分子间相互作用的量子化学研究方法

分子间相互作用是一类十分重要的作用, 这类作用的实验和理论研究越来越受到化学家、生物学家、材料科学家等的重视。本文综述了这种相互作用的量子化学研究现状和特点, 主要集中于常见的3 种量子化学方法。并对该领域的研究前景作了展望。     

Influence of Substitution on the Supramolecular Chemistry of Cycloparaphenylene-Fullerene Complexes

We present a comprehensive host-guest study of four substituted and unsubstituted [10]cycloparaphenylenes with the fullerenes C₆₀ and C₇₀. Within this study, the influence on the complexation behavior was investigated experimentally and computationally. Due to the increased steric demand the substitution on the nanohoop results in an energetic penalty, which could be partially compensated by additional substituent-fullerene interactions. These attractive interactions are intensified in the C₇₀ complexes and with an increased degree of substitution. For the computational investigation conformer ensembles were taken into account, providing reliable structures with Boltzmann weighted energies. An analysis of the noncovalent interactions elucidated the origin of the enhanced substituent-C₇₀ interaction. The ellipsoid fullerene C₇₀ can be considered as a π-extended version of C₆₀, which is able to increase the attractive van der Waals interactions within these supramolecular complexes.     

Halogen‐Bonding Interactions with π Systems: CCSD(T), MP2, and DFT Calculations

Halogen bonding is a noncovalent interaction between a halogen atom and a nucleophilic site. Interactions involving the π electrons of aromatic rings have received, up to now, little attention, despite the large number of systems in which they are present. We report binding energies of the interaction between either NCX or PhX (X=F, Cl, Br, I) and the aromatic benzene system as determined with the coupled cluster with perturbative triple excitations method [CCSD(T)] extrapolated at the complete basis set limit. Results are compared with those obtained by Møller–Plesset perturbation theory to second order (MP2) and density functional theory (DFT) calculations by using some of the most common functionals. Results show the important role of DFT in studying this interaction.     

Targeting the Rich Conformational Landscape of N-Allylmethylamine Using Rotational Spectroscopy and Quantum Mechanical Calculations

The highly variable conformational landscape of N-allylmethylamine (AMA) was investigated using Fourier transform microwave spectroscopy aided by high-level theoretical calculations to understand the energy relationship governing the interconversion between nine stable conformers. Spectroscopically, transitions belonging to four low energy conformers were identified and their hyperfine patterns owing to the ¹⁴N quadrupolar nucleus were unambiguously resolved. The rotational spectrum of the global minimum geometry, conformer I, shows an additional splitting associated with a tunneling motion through an energy barrier interconnecting its enantiomeric forms. A two-step tunneling trajectory is proposed by finding transition state structures corresponding to the allyl torsion and NH inversion. Natural bond orbital and non-covalent interaction analyses reveal that an interplay between steric and hyperconjugative effects rules the conformational preferences of AMA.     

Plasma Modeling and Prebiotic Chemistry: A Review of the State-of-the-Art and Perspectives

We review the recent progress in the modeling of plasmas or ionized gases, with compositions compatible with that of primordial atmospheres. The plasma kinetics involves elementary processes by which free electrons ultimately activate weakly reactive molecules, such as carbon dioxide or methane, thereby potentially starting prebiotic reaction chains. These processes include electron–molecule reactions and energy exchanges between molecules. They are basic processes, for example, in the famous Miller-Urey experiment, and become relevant in any prebiotic scenario where the primordial atmosphere is significantly ionized by electrical activity, photoionization or meteor phenomena. The kinetics of plasma displays remarkable complexity due to the non-equilibrium features of the energy distributions involved. In particular, we argue that two concepts developed by the plasma modeling community, the electron velocity distribution function and the vibrational distribution function, may unlock much new information and provide insight into prebiotic processes initiated by electron–molecule collisions.     

On the Prebiotic Synthesis of D‐Sugars Catalyzed by L‐Peptides: Assessments from First‐Principles Calculations

What accounts for a particular chiral selection in the case of a few sugars of prebiotic relevance, thereby mirroring the asymmetry observed in nature? By using first‐principles calculations, the generation of pentoses from glycolaldehyde (the initial product of the autocatalytic formose reaction), which has been detected in outer space), has been modeled by using L ‐Val‐L ‐Val as a primeval catalyst. Our theoretical study provides insight into the mechanism of this reaction and satisfactorily explains a few key molecular events. Our rationale agrees with the reported experimental data and shows that the D ‐configuration is only favored for ribose. L ‐pentoses are usually favored in the presence of L ‐configured dipeptides, as observed experimentally, although no chiral selection could be observed in the case of xylose. These results confirm that a prebiotic sugar soup could be fine‐tuned in the presence of shorter peptides as catalysts and that D ‐ribose would have also resulted in an advantageous imbalance for further amplification and chemical evolution.     

Interactions of Aromatic Heterocycles with Water: The Driving Force from Free‐Jet Rotational Spectroscopy and Model Electrostatic Calculations

The interaction of isolated aromatic nitrogen atoms with water is explored within free jets by using rotational spectroscopy. To the existing data on diazines, we add the case of the 1:1 complex of 1,3,5‐triazine and water (where water donates a proton to one of the nitrogen heterocyclic atoms to form a planar adduct). An electrostatic model based on distributed multipoles accurately reproduces the structures of the four azine–water complexes and allows us to understand the forces that stabilize these structures. The applied intermolecular potential allows us to estimate the changes in the thermodynamic functions of the complexes—compared to the separated constituents—and evaluate the temperature at which the complexes are stable under standard conditions.     

Binding Energies of the π‐Stacked Anisole Dimer: New Molecular Beam—Laser Spectroscopy Experiments and CCSD(T) Calculations

Among noncovalent interactions, π–π stacking is a very important binding motif governed mainly by London dispersion. Despite its importance, for instance, for the structure of bio‐macromolecules, the direct experimental measurement of binding energies in π–π stacked complexes has been elusive for a long time. Only recently, an experimental value for the binding energy of the anisole dimer was presented, determined by velocity mapping ion imaging in a two‐photon resonant ionisation molecular beam experiment. However, in that paper, a discrepancy was already noted between the obtained experimental value and a theoretical estimate. Here, we present an accurate recalculation of the binding energy based on the combination of the CCSD(T)/CBS interaction energy and a DFT‐D3 vibrational analysis. This proves unambiguously that the previously reported experimental value is too high and a new series of measurements with a different, more sensitive apparatus was performed. The new experimental value of 1800±100 cm^?1 (5.15±0.29 kcal mol^?1) is close to the present theoretical prediction of 5.04±0.40 kcal mol^?1. Additional calculations of the properties of the cationic and excited states involved in the photodissociation of the dimer were used to identify and rationalise the difficulties encountered in the experimental work.     

Non‐enzymatic Ribonucleotide Reduction in the Prebiotic Context

Model studies of prebiotic chemistry have revealed compelling routes for the formation of the building blocks of proteins and RNA, but not DNA. Today, deoxynucleotides required for the construction of DNA are produced by reduction of nucleotides catalysed by ribonucleotide reductases, which are radical enzymes. This study considers potential non‐enzymatic routes via intermediate radicals for the ancient formation of deoxynucleotides. In this context, several mechanisms for ribonucleotide reduction, in a putative H₂S/HS^. environment, are characterized using computational chemistry. A bio‐inspired mechanistic cycle involving a keto intermediate and HSSH production is found to be potentially viable. An alternative pathway, proceeding through an enol intermediate is found to exhibit similar energetic requirements. Non‐cyclical pathways, in which HSS^. is generated in the final step instead of HS^., show a markedly increased thermodynamic driving force (ca. 70 kJ mol^?1) and thus warrant serious consideration in the context of the prebiotic ribonucleotide reduction.     

Reconciling Electrostatic and n→π* Orbital Contributions in Carbonyl Interactions

Interactions between carbonyl groups are prevalent in protein structures. Earlier investigations identified dominant electrostatic dipolar interactions, while others implicated lone pair n→π* orbital delocalisation. Here these observations are reconciled. A combined experimental and computational approach confirmed the dominance of electrostatic interactions in a new series of synthetic molecular balances, while also highlighting the distance‐dependent observation of inductive polarisation manifested by n→π* orbital delocalisation. Computational fiSAPT energy decomposition and natural bonding orbital analyses correlated with experimental data to reveal the contexts in which short‐range inductive polarisation augment electrostatic dipolar interactions. Thus, we provide a framework for reconciling the context dependency of the dominance of electrostatic interactions and the occurrence of n→π* orbital delocalisation in C=O???C=O interactions.     

两亲分子组装介导的化学反应及相关生命起源化学

化学反应会受其所处微环境影响,因此不同分子间相互作用对反应进程的调控不容忽视.水溶液作为优良的反应介质,其应用常受到反应物溶解性差的限制.在水溶液中引入胶束或囊泡等两亲分子组装,可在一定程度上克服这种不足.这些均匀分散的动态组装,提供了有别于本体水溶液的微环境,以非共价的方式,将单体结合到其极性表面或疏水内核.通过加速...     

Sequence and Chiral Selectivity of Drug–DNA Interactions Revealed by Force Spectroscopy

Differential binding force has been used to precisely characterize the mechanical effect of a drug molecule binding to a DNA duplex. The high‐resolution binding forces measured by the force‐induced remnant magnetization spectroscopy (FIRMS) enable the binding behavior of drug molecules with different chirality and DNA of various sequences to be distinguished. The sequence specificity of Hg²⁺ and daunomycin was revealed by force spectroscopy for the first time, and the results are consistent with those obtained by other techniques. Furthermore, the two isomers of d,l ‐tetrahydropalmatine showed selectivity for two different DNA sequences. One particular useful feature of this approach is that the small molecules under study do not require any labels.     

Synthesis of Pyrimidines and Triazines in Ice: Implications for the Prebiotic Chemistry of Nucleobases

From urea to nucleobases : Freeze–thaw cycles in urea ( 1 ) solutions under methane/nitrogen atmospheres lead, with application of an energy source, to the synthesis of pyrimidines (mainly cytosine ( 2 ) and uracil ( 3 )), triazines (such as cyanuric acid ( 4 )), and adenine. This synthesis appears to be dependent on the atmosphere and the freezing conditions. At room temperature, hydantoin ( 5 ) is obtained. However, a freezing urea/water system subjected to an energy source under an inert atmosphere generates s‐triazines.

     

A Universal Geochemical Scenario for Formamide Condensation and Prebiotic Chemistry

The condensation of formamide has been shown to be a robust chemical pathway affording molecules necessary for the origin of life. It has been experimentally demonstrated that condensation reactions of formamide are catalyzed by a number of minerals, including silicates, phosphates, sulfides, zirconia, and borates, and by cosmic dusts and meteorites. However, a critical discussion of the catalytic power of the tested minerals, and the geochemical conditions under which the condensation would occur, is still missing. We show here that mineral self-assembled structures forming under alkaline silica-rich solutions are excellent catalysts for the condensation of formamide with respect to other minerals. We also propose that these structures were likely forming as early as 4.4 billion years ago when the whole earth surface was a reactor, a global scale factory, releasing large amounts of organic compounds. Our experimental results suggest that the conditions required for the synthesis of the molecular bricks from which life self-assembles, rather than being local and bizarre, appears to be universal and geologically rather conventional.     

计算化学在紫外可见吸收光谱教学中的应用

以L-酪氨酸为案例,结合计算化学手段,设计了采集紫外可见吸收光谱的教学方案,并探讨了计算化学在紫外可见吸收光谱教学中的具体应用。通过对该分子紫外可见光谱的模拟与指认,以及利用多种方法对其不同电子激发过程开展分析,不仅可以有效解释实验光谱吸收峰的来源,还能获取一系列具有教学意义的等值面图形与数据,来帮助学生加强对轨道跃迁类型、电子转移与空穴-电子分布等电子激发特性方面的感性认识,从而使得教学内容既有趣生动,又富有理论深度。