [N(2)](delta-)-[CuX](delta+) formula. According to the NBO analysis, the Cu-N coordinate bonds are governed by predominant LP(N2)-->sigma*(Cu-X) "2e-delocalization" in the most stable N[triple bond]N-CuX systems, meanwhile back donation LP(Cu)-->pi*(N-N) prevails in less stable N(2)-CuX molecules. A topological analysis of the electron density (AIM) presents single BCP between the Cu and N nuclei in the N[triple bond]N-CuX, two BCPs corresponding to two donor-acceptor Cu-N bonds in the N(2)-CuX and single BCP between electron density maximum of the N[triple bond]N bond and halogen nucleus in the van der Waals complexes N(2)...XCu. In all systems values of the Laplacian nabla(2)rho(r)(r(BCP)) are positive and they decrease following a trend of the complex stability i.e. N[triple bond]N-CuX (C(infinity v)) > N(2)-CuX (C(2v)) > N(2)...XCu (C(2v)). A topological analysis of the electron localization function (ELF) reveals strongly ionic bond in isolated CuF and a contribution of covalent character in the Cu-Cl and Cu-Br bonds. The donor-acceptor bonds Cu-N are characterized by bonding disynaptic basins V(Cu,N) with attractors localized at positions corresponding to slightly distorted lone pairs V(N) in isolated N(2). In the N[triple bond]N-CuX systems, there were no creation of any new bonding attractors in regions where classically the donor-acceptor bonds are expected and there is no sign of typical covalent bond Cu-N with the bonding pair. Calculations carried out for the N[triple bond]N-CuX reveal small polarization of the electron density in the N[triple bond]N bond, which is reflected by the bond polarity index being in range of 0.14 (F) to 0.11 (Cl).  相似文献   

7.
A set of four reactions, XCH3+X? (X=F, Cl, Br) and ClSiH3+Cl?, is investigated by means of the joint use of the electron localization function (ELF) and catastrophe theory (CT) analysis in order to obtain new insights into the bond breaking/forming processes for identity SN2 gas-phase reactions. Using DFT calculations at the OLYP/6-311++G(d,p) level, the effect of nucleophile (F, Cl, and Br anions) and the role of reacting centers (C or Si) on the reaction mechanisms are investigated. The charge-shift character of carbon–halogen bonds is studied by determination of the weights of the Lewis resonance structures. In all SN2 reactions at the carbon atom, there is a progressive reduction on the covalent character of the C–X bond from the reactant complex (0.41, 0.57, 0.58 for F, Cl, and Br, respectively) until the bond-breaking process, occurring before the transition structure is reached. On the other hand, the Si–Cl bond maintains its degree of covalent character (0.51) from the isolated fragments to the formation of a stable transition complex, presenting two silicon–chlorine charge-shifted bonds. The analysis of the ELF topology along the reaction path reveals that all reactions proceed via the same turning points of fold-type but the order is inverted for reactions taking place at C or Si atoms.  相似文献   

8.
The chemisorption of C8H8 bicyclo[2.2.2]-2,5,7-octatriene (barrelene) on the Si(100) surface is studied from first principles calculations. We find that, in the most stable configuration, barrelene is bonded to Si(100) through four Si-C bonds, with the C-C bonds which are orthogonal to the underlying Si dimers. The chemisorption reaction responsible for this structure is driven by the biradical nature of the Si-Si dimer bond. Two others, slightly less stable configurations, exist which are also characterized by four Si-C bonds but have a different orientation or location with respect to the Si(100) surface. The properties of these and other, less stable configurations have been investigated. For the most stable structures, the effect of different surface coverages has been also studied, showing a tendency to easily form complete monolayers of barrelene on the Si surface. On the basis of energetic and kinetic considerations, we expect that chemisorption of barrelene monolayers on the Si(100) surface will be characterized however by a certain amount of disorder. Finally, several possible reaction pathways, leading from one stable structure to another of lower energy or from a molecule in the gas phase to a chemisorbed configuration, have been investigated in detail and estimates of the relative energy barriers are given.  相似文献   

9.
The nature of the bonding of a series of gas-phase all-metal clusters containing the Al4 unit attached to an alkaline, alkaline earth, or transition metal is investigated at the DFT level using Mulliken, quantum theory of atoms in molecules (QTAIM), and Hirshfeld iterative (Hirshfeld-I) atomic partitionings. The characterization of ionic, covalent, and metallic bonds is done by means of charge polarization and multicenter electron delocalization. This Article uses for the first time Hirshfeld-I multicenter indices as well as Hirshfeld-I based atomic energy calculations. The QTAIM charges are in line with the electronegativity scale, whereas Hirshfeld-I calculations display deviations for transition metal clusters. The Mulliken charges fail to represent the charge polarization in alkaline metal clusters. The large ionic character of Li-Al and Na-Al bonds results in weak covalent bonds. On the contrary, scarcely ionic bonds (Be-Al, Cu-Al and Zn-Al) display stronger covalent bonds. These findings are in line with the topology of the electron density. The metallic character of these clusters is reflected in large 3-, 4- and 5-center electron delocalization, which is found for all the molecular fragments using the three atomic definitions. The previously reported magnetic inactivity (based on means of magnetic ring currents) of the pi system in the Al42- cluster contrasts with its large pi electron delocalization. However, it is shown that the different results not necessary contradict each other.  相似文献   

10.
The metal-ligand bonds of the title compounds have been investigated with the help of an energy partitioning analysis at the DFT level. It was found that the attractive orbital interactions between Fe and ER in (CO)(4)Fe-ER arise mainly from Fe <-- ER sigma donation. Only the boron diyl complexes (CO)(4)Fe-BR have significant contributions by Fe --> ER pi back-donation, but the Fe <-- BR sigma-donation remains the dominant orbital interaction term. The relative contributions of Fe-ER sigma donation and pi back-donation are only slightly altered when R changes from a good pi donor to a poor pi donor. Electrostatic forces between the metal fragment and the diyl ligand are always attractive, and they are very strong. They arise from the attraction between the local negative charge concentration at the overall positively charged donor atom E of the Lewis base ER and the positive charge of the iron nucleus. Electrostatic interactions and covalent interactions in (CO)(4)Fe-ER complexes have a similar strength when E is Al--Tl and when R is a good pi donor substituent. The Fe-BR bonds of the boron carbonyldiyl complexes have a significantly higher ionic character than the heavier group-13 analogues. Weak pi donor substituents R enhance the ionic character of the (CO)(4)Fe-ER bond. The metal-ligand bonds in the homoleptic complexes Fe(EMe)(5) and Ni(EMe)(4) have a higher ionic character than in (CO)(4)Fe-ER. The contribution of the TM --> ER pi back-donation to the Delta E(orb) term becomes clearly higher and contributes significantly to the total orbital interactions in the homoleptic complexes where no other pi acceptor ligands are present. The ligand BMe is nearly as strong a pi acceptor in Fe(BMe)(5) as CO is in Fe(CO)(5).  相似文献   

11.
作者曾系统研究[Ln(CCl_3COO)_3·dipy·H_2O]2配合物的合成和性质,并测定了[La(CCl_3COO)_3·dipy·H_2O]_2的晶体结构(待发表)。本文用量子化学INDO方法探讨镧配合物的电子结构和化学键。程序和参数见文献[1]。分子结构采用晶体结构数据。计算模型取配合物的一半,用HCOO~-代CCl_3COO~-,这样的近似对结果可能有影响,但在讨论羧基与La配位以及双聚机理时使图象更为简明清晰。分子骨架结构见图1,其中HCO_1O_5~-的一个氧  相似文献   

12.
The structures, infrared spectra, and electronic properties of the N7,N9-dimethylguaninium chloride have been studied. The interaction of one cation with one to four Cl anions and one Cl anion with two cations were investigated. Fifteen stable conformers are obtained. It is found that there are four acidic regions in the vicinity of the guaninium cations. In these regions, the cation could H-bond with one to three Cl anions but no more than three nearest anions. One Cl anion could H-bond with two cations. Additionally, evidence of a Cl...pi interaction between the anion and cation is observed. Among these structures, one cation interaction with two anions and two cations interaction with one anion have the larger interaction energies than the other series. Natural bond orbital analyses and molecular orbitals reveal that the charge transfer from anion(s) to the cation(s) occurs mainly through either the Cllp --> sigma C-H, Cllp --> sigma N-H, or Cllp --> pi C8-N7 interactions. The interaction between Cl and sigma (C/N-H) or pi C-N produces a small bond order. This indicates that the Cl...H (Cl...pi) interaction exhibits a weak covalent character and suggests a strong ionic H-bond (Cl...pi bond). What's more, formation of Cl...H/Cl...pi bond decreases the bond order of the associated C/N-H bond or C8-N7 bond. In addition, examination of vibrational spectrum of each conformer explains the origin of H-bonding character.  相似文献   

13.
The equilibrium geometries, energies, harmonic vibrational frequencies, and nucleus independent chemical shifts (NICSs) of the ground state of P5(-) (D(5h)) anion, the [Ti (eta(5)-P5)]- fragment (C(5v)), and the sandwich complex [Ti(eta(5)-P5)2]2- (D(5h) and D(5d)) are calculated by the three-parameter fit of the exchange-correlation potential suggested by Becke in conjunction with the LYP exchange potential (B3LYP) with basis sets 6-311+G(2d) (for P) and 6-311+G(2df) (for Ti). In each of the three molecules, the P-P and Ti-P bond distances are perfectly equal: five P atoms in block P5(-) lie in the same plane; the P-P bond distance increases and the Ti-P bond distance decreases with the order P5(-), [Ti(eta(5)-P5)2]2-, and [Ti (eta(5)-P5)]-. The binding energy analysis, which is carried out according to the energy change of hypothetic reactions of the three species, predicts that the three species are all very stable, and [Ti (eta(5)-P5)]- (C(5v)), more stable than P5(-) and [Ti(eta(5)-P5)2]2- synthesized in the experiment, could be synthesized. NICS values, computed for the anion and moiety of the three species with GIAO-B3LYP, reveal that the three species all have a larger aromaticity, and NICS (0) of moiety, NICS (1) of moiety, and minimum NICS of the inner side of ring P5 plane in magnitude increase with the order P5(-), [Ti(eta(5)-P5)2]2-, and [Ti (eta(5)-P5)]-. By analysis of the binding energetic and the molecular orbital (MO) and qualitative MO correlation diagram, and the dissection of total NICS, dissected as NICS contributions of various bonds, it is the main reason for P5(-) (D(5h)) having the larger aromaticity that the P-P sigma bonds, and pi bonds have the larger diatropic ring currents in which NICS contribution are negative, especially the P-P sigma bond. However, in [Ti (eta(5)-P5)]- (C(5v)) and [Ti(eta(5)-P5)2]2- (D(5h), and D(5d)), the reason is the larger and more negative diatropic ring currents in which the NICS contributions of P-P pi bonds and P5-Ti bonds including pi, delta, and sigma bonds, especially P5-Ti bonds, are much more negative and canceled the NICS contributions of P and Ti core and lone pair electrons.  相似文献   

14.
Adsorption structures of the dibenzo[a,j]coronene (C(32)H(16)) molecule on the clean Si(001)-2 X 1 surface were investigated by scanning tunneling microscopy (STM) in conjunction with electronic structure calculations. The dibenzo[a,j]coronene molecules were found to adsorb on three different sites: one major adsorption site and two minor adsorption sites. The formation of four to eight Si-C covalent bonds is responsible for the different surface bonding structures observed. Bond strain effects due to out-of-plane bending of the molecule play a significant role in governing the surface bond energies. The geometries of the three adsorption sites were established by comparison of the experimental and simulated STM images. By applying an electrical pulse, the molecule can be made to hop from one site to another site without breaking the dibenzo[a,j]coronene molecular structure.  相似文献   

15.
作者曾系统研究[Ln(CCl3COO)3·dipy·H2O]2配合物的合成和性质,并测定了[La(CCl3COO)3·dipy·H2O]2的晶体结构(待发表)。  相似文献   

16.
The flexibility of valence bond (VB) theory provides a new method of calculating pi-bond energies in the double-bonded species H(m)A=BH(n), where A, B = C, N, O, Si, P, S. This new method circumvents the problems usually associated with obtaining pi-bond strengths by targeting only the pi bond, while all other factors remain constant. In this manner, a clean separation between sigma- and pi effects can be achieved which highlights some expected trends in bond strength upon moving from left to right and up and down the Periodic Table. Intra-row pi bonds conform to the classic statement by Pauling [L. Pauling, The Natiure of the Chemical Bond, Cornell University Press, Ithaca, 1960, 3rd edition] regarding the relationship of heteronuclear bond strengths to their homonuclear constituents whereas inter-row pi bonds do not. This variance with Pauling's statement is shown to be due to the constraining effect of the underlying sigma bonds which prevents optimal p(pi)-p(pi) overlap. While Pauling's statement was based on the assumption that the resonance energy (RE) would be large for heteronuclear and small for homonuclear bonds, we have found large REs for all bonds studied herein; this leads to the conclusion that REs are dependent not only on the electronegativity difference but also the electronegativity sum of the constituent atoms. This situation where the bond is neither covalent nor ionic but originates in the covalent-ionic mixing has been termed charge shift (CS) bonding [S. Shaik, P. Maitre, G. Sini, P. C. Hiberty, J. Am. Chem. Soc. 1992, 114, 7861]. We have shown that CS bonding extends beyond single sigma bonds in first row molecules, thus supporting the idea that CS-bonding is a ubiquitous bonding form.  相似文献   

17.
Atomic interaction lines (AILs) and the QTAIM's molecular graphs provide a predominantly two‐center viewpoint of interatomic interactions. While such a bicentric interpretation is sufficient for most covalent bonds, it fails to adequately describe both formal multicenter bonds as well as many non‐covalent interactions with some multicenter character. We present an extension to our Fragment, Atomic, Localized, Delocalized and Interatomic (FALDI) electron density (ED) decomposition scheme, with which we can measure how any atom‐pair's delocalized density concentrates, depletes or reduces the electron density in the vicinity of a bond critical point. We apply our method on five classical bonds/interactions, ranging from formal either two‐ or three‐center bonds, a non‐covalent interaction (an intramolecular hydrogen bond) to organometallic bonds with partial multicenter character. By use of 3D representation of specific atom‐pairs contributions to the delocalized density we (i) fully recover previous notion of multicenter bonding in diborane and predominant bicentric character of a single covalent C C bond, (ii) reveal a multicenter character of an intramolecular H‐bond and (iii) illustrate, relative to a Schrock carbene, a larger degree of multicenter M C interaction in a Fischer carbene (due to a presence of a heteroatom), whilst revealing the holistic nature of AILs from multicenter ED decomposition. © 2018 Wiley Periodicals, Inc.  相似文献   

18.
What is the nature of the C? C bond? Valence bond and electron density computations of 16 C? C bonds show two families of bonds that flesh out as a phase diagram. One family, involving ethane, cyclopropane and so forth, is typified by covalent C? C bonding wherein covalent spin‐pairing accounts for most of the bond energy. The second family includes the inverted bridgehead bonds of small propellanes, where the bond is neither covalent nor ionic, but owes its existence to the resonance stabilization between the respective structures; hence a charge‐shift (CS) bond. The dual family also emerges from calculated and experimental electron density properties. Covalent C? C bonds are characterized by negative Laplacians of the density, whereas CS‐bonds display small or positive Laplacians. The positive Laplacian defines a region suffering from neighbouring repulsive interactions, which is precisely the case in the inverted bonding region. Such regions are rich in kinetic energy, and indeed the energy‐density analysis reveals that CS‐bonds are richer in kinetic energy than the covalent C? C bonds. The large covalent–ionic resonance energy is precisely the mechanism that lowers the kinetic energy in the bonding region and restores equilibrium bonding. Thus, different degrees of repulsive strain create two bonding families of the same chemical bond made from a single atomic constituent. It is further shown that the idea of repulsive strain is portable and can predict the properties of propellanes of various sizes and different wing substituents. Experimentally (M. Messerschmidt, S. Scheins, L. Bruberth, M. Patzel, G. Szeimies, C. Paulman, P. Luger, Angew. Chem. 2005 , 117, 3993–3997; Angew. Chem. Int. Ed. 2005 , 44, 3925–3928), the C? C bond families are beautifully represented in [1.1.1]propellane, where the inverted C? C is a CS‐bond, while the wings are made from covalent C? C bonds. What other manifestations can we expect from CS‐bonds? Answers from experiment have the potential of recharting the mental map of chemical bonding.  相似文献   

19.
This paper deals with a central paradigm of chemistry, the electron-pair bond. Valence bond (VB) theory and electron-localization function (ELF) calculations of 21 single bonds demonstrate that along the two classical bond families of covalent and ionic bonds, there exists a class of charge-shift bonds (CS bonds) in which the fluctuation of the electron pair density plays a dominant role. In VB theory, CS bonding manifests by way of a large covalent-ionic resonance energy, RE(CS), and in ELF by a depleted basin population with large variances (fluctuations). CS bonding is shown to be a fundamental mechanism that is necessary to satisfy the equilibrium condition, namely the virial ratio of the kinetic and potential energy contributions to the bond energy. The paper defines the atomic propensity and territory for CS bonding: Atoms (fragments) that are prone to CS bonding are compact electronegative and/or lone-pair-rich species. As such, the territory of CS bonding transcends considerations of static charge distribution, and involves: a) homopolar bonds of heteroatoms with zero static ionicity, b) heteropolar sigma and pi bonds of the electronegative and/or electron-pair-rich elements among themselves and to other atoms (e.g., the higher metalloids, Si, Ge, Sn, etc), c) all hypercoordinate molecules. Several experimental manifestations of charge-shift bonding are discussed, such as depleted bonding density, the rarity of ionic chemistry of silicon in condensed phases, and the high barriers of halogen-transfer reactions as compared to hydrogen-transfers.  相似文献   

20.
Bonding in the series ONXYZ (X, Y, Z=H, F, Cl), HNNX3, HNNX2Y, HNNXY2 (X, Y=H, F), and OCX3-, OCX2Y-, OCXY2- (X, Y=H, F) shows evidence of a significant ionic contribution modifying the underlying covalent bonding. Increased ionic character can be correlated with oxidation-state differences between the bound atoms and is expressed in terms of shorter bond lengths. All members of the series, with the exception of ONH3, HNNH3, and OCH3-, possess a multiple O-N, N-N, or C-O bond modified by the ionic character of that bond. The O-N, N-N, and O-C single bonds in ONH3, HNNH3, and OCH3-, respectively, show some variation in length relative to "typical" single bonds of these types due to differences in ionic character. The two highest-occupied molecular orbitals in the ONXYZ or OCXYZ- (X, Y, Z=H, F) series which are piNO or piCO (when X=Y=Z=H) exhibit a distinct shift in their nodal plane as hydrogen is replaced by fluorine. The nodal plane moves from a location between the oxygen and the nitrogen or carbon to between the nitrogen or carbon and the fluorines impacting on the nature and length of the bonds joining these atoms. The pattern of N-F and C-F bond lengths in the series, ONH3-ONF3 and OCH3--OCF3-, respectively, lends support to the idea of resonance structures of the form ONXY+ F- or OCXY F- (where X, Y=H, F).  相似文献   

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