Comparison of Bifurcated Halogen with Hydrogen Bonds

Bifurcated halogen bonds are constructed with FBr and FI as Lewis acids, paired with NH₃ and NCH bases. The first type considered places two bases together with a single acid, while the reverse case of two acids sharing a single base constitutes the second type. These bifurcated systems are compared with the analogous H-bonds wherein FH serves as the acid. In most cases, a bifurcated system is energetically inferior to a single linear bond. There is a larger energetic cost to forcing the single σ-hole of an acid to interact with a pair of bases, than the other way around where two acids engage with the lone pair of a single base. In comparison to FBr and FI, the H-bonding FH acid is better able to participate in a bifurcated sharing with two bases. This behavior is traced to the properties of the monomers, in particular the specific shape of the molecular electrostatic potential, the anisotropy of the orbitals of the acid and base that interact directly with one another, and the angular extent of the total electron density of the two molecules.     

Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions, n→π* is the best understood with studies ranging from small molecules to β-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the β-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as n→σ* and π→π* that are energetically comparable to or larger than n→π*. We find that these interactions are sensitive to changes in the side chain of the residues in the β-turn of GB1, suggesting that the n→π* may not be the only component in dictating β-turn conformation and stability. Furthermore, a database search of n→σ* and π→π* in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches.     

Halogen Interactions in Halogenated Oxindoles: Crystallographic and Computational Investigations of Intermolecular Interactions

X-ray structural determinations and computational studies were used to investigate halogen interactions in two halogenated oxindoles. Comparative analyses of the interaction energy and the interaction properties were carried out for Br···Br, C-H···Br, C-H···O and N-H···O interactions. Employing Møller–Plesset second-order perturbation theory (MP2) and density functional theory (DFT), the basis set superposition error (BSSE) corrected interaction energy (E_int(BSSE)) was determined using a supramolecular approach. The E_int(BSSE) results were compared with interaction energies obtained by Quantum Theory of Atoms in Molecules (QTAIM)-based methods. Reduced Density Gradient (RDG), QTAIM and Natural bond orbital (NBO) calculations provided insight into possible pathways for the intermolecular interactions examined. Comparative analysis employing the electron density at the bond critical points (BCP) and molecular electrostatic potential (MEP) showed that the interaction energies and the relative orientations of the monomers in the dimers may in part be understood in light of charge redistribution in these two compounds.     

含能材料六硝基六氮杂异伍兹烷分子的B3LYP研究

在B3LYP/6-31G^**水平上对六硝基六氮杂异伍兹烷(CL-20)分子进行结构优化、集居数分析、自然键轨道和振动频率计算,得到与实验值相符的稳定构型.根据计算结果,讨论了键特性对分子性质的影响.     

(BN)_n团簇的结构和稳定性

用HF方法、密度泛函理论的B3LYP以及微扰理论的MP2方法 ,在 6 3 1G(d)基组水平上 ,对 (BN) n(n =1～ 16)团簇的各种可能结构进行了优化 .讨论了环状与笼状稳定团簇的几何构型、自然键轨道 (NBO)、振动频率、结合能、核独立化学位移 (NICS)和能量二次差分 ,得到了 (BN) n(n =1～ 16)团簇结构的稳定性信息 .比较了HF ,B3LYP以及MP2三种理论方法对(BN) n 团簇的适应性所表现出的差异 .     

A−H…σ Hydrogen Bonds: Dihydrogen and Cycloalkanes as Proton Acceptors

ωB97XD/aug-cc-pVTZ calculations were performed for complexes of dihydrogen, cyclopropane, cyclobutane and cyclopentane, with simple proton donating species such as hydrogen fluoride, hydrogen chloride, water, hydrogen cyanide and acetylene. Numerous dependencies between geometrical, energetic and topological parameters of complexes considered were found, since various theoretical approaches were applied: Quantum Theory of ‘Atoms in Molecules’ (QTAIM), Natural Bond Orbital (NBO) method and energy decomposition analysis (EDA). It was confirmed that complexes of dihydrogen and cyclopropane are linked through the A−H…σ interactions that may be classified as hydrogen bonds. In the case of complexes of cyclobutane such hydrogen bonds are rather weak. Other type and also weak A−H…C hydrogen bonds are formed for complexes with cyclopentane.     

1-取代-2-氨基苯并咪唑衍生物的理论计算及QSAR研究

在B3LYP/6-31＋g(d)计算水平下, 通过运用密度泛函理论(DFT)量子化学方法, 对7种1-取代-2-氨基苯并咪唑衍生物的电子结构特征进行了研究, 获得了它们的电离能、亲合能、化学硬度、化学软度、化学势、电负性、亲电性、分配系数、折射率、极化率、分子体积和分子表面积等参数. 结果表明, 在2-氨基苯并咪唑衍生物的1位引入取代基团, 对化合物的电荷布居和结构性质都有较大的影响|关联了定量结构-活性关系(QSAR), 7种化合物的半数致死量LD₅₀与极化率等有较好的相关性. 这些结果可为1-取代-2-氨基苯并咪唑衍生物的氧化代谢实验研究和毒性机理揭示等提供重要信息.     

Thermal Decomposition Kinetics of Ethane Halides and Derivatives（C_2H_（6-n）X_n（n = 1～3）;X = F,Cl,Br）：DFT Study and NBO Analysis

A theoretical study of the thermal decomposition kinetics of ethane halides(C2H6-nXn(n = 1～3);X = F,Cl,Br) has been carried out at the B3LYP/6-31++G** and B3PW91/631++G** levels of theory.Among these methods and comparison of activation parameters with available experimental values,the B3PW91/6-31++G** method is in good agreement with the experimental data.The analysis of bond order and natural bond orbital(NBO) charges,bond indexes,and synchronicity parameters suggest the elimination of HX in reactions 1～9(HF:compounds 1～3,HCl:compounds 4～6,and HBr:compounds 7～9) occur through a concerted and slightly asynchronous four-membered cyclic transition state type of mechanism.     

DFT Calculations of the Elimination Kinetics of Silacyclobutanes and its Methyl Derivatives in the Gas-Phase

Abstract

The gas-phase thermal decomposition kinetics of silacyclobutane (1), 1-methyl- silacyclobutane (2), and 1,1-dimethyl-1-silacyclobutane (3) has been theoretically studied at the B3LYP/6-311G**, B3PW91/6-311G**, and MPW1PW91/6-311G** levels. The B3LYP/6-311G** method was found to give a reasonable good agreement with the experimental kinetics and thermodynamic parameters. The decomposition reaction of compounds 1–3 yields ethylene and the corresponding silene. Based on the optimized ground state geometries using B3LYP/6-311G** method, the natural bond orbital (NBO) analysis of donor-acceptor (bonding–antibonding) interactions revealed that the perturbation energies (E₂) associated with the electronic delocalization from σ_Si1–C2 to σ*_C4–Si1 orbitals increase from compounds 1 to 3. The σ_Si1–C2→σ*_C4–Si1 resonance energies for compounds 1–3 are 1.17, 1.26, and 1.43 kcal/mol, respectively. Also, the decomposition process in these compounds is controlled by σ→σ* resonance energies. Moreover, the obtained order of energy barriers could be explained by the number of electron-releasing methyl groups substituted to the Si_sp2 atom. NBO analysis shows that the occupancies of σ_Si1–C2 bonds decrease for compounds 1–3 as 3 < 2 < 1, and the occupancies of σ*_Si1–C2 bonds increase in the opposite order (3 > 2 > 1). Moreover, these results can fairly explain the decrease of the energy barriers (ΔE_o) of the decomposition reaction of compounds 1 to 3. The calculated data demonstrate that in the decomposition process of the studied compounds, the polarization of the C₃–C₄ bond is the rate determining factor. Analysis of bond orders, NBO charges, bond indexes, synchronicity parameters, and IRC calculations indicate that these reactions are occurring through a concerted and asynchronous four-membered cyclic transition state type of mechanism.     

Comparison between Hydrogen and Halogen Bonds in Complexes of 6-OX-Fulvene with Pnicogen and Chalcogen Electron Donors

Quantum chemical calculations are applied to complexes of 6-OX-fulvene (X=H, Cl, Br, I) with ZH₃/H₂Y (Z=N, P, As, Sb; Y=O, S, Se, Te) to study the competition between the hydrogen bond and the halogen bond. The H-bond weakens as the base atom grows in size and the associated negative electrostatic potential on the Lewis base atom diminishes. The pattern for the halogen bonds is more complicated. In most cases, the halogen bond is stronger for the heavier halogen atom, and pnicogen electron donors are more strongly bound than chalcogen. Halogen bonds to chalcogen atoms strengthen in the order O<S<Se<Te, whereas the pattern is murkier for the pnicogen donors. In terms of competition, most halogen bonds to pnicogen donors are stronger than their H-bond analogues, but there is no clear pattern with respect to chalcogen donors. O prefers a H-bond, while halogen bonds are favored by Te. For S and Se, I-bonds are strongest, followed Br, H, and Cl-bonds in that order.