非手性的酞菁铜分子在Bi(111)表面上的手性特征

利用低温扫描隧道显微镜（LT-STM）研究了酞菁铜（CuPc）分子在Bi（111）表面上的吸附和手性自组装结构。由于较弱的分子-衬底相互作用,我们发现在液氮温度（78 K）下吸附在Bi（111）表面上的单个CuPc分子围绕着分子中心发生旋转,直到遇到其他分子形成团簇为止。随着分子覆盖度的增加,CuPc分子形成了自组装分子单层。高分辨STM图表明,非手性的CuPc分子出现了手性特征：两个相对的酞菁基团发生了弯曲。当覆盖度超过一个分子层,酞菁铜分子的吸附取向由“平躺”转变到“站立”姿态。我们认为,酞菁铜分子的手性起源是由两种因素共同导致的结果：一种是分子-衬底之间的非对称电荷转移,另一种是相邻分子间的非对称性的范德华力作用。     

Investigation of mandelic acid bonding on Pirkle type chromatographic stationary phases by Raman spectroscopy

The bonding of mandelic acid enantiomers has been studied on benzene-leucine, dinitrobenzene-leucine and dinitrobenzene-phenylalanine type chiral stationary phases connected to zeolite A supports. The pi-donor, pi-acceptor and H-bonding interactions responsible for diastereomer pair formations can be studied under quasi in situ chromatographic conditions by Fourier transform Raman and surface enhanced Raman spectroscopic techniques. Structural differences between diastereomer pairs result in observable spectral differences at a phase load of approx. 50%. It was shown that the decreasing pi-acceptor character of the phase is associated with its increasing capability of H-bond formation. Correlating spectral data to chromatographic results it can be concluded that, in addition to H-bonding as well as to pi-donor-pi-acceptor interactions, steric hindrances due to bulky moieties of either the stationary phase or the analyte molecules are of importance in successful separations.     

Dynamics and Kinetics of Methanol-Graphite Interactions at Low Surface Coverage

The processes of molecular clustering, condensation, nucleation, and growth of bulk materials on surfaces, represent a spectrum of vapor-surface interactions that are important to a range of physical phenomena. Here, we describe studies of the initial stages of methanol condensation on graphite, which is a simple model system where gas–surface interactions can be described in detail using combined experimental and theoretical methods. Experimental molecular beam methods and computational molecular dynamics simulations are used to investigate collision dynamics and surface accommodation of methanol molecules and clusters at temperatures from 160 K to 240 K. Both single molecules and methanol clusters efficiently trap on graphite, and even in rarified systems methanol-methanol interactions quickly become important. A kinetic model is developed to simulate the observed behavior, including the residence time of trapped molecules and the quantified Arrhenius kinetics. Trapped molecules are concluded to rapidly diffuse on the surface to find and/or form clusters already at surface coverages below 10⁻⁶ monolayers. Conversely, clusters that undergo surface collisions fragment and subsequently lose more loosely bound molecules. Thus, the surface mediates molecular collisions in a manner that minimizes the importance of initial cluster size, but highlights a strong sensitivity to surface diffusion and intermolecular interactions between the hydrogen bonded molecules.     

Concept of Absolute Enantioselective Separation

A novel approach to separations of racemates is described. It is a chromatography-like process in which molecules to be separated are oriented in two directions perpendicular to each other and parallel to the surface. If this requirement is met the opposite enantiomers differ in the energy of interaction with the surface. We call the process Absolute Enantioselective Separation (AES). Surface requirements for resolving a racemate to enantiomers are discussed. AES can be accomplished either by interaction of racemate components with a repeating pattern on the not necessarily chiral surface and interaction with a static electric field or by interaction with two repeating patterns defining the chirality of the surface. Additionally, a multiple use of electric fields to enable a separation in bulk is described. The ease of separation of selected natural compounds (amino acids and monosaccharides) in the AES process is also discussed.     

Feature vector clustering molecular pairs in computer simulations

A clustering framework is introduced to analyze the microscopic structural organization of molecular pairs in liquids and solutions. A molecular pair is represented by a representative vector (RV). To obtain RV, intermolecular atom distances in the pair are extracted from simulation trajectory as components of the key feature vector (KFV). A specific scheme is then suggested to transform KFV to RV by removing the influence of permutational molecular symmetry on the KFV as the predicted clusters should be independent of possible permutations of identical atoms in the pair. After RVs of pairs are obtained, a clustering analysis technique is finally used to classify all the RVs of molecular pairs into the clusters. The framework is applied to analyze trajectory from molecular dynamics simulations of an ionic liquid (trihexyltetradecylphosphonium bis(oxalato)borate ([P_6,6,6,14][BOB])). The molecular pairs are successfully categorized into physically meaningful clusters, and their effectiveness is evaluated by computing the product moment correlation coefficient (PMCC). (Willett, Winterman, and Bawden, J. Chem. Inf. Comput. Sci. 1986, 26, 109–118; Downs, Willett, and Fisanick, J. Chem. Inf. Comput. Sci. 1994, 34, 1094–1102) It is observed that representative configurations of two clusters are related to two energy local minimum structures optimized by density functional theory (DFT) calculation, respectively. Several widely used clustering analysis techniques of both nonhierarchical (k-means) and hierarchical clustering algorithms are also evaluated and compared with each other. The proposed KFV technique efficiently reveals local molecular pair structures in the simulated complex liquid. It is a method, which is highly useful for liquids and solutions in particular with strong intermolecular interactions. © 2019 Wiley Periodicals, Inc.     

Chiral recognition by enantioselective liquid chromatography: Mechanisms and modern chiral stationary phases

An overview of the state-of-the-art in LC enantiomer separation is presented. This tutorial review is mainly focused on mechanisms of chiral recognition and enantiomer distinction of popular chiral selectors and corresponding chiral stationary phases including discussions of thermodynamics, additivity principle of binding increments, site-selective thermodynamics, extrathermodynamic approaches, methods employed for the investigation of dominating intermolecular interactions and complex structures such as spectroscopic methods (IR, NMR), X-ray diffraction and computational methods. Modern chiral stationary phases are discussed with particular focus on those that are commercially available and broadly used. It is attempted to provide the reader with vivid images of molecular recognition mechanisms of selected chiral selector–selectand pairs on basis of solid-state X-ray crystal structures and simulated computer models, respectively. Such snapshot images illustrated in this communication unfortunately cannot account for the molecular dynamics of the real world, but are supposed to be helpful for the understanding. The exploding number of papers about applications of various chiral stationary phases in numerous fields of enantiomer separations is not covered systematically.     

Chirality Discrimination at Binary Organic|Water Interfaces Monitored by Interfacial Tension Measurements with Preliminary Comparison with Molecular Dynamics Simulations

Chirality discrimination at a binary toluene (organic)/water(aqueous) interface between R- or S-Tol-BINAP (2,2′-Bis(di-p-tolylphosphino)-1,1′-binaphthyl) molecules and the water-soluble serine chiral specie is examined for the first time, using a combination of interfacial tension measurements and molecular dynamic simulations. Experimental interfacial measurements exhibit a clear chirality-controlled difference when a homochiral versus a heterochiral enantiomeric pairs are introduced at the interfaces. The related molecular dynamics simulations support the experimental results and provide further molecular insight of intermolecular interactions at the interfaces. The results indicate that interfacial tension measurements can capture the preferential interactions which exist between different pairs of enantiomers at the binary interfaces, opening up a new way for probing chirality discrimination at liquid-liquid interfaces.     

Molecular Recognition in Organic Crystals: Directed Intermolecular Bonds or Nonlocalized Bonding?

Molecules are held together mainly by forces acting between individual atoms. Does the same apply to molecular clusters? Does intermolecular cohesion depend on weak bonds between individual atoms in different molecules or on less localized, more diffuse interactions between molecules? We discuss these questions from several viewpoints and in particular compare interpretations based on the extension of Bader's atoms in molecules (AIM) theory to cover closed‐shell intermolecular interactions with interpretations based on the new pixel method for the calculation of coulombic, polarization, dispersion, and repulsion energies from the electron density of molecular clusters.     

Ethyl 1‐ethyl‐7‐fluoro‐4‐oxo‐1,4‐dihydroquinoline‐3‐carboxylate: X‐ray and DFT studies

The basic building unit in the structure of the title compound, C₁₄H₁₄FNO₃, is pairs of molecules arranged in an antiparallel fashion, enabling weak C—H...O interactions. Each molecule is additionally involved in π–π interactions with neighbouring molecules. The pairs of molecules formed by the C—H...O hydrogen bonds and π–π interactions form ribbon‐like chains running along the c axis. Theoretical calculations based on these pairs showed that, although the main intermolecular interaction is electrostatic, it is almost completely compensated by an exchange–repulsion contribution to the total energy. As a consequence, the dominating force is a dispersion interaction. The F atoms form weak C—F...H—C interactions with the H atoms of the neighbouring ethyl groups, with H...F separations in the range 2.59–2.80 Å.     

Investigation of chiral recognition by molecular micelles with molecular dynamics simulations

Molecular dynamics simulations were used to characterize the binding of the chiral drugs chlorthalidone and lorazepam to the molecular micelle poly-(sodium undecyl-(L)-leucine-valine). The project’s goal was to characterize the nature of chiral recognition in capillary electrophoresis separations that use molecular micelles as the chiral selector. The shapes and charge distributions of the chiral molecules investigated, their orientations within the molecular micelle chiral binding pockets, and the formation of stereoselective intermolecular hydrogen bonds with the molecular micelle were all found to play key roles in determining where and how lorazepam and chlorthalidone enantiomers interacted with the molecular micelle.     

Origin of short-range repulsion between hydrated phospholipid bilayers: a computer simulation study

The grand canonical Monte Carlo technique is used to simulate the pressure-distance dependence for supported dilauroylphosphatidylethanolamine (DLPE) membranes. The intra- and intermolecular interactions in the system are described with a combination of an AMBER-based force field for DLPE and a TIP4P model for water. To improve the balance between the pair interactions of like and unlike molecules, the water-lipid interaction potentials are scaled to reproduce the hydration level and intermembrane separation at full hydration. It is found that the short-range water-mediated repulsion originates from the hydration component of the intermembrane pressure, whereas the direct interaction between the membranes remains attractive throughout the pressure range studied (0-5 kbar).     

Comparison of the intermolecular energy surfaces of amino acids: orientation-dependent chiral discrimination

In the present work, we compare the intermolecular energy surfaces of the alanine molecule in its neutral and zwitterionic state using ab initio theory (HF/6-311++G) as a function of mutual orientation. Starting from the optimized structures of the nonbonded homochiral (l-l) and heterochiral (d-l) pairs of molecules, the energy surfaces are studied with rigid geometry by varying the distance and orientation. The potential energy surfaces of the l-l and d-l pairs are found to be dissimilar and reflect the underlying chirality of the homochiral pair and racemic nature of the heterochiral pair. The intermolecular energy surface of the l-l pair is more favorable than the corresponding energy surface of the d-l pair. The study, for the first time, reveals clear homochiral preference without use of parameters, which was unobserved in previous detailed simulations but predicted by theory. The electrostatic interaction further augments the chiral discrimination. The basis set superposition error (BSSE) corrected results show enhanced discrimination. Use of higher-level M?ller-Plesset perturbation theory (MP2) and further BSSE correction do not change the conclusions made at the Hartree-Fock (HF) level. The major conclusions based on HF and MP2 level calculations remain unaltered when the calculations of the potential energy surfaces for the neutral and zwitterionic pairs are repeated using the density functional theory (DFT) (B3LYP/6-311++G). The observed orientation dependence has significance in the biological chiral recognition as well as peptide synthesis at the peptidyl transferase center where the amino terminal and peptidyl terminal undergo mutual rotatory motion.     

Ion pairs in aqueous electrolyte microdrops under conditions of a flat nanopore

The molecular mechanisms of aqueous solvent penetration into a flat nanopore with hydrophobic structureless walls containing a Na⁺Cl^? ion pair with nonfixed distance between ions is studied by computer simulations. A detailed many-body polycenter model of intermolecular interactions calibrated with respect to experimental data for the free energy of attachment of water vapor molecules and quantum-chemical calculations in clusters is used. The ion pair hydration results in its decomposition. Drawing the molecules into the gap between ions makes easier penetration of solvent and filling of the nanopore with electrolyte. The ion-pair dissociation is accompanied by dramatic changes in the chemical potential of molecules and electric properties of the whole system. The thermodynamic characteristics of decomposition are stable as regards variations in the pore width. The post-decomposition electric polarizability demonstrates strong anisotropy associated with the nanopore flatness.     

π-Molecular complexes: A modified CNDO study of the benzene-borazine system

The standard CNDO/2 method is shown to be unable to produce meaningful potential curves for π-π-type molecular complexes. A modification of this method in which pairs of atoms associated with the same molecule and with different molecules are differentiated leads to reduced intermolecular bonding and provides reasonable stabilization energies and intermolecular separations. Calculations based on this modified method indicate that benzene-borazine and borazine-borazine complexes in which the molecules are symmetrically disposed in parallel planes can exist in the ground state. The stabilization energies are calculated to be in the range 2–5 kcal/mole for benzene-borazine and 5–18 kcal/mole for borazine-borazine, with interplanar separations near 3 Å in both cases.     

A high energy barrier to charge recombination in ionized water vapor

A quantitative kinetic theory has been developed to explain the results of experimental observation of the abnormally intense clustering of water molecules in the vapor phase in an ionizing radiation field at a moderate dose rate. The recombination is impeded because of the hydration of ion pairs and the formation of an abnormally high energy barrier (∼100 k _B T) in molecular clusters. The buildup of the clusters of water molecules stabilized in the electric field of ion pairs results in a dramatic enhancement of the effect of ionizing radiation on the electric properties of the vapor. The values of the coefficients to the rate equation of ionization-recombination equilibrium were calculated on the molecular level by computer simulation of the hydration of the H₃O⁺(H₂O) _n OH⁻ ion pair using the detailed model of intermolecular interactions.     

Solvation of sodium-chloride ion pair in water cluster at atmospheric conditions: grand canonical ensemble Monte Carlo simulation

Open statistical ensemble simulations are used to study the mechanism of nucleation of atmospheric water on sodium-chloride ion pair in a wide range of temperature and relative humidity values. The extended simple point-charge model is used for water molecules. Ions-water nonadditive interactions are taken into account by introducing the mutual polarization of ions and water in the field of each other. Gibbs free-energy variations are calculated from Na+-Cl- pair-correlation function and used as a criterion for determining the possible stable states of the cluster. In this relation, it was found that the dissociation of ion pairs in water clusters occurs even at vapor pressures of only a few millibars. In the conditions under consideration solvent-separated ion-pair states are found to be more probable than contact ion-pair configurations. The susceptibilities of water and ions are found to play an essential role in the stabilization of ions at large separations. The structure of ion-induced clusters is analyzed in terms of binary correlation functions. The non-pair interactions influence essentially the structure of ion solvation shells. The results of simulation show that the separation of the charges in water clusters containing simple ions can take place under atmospheric conditions.     

Disappearing Enantiomorphs: Single Handedness in Racemate Crystals

Although crystallization is the most important method for the separation of enantiomers of chiral molecules in the chemical industry, the chiral recognition involved in this process is poorly understood at the molecular level. We report on the initial steps in the formation of layered racemate crystals from a racemic mixture, as observed by STM at submolecular resolution. Grown on a copper single‐crystal surface, the chiral hydrocarbon heptahelicene formed chiral racemic lattice structures within the first layer. In the second layer, enantiomerically pure domains were observed, underneath which the first layer contained exclusively the other enantiomer. Hence, the system changed from a 2D racemate into a 3D racemate with enantiomerically pure layers after exceeding monolayer‐saturation coverage. A chiral bias in form of a small enantiomeric excess suppressed the crystallization of one double‐layer enantiomorph so that the pure minor enantiomer crystallized only in the second layer.     

Comparative study of three teicoplanin-based chiral stationary phases using the linear free energy relationship model

Teicoplanin (T) is a macrocyclic glycopeptide that is highly effective as a chiral selector for enantiomeric separations. In this study, we used three teicoplanin-based chiral stationary phases (CSPs) - native teicoplanin, teicoplanin aglycon (TAG) and recently synthesized methylated teicoplanin aglycon (MTAG). In order to examine the importance of various interaction types in the chiral recognition mechanism the three related CSPs were evaluated and compared using a linear free energy relationship (LFER). The capacity factors of 19 widely different solutes, with known solvation parameters, were determined on each of the columns under the same mobile phase conditions used for the chiral separations. The regression coefficients obtained revealed the magnitude of the contribution of individual interaction types to the retention on the compared columns under those specific experimental conditions. Statistically derived standardized regression coefficients were used to evaluate the contribution of individual molecular interactions within one stationary phase. It has been concluded that intermolecular interactions of the hydrophobic type significantly contribute to retention on all the CSPs studied here. Other retention increasing factors are n- and pi-electron interactions and dipole-dipole or dipole-induced dipole ones, while hydrogen donating or accepting interactions are more predominant with the mobile phase than with the stationary phases. However, these types of interactions are not equally significant for all the CSPs studied.     

Surface facetting induced by adsorbates

The presence of adsorbates can modify the morphology of the underlying substrate. The modifications are the results of a subtle thermodynamic balance between intermolecular and molecular-substrate interactions together with the surface relaxation energy. The information on how the substrate structures are influenced by the adsorbates, and therefore, the physical and chemical properties of the resulting interface is fundamentally important. In this review, we examine facetting of transition metals induced by either atomic species or organic molecules. First we focus on facetting induced by atomic species and small molecules under high pressure or UHV conditions. Following that, organic molecules containing several electronegative elements, such as amino acids, benzoic acid and aminobenzoic acid, are examined. These organic molecules can induce large scale facets with great similarity on fcc crystal surfaces. Learning from the correlation between the facetting induced by these molecules and those of atomic species, we try to rationalise the molecular mechanism for the formation of adsorbate induced facets.