Investigation of Highly Designable Dented Structures in HP Model with Hydrogen Bond Energy

Some highly designable protein structures have dented on the surface of their native structures, and are not full compactly folded. According to hydrophobic-polar （HP） model the most designable structures are full compactly folded. To investigate the designability of the dented structures, we introduce the hydrogen bond energy in the secondary structures by using the secondary-structure-favored HP model proposed by Ou-yang etc. The result shows that the average designability increases with the strength of the hydrogen bond. The designabilities of the structures with same dented shape increase exponentially with the number of secondary structure sites. The dented structures can have the highest designabilities for a certain value of hydrogen bond energy density.

Average Bond Energy and Fermi Level on Free Electronic Band Model

On the basis of free-electronic bands, the Fermi energy is calculated by summing the band eigenvalues over Brillouin-zones ,and the results may lead to understand the physical basis of the average-bond-energy model in the calculation of valence-band offsets.

A neural network protocol for predicting molecular bond energy

Molecular bond energy is a key parameter for analyzing the properties of chemical activity,stability and flexibility.Calculating bond energy is a challenge due to the cost of first-principles simulations and unsatisfactory prediction using empirical formula.Here we show that a neural network(NN)machine-learning method can achieve quick prediction of bond energies of organic molecules.Using atomic species and charge information as descriptors,we trained a NN protocol and applied it to predict the bond energy in a certain chemical bond that agreed with density functional theory calculations.This protocol also provided a way to evaluate the effects of different methods of atomic charge analysis on NN training.Trained to accurately estimate bond energies,this NN protocol provides a cost-effective tool for optimizing chemical reactions,accelerating molecular design,and other important applications.

Bonding Energy of a Molecular Orbital(Ⅱ)——Ab initio Calculation

Calculation of the bonding energy of a molecular orbital for a series of small molecules has been carried out by using ab initio STO-3G method. The results obtained demonstrate that the concept of the molecular orbital bonding energy is applicable for judging whether a molecular orbital is bonding, nonbonding or antibonding besides Mulliken overlap criterion.

Prediction of Bond Dissociation Energy for Organic Molecules Based on a Machine-Learning Approach

Bond dissociation energy(BDE),which refers to the enthalpy change for the homolysis of a specific covalent bond,is one of the basic thermodynamic properties of molecules.It is very important for understanding chemical reactivities,chemical properties and chemical transformations.Here,a machine learning-based comprehensive BDE prediction model was established based on the iBonD experimental BDE dataset and the calculated BDE dataset by St.John et al.Differential Structural and PhysicOChemical(D-SPOC)descriptors that reflected changes in molecules'structural and physicochemical features in the process of bond homolysis were designed as input features.

THE CALCULATION OF THE COHESIVE ENERGY OFГPHASE IN THE TRANSITIONAL LAYER FE ZN OF HEAT GALVANIZED SHEET USED IN CARS

hethesisanalysesthevalenceelectronstructuresof phase Γin Fe Zn transitionallayerof heat galvanized sheet used in cars by applying the Empirical Electron Theory of Solids andMolecules, and calculatesthebond energy ofthe major bondsand cohesiveenergy ofcrystals,from which we draw theconclusion:sincecrystal has alargercohesiveenergy, it has higherhardness, butsinceitsbondenergyisratherlow ,itiseasytobreak under pressurefrom out side, and thecrackiseasytocome up andspreadin phase Γ.

Diffusion Monte Carlo Study of Bond Dissociation Energies for BH2, B（OH）2, BCl2, and BCI

On basis of bond dissociation energies （BDEs） for BH2, B（OH）2, BCl2, and BCl, the diffusion Monte Carlo （DMC） method is applied to explore the BDEs of HB-H, HOB-OH, ClB-Cl, and B-Cl. The effect of the choice of orbitals, as well as the backflow transformation, is studied. The Slater-Jastrow DMC algorithm gives BDEs of 359.1±0.12 kJ/mol for HB-H, 410.5±0.50 kJ/mol for HOB-OH, 357.8±1.46 kJ/mol for ClB-Cl, and 504.5±0.96 kJ/mol for B-Cl using B3PW91 orbitals and similar BDEs when B3LYP orbitals are used. DMC with backflow corrections （BF-DMC） gives a HB-H BDE of 369.9±0.12 kJ/mol which is close to one of the available experimental value （375.8 kJ/mol）. In the case of HOB-OH BDE, the BF-DMC calculation is 446.04-1.84 k J/mol that is closer to the experimental BDE. The BF-DMC BDE for ClB-Cl is 343.2±2.34 kJ/mol and the BF-DMC B-Cl BDE is 523.3±0.33 kJ/mol, which are close to the experimental BDEs, 341.9 and 530.0 kJ/mol, respectively.

Is HOMO Energy Level a Good Parameter to Characterize Antioxidant Activity

Semiempirical quantum chemical method AM1 was employed to calculate the highest occupied molecular orbital (HOMO) energy levels (E-HOMO) for various types of antioxidants. It was verified that the correlation between logarithm of free radical scavenging rate constants (1gks) and E-HOMO substantially arises from the correlation between E-HOMO and O-H bond dissociation energies (BDE) of antioxidants. Furthermore, E-HOMO were poorly correlated with the logarithm of relative free radical scavenging rate constants (1gk(3)/k(1)) for various types of antioxidants that possess complex structures (r = 0.5602). So in a broad sense, E-HOMO was not an appropriate parameter to characterize the free radical scavenging activity of antioxidants.

The evaluation of bond dissociation energies for NO2 scission in nitro compounds using density functional and complete basis set methods

By using the density functional theory （B3LYP） and four highly accurate complete basis set （CBS-Q, CBS-QB3, CBS-Lq, and CBS-4M）ab initio methods, the X（C, N, O）-NO2 bond dissociation energies （BDEs） for CH3NO2, C2H3NO2, C2H5NO2, HONO2, CH3ONO2, C2H5ONO2, NH2NO2 （CH3）2NNO2 are computed. By comparing the computed BDEs and experimental results, it is found that the B3LYP method is unable to predict satisfactorily the results of bond dissociation energy （BDE）; however, all four CBS models are generally able to give reliable predication of the X（C, N, O）-NO2 BDEs for these nitro compounds. Moreover, the CBS-4M calculation is the least computationally demanding among the four CBS methods considered, Therefore, we recommend CBS-4M method as a reliable method of computing the BDEs for this nitro compound system.

Quantum chemical calculations of bond dissociation energies for COOH scission and electronic structure in some acids

Quantum chemical calculations are performed to investigate the equilibrium C-COOH bond distances and the bond dissociation energies（BDEs） for 15 acids.These compounds are studied by utilizing the hybrid density functional theory（DFT）（B3LYP,B3PW91,B3P86,PBE1PBE） and the complete basis set（CBS-Q） method in conjunction with the 6311G^＊＊ basis as DFT methods have been found to have low basis sets sensitivity for small and medium molecules in our previous work.Comparisons between the computational results and the experimental values reveal that CBS-Q method,which can produce reasonable BDEs for some systems in our previous work,seems unable to predict accurate BDEs here.However,the B3P86 calculated results accord very well with the experimental values,within an average absolute error of 2.3 kcal/mol.Thus,B3P86 method is suitable for computing the reliable BDEs of C-COOH bond for carboxylic acid compounds.In addition,the energy gaps between the highest occupied molecular orbital（HOMO） and the lowest unoccupied molecular orbital（LUMO） of studied compounds are estimated,based on which the relative thermal stabilities of the studied acids are also discussed.

Density Functional Calculations of C–NO_2 Bond Dissociation Energies for Nitroalkanes Molecules

Bond dissociation energies for the removal of nitrogen dioxide group in some nitroalkane energetic materials have been calculated by using the three hybrid density functional theory （DFT） methods B3LYP, B3PW91 and B3P86 with 6-31g^＊＊ and 6-311g^＊＊ basis sets. The computed BDEs have been compared with the available experimental results. It is found that the B3P86 method with 6-31g^＊＊ and 6-311g^＊＊ basis sets can obtain satisfactory bond dissociation energies （BDEs）, which are in extraordinary agreement with the experimental data. Considering the smaller mean absolute deviation and maximum difference, the reliable B3P86/6-311g^＊＊ method was recommended to compute the BDEs for the removal of nitrogen dioxide group in the nitroalkane energetic materials. Using the method, the BDEs of 8 other nitroalkane energetic materials have been calculated and the maximum difference from experimental value is 1.76 kcal.mo1^-1 （for the BDE of tC4Hg-NOz）, which further proves the reliability of B3P86/6-311g^＊＊ method. In addition, it is noted that the BDEs of C-NO2 bond change slightly for main chain nitroalkane compounds with the maximum difference of only 3.43 kcal mo1^-1.

Theoretical Study of the N-NO_2 Bond Dissociation Energies for Energetic Materials with Density Functional Theory

The N-NO2 bond dissociation energies （BDEs） for 7 energetic materials were computed by means of accurate density functional theory （B3LYP, B3PW91 and B3P86） with 6-31G＊＊ and 6-311G＊＊ basis sets. By comparing the computed energies and experimental results, we find that the B3P86/6-311G＊＊ method can give good results of BDE, which has the mean absolute deviation of 1.30kcal/mol. In addition, substituent effects were also taken into account. It is noted that the Hammett constants of substituent groups are related to the BDEs of the N-NO2 bond and the bond dissociation energies of the energetic materials studied decrease when increasing the number of NO2 group.

Research on C—C Bond Length Distribution in Hydrocarbon Molecules

The C--C bond dissociation energy （BDE） is a very important data in research of hydrocarbon cracking reactions, because it reflects the difficulty level of chemical reactions. But it is very difficult to obtain the C--C bond dissociation energy （BDE） by experiments, so using quantum chemistry calculation such as density functional theory （DFT） to study the C--C bond dissociation energy is a very useful means. The impact of acceptor substituents and donor substituents on the C--C bond length distribution was studied.

Bonding Energies and Structural Study of Alkylaluminium

Neutral aluminium alkyls are well known to act as ethylene oligomerization and polymerization catalysts and cocatalysts.On the basis of the full optimization of alkylaluminium compounds with Gaussian 98 program package at the B3LYP/6-31G＊＊ level,the selected structures and bonding energies were investigated extensively.The geometries and bonding energies of AlR3（R = H,CH3,C2H5,C3H7,C4H9） and Al（C2H5）2R＇（R＇ = C2H5,C3H7,C4H9,C5H11,C6H13） were investigated extensively,and we found that,along with the prolongation of carbon chains the terminal C-C bond is shortened gradually until to a constant value of about 0.1532 nm in C4H9;and the bonding energy almost remains constant.The dative bonding of C2H4 to Al（C2H5）3,whose bonding energy is only 15.30 kJ/mol,is very weak.

Covalent electron density analysis and surface energy calculation of gold with the empirical electron surface model

Based on the empirical electron surface model （EESM）,the covalent electron density of dangling bonds （CEDDB） was calculated for various crystal planes of gold,and the surface energy was calculated further.Calculation results show that CEDDB has a great influence on the surface energy of various index surfaces and the anisotropy of the surface.The calculated surface energy is in agreement with experimental and other theoretical values.The calculated surface energy of the close-packed （111） surface has the lowest surface energy,which agrees with the theoretical prediction.Also,it is found that the spatial distribution of covalent bonds has a great influence on the surface energy of various index surfaces.Therefore,CEDDB should be a suitable parameter to describe and quantify the dangling bonds and surface energy of various crystal surfaces.

Density Functional Theory Study of Marine Polybrominated Diphenyl Ethers in Anaerobic Degradation

Polybrominated diphenyl ethers(PBDEs)are a kind of serious pollutants in the ocean.Biodegradation is considered as an economical and safe way for PBDEs removal and reductive debromination dominates the initial pathway of anaerobic degradation.On the basis of experimental study,Octa-BDE 197,Hepta-BDE 183,Hexa-BDE 153,Penta-BDE 99 and Tetra-BDE 47 were selected as the initial degradation objects,and their debromination degradation were studied using density functional theory.The structures were optimized by Gaussian 09 program.Furthermore,the molecular orbitals and charge distribution were analyzed.All C-Br bond dissociation energies at different positions including ortho,meta and para bromine atoms were calculated and the sequence of debromination was obtained.There is a close relationship between molecular structure,charge,molecular orbital and C-Br bond.All PBDEs exhibited similar debromination pathways with preferential removal of meta and para bromines.

Structures and electronic properties of AUn-1Cu and AUn （n ≤ 9） clusters

A systematic study on the structure and electronic properties of gold clusters doped each with one copper atom has been performed using the density functional theory. The average bond lengths in the Aun-1Cu （n ≤ 9） bimetallic clusters are shorter than those in the corresponding pure gold clusters. The ionization potentials of the bimetallic clusters Aun-1Cu （n 〈 9） are larger than those of the corresponding homoatomic gold clusters except for Aus. The energy gaps of the Au-Cu binary clusters are narrower than those of the Aun clusters except AuCu and Au3Cu. No obvious even-odd effect exists in the variations of the electron affinities and ionization potentials for the Aun-1Cu （n ≤ 9） clusters, which is in contrast to the case of gold clusters Aun.

Effects of Bases on the Stabilities of Nucleoside C4'Radicals

C4'-H bond dissociation enthalpies of nucleosides were predicted using theoretical methods to a precision of 1-2 Kcal/mol. It was found that the stability of the C4' nucleoside radical is slightly dependent on the base. The orders of stability are dA < dG < dT < dC for deoxynucleosides and U < G < A = C for nucleosides.