Bond length and the electron density at the bond critical point: X--X, Z--Z, and C--Z bonds (X = Li-F, Z = Na-Cl)

The aim was to investigate the relationship between the bond length and the electron density at the bond critical point in homonuclear X--X and Z--Z and heteronuclear C--Z bonds (X = Li-F, Z = Na-Cl). The d,rho(c) pairs were obtained from 472 target bonds in DFT-optimized (B3LYP/6-311+G(d,p)) small molecular species. These species were selected arbitrarily but with a view to maximize the range widths WR for each atom combination. It was found that (i) with one clear exception, the d(A - A) means (A = X or Z) correlate linearly with the bond lengths d(A(2)) of the respective diatomic molecules; (ii) the d(A - A) means correlate parabolically with n, the formal number of valence electrons in the atoms of the bond; and (iii) with increasing sample size N the ratio WR(rho(c))/WR(d) appears to converge toward a representation f [WR(rho(c))/WR(d)](N-->infinity) characteristic of A. Detailed analysis of the d,rho(c) relationship has shown that by and large simple power regression accounts best for the DFT data. The regression coefficients of d = arho(c) (-b) and rho(c) = alphad(-beta) (b, beta > 0) vary with n in a seemingly irregular manner but one that is consistent with simple chemical notions. The d(A(2)) can be approximated in terms of multilinear MO electron occupancies.     

HCHO+X(X=F、Cl、Br)的反应机理

采用CCSD/6-311++G(d,p)//B3LYP/6-311++G(d,p)方法研究了HCHO与卤素原子X(X=F、Cl、Br)的反应机理. 计算结果表明, 卤素原子X(X=F、Cl、Br)主要通过直接提取HCHO中的H原子生成HCO+HX(X=F、Cl、Br). 另外还可以生成稳定的中间体, 中间体再通过卤原子夺氢和氢原子直接解离两个反应通道分别生成HCO+HX(X=F、Cl、Br)和H+XCHO(X=F、Cl、Br). 其中卤原子夺氢通道为主反应通道, HCO和HX(X=F、Cl、Br)为主要的反应产物; 且三个反应的活化能均较低, 说明此类反应很容易进行, 计算结果与实验结果符合很好. 电子密度拓扑分析显示, 在HCHO+X反应通道(b)中出现了T型结构过渡态, 结构过渡态(STS)位于能量过渡态(ETS)之后. 并且按F、Cl、Br的顺序, 结构过渡态出现得越来越晚.     

Structures and Aromaticity of Three-membered BeXP （X = C,Si, Ge） and CYP （Y = O,S, Se） Rings

Three-membered BeXP （X = C, Si, Ge） and CYP （Y = O, S, Se） rings are theoretically investigated using density functional theory （DFT） methods at the B3LYP/6-311＋G^＊ and B3PW91/6-311＋G^＊ levels of theory. The research results show that the size of atoms has a great influence on the structural stability of these species. The wiberg bond indexs （WBIs） suggest the existence of delocalization in these structures. Negative nucleus-independent chemical shift （NICS） values for these species indicate that a strong ring current exists in these three-membered structures （Cs symmetry）. A detailed molecular orbital （MO） analysis further reveals that a delocalized π MO strengthens the structural stability and makes these species show strong aromatic characters.     

Redox energetics of hypercloso boron hydrides B(n)H(n) (n = 6-13) and B12X12 (X = F, Cl, OH, and CH3)

The reduction potentials (E°(Red) versus SHE) of hypercloso boron hydrides B(n)H(n) (n = 6-13) and B(12)X(12) (X = F, Cl, OH, and CH(3)) in water have been computed using the Conductor-like Polarizable Continuum Model (CPCM) and the Solvation Model Density (SMD) method for solvation modeling. The B3LYP/aug-cc-pvtz and M06-2X/aug-cc-pvtz as well as G4 level of theory were applied to determine the free energies of the first and second electron attachment (ΔG(E.A.)) to boron clusters. The solvation free energies (ΔG(solv)) greatly depend on the choice of the cavity set (UAKS, Pauling, or SMD) while the dependence on the choice of exchange/correlation functional is modest. The SMD cavity set gives the largest ΔΔG(solv) for B(n)H(n)(0/-) and B(n)H(n)(-/2-) while the UAKS cavity set gives the smallest ΔΔG(solv) value. The E°(Red) of B(n)H(n)(-/2-) (n = 6-12) with the G4/M06-2X(Pauling) (energy/solvation(cavity)) combination agrees within 0.2 V of experimental values. The experimental oxidative stability (E(1/2)) of B(n)X(n)(2-) (X = F, Cl, OH, and CH(3)) is usually located between the values predicted using the B3LYP and M06-2X functionals. The disproportionation free energies (ΔG(dpro)) of 2B(n)H(n)(-) → B(n)H(n) + B(n)H(n)(2-) reveal that the stabilities of B(n)H(n)(-) (n = 6-13) to disproportionation decrease in the order B(8)H(8)(-) > B(9)H(9)(-) > B(11)H(11)(-) > B(10)H(10)(-). The spin densities in B(12)X(12)(-) (X = F, Cl, OH, and CH(3)) tend to delocalize on the boron atoms rather than on the exterior functional groups. The partitioning of ΔG(solv)(B(n)H(n)(2-)) over spheres allows a rationalization of the nonlinear correlation between ΔG(E.A.) and E°(Red) for B(6)H(6)(-/2-), B(11)H(11)(-/2-), and B(13)H(13)(-/2-).     

Theoretical study of (CH...C)- hydrogen bonds in CH(4-n)X(n) (X = F, Cl; n = 0, 1, 2) systems complexed with their homoconjugate and heteroconjugate carbanions

This work deals with a theoretical study of the (CH...C)- hydrogen bonds in CH4, CH3X, and CH2X2 (X = F, Cl) complexed with their homoconjugate and heteroconjugate carbanions. The properties of the complexes are calculated with the B3LYP method using the 6-311++G(d,p) or 6-311++G(2df,2p) basis sets. The deprotonation enthalpies (DPE) of the CH bond or the proton affinities of the carbanions (PA(C-) are calculated as well. All the systems with the exception of the CH4...CHCl2(-) one are characterized by a double minimum potential. In some of the complexes, the (CH(b)...C)- hydrogen bond is linear. In other systems, such as CH3F...CH2F- and CH3F...CHF2(-), there is a large departure from linearity, the systems being stabilized by electrostatic interactions between the nonbonded H of the neutral molecule and the F atom of the carbanion. In the transition state, the (CH(b)...C)- bond is linear, and there is a large contraction of the intermolecular C...C distance. The binding energies vary within a large range, from -1.4 to -11.1 kcal mol(-1) for the stable complexes and -8.6 to -44.1 kcal mol(-1) for the metastable complexes. The energy barriers to proton transfer are between 5 and 20 kcal mol(-1) for the heteroconjugate systems and between 3.8 and 8.3 kcal mol(-1) for the homoconjugate systems. The binding energies of the linear complexes depend exponentially on 1.5DPE - PA(C-), showing that the proton donor is more important than the proton acceptor in determining hydrogen bond strength. The NBO analysis indicates an important electronic reorganization in the two partners. The elongations of the CH bond resulting from the interaction with the carbanion depend on the occupation of the sigma*(CH(b)) antibonding orbitals and on the hybridization of the C bonded to H(b). The frequency shifts of the nu(CH)(A1) stretching vibration range between 15 and 1150 cm(-1). They are linearly correlated to the elongation of the CH(b) bond.     

Quantum-chemical Study on the Structures and Properties of Uracil-BX3 （X = F, Cl） Complexes

1 INTRODUCTION The intermolecular interaction of bases in DNA or RNA is of immense interest and significance to che- mists and biologists alike. The interactions of these bases with metal cations, solvent molecules and other small molecules or ions would affect the struc- ture and biological properties or recognition process,which has been investigated widely[1～8]. Boron contained compounds are electron deficient com- pounds and have been extensively used as catalysts in chemical react…     

C6F5X＋（X=Cl,Br,I,CH3）离子的理论研究

用DFT B3LYP方法及6-311G（d,p）,6-311＋G（d,p）和LanL2dz基组,对C6F5X＋（X=Cl,Br,I,CH3）阳离子做了理论研究,优化了它们的电子基态的构型,计算了对应分子的垂直电离势（VIP）和绝热电离势（AIP）.结果表明四种离子的构型的对称点群和对应分子相同,但构型参数有明显差别.B...     

Transition state structure and energetics of the N(2)O + X (X = Cl,Br) reactions

The structural and vibrational properties of the transition state of the N(2)O + X (X = Cl,Br) reactions have been characterized by ab initio methods using density functional theory. We have employed Becke's hybrid functional (B3LYP), and transition state optimizations were performed with 6-31G(d), 6-311G(2d,2p), 6-311+G(3d,2p), and 6-311+G(3df,2p) basis sets. For the chlorine atom reaction the coupled-cluster method (CCSD(T)) with 6-31G(d) basis set was also used. All calculations resulted in transition state structures with a planar cis arrangement of atoms for both reactions. The geometrical parameters of transition states at B3LYP are very similar, and the reaction coordinates involve mainly the breaking of the N-O bond. At CCSD(T)/6-31G(d) level a contribution of the O-Cl forming bond is also observed in the reaction coordinate. In addition, several highly accurate ab initio composite methods of Gaussian-n (G1, G2, G3), their variations (G2(MP2), G3//B3LYP), and complete basis set (CBS-Q, CBS-Q//B3LYP) series of models were applied to compute reaction energetics. All model chemistries predict exothermic reactions. The G3 and G2 methods result in the smallest deviations from experiment, 1.8 and 0 kcal mol(-1), for the enthalpies of reaction for N(2)O reaction with chlorine and bromine, respectively. The G3//B3LYP and G1 methods perform best among the composite methods in predicting energies of the transition state, with a deviation of 1.9 and 3.0 kcal mol(-1), respectively, in the activation energies for the above processes. However, the B3LYP/6-311+G(3df,2p) method gives smaller deviations of 0.4 and -1.0 kcal mol(-1), respectively. The performance of the methodologies applied in predicting transition state energies was analyzed.     

Topological characteristics of electron density distribution in SSXY --> XSSY (X or Y = F, Cl, Br, I) isomerization reactions

The reactions of SSXY to XSSY (X or Y = F, Cl, Br, I) have been studied at B3LYP/6-311++G(2df) and MP2/6-311++G(2df) levels based on B3LYP/6-311++G(2df) optimized geometries. There are two pathways (X or Y atom transferring) for each reaction of SSXY to XSSY(X or Y = F, Cl, Br, I). The "Atoms in Molecules" theory has been applied to analyze the topological characteristics of electron density distribution along the reaction path. (a) The S-S-X or S-S-Y ring structure transition region (STR) is contributed to S(1)-X or S(1)-Y bond formation and S(2)-X or S(2)-Y bond annihilation. The STR and structure transition state (STS) are defined. (b) Comparing the two pathways of each SSXY --> XSSY (X, Y = F, Cl, Br, I) reaction, X or Y atom transferring, the broader the STR is, the later the STS appears, and the pathway is easier. (c) When X linked to the same S site of a three-member ring (S-S-F, S-S-Cl, S-S-Br, or S-S-I), the ring STR becomes broader and the STS appears later according to the sequence of X = F, Cl, Br, and I. And in these cases, for exothermic reactions, the higher the DeltaE(P-->TS1) is, the broader the STR is and the later the STS appears. (d) When the same Y atom linked to different three-member-ring S-S-X, the STR becomes broader and the STS appears later according to the sequence of X = F, Cl, Br, and I in the ring. And in these cases, for exothermic reactions, the lower the DeltaE(P-->TS2) is, the broader the STR is and the later the STS appears.     

Theoretical investigation of adenine–BX3 (X=F,Cl) complex

Geometries and binding energies are predicted at B3LYP/6-311+G* level for the adenine–BX₃ (X=F,Cl) systems and four conformers with no imaginary frequencies have been obtained for both adenine–BF₃ and adenine–BCl₃, respectively, and single energy calculations using much larger basis sets (6-311+G(2df,p)) and aug-cc-pVDZ were carried out as well. The most stable conformer is BF₃ or BCl₃ connected to N₃ of adenine and with the stabilization energy of 22.55 or 20.59 kcal/mol at B3LYP/6-311+G* level (BSSE corrected). The analyses for the combining interaction between BX₃ and adenine with natural bond orbital method (NBO) and the atom-in-molecules theory (AIM) have been performed. The results indicate that all the conformers were formed with σ–p type interactions between adenine and BX₃, in which pyridine-type nitrogen or nitrogen atom of amino group offers its lone pair electron to the empty p orbital of boron atom and the concomitances of charge transference from adenine to BX₃ were occurred. Frequency analysis suggested that the stretching vibration of BX₃ underwent a red shift in complexes. Adenine–BF₃ complex was more stable than adenine–BCl₃ although the distance of B–N is shorter in the later.     

氮原子与卤代甲烷反应的直接氢抽提过程研究

利用B3LYP理论研究了N(~4S)+CH_3X(X = H, F, Cl)反应体系的直接氢抽提过 程,分别得到了各反应物、产物和过渡态的优化构型和谐振频率。同时应用了6- 31G(d), 6-311+G(d,p)和6-311+ + G(2d,2p)基组,考察其大小对反应体系中各物 种构型及能量的影响。理论计算表明,随着基组的增加,反应势垒逐渐降低,反应 吸热减少。对比取代甲烷的情形,结果表明反应过程中卤素原子具有典型的诱导效 应,降低了抽提势垒。     

CAl4X (X=Si,Ge): molecules with simultaneous planar tetracoordinate carbon, aluminum, and silicon/germanium

The authors report the first theoretical study on the hexa-atomic molecules CAl(4)X (X=Si,Ge) at the B3LYP/6-311++G(2d), MP2/6-311++G(2d), and CCSD(T)/6-311++G(3df) (single point) levels. Three low-lying isomers (within 2.0 kcal/mol) can be formally viewed as constructed by one Al+ interacting with the planar CAl3X- at the side Al-X bond (X-1), side Al-Al bond (X-2), and central C atom (X-3). The isomers X-1 and X-2 both have planar structures that include the planar tetracoordinate carbon, aluminum, and silicon/germanium, while the three-dimensional isomer X-3 has the pentacoordinate carbon. The planarity of X-1 and X-2 is ascribed to the ligand five-center two-electron bonding molecular orbital, similar to the orbital responsible for the planarity of CAl3X- (X=Si,Ge). Kinetically, the two planar structures X-1 and X-2 can be easily interconverted to each other via the intermediate X-3, indicative of their coexistence. Of particular interest, isomer X-1 represents the first example that simultaneously contains three types of planar centers in a single molecule, to the best of our knowledge. The three low-lying and structurally interesting isomers X-1, X-2, and X-3 await future experimental verification. The present results could enrich the planar chemistry.     

BX4- and AlX4- superhalogen anions (X = F, Cl, Br): an ab initio study

The vertical electron detachment energies (VDEs) of 30 MX 4 (-) (M = B, Al; X = F, Cl, Br) anions were calculated at the OVGF level with the 6-311+G(3df) basis sets. The largest vertical electron binding energy was found for the AlF 4 (-) system (9.789 eV). The strong VDE dependence on the symmetry of the species, ligand type, ligand-central atom distance, and bonding/nonbonding/antibonding character of the highest occupied molecular orbital was observed and discussed.     

Density functional theoretical study of a series of binary azides M(N3)n (n = 3, 4)

Geometrical structures of a series of binary azides M(N3)n (M = elements in groups 3 and 13 (n = 3) and in groups 4 and 14 (n = 4)) were investigated at the B3LYP/6-311+G level of theory. Our calculations found that binary group 3 triazides M(N3)3 (M = Sc, Y, La) and binary group 4 tetraazides M(N3)4 (M = Ti, Zr, Hf) turn out to be stable with all frequencies real having a similar linear M-N-NN structural feature, as previously reported for M(N3)4 (M = Ti, Zr, Hf). However, binary azides of group 13 M(N3)3 (M = B, Al, Ga, In, Tl) and group 14 elements M(N3)4 (C, Si, Ge, Sn, Pb) with bent M-N-NN bond angles differ obviously from binary group 3 and 4 azides in geometrical structure. These facts are mainly explained by the difference in electronic density overlap between the central atom and the alpha-N atoms of the azido groups. Two lone-pair electrons on the sp hybridization alpha-N atoms in the binary group 3 and 4 azides donate electron density into two empty d orbitals of the central transition metal atom and a pair of valence bonding electrons, resulting in the alpha-N atoms acting as a tridentate ligand. The sp2 hybridization alpha-N atoms of the binary group 13 and 14 azides only give one valence electron to form one valence bonding electron pair acting virtually as monodentate donors.     

Carbon-to-carbon identity proton transfer from allene, ketene, ketenimine, and thioketene to their respective conjugate anions in the gas phase. An ab initio study.

Gas-phase acidities of CH2=C=X (X = CH2, NH, O, and S) and barriers for the identity proton transfers (X=C=CH2 + HC triple bond C-X- right harpoon over left harpoon -X-C triple bond CH + CH2=C=X) as well as geometries and charge distributions of CH2=C=X, HC triple bond C-X- and the transition states of the proton transfer were determined by ab initio methods at the MP2/6-311+G(d,p)//MP2/6-311+G(d,p) and B3LYP/6-311+G(d,p) levels of theory. The acidities were also calculated at the CCSD(T)/6-311+G(2df,p) level. A major objective of this study was to examine how the enhanced unsaturation of CH2=C=X compared to that of CH3CH=X may affect acidities, transition state imbalances, and intrinsic barriers of the identity proton transfer. The results show that the acidities are all higher while the barriers are lower than for the corresponding CH3CH=X series. The transition states are all imbalanced but less so than for the reactions of CH3CH=X.     

N, P, and As ylides and aza- and arsa-Wittig reactions from topological analyses of electron density

The nature of bonding between N, P, and As constituent atoms in ylide systems with the R(3)XYR' formula (X = N, P, As; Y = N, P, As; R = F, H; R' = H, CH(3)) has been characterized by ab initio (MP2/6-311++G**) and density functional theory (B3LYP/6-311++G**) calculations. Its electronic structure has been analyzed through electron density with the quantum theory of atoms in molecules and the electron localization function (ELF). The characteristics of the central bond are inspected with the calculated rotational barriers. The results show that N has a behavior different from that of the remaining pnicogen atoms (P, As), where the bond is much stronger. Fluorine substituents strengthen the X-Y bond, reduce the bond distance, and increase the electron density in the central bond so that the substituent pulls charge from the bond in the pnicogen X atom. For the N-pnicogen ylides, the results showed different bonding characters between F and X atoms; depending on the position of the F atom, the difference of the bond character is sensed by the basin synaptic order, as it is deduced from the analysis of the ELF basins. The energy profiles of the rotational barriers have been calculated at the MP2/6-311++G** level, indicating that the electronegativity of the substituents is a relevant factor that has consequences in the characteristics of the X-Y bond.     

NXAl(3)+ (X = N, P, As): penta-atomic planar tetracoordinate nitrogen with N-X multiple bonding

Planar tetracoordinate nitrogen (ptN) has been successfully extended as a new branch of planar chemistry. As the simplest type of ptN, penta-atomic species (pptN, e.g., NAl(4)(-)) are known to have a "delocalized" molecular environment with a single bond between the central N and the ligand. In this paper, through an extensive isomeric search of a series of group V-based systems NXAl(3)(+) (X = N, P and As) in both singlet and triplet electronic states at the B3LYP/6-311+G(d) level, we report a class of novel pptN with unique chemical bonding, i.e., the central nitrogen and the connected ligand X (X = N, P and As) effectively form a highly "localized" N-X multiple bond, as confirmed by the aug-cc-pVTZ-B3LYP and MP2 calculations. The high-level CCSD(T)/aug-cc-pVTZ energetic calculations show that the three pptN species each have appreciable kinetic stability against structural transformation and fragmentation, which is confirmed by the Born-Oppenheimer molecular dynamics calculations. Possible formation pathways of the three pptNs are discussed. In particular, the pptN isomer with X = P, i.e., NPAl(3)(+), is the global minimum, making the pptN-based NPAl(3)(+) the most accessible via mass spectroscopic characterization. The present work demonstrates that the frequently used concept "localization vs. delocalization" in organic chemistry can also be transplanted to exotic planar chemistries like pptN.     

杂硼原子簇XB6+ (X=C,Si, Ge,Sn, Pb)的稳定性和芳香性

利用从头算MP2方法和密度泛函理论B3LYP和B3PW91方法, 研究了杂硼原子簇XB₆⁺ (X=C, Si, Ge, Sn, Pb)的结构、稳定性及化学键合情况. 对C, Si, Ge, B使用6-311+G(d)基组, 对Sn和Pb使用LANL2DZ赝势基组. 研究结果表明, 具有C_s对称性的假平面XB₆⁺ (X=C, Si, Ge, Sn, Pb)结构是势能面上的全域极小点, 其稳定性要高于C_6v对称性的锥形结构和C₂对称性的假锥形结构. 在B3LYP水平上, 对这些异构体的势能面的极小点进行了自然键轨道(NBO)的分析; 对最稳定构型的最高占据分子轨道(HOMO)和最低空轨道(LUMO)能级差、分子轨道(MO)和核独立化学位移(NICS)进行了计算和讨论. 分析了杂原子和硼原子间、相邻硼原子间的键合情况, 讨论了最稳定构型的芳香性质.     

((Fluoroformyl)imido)sulfuryl difluoride, FC(O)N=S(O)F2: structural, conformational, and configurational properties in the gaseous and condensed phases

Structural, conformational, and configurational properties of the gaseous molecule ((fluoroformyl)imido)sulfuryl difluoride, FC(O)N=S(O)F(2), have been studied by vibrational spectroscopy (IR (gas) and Raman (liquid)) and quantum chemical calculations (HF, MP2, and B3LYP with 6-31+G* and 6-311+G* basis sets); in addition, the solid-state structure has been determined by X-ray crystallography. FC(O)N=S(O)F(2) exists in the gas phase as a mixture of a favored antiperiplanar-synperiplanar form (the S=O double bond antiperiplanar with respect to the C-N single bond, and the C=O group synperiplanar with respect to the S=N double bond) in equilibrium with less abundant antiperiplanar-antiperiplanar, synclinal-synperiplanar, and synclinal-antiperiplanar structures. The crystalline solid at 163 K (monoclinic, P2(1)/c, a = 5.1323(7) A, b = 15.942(2) A, c = 16.798(2) A, beta = 95.974(3) degrees , Z = 12) consists of three similar antiperiplanar-synperiplanar forms.     

Theoretical study on the structure and formation mechanism of [C6H5Mm]- (M=Ag, Au; m=1-3)

The structures and formation mechanisms of the important intermediate phenyl-coinage metal complexes [C(6)H(5)M(m)](-) (M==Ag, Au, m = 1-3) are investigated at B3LYP//6-311G(d, p)/Lanl2dz level using Gaussian 03 program. The adiabatic electron affinity and vertical dissociation energy of [M(m)](-) and [C(6)H(5)M(m)](-) are calculated, which are excellently coincident with the experimental determination. The C(6)H(5) group bonds on metal clusters through M--C sigma bond in the complex [C(6)H(5)M(m)](-). The complexes [C(6)H(5)M(m)](-) (M==Ag, Au; m = 2-3) are generated through a stepwise reaction. The first step is a direct insertion reaction between [M(m)](-) (M==Ag, Au, m = 1-3) and C(6)H(6,) which leads to the generation of intermediate [C(6)H(5)M(m)H](-) (m = 1-3) with the activation and cleavage of C--H bond. The second step is the neutral metal atom abstracting the H atom to yield the product [C(6)H(5)M(m)](-).