1,3,3-三硝基氮杂环丁烷及其衍生物的热解机理的AM1研究

用ＳＣＦ－ＭＯ－ＡＭ１方法计算研究了１，３，３－三硝基氮杂环丁烷和它的三个衍生物的分子几何构型，电子结构和热解机理，分子中连结偕二硝基的两个Ｃ－Ｎ键级较小，均裂该建所需活化能较低，可能是优先发生的主要热解引发反应，四个标题物均裂该键的活化能和该键的Ｗｉｂｅｒｇ键级之间存在良好的线性关系，线性相关系数为０．９９。     

Density-functional theory study of Iron(III) hydrolysis in aqueous solution

Fe(III) hydrolysis in aqueous solution has been investigated using density-functional methods (DFT). All possible structures arising from different tautomers and multiplicities have been calculated. The solvation energy has been estimated using the UAHF-PCM method. The hydrolysis free energies have been estimated and compared with the available experimental data. The different hydrolysis species have distinct geometries and electronic structures. We have shown that improvement of theory level in calculating the electronic energy does not necessarily improve the estimated free energies in aqueous solution since the UAHF-PCM is a simple method that neglects specific interactions with the solvent. Therefore, it is important to have the correct balance between theory level used in the electronic calculation and the UAHF-PCM. The PBE/TZVP/UAHF-PCM method has been found to describe correctly the hydrolysis energies of Fe(III), deviating about 3.0 kcal mol(-1) from experimental values.     

Modeling the dynamic equilibrium between oligomers of (AlOCH3)n in methylaluminoxane (MAO). A theoretical study based on a combined quantum mechanical and statistical mechanical approach

Density functional theory (DFT) has been used to calculate the energies of 36 different methylaluminoxane (MAO) cage structures with the general formula (MeAlO)n, where n ranges from 4 to 16. A least-squares fit has been used to devise a formula which predicts the total energies of the MAO with different n's giving an rms deviation of 4.70 kcal/mol. These energies in conjunction with frequency calculations based on molecular mechanics have been used to estimate the finite temperature enthalpies, entropies, and free energies for these MAO structures. Furthermore, formulas have been devised which predict finite temperature enthalpies and entropies for MAO structures of any n for a temperature range of 198.15-598.15 K. Using these formulas, the free energies at different temperatures have been predicted for MAO structures where n ranges from 17 to 30. The free energy values were then used to predict the percentage of each n found at a given temperature. Our calculations give an average n value of 18.41, 17.23, 16.89, and 15.72 at 198.15, 298.15, 398.15, and 598.15 K, respectively. Topological arguments have also been used to show that the MAO cage structure contains a limited amount of square faces as compared to octagonal and hexagonal ones. It is also suggested that the limited number of square faces with their strained Al-O bonds explain the high molar Al:catalyst ratio required for activation. Moreover, in this study we outline a general methodology which may be used to calculate the percent abundance of an equilibrium mixture of oligomers with the general formula (X)n.     

Quantum-Chemical Study of the Oxidative Ability of Nitro Compounds Using Decomposition of Some Simple Amines in the Presence of Triplet Nitromethane as an Example

The photooxidation of amines with triplet nitromethane has been studied using the uB3LYP/6-311g* method. The activation energies for hydrogen atom abstraction from ammonia and the amino group of methylamine or aniline have been found to be 14.1, 4.9, and 6.3 kJ mol^?1, respectively. Details of the hydrogen atom transfer mechanism have been studied, the structures of transition complexes have been revealed, and noncovalent interaction energies have been evaluated in terms of the theory of atoms in molecules.     

Theoretical study on the DNA interaction properties of copper(II) complexes

Theoretical studies on DNA-cleavage and DNA-binding properties of a series of Cu(II) complexes [Cu(bimda)(diimine)] 1–5 have been carried out by density functional theory (DFT). The optimized structures of Cu(II) complexes were docked into parallel, antiparallel and mixed G-quadruplexes, with which the binding energies of complexes 1–5 were obtained. The cytotoxicities of these complexes can be predicted preliminarily by the binding energies. To explore the energy changes of Cu(II) complexes in duplex DNA, the optimized structures of these complexes were docked into the duplex DNA, and the obtained docking models were further optimized using QM/MM method. The DNA-cleavage abilities of complexes 1–5 can be predicted accurately and explained reasonably by the computed intra-molecular reorganization energies of these complexes. This work reported here has implications for the understanding of the interaction Cu(II) complexes with the DNA, which might be helpful for the future directing the design of novel anticancer Cu(II) complexes.     

新的异体四氢键二聚体结构的理论研究

研究了一系列由不同单位通过DAAD－ADDA方式结合的新的异体二聚体体系。运 用密度泛函B31YP方法在3－21g水平上完全优化了单位和二聚体的结构，通过对体 系的结构特征、能量、相互作用能的分析研究，证实了这类新的超分子聚集体可通 过四重氢键自组装形成。     

SCMEH-MO calculations on lanthanide systems. III. Ln(CO)6, Ln(OC)6 (Ln = Nd,Sm)

The SCMEH-MO method with average relativistic and spin-orbit effects has recently been applied to study the electronic structure and bonding in samarium pentamethylcyclopentadienyls. In this report the same approach has been utilized in studying the electronic structures of Nd and Sm hexacarbonyls. In contrast to the stable transition metal d-block carbonyls, these lanthanide carbonyls are found to be quite unstable. These findings are based on calculated electronic structures and bond energies. © 1996 John Wiley & Sons, Inc.     

Large-Sized Ammonia Clusters and Solvation Energies of the Proton in Ammonia

The absolute solvation energies (free energies and enthalpies) of the proton in ammonia are used to compute the pK_a of species embedded in ammonia. They are also used to compute the solvation energies of other ions in ammonia. Despite their importance, it is not possible to determine experimentally the solvation energies of the proton in a given solvent. We propose in this work a direct approach to compute the solvation energies of the proton in ammonia from large-sized neutral and protonated ammonia clusters. To undertake this investigation, we performed a geometry optimization of neutral and protonated ammonia 30-mer, 40-mer, and 50 mer to locate stable structures. These structures have been fully optimized at both APFD/6-31++g(d,p) and M06-2X/6-31++g(d,p) levels of theory. An infrared spectroscopic study of these structures has been provided to assess the reliability of our investigation. Using these structures, we have computed the absolute solvation free energy and the absolute solvation enthalpy of the proton in ammonia. It comes out that the absolute solvation free energy of the proton in ammonia is calculated to be −1192 kJ mol^–1, whereas the absolute solvation enthalpy is evaluated to be −1214 kJ mol^–1. © 2019 Wiley Periodicals, Inc.     

Hydride dissociation energies of six-membered heterocyclic organic hydrides predicted by ONIOM-G4Method

Hydride dissociation energy is of great importance in understanding the hydride-donating abilities of organic hydrides. Although the hydride dissociation energies of some organic hydrides have been experimentally measured, much less attention has been focused on the investigation of these quantities from the first principles of physics. Herein, we developed an ONIOM-G4 method and carefully benchmarked this new method against 48 experimental hydride dissociation energies of diverse bulky molecules. It was found that with the combined methods of the HF/6-31+G(d,p)//IEFPCM/Bondi1.15 solvation model, the ONIOM-G4 method can predict the hydride dissociation energies with an error bar of only 1.7 kcal/mol. With the newly developed ONIOM-G4 method, we then systematically studied the hydride dissociation energies of six categories of biologically and pharmaceutically important six-membered heterocyclic organic hydrides, namely, the organic hydrides containing 1,4-dihydropyridine, 1,4-dihydropyrazine, 1,4-oxazine, 1,4-thiazine, 4H-pyran, and 4H-thiopyran ring structures. An extensive hydride dissociation energy scale containing over 100 six-memebered heterocyclic organic hydrides has been established, which may find applications in both synthetic organic chemistry and mechanistic studies of various chemical or biological processes involving transferring of the hydride anion.     

The effect of aqueous solvation upon alpha-helix formation for polyalanines

The incremental free energies of aqueous solution for acetyl(ala)NNH2 in its extended unfolded and alpha-helical conformations are compared using the SM5.2 solvation method of Cramer and Truhlar. A combination of density functional theory (DFT) at the B3LYP/D95(d,p) and AM1 has been employed using the ONIOM method. The incremental solvation energies of alpha-helical structures are very similar for both ONIOM and AM1 optimized structures as these structures do not significantly change upon solution. However, the conformations of the unfolded peptides change from extended beta-strand to polyproline II conformations upon aqueous solution. The incremental solvation free energy per residue of the polyproline II structure is about 2 kcal/mol/residue greater than that for the alpha-helix, representing an upper limit for the difference between the solvation energies. However, most of this difference disappears when the energy required to distort the optimized gas-phase extended beta-strand structure to the optimized polyproline II solution structure is included in the analysis, leaving an estimated difference in incremental solvation free energy of 0.3-0.5 kcal/mol favoring the unfolded structure. The solution structure sacrifices the stability derived from the intramolecular C5 H-bonds for more favorable interactions with the aqueous solvent.     

Microsolvation of protonated methane: structures and energetics of CH5(+)(H2)n

Effects of microsolvating CH(5)(+) with up to four H(2) molecules have been investigated in terms of structures and energies. For the smaller complexes, benchmark calculations have been carried out using MP2 and CCSD(T) with basis sets up to aug-cc-pV5Z quality and energies have been extrapolated to the infinite basis set limit. It is found that MP2 calculations using the aug-cc-pVQZ basis set or better yield robust reference data for both structures and energies. More than 30 stationary points including minima and first-order as well as second-order stationary points have been characterized by this method and are discussed in terms of solvation motifs. Finally, the performance of several density functionals has been assessed for this very demanding case. Popular GGA functionals such as BLYP and PBE fail, whereas the TPSS meta-GGA functional captures many structural and energetic aspects of microsolvation satisfactorily.     

硝酸甲酯分子间相互作用的DFT和ab initio比较

用密度泛函理论(DFT)和从头算(ab initio)方法,分别在B3LYP/6 31G和HF/6 31G水平上求得硝酸甲酯三种二聚体的全优化几何构型和电子结构,并用6 311G和6 311＋＋G基组进行总能量计算.对HF/6 31G计算结果进行MP4SDTQ电子相关校正.在各基组下均进行基组叠加误差(BSSE)和零点能(ZPE)校正求得结合能.对6 31G优化构型作振动分析并基于统计热力学求得200～600 K温度下单体和二聚体的热力学性质.详细比较两种方法的相应计算结果,发现DFT求得的分子间距离较短,分子内键长较长,所得结合能均小于相应ab initio计算值.     

Correlation between the transport behavior of polyimides and the conformational rigidity of their chains

For a number of polyimides, Kuhn segment lengths have been calculated by the Monte Carlo method under the free-rotation approximation and the energies of cohesion have been estimated by the group-contribution method. It has been shown that, in the case of isomeric polyimides characterized by close energies of interchain interactions, a decrease in the rigidity of chains always leads to reductions in the free volume and gas permeability. For polyimides of allied structures, the simultaneous (and frequently oppositely directed) effects of chain rigidity and the energy of interchain interactions ambiguously influence gas permeability. Both factors should be taken into account during estimation of the influence of chain rigidity on the transport characteristics of polymers. Small-scale effects of packing and mobility of chain fragments exert the decisive effect on the transport characteristics of polyimides possessing a decreased mobility of chains.     

Anchoring the potential energy surface of the cyclic water trimer

Six cyclic stationary points on the water trimer potential energy surface have been fully optimized at the MP2 level with the aug-cc-pVQZ basis set. In agreement with previous work, harmonic vibrational frequencies indicate that two structures are minima, three are transition states connecting minima on the surface while the remaining stationary point is a higher-order saddle point. The 1- and n-particle limits of the electronic energies of each of these six structures were estimated by systematically varying both the basis sets and theoretical methods. The former limit was approached with the cc-pVXZ and aug-cc-pVXZ families of basis sets (X=2-7) while MP2, CCSD(T), and BD(TQ) calculations helped examine the latter. Core correlation effects have also been assessed at the MP2 level with the cc-pCVXZ series of basis sets (X=2-5). These data have been combined to provide highly accurate relative energies and dissociation energies for these stationary points.     

Quantum-Chemical Modeling of B<Subscript>32</Subscript> Complexes with Nitrogen: Endo or Exo?

Computational modeling of borospherene B₃₂ complexes with nitrogen has been performed by the density functional theory method (DFT UB3LYP*/6-311+G(d)). The geometry of isomers of these complexes with a different starting orientation of N has been found, their relative energies have been calculated, and the spin density distribution has been studied. Computation results predict that the structures with a nitrogen atom or ion built into the boron cage are more favorable than the endohedral isomers.     

Interaction between uracil nucleobase and phenylalanine amino acid: the role of sodium cation in stacking

The stacking interactions in the uracil:phenylalanine (U:PHE) and (U:PHE)···Na⁺ complexes have been studied at different levels of theory, in which the structures were optimized by both standard and gradient counterpoise corrected methods. The Na⁺ cation can interact with different sites of stacked U:PHE unit. The geometrical parameters of the optimized structures and the calculated binding energies reveal the influence of cation interaction on π–π stacking and vice versa. The interplay between π–π stacking and cation interaction has also been investigated by topological analysis of electron charge density using atoms in molecules (AIM) method. A good agreement between the results of AIM analysis and calculated binding energies has been observed in dimer and complexes.     

Ab initio SCF calculations of the linear infinite chain of LiH according to the pseudo-lattice method

The pseudo-lattice (PL) method has been reformulated for ab initio self-consistent-field (SCF) calculations. The translational symmetries of infinite systems have been applied to the finite model chain by manipulating all the intramolecular and intermolecular Fock matrices. The nuclear repulsion energy has been corrected accordingly. The method has been tested for the linear chain of lithium hydride under the constraint of equidistance between all neighboring lithium and hydrogen atoms. The calculated results of the infinite chain have been compared with those of finite chains of lithium hydride under the same geometric constraint. The equilibrium geometries, band structures, intermolecular stabilization energies and potential curves have been studied. It is found that the infinite systems cannot be described by considering only first nearest neighbor interactions, and the intermolecular interactions must be considered at least up to third nearest neighbors in order to obtain accurate value of force constant of infinite systems. We can conclude from band structures of infinite chains that the boundary effect of the finite model chain is effectively removed by the PL method.     

原子团簇Ge11同分异体的密度泛函研究

用分子图形软件设计出多种Ge_11原子团簇模型,使用B3LYP密度泛函方法进行几何构型优化和振动频率计算,比较了14种同分异构体的总能量,得到了新的基态构型。锗原子团簇的大部分原子以三、四、五和六配位成键。在Ge11原子团簇中,双角反四棱柱衍生出来的构型能量较低,它是设计大分子锗原子团簇初始模型的重要结构单元。由三棱柱演变的构型能量居中。带心结构和共边构型带有高配位原子,其总能量较高,是不稳定的结构。     

基态氧(3^O2)氧化硅烯的密度泛函计算研究

采用密度泛函[B3LYP(full)/6-311+G^*]方法研究了基态氧(3^O2)氧化硅烯(Si2H4)的机理。计算了三重态初始中间体(IM(T1)到单重态中间体IM2(S0)反应交叉势能面,报道了各反应中间体、产物和过渡态的构型和能量,用频率分析方法对各过渡态进行了验证,进一步用IRC方法对主要的基元反应进行了考察,确定了历经生成1,2-二氧环氧硅烷中间体的氧化过程的主要反应通道。     

Density functional studies on hydrogen‐bonded clusters of hydrogen halides and the interaction on halide anions

Density functional theory (DFT) calculations have been performed to study the structures and stability of X^?·(HX)_n=2–5 clusters where X = F, Cl, Br at B3LYP/6‐311++G** level of theory. The presence of halide ions in these clusters disintegrates the hydrogen halide clusters. All the hydrogen halides are then hydrogen bonded to the centrally placed halide ions, thereby forming multiple hydrogen bonds. The interaction energies have been corrected for the basis set superposition error (BSSE) using Boy's counterpoise correction method. Evidence for the destruction of hydrogen bonds in hydrogen halide clusters due to the presence of halide ions is further obtained from topological analysis and natural bond orbital analysis. The chemical hardness and chemical potential have been calculated for all the anion clusters. The above analysis reveals that hydrogen bonding in these systems is not an essentially electrostatic interaction. The nature of the stabilization interactions operative in these multiple hydrogen‐bonded clusters has been explained in terms of many‐body contribution to interaction energies. From these studies, an attempt has been made to understand the nature of the molecular properties resulting from different electronegativities of the halogens. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005