Fe–Hg Interactions and P Chemical Shifts in [Fe(CO)3 (PPh2R)2(HgCl2)] (R=pym, fur, py, thi)

In order to study the effects of R group on Fe–Hg interactions and 31P chemical shifts, the structures of mononuclear complexes Fe(CO)₃(PPh₂R)₂ (R=pym:1, fur: 2, py: 3,thi: 4; pym=pyrimidine, fur=furyl, py=pyridine, thi=thiazole) and binuclear complexes [Fe(CO)₃(PPh₂R)₂(HgCl₂)] (R=pym: 5, fur: 6, py: 7, thi: 8) were studied using the density functional theory (DFT) PBE0 method. The 31P chemical shifts were calculated by PBE0-GIAO method. Nature bond orbital (NBO) analyses were also performed to explain the nature of the Fe–Hg interactions. The conclusions can be drawn as follows: (1) The complexes with nitrogen donor atoms are more stable than those with O or S atoms. The more N atoms there are, the higher is the stabilility of the complex. (2) The Fe–Hg interactions play a dominant role in the stabilities of the complexes. In 5 or 6, thereisa σ-bond between Fe and Hg atoms. However, in 7 and 8, the Fe–Hg interactions act as σ_P–Fe→n_Hg and σ_C–Fe→n_Hg delocalization. (3) Through Fe→Hg interactions, there is charge transfer from R groups towards the P, Fe, and Hg atoms, which increases the electron density on P nucleus in binuclear complexes. As a result, compared with their mononuclear complexes, the 31P chemical shifts in binuclear complexes show some reduction.     

C30卡宾三叶结分子结构与稳定性的理论研究

三叶结分子是最简单的非平凡纽结分子, C₃₀卡宾三叶结分子是由一条闭合的(C≡C—)₁₅ sp杂化碳链组成的, 是具有D₃对称性的拓扑手性分子. 本文用密度泛函方法[DFT/RB3LYP/6-31G(D)]对分子结构和光谱性质进行了研究, 在优化构型的基础上通过自然键轨道(NBO)方法和轨道能级研究了它的共轭性、成键情况和稳定性, 并与平面型C₃₀卡宾环分子进行了比较. 计算结果表明三叶结分子的三叶弧上形成了非平面的C≡C共轭和扭曲的内螺旋结构, 交叉处具有弱成键作用, 且分子轨道也发生了扭曲; 三叶结分子比卡宾环的共轭性和赝Jahn-Teller效应都明显小, 而总能量高. 因此, 分子打结是一个能量升高的过程.     

双核金属茂合物Zn2(η5-E5)2(E=N, P, As, Sb)电子结构和三阶非线性光学性质的理论研究

运用密度泛函PBE0方法研究了双核金属茂合物Zn2(η5-E5)2(E=N, P, As, Sb)的电子结构, 运用自然键轨道(NBO)方法对该体系的电荷分布及成键特征进行了分析. 此类体系中存在Zn—Zn的σ单键, 为近似纯s成分的成键方式. 用含时密度泛函理论(TDDFT ) 完全态求和(SOS) 方法计算了该体系的三阶非线性光学系数, 结果表明, γ值与最大吸收波长λmax成正比, 在各个分量中, 对〈γ〉起主要贡献的是γzzzz, 最大吸收波长对应的电子跃迁是从Zn—Zn的σ成键轨道到Zn—Zn的σ*反键轨道.     

吡啶酮系偶氮类化合物可见吸收光谱的预测

利用密度泛函的B3LYP方法, 在6-311G*基组水平对吡啶酮系偶氮类化合物进行构型优化, 并进行了自然键轨道(NBO)分析, 然后用TDDFT方法和ZINDO/S方法分别计算了它们的可见吸收光谱, 结果均与实验值十分吻合. 通过对比发现, 对于最高吸收波长的计算, ZINDO/S能以较快的速度得到较好的结果. 在用ZINDO/S计算的过程中, 回归分析发现π-π重叠加权因子(OWF_π-π)与染料分子吡啶环上两个羰基氧原子平均电荷Z_O有较好的线性关系: OWF_π-π＝0.11425－1.04178ZO, 这一关系不仅可从量子化学的角度进行解释, 而且可用于同类染料可见吸收光谱的预测. 分子轨道的研究表明, 这些化合物的最高可见吸收波长主要对应着共轭体系中给电子体到受电子体的电子跃迁.     

HCN(HNC)与NH3, H2O和HF分子间相互作用的理论研究

在MP2/aug-cc-pVTZ水平上, 对HCN(HNC)与NH3, H2O和HF分子间可能存在的氢键型复合物进行了全自由度能量梯度优化, 通过在相同水平上的频率验证分析发现了稳定的分子间相互作用形式是HCN(HNC)作为质子供体或作为质子受体形成的复合物. 基组重叠误差对总相互作用能的影响均小于3.34 kJ/mol. 通过自然键轨道(NBO)分析, 研究了单体和复合物中的原子电荷和电荷转移对分子间相互作用的影响. 对称性匹配微扰理论(SAPT, Symmetry Adapted Perturbation Theory)能量分解结果表明, 在分子间相互作用中, 静电作用与诱导作用占主导地位, 而诱导作用与复合物的电荷转移之间具有良好的正相关性.     

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.     

The Electronic Nature of the 1,4‐β‐Glycosidic Bond and Its Chemical Environment: DFT Insights into Cellulose Chemistry

The molecular understanding of the chemistry of 1,4‐β‐glucans is essential for designing new approaches to the conversion of cellulose into platform chemicals and biofuels. In this endeavor, much attention has been paid to the role of hydrogen bonding occurring in the cellulose structure. So far, however, there has been little discussion about the implications of the electronic nature of the 1,4‐β‐glycosidic bond and its chemical environment for the activation of 1,4‐β‐glucans toward acid‐catalyzed hydrolysis. This report sheds light on these central issues and addresses their influence on the acid hydrolysis of cellobiose and, by analogy, cellulose. The electronic structure of cellobiose was explored by DFT at the BB1 K/6‐31++G(d,p) level. Natural bond orbital (NBO) analysis was performed to grasp the key bonding concepts. Conformations, protonation sites, and hydrolysis mechanisms were examined. The results for cellobiose indicate that cellulose is protected against hydrolysis not only by its supramolecular structure, as currently accepted, but also by its electronic structure, in which the anomeric effect plays a key role.     

Design,synthesis, crystal structure and in vitro cytotoxic properties of a novel Schiff base derived from indole and biphenyl

A novel and potentially active dihydroorotate dehydrogenase (DHODH) inhibitor, namely 3‐({(E )‐[(E )‐1‐(biphenyl‐4‐yl)ethylidene]hydrazinylidene}methyl)‐1H‐indole (BEHI) acetonitrile disolvate, C₂₃H₁₉N₃·2CH₃CN, has been designed and synthesized. The structure of BEHI was characterized by elemental analysis, Q‐TOF (quadrupole time‐of‐flight) MS, NMR, UV–Vis and single‐crystal X‐ray diffraction. The antitumour activity of the target molecule was evaluated by the MTT method. Results indicated that BEHI exhibited rather potent cytotoxic activity against human A549 (IC₅₀ = 20.5 µM ) and mouse breast 4T₁ (IC₅₀ = 18.5 µM ) cancer cell lines. Meanwhile, to rationalize its potencies in the target, BEHI was docked into DHODH and the interactions with the active site residues were analyzed. Single‐crystal structure analysis indicated that hydrogen bonds are present only between BEHI and acetonitrile solvent molecules in the asymmetric unit. The interplay of weak π–π stacking and weak C(N)—H…π interactions between neighbouring BEHI molecules play crucial roles in the formation of the final supramolecular frameworks.     

Structural studies and quantum chemical calculations of Cr(III), Fe(III) and Ru(III) bromazepam complexes

The reaction of bromazepam (7‐bromo‐1,3‐dihydro‐5‐(2‐pyridyl)‐2H ‐1,4‐benzodiazepin‐2‐one, BZM) with Cr(III) ( 1 ), Fe(III) ( 2 ) and Ru(III) ( 3 ) salts gives complexes of the type [M(BZM)₃]⋅3X (X = Cl or NO₃). Structural characterization was extensively carried out using various analytical and spectral tools such as infrared, ¹H NMR and UV–visible spectroscopies and magnetic, conductance, elemental and thermal analyses. BZM is a bidentate ligand and interacts with the metal ions via the pyridine and benzodiazepin‐2‐one nitrogen atoms. The magnetic and electronic properties of 2 and 3 are consistent with low‐spin octahedral complexes. The three BZM molecules are non‐isoenergetically coordinated to the metal ions and this is reflected in the values of the second‐order interaction energy. The antibacterial activity was studied using Staphylococcus aureus and Escherichia coli . Coordination of BZM to Cr(III) or Ru(III) ions leads to a marked increase in toxicity with respect to the inactive Fe(III) complex 2 .     

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.