The Nature of Activated Non‐classical Hydrogen Bonds: A Case Study on Acetylcholinesterase–Ligand Complexes

Molecular recognition events in biological systems are driven by non‐covalent interactions between interacting species. Here, we have studied hydrogen bonds of the CH???Y type involving electron‐deficient CH donors using dispersion‐corrected density functional theory (DFT) calculations applied to acetylcholinesterase–ligand complexes. The strengths of CH???Y interactions activated by a proximal cation were considerably strong; comparable to or greater than those of classical hydrogen bonds. Significant differences in the energetic components compared to classical hydrogen bonds and non‐activated CH???Y interactions were observed. Comparison between DFT and molecular mechanics calculations showed that common force fields could not reproduce the interaction energy values of the studied hydrogen bonds. The presented results highlight the importance of considering CH???Y interactions when analysing protein–ligand complexes, call for a review of current force fields, and opens up possibilities for the development of improved design tools for drug discovery.     

Ni(510)台阶面对氢分子解离吸附的影响

应用对势方法获得Ｈ２／Ｎｉ（１００）和Ｈ２／Ｎｉ（５１０）相互作用体系的ＬＥＰＳ势能面，考察了氢分子在Ｎｉ（１００）面上的解离吸附行为。理论计算结果和实验结果符合很好，对Ｈ２／Ｎｉ（５１０）体系的研究表明，台阶的作用为：（１）在台阶下部，氢分子直接解离的最低能量反应途径密度增大，且平动活化垒降低，（２）在台阶上部及台阶边棱处，前驱态的最低能量反应途径密度增大。因此，台阶处成为氢分子解离和复合的活性     

尿酸分子互变异构体平面构象的理论研究

使用半经验量子化学中的AM1方法、从头计算Hartree-Fock理论(在3-21G*水平)和密度泛函理论中的B3LYP方法(使用6-31G(d)基组),研究了尿酸分子的所有35种互变异构体。计算结果表明,三羰基互变异构体是所有异构体中能量最低的,其次为单羟基异构体和双羟基异构体,而含有三羟基的互变异构体相对能量最高。随着羟基数的增加, C-N键的平均键长从1.395逐渐缩短到1.351,而CC键的平均键长基本保持不变(1.400~1.406)。     

2-羟基吡啶与水氢键作用的理论研究

本文采用量子化学的Hatree-Fock方法和密度泛函理论(DFT)的B3LYP方法,在6-31G(d)水平上,研究了2-羟基吡啶分子(Hy)及其酮式互变异构体2(1H)-吡啶酮(Py)与水的相互作用。考察它们之间在形成Hy…H2O,Py…H2O,Hy…Hy,Py…Py和Hy…Py等复合物前后的能量变化和分子结构参数变化特点。计算结果表明,在这些复合物中都形成了较强的氢键作用,在水合物中,Py与水形成复合物时能量降低较多,与实验结果一致。经过零点振动能(ZPVE)和基组叠加误差(BSSE)校正后的复合物离解能分别为38.3,40.8,73.0,82.7和71.1 kJ/mol(B3LYP/6-31G(d)),水合物的离解能远小于二聚体复合物,而酮式结构的二聚体的离解能最大。     

MgCl2/甲醇溶液的近红外光谱研究及量子计算

利用近红外光谱研究了MgCl2/甲醇溶液中的氢键种类及其变化和溶液离子化作用. 近红外光谱结果分析表明, Mg2＋与溶剂发生了强烈的相互作用导致溶液中的氢键发生变化. 随着MgCl2浓度的增加, 多聚体氢键(δ-OHs)减少, 低聚体和二聚体氢键(γ-OHs)增加, OHs总数维持不变. 通过对光谱曲线的分解拟合, 定量地计算了不同浓度范围(0.21～0.62 mol•kg－1)内Mg2＋的溶剂化数为5.5到5.0. 并利用量子化学方法对溶剂化数为5和6的配合物结构进行优化及热力学性质的计算, 通过光谱变化及理论计算推断Cl－可能会以氢键结合甲醇分子的形式存在.     

A Single‐Molecule Perspective on the Role of Solvent Hydrogen Bonds in Protein Folding and Chemical Reactions

We present an array of force spectroscopy experiments that aim to identify the role of solvent hydrogen bonds in protein folding and chemical reactions at the single‐molecule level. In our experiments we control the strength of hydrogen bonds in the solvent environment by substituting water (H₂O) with deuterium oxide (D₂O). Using a combination of force protocols, we demonstrate that protein unfolding, protein collapse, protein folding and a chemical reaction are affected in different ways by substituting H₂O with D₂O. We find that D₂O molecules form an integral part of the unfolding transition structure of the immunoglobulin module of human cardiac titin, I27. Strikingly, we find that D₂O is a worse solvent than H₂O for the protein I27, in direct contrast with the behaviour of simple hydrocarbons. We measure the effect of substituting H₂O with D₂O on the force dependent rate of reduction of a disulphide bond engineered within a single protein. Altogether, these experiments provide new information on the nature of the underlying interactions in protein folding and chemical reactions and demonstrate the power of single‐molecule techniques to identify the changes induced by a small change in hydrogen bond strength.     

Response to: “Comment on ‘The effect of confinement on the electronic energy and polarizability of a hydrogen molecular ion’”

In this reply we clarify questions point out in the Comment on: “The Effect of Confinement on the Electronic Energy and Polarizability of a Hydrogen Molecular Ion” by J. F. da Silva, F. R. Silva and E. Drigo Filho, Int. J. Quantum Chem.2016, 116, 497–503 written by S. A. Cruz and H. Olivares‐Pilón. In particular, we show how we made the calculations of ground state energy from the confined hydrogen molecule ion for cavities of different volumes. The internuclear distances to the excited state 2pσ_u are also presented.     

分子团簇的量子化学研究

采用Hartree-Fock方法、密度泛函(DFT)方法(BLYP、B3LYP)和MP2方法对Se4分子团簇的各种可能构型进行了结构优化和频率分析, 结果表明有5种构型是势能面上的稳定驻点, 同时对上述4种量子化学方法计算结果的差异进行了分析。并对这5种构型的结构稳定性、几何构型、前线分子轨道、Mulliken布局分析和偶极矩进行了分析, 根据分析结果对Se4分子的某些物理和化学性质进行了预测。     

Structure Elucidation of a Melam–Melem Adduct by a Combined Approach of Synchrotron X-ray Diffraction and DFT Calculations

Melam-melem (1:1), an adduct compound that can be obtained from dicyandiamide in autoclave reactions at 450 °C and elevated ammonia pressure, had previously been described based on mass spectrometry and NMR spectroscopy, but only incompletely characterized. The crystal structure of this compound has now been elucidated by means of synchrotron microfocus diffraction and subsequent quantum-chemical structure optimization applying DFT methods. The structure was refined in triclinic space group P based on X-ray data. Cell parameters of a=4.56(2), b=19.34(8), c=21.58(11) Å, α=73.34(11)°, β=89.1(2)°, and γ=88.4(2)° were experimentally obtained. The resulting cell volumes agree with the DFT optimized value to within 7 %. Molecular units in the structure form stacks that are interconnected by a vast array of hydrogen bridge interactions. Remarkably large melam dihedral angles of 48.4° were found that allow melam to interact with melem molecules from different stack layers, thus forming a 3D network. π-stacking interactions appear to play no major role in this structure.     

Nuclear Dynamics and Electronic Effects of Hydrogen on Solid Surfaces

Hydrogen is involved in a variety of chemical processes on surfaces. While hydrogen exhibits vibrational and rotational dynamics in its adsorption state, it in some cases undergoes diffusion into the substrate as well as on the surface, and participates in chemical reactions. Furthermore, hydrogen exchanges an electron with surfaces having a significant effect on the surface electronic structure. In this personal account, we review our recent studies on surface nuclear dynamics of hydrogen, hydrogen transport across surfaces, catalytic hydrogenation/isotope exchange reactions, and charge transfer between the surface and hydrogen by using a depth‐resolved technique of nuclear reaction analysis and a quantum‐state‐selective detection of resonance enhanced multiphoton ionization in combination with surface science techniques. As a future prospect, we refer to ultraslow μ spin rotation spectroscopy for a direct probe of the hydrogen charge state at surfaces.     

药物小分子与生物大分子相互作用的研究方法进展

评述了药物小分子与血清白蛋白、DNA相互作用的模式和近几年来国内外相关研究方法进展。引用文献57篇。     

适用于液晶大分子的量子化学计算方法以及六烷氧基苯并菲取代的1,3,5-三酰胺苯液晶的研究

盘状液晶分子之间的相互作用决定液晶的性质. 为了选择合适的计算方法, 以便用量子化学研究液晶大分子, 设计了对位取代苯和三酰胺苯作为模型分子, 用高水平的ONIOM [MP2/6-31G*(0.25):HF/6-31G(d,p)]计算提供了与晶体结构资料相符合的较准确的二体相互作用结果. 然后与各种较低级别的计算进行比较, 说明ONIOM (HF/STO-3G: AM1:UFF)水平比较合适. 盘重叠部分的相互作用主要是色散作用, 用UFF力场处理, 氢键主要是静电作用, 用HF/STO-3G处理, 其余部分用AM1处理. 通过对苯取代的1,3,5-三酰胺苯的双分子构型优化, 并与晶体结构数据进行比较, 进一步说明ONIOM (HF/STO-3G:AM1:UFF)水平计算的适用性. 在此基础上, 对六烷氧基苯并菲取代的1,3,5-三酰胺苯的双分子构型进行了优化, 为解释它所形成的液晶具有较高的电荷传输能力提供了有用的信息.