The ring opening of cyclopropylidene to allene: key features of the accurate reaction surface

Summary The global potential energy surface, determined in the first paper [1] for the groundstate ring opening of cyclopropylidene to allene, is complemented by accurate calculations of its key regions. The basis set is extended and polarization functions are included. The full configuration space of four electrons in four reactive orbitals is enlarged to the full configuration space of eight electrons in eight active orbitals by including correlations in the unbroken, but stretched CC sigma bonds. The effect of further single and double excitations is examined. The geometries and relative energies of the critical regions are found to change only little except for the ring-opening energy barrier which is lowered to about 7 kcal/mol, in good agreement with the experimental estimate of about 6 kcal/mol. Furthermore, the bifurcation is shown to occurafter the transition state, in the neighborhood of a conical intersection on the steepest descent path from the ring-opening transition state to the allene isomerization transition state. The steepest descent paths and the conical intersection are documented in detail. The cogwheel-like free internal rotation of the two methyl groups is confirmed by the accurate calculations. A similar richness of features is believed to exist on many potential energy surfaces governing chemical reactions.Operated for the U.S. Department of Energy by Iowa State University under Contract No. 7405-Eng-82. This work was supported by the Office of Basic Energy Sciences     

The ring opening of cyclopropylidene to allene and the isomerization of allene:ab initio interpretation of the electronic rearrangements in terms of quasi-atomic orbitals

Summary A full optimized reaction space (FORS) remains invariant under arbitrary orthogonal transformations among its configuration-generating molecular orbitals. Localization of the latter for a FORS wavefunction yields molecular orbitals withquasi-atomic character which can be interpreted asmolecule-adapted minimal-basis-set atomic orbitals. In terms of these quasi-atomic FORS MOs, the configuration mixing in the FORS wavefunction, the representation of the density matrix, and the expansions of the natural orbitals provide information about the interactions that are responsible for the molecular energy changes. A basis-set-independent population analysis can be formulated which accomplishes the objectives of Mulliken's population analysis without the drawbacks stemming from the basis-set dependence of the latter. Through application of these procedures, explanations can be found for various features of the potential energy surface governing the ring opening of cyclopropylidene and the isomerization of allene.Operated for the U.S. Department of Energy by Iowa State University under contract No. 7405-ENG-82. This work was supported by the Office of Basic Energy Sciences     

The ring opening of substituted cyclopropylidenes to substituted allenes: the effects of steric and long-range electrostatic interactions

Summary It is shown that all stereospecific preferences found experimentally for the ring opening of substituted cyclopropylidenes are satisfactorily reproduced by adding steric and long-range electrostatic interactions to the cyclopropylidene reaction surface. The corresponding surface for dimethyl cyclopropylidene is mapped out in detail. The surface for 3-methyl- and 2-bromo-3-methyl-cyclopropylidene is explored around the transition region. From the success of this approach it is inferred that short-range covalent interactions are unlikely to be responsible for sterospecific preferences found in these systems.Operated for the U.S. Department of Energy by Iowa State University under Contract No. 7405-ENG-82. This work was supported by the office of Basic Energy Sciences     

Cyclopropane ring opening in the reaction of methylenecyclopropane with silyl radicals stabilized on an activated Aerosil surface

Alkyl type radicals stable at room temperature and incorporating a double bond not conjugated with the free valence, ≡Si−C(=CH₂)−CH₂−CH₂, are formed in the reaction of methylenecyclopropane with silyl radicals (≡SiO)₃Si on an activated Aerosil surface. Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 5, pp. 1065–1066, May, 1997.     

Theoretical study of the reaction of Ni with OCS

The reactivity of Ni⁺ with OCS on both doublet and quartet potential energy surfaces (PES) has been investigated at the B3LYP/6-311+G(d) level. The object of this investigation was the elucidation of the reaction mechanism. The calculated results indicated that both the CS and CO bond activations proceed via an insertion–elimination mechanism. Intersystem crossing between the doublet and quartet surfaces may occur along both the CS and CO bond activation branches. The ground states of NiS⁺ and NiO⁺ were found to be quartets, whereas NiCO⁺ and NiCS⁺ have doublet ground states. The CS bond activation is energetically much more favorable than the CO bond activation. All theoretical results are in line with early experiments.     

Potential energy surface and thermochemistry for the direct gas phase reaction of germane and water

Gas phase reaction between germane GeH₄ and water H₂O was investigated at CCSD(T)/[aug-cc-pVTZ-pp for Ge + Lanl2dz for H and O]//MP2/6-31G(d,p) level. Only the hydrogen elimination channels are monitored. Within the energy range of 100 kcal/mol, we located nine equilibrium and six transition states on the potential energy surface (PES) of the Ge–O–H systems. GeH₄ reacts with H₂O exothermically (by 2.37 kcal/mol) without a barrier to form a non-planar complex GeH₄·H₂O which isomerizes to GeH₃OH·H₂ and H₂GeOH₂·H₂ with a barrier of 44.34 kcal/mol and 53.75 kcal/mol respectively. The first step of hydrogen elimination gives two non-planar species, GeH₃OH and H₂GeOH₂ but germinol GeH₃OH is found to be more stable. Further thermal decomposition reactions of GeH₃OH involving hydrogen elimination have been studied extensively using the same method. The final hydrogen elimination step gives HGeOH which can exist in cis and trans forms. As the trans form is more stable, only the trans form is considered on the potential energy surface (PES) of the reaction. The important thermochemical parameters (∆_rE_tot + ZPE), ∆_rH and ∆_rG for the H₂ elimination pathways are predicted accurately.     

Theoretical study on the mechanism of cycloaddition reaction between dimethyl germylidene and formaldehyde

The cycloaddition mechanism of the reaction between singlet dimethyl germylidene and formaldehyde has been investigated with MP2/6-31G* method, including geometry optimization and vibrational analysis for the involved stationary points on the potential energy surface. The energies of the different conformations are calculated with CCSD (T)//MP2/6-31G* method. From the potential energy profile, we predict that the cycloaddition reaction between singlet dimethyl germylidene and formaldehyde has two dominant reaction pathways. First dominant reaction pathway consists of three steps: (1) the two reactants (R1, R2) firstly form an intermediate INT1a through a barrier-free exothermic reaction of 43.0 kJ/mol; (2) INT1a then isomerizes to a four-membered ring compound P1 via a transition state TS1a with an energy barrier of 24.5 kJ/mol; (3) P1 further reacts with formaldehyde(R2) to form a germanic heterocyclic compound INT3, which is also a barrier-free exothermic reaction of 52.7 kJ/mol; Second dominant reaction pathway is as following: (1) the two reactants (R1, R2) firstly form a planar four-membered ring intermediate INT1b through a barrier-free exothermic reaction of 50.8 kJ/mol; (2) INT1b then isomerizes to a twist four-membered ring intermediate INT1.1b via a transition state TS1b with an energy barrier of 4.3 kJ/mol; (3) INT1.1b further reacts with formaldehyde(R2) to form an intermediate INT4, which is also a barrier-free exothermic reaction of 46.9 kJ/mol; (4) INT4 isomerizes to a germanic bis-heterocyclic product P4 via a transition state TS4 with an energy barrier of 54.1 kJ/mol.     

Thermochemistry data from kinetics results: A test of quality of the potential energy surface

A straightforward test of the quality of potential energy surfaces in polyatomic systems is proposed based on obtaining thermochemical properties, in this case, standard enthalpies of formation, from kinetics results. Agreement with experiment lends confidence to the PESs, and the disagreement serves to help improve them.     

Potential energy surface of the (H2)2 dimer: an MP2 study

Fifteen structures of the (H₂)₂ dimer have been investigated at the MP2/[4s3p] level. The SCF and MP2 (2nd order Møller-Plesser treatment) interaction energies have been corrected for the basis set superposition error. Only the T-shaped structure has been established as a minimum on the potential energy surface. Two equivalent T-shaped structures are connected by a saddle point with a rhomboid structure.Dedicated to Professor J. Koutecký on the occasion of his 65th birthday     

The READY program: Building a global potential energy surface and reactive dynamic simulations for the hydrogen combustion

READY (REActive DYnamics) is a program for studying reactive dynamic systems using a global potential energy surface (PES) built from previously existing PESs corresponding to each of the most important elementary reactions present in the system. We present an application to the combustion dynamics of a mixture of hydrogen and oxygen using accurate PESs for all the systems involving up to four oxygen and hydrogen atoms. Results at the temperature of 4000 K and pressure of 2 atm are presented and compared with model based on rate constants. Drawbacks and advantages of this approach are discussed and future directions of research are pointed out. © 2014 Wiley Periodicals, Inc.     

The Role of High Excitations in Constructing Sub-spectroscopic Accuracy Intermolecular Potential of He-HCN: Critically Examined by the High-Resolution Spectra with Resonance States

Interpreting high-resolution rovibrational spectra of weakly bound complexes commonly requires spectroscopic accuracy (<1 cm^-1) potential energy surfaces (PES). Constructing high-accuracy ab initio PES relies on the high-level electronic structure approaches and the accurate physical models to represent the potentials. The coupled cluster approaches including single and double excitations with a perturbational estimate of triple excitations (CCSD(T)) have been termed the "gold standard" of electronic structure theory, and widely used in generating intermolecular interaction energies for most van der Waals complexes. However, for HCN-He complex, the observed millimeter-wave spectroscopy with high-excited resonance states has not been assigned and interpreted even on the ab initio PES computed at CCSD(T) level of theory with the complete basis set (CBS) limit. In this work, an effective three-dimensional ab initio PES for HCN-He, which explicitly incorporates dependence on the Q₁ (C-H) normal-mode coordinate of the HCN monomer has been calculated at the CCSD(T)/CBS level. The post-CCSD(T) interaction energy has been examined and included in our PES. Analytic two-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies for v₁(C-H)=0, and 1 to the Morse/Long-Range potential function form with root-mean-square deviations (RMSD) smaller than 0.011 cm^-1. The role and significance of the post-CCSD(T) interaction energy contribution are clearly illustrated by comparison with the predicted rovibrational energy levels. With or without post-CCSD(T) corrections, the value of dissociation limit (D₀) is 8.919 or 9.403 cm^-1, respectively. The predicted millimeter-wave transitions and intensities from the PES with post-CCSD(T) excitation corrections are in good agreement with the available experimental data with RMS discrepancy of 0.072 cm^-1. Moreover, the infrared spectrum for HCN-He complex is predicted for the first time. These results will serve as a good starting point and provide reliable guidance for future infrared studies of HCN doped in (He)_n clusters.     

值得引入物理化学教材的重要内容:势能面交叉

势能面交叉既是内转换和系间窜越的实际通道,也是联系光化学和热化学的重要桥梁。势能面交叉引起的非绝热过程广泛存在于各种生物、化学和材料的体系当中。笔者建议将势能面交叉的相关内容引入物理化学课程的教材中,因为这不但会使教材内容更加丰富和成体系,而且有利于学生了解科技发展前沿,激发他们探索未知的兴趣。     

C2H3和NO2反应势能面的理论研究

在CCSD(T)／6—311G(d，p)／／B3LYP／6—3llG(d，p)水平上给出了反应C2H3 NO2的详细势能面信息，并列出了中间体和过渡态的几何构型．通过深入分析反应路径及反应机理，得到5个能量可行的产物和6条反应通道，其中产物C2H3O NO的形成又有利，而产物CH2CO HNO则是次要产物，其他产物在通常条件下可以忽略．     

The new theory of electron transfer: application to the photosynthetic reaction centre

Based on recent developments in the theory of electron transfer, we prove that a non-polar environment is needed to maintain the high efficiency and chemical integrity of the photosynthetic reaction centre. We also determine the Gibbs energy diagram for the primary act of charge separation in photosynthesis, and propose an equivalent circuit that captures the principal features of the entire acceptor side of the electron transport chain in photosystem II.     

CH自由基和NO~2反应研究: II.反应的动力学计算

采用MP2(FULL)/6-31G(d)方法从动力学计算上探讨了CH自由基与NO~2反应的可能途径,找到了反应物,中间体及产物之间的能量通道和过渡态,报道了它们的构型、电子态及能量。并通过频率分析和IRC方法对所有的过渡态进行了验证。在此基础上求出了各步反应的活化能。在以前热力学研究的基础上,对于可能的反应通道进一步作了动力学分析,找到了反应主产物通道的分支比,与实验得到的分支比基本吻合。     

Potential energy surface of the reaction of imidazole with peroxynitrite: Density functional theory study

This article presents a theoretical investigation of the reaction mechanism of imidazole nitration by peroxynitrite using density functional theory calculations. Understanding this reaction mechanism will help in elucidating the mechanism of guanine nitration by peroxynitrite, which is one of the assumed chemical pathways for damaging DNA in cells. This work focuses on the analysis of the potential energy surface (PES) for this reaction in the gas phase. Calculations were carried out using Hartree–Fock (HF) and density functional theory (DFT) Hamiltonians with double‐zeta basis sets ranging from 6‐31G(d) to 6‐31++G(d,p), and the triple‐zeta basis set 6‐311G(d). The computational results reveal that the reaction of imidazole with peroxynitrite in gas phase produces the following species: (i) hydroxide ion and 2‐nitroimidazole, (ii) hydrogen superoxide ion and 2‐nitrosoimidazole, and (iii) water and 2‐nitroimidazolide. The rate‐determining step is the formation of a short‐lived intermediate in which the imidazole C₂ carbon is covalently bonded to peroxynitrite nitrogen. Three short‐lived intermediates were found in the reaction path. These intermediates are involved in a proton‐hopping transport from C₂ carbon to the terminal oxygen of the ? O? O moiety of peroxynitrite via the nitroso (ON? ) oxygen. Both HF and DFT calculations (using the Becke3–Lee–Yang–Parr functional) lead to similar reaction paths for proton transport, but the landscape details of the PES for HF and DFT calculations differ. This investigation shows that the reaction of imidazole with peroxynitrite produces essentially the same types of products (nitro‐ and nitroso‐) as observed experimentally in the reaction of guanine with peroxynitrite, which makes the former reaction a good model to study by computation the essential characteristics of the latter reaction. Nevertheless, the computationally determined activation energy for imidazole nitration by peroxynitrite in the gas phase is 84.1 kcal/mol (calculated at the B3LYP/6‐31++G(d,p) level), too large for an enzymatic reaction. Exploratory calculations on imidazole nitration in solution, and on the reaction of 9‐methylguanine with peroxynitrite in the gas phase and solution, show that solvation increases the activation energy for both imidazole and guanine, and that the modest decrease (15 kcal mol^?1) in the activation energy, due to the adjacent six member ring of guanine, is counterbalanced by solvation. These results lead to the speculation that proton tunneling may be at the origin of experimentally observed high reaction rate of guanine nitration by peroxynitrite in solution. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Bifurcation of reaction pathways: the set of valley ridge inflection points of a simple three-dimensional potential energy surface

This paper serves for the better understanding of the branching phenomenon of reaction paths of potential energy hypersurfaces in more than two dimensions. We apply the recently proposed reduced gradient following (RGF) method for the analysis of potential energy hypersurfaces having valley-ridge inflection (VRI) points. VRI points indicate the region of possible reaction path bifurcation. The relation between RGF and the so-called global Newton search for stationary points (Branin method) is shown. Using a 3D polynomial test surface, a whole 1D manifold of VRI points is obtained. Its relation to RGF curves, steepest descent and gradient extremals is discussed as well as the relation of the VRI manifold to bifurcation points of these curves. Received: 8 July 1998 / Accepted: 24 August 1998 / Published online: 23 November 1998     

The use of N-sulfenylimines in the β-lactam synthon method: Staudinger reaction, oxidation of the cycloadducts and ring opening of β-lactams

Selected N-sulfenylimines act as good nucleophilic partners in the Staudinger reaction with methoxy- and benzyloxy-ketenes. The choice of diisopropylethylamine as a non-nucleophilic Lewis base for the generation of ketenes from acid chlorides is a determining factor for the success of the reaction. N-Sulfenyl-β-lactams are obtained in good to excellent yields and with moderate cis/trans diastereoselectivity. Then, they are quantitatively and selectively transformed to N-sulfinyl- or N-sulfonyl-β-lactams, by adjusting the oxidation state of the sulfur atom. The oxidation process induces an inversion of polarity of the nitrogen atom's substituent and allows a subsequent smooth ring opening by reaction of N-thiolated-β-lactams with various nucleophiles. The overall sequence provides straightforward and efficient route to highly functionalized-β-amino acid derivatives.