Cold Molecules: Preparation,Applications, and Challenges

Research with cold molecules has developed rapidly in recent years. There is now a variety of established methods for cooling molecules into the millikelvin range. Nevertheless, a focal point of current research is directed toward finding new ways to bring the temperature of molecules even closer to absolute zero. Samples of cold molecules offer not only important applications for high‐resolution spectroscopy, which benefit from the increased interaction time of slow molecules with electromagnetic radiation; they also promise access to an exotic regime of chemical reactivity, in which phenomena such as quantum tunneling and quantum resonances predominate. This review begins with an introduction to the methods by which cold molecules can be prepared, with special emphasis on Stark deceleration and traps. In addition to applications of cold molecules that have already been partially achieved, an important focus of the review concentrates on possible future applications, and both aspects are illustrated with selected examples.     

Charge Transport Properties of Tetrabenz[a,c,h,j]-anthracene Derivatives

Charge transport properties of F, OH, OCH3, SH and SCH3-substituted tetra- benz[a,c,h,j]- anthracene derivative molecules have been investigated theoretically at the B3LYP/6-31G** level using Marcus theory. The results showed that at 300 K, the hole or electron transport capability of F or SH-substituted molecules was better obviously than that of OH or OCH3-substituted molecules. The electron transport capability of SCH3-substituted and F or SH-substituted molecules was superior to their hole transport capability, respectively. F, SH or SCH3-substituted tetrabenz[a,c,h,j]-anthracene derivative molecules can be used as electron transport materials.     

Halogenated xenon cyanides ClXeCN, ClXeNC, and BrXeCN

We report on the preparation and characterization of three new noble-gas molecules ClXeCN, ClXeNC, and BrXeCN. These molecules are synthesized by 193 nm photolysis and thermal annealing of ClCN and BrCN in a xenon matrix. The absorption spectra are measured in the mid- and far-infrared regions, and the assignment is supported by isotope substitution and quantum chemical calculations at the B3LYP and MP2 levels of theory. The present results demonstrate a way to prepare other noble-gas molecules of this type.     

Molecular topology analysis of the differences between drugs, clinical candidate compounds, and bioactive molecules

A new method to decompose molecules is proposed and used to analyze drugs, clinical candidate compounds and bioactive molecules. The method classifies a set of molecules into a few well-defined classes based on their molecular framework. It is then possible to use these classes to investigate differences between drugs, clinical candidates and bioactive molecules. The analysis shows that in comparison with clinical candidates and bioactive compounds, drugs have a higher fraction of compounds with only one ring system. This conclusion is still valid after correcting for lipophilicity (ClogP) and molecular size, as well as any potential protein target bias in the data sets. Furthermore the molecular bridge part of compounds in the drug set has on average fewer ring systems than molecules from the other sets. The ring system complexity (RSC) was also investigated and for most topological classes drugs have a lower RSC than the clinical candidates and bioactive molecules. Hence, this study highlights differences in topology between drugs, clinical candidate compounds and bioactive molecules.     

Highly fluorescent N,N-dimethylaminophenylethynylarenes: synthesis, photophysical properties, and electrochemiluminescence

A new family of aryl-pi-donor-aryl molecules has been synthesized and studied with respect to their photophysical properties and electrogenerated chemiluminscence (ECL) for the first time. Anthracene, phenanthrene, naphthalene, biphenyl, and fluorene were coupled with N,N-dimethylanilino moiety via a C-C triple bond (1-7). Introduction of such a strong electron-donating moiety as N,N-dimethylanilino group through a triple bond imparts new properties to the resultant molecules that are not commonly observed for the parent arenes. All molecules show absorption in the near-visible region and emission totally in the visible region with high fluorescence quantum yields. Bright solid-state photoluminescence has also been noticed for all the compounds in the visible region. 9-Anthryl- and 1-naphthyl- derivatives exhibited blue-shifted electrochemiluminescence (ECL) relative to their photoluminescence because of aggregation. 9-Phenanthryl- and 2-naphthyl- derivatives did not show ECL. 2-Biphenyl derivative showed monomeric ECL while 4-biphenyl counterpart exhibited excimer ECL. No ECL was observed for 2-fluorenyl derivative. The observed electronic properties are discussed with regard to the structure of the molecules. The characteristics of the molecules chosen in the present study open up new prospects and promises for novel tunable organic materials, on the basis of simple extension of conjugation to promote intramolecular communication, for ECL, OLED, and other optoelectronic applications.     

Monomolecular films of phthalocyanines: formation, characterization, and expelling by alkanethiols

Adsorption of aluminum-2,3-naphthalocyanine (Al-PC) onto gold (111) substrate from the pure and mixed (with alkanethiols) solutions of the target molecules in ethanol was studied. The resulting films were characterized by X-ray photoelectron spectroscopy and near-edge X-ray absorption fine structure spectroscopy. The adsorption from the pure solution resulted in formation of an Al-PC monolayer composed of the strongly inclined molecules. However, a presence of only one molar percent of a thiolated compound (alkanethiol) in the primary solution led to the complete expelling of the Al-PC molecules from the substrate and formation of a one-component alkylthiolate monolayer. The results indicate that an equilibrium formation of mixed monolayers of rodlike thiolated molecules and relatively large planar-geometry molecules, whose interaction with the metal surface is mainly provided by the pi-electron system, is difficult to achieve or is in most cases even impossible under equilibrium conditions and requires an introduction of additional anchor moieties (e.g., thiols) into these molecules, as has been demonstrated by successful coadsorption of hexadecanethiol and thiolated tetraphenylporphyrin.     

Force Field Benchmark of Organic Liquids: Density, Enthalpy of Vaporization, Heat Capacities, Surface Tension, Isothermal Compressibility, Volumetric Expansion Coefficient, and Dielectric Constant

The chemical composition of small organic molecules is often very similar to amino acid side chains or the bases in nucleic acids, and hence there is no a priori reason why a molecular mechanics force field could not describe both organic liquids and biomolecules with a single parameter set. Here, we devise a benchmark for force fields in order to test the ability of existing force fields to reproduce some key properties of organic liquids, namely, the density, enthalpy of vaporization, the surface tension, the heat capacity at constant volume and pressure, the isothermal compressibility, the volumetric expansion coefficient, and the static dielectric constant. Well over 1200 experimental measurements were used for comparison to the simulations of 146 organic liquids. Novel polynomial interpolations of the dielectric constant (32 molecules), heat capacity at constant pressure (three molecules), and the isothermal compressibility (53 molecules) as a function of the temperature have been made, based on experimental data, in order to be able to compare simulation results to them. To compute the heat capacities, we applied the two phase thermodynamics method (Lin et al. J. Chem. Phys.2003, 119, 11792), which allows one to compute thermodynamic properties on the basis of the density of states as derived from the velocity autocorrelation function. The method is implemented in a new utility within the GROMACS molecular simulation package, named g_dos, and a detailed exposé of the underlying equations is presented. The purpose of this work is to establish the state of the art of two popular force fields, OPLS/AA (all-atom optimized potential for liquid simulation) and GAFF (generalized Amber force field), to find common bottlenecks, i.e., particularly difficult molecules, and to serve as a reference point for future force field development. To make for a fair playing field, all molecules were evaluated with the same parameter settings, such as thermostats and barostats, treatment of electrostatic interactions, and system size (1000 molecules). The densities and enthalpy of vaporization from an independent data set based on simulations using the CHARMM General Force Field (CGenFF) presented by Vanommeslaeghe et al. (J. Comput. Chem.2010, 31, 671) are included for comparison. We find that, overall, the OPLS/AA force field performs somewhat better than GAFF, but there are significant issues with reproduction of the surface tension and dielectric constants for both force fields.     

FragNet,a Contrastive Learning-Based Transformer Model for Clustering,Interpreting, Visualizing,and Navigating Chemical Space

The question of molecular similarity is core in cheminformatics and is usually assessed via a pairwise comparison based on vectors of properties or molecular fingerprints. We recently exploited variational autoencoders to embed 6M molecules in a chemical space, such that their (Euclidean) distance within the latent space so formed could be assessed within the framework of the entire molecular set. However, the standard objective function used did not seek to manipulate the latent space so as to cluster the molecules based on any perceived similarity. Using a set of some 160,000 molecules of biological relevance, we here bring together three modern elements of deep learning to create a novel and disentangled latent space, viz transformers, contrastive learning, and an embedded autoencoder. The effective dimensionality of the latent space was varied such that clear separation of individual types of molecules could be observed within individual dimensions of the latent space. The capacity of the network was such that many dimensions were not populated at all. As before, we assessed the utility of the representation by comparing clozapine with its near neighbors, and we also did the same for various antibiotics related to flucloxacillin. Transformers, especially when as here coupled with contrastive learning, effectively provide one-shot learning and lead to a successful and disentangled representation of molecular latent spaces that at once uses the entire training set in their construction while allowing “similar” molecules to cluster together in an effective and interpretable way.     

Design,Synthesis, and In Vitro Evaluation of Novel Indolyl DiHydropyrazole Derivatives as Potential Anticancer Agents

Indoles derived from both natural sources or artificial synthetic methods have been known to interact with aryl hydrocarbon receptors (AhR), and exhibit anticancer activity. In light of these attractive properties, a series of hybrid molecules with structural features of indoles, i.e., those bearing a pyrazoline nucleus, were evaluated for their enhanced anticancer activity. The designed molecules were subjected to molecular docking in order to screen for potential AhR interacting compounds, and the identified indolyl dihydropyrazole derivatives were synthesized. The synthesized compounds were characterized, and their cytotoxicity was evaluated against four human cancer cell lines using the MTT assay. Based on the Glide g-score, H-bonding interactions and bonding energy of 20 candidate molecules were selected for further analysis from the 64 initially designed molecules. These candidate molecules have shown promising anti-proliferative activity against the cell lines tested. Among these candidate molecules, the compounds with hydroxy phenyl substitution on the pyrazoline ring have shown potent activity across all the tested cell lines. The designed scaffold was proven effective for screening potential candidate molecules with anticancer properties, and may be further optimized structurally for yielding the ideal anti-tumorigenic compound for the treatment of various cancers.     

Generation, spectroscopy, and structure of cyanoformyl chloride and cyanoformyl bromide, XC(O)CN

Cyanoformyl chloride and cyanoformyl bromide, XC(O)CN (X = Cl and Br), have been investigated in the gas phase by UV photoelectron and mid-infrared spectroscopies. The ground-state geometries of the neutral molecules have been obtained from quantum-chemical calculations at the B3LYP and CCSD(T) levels using the aug-cc-pVTZ basis set. The individual spectroscopies provide a detailed investigation into the vibrational and electronic character of the molecules and are supported by quantum-chemical calculations. The results are compared to data for structurally and chemically related molecules.     

All-aromatic, nanometer-scale, gold-cluster thiolate complexes

We report a method to generate and isolate 22 and 29 kDa core mass gold:benzenethiolate monolayer-protected cluster (MPC) molecules and a subsequent reaction to yield [(octyl)4N]2[Au44(SC6H5)28] (8.7 kDa core) clusters from these materials. Characterization methods for these 1.0-1.7 nm molecules include vibrational, electronic, 1H NMR, and mass spectrometry, as well as powder X-ray diffraction. The clusters are anionic and charge balanced by tetraoctylammonium. They possess size-dependent optical absorbance bands consistent with size-quantized gold cores and are susceptible to electrochemical degradation in polar organic solvents. To our knowledge this is the first report of all arylthiolate gold MPC molecules, and they represent ideal materials for crystallization and total structural characterization.     

Stability of nitrogen-oxygen cages N12O2, N14O2, N14O3, and N16O4

Molecules consisting entirely of nitrogen have been studied extensively for their potential as high energy density materials (HEDM). However, many such molecules are too unstable to serve as practical energy sources. This has prompted many studies of molecules that are mostly nitrogen but which incorporate heteroatoms into the structure to provide additional stability. In the current study, cages of three-coordinate nitrogen are viewed as candidates for stabilization by insertion of oxygen atoms into the nitrogen framework. Cages of N12, N14, and N16 with four-membered rings are studied because four-membered rings have been previously shown to be a destabilizing influence. Insertion of oxygen atoms, which converts N-N bonds to N-O-N bonding groups, relieves ring strain and can potentially result in stable molecules. These molecules are studied by theoretical calculations, using Hartree-Fock and Moller-Plesset (MP3 and MP4) theories, to determine the dissociation energies of the molecules. The primary result of the study is that stable molecules can result from oxygen insertion but that oxygen-oxygen proximity destabilizes the insertion products.     

Calculations of molecules,clusters, and solids with a simplified LCAO-DFT-LDA scheme

A simplified LCAO-DFT-LDA scheme for calculations of structure and electronic structure of large molecules, clusters, and solids is presented. Forces on the atoms are calculated in a semiempirical way considering the electronic states. The small computational effort of this treatment allows one to perform molecular dynamics (MD ) simulations of molecules and clusters up to a few hundred atoms as well as corresponding simulations of condensed systems within the Born-Oppenheimer approximation. The accuracy of the method is illustrated by the results of calculations for a series of small molecules and clusters. © 1996 John Wiley & Sons, Inc.     

Molekulare Wortspiele: Anagramme,Metagramme, Palindrome

Words and molecules are comparable. Words are a string of letters just as molecules are linked atoms. Isomers can be considered as molecular anagrams. Isosteres correspond to verbal metagrams. The linkage of identic syllables in a word is comparable with the linkage of same atomic groups in a molecule. Numerous natural substances and active compounds (drugs) correspond in their structure to a palindrom, which results in the same sense read from left to the right as in reverse.     

Surface ordering of a perfluorinated, self-assembled, dendrimer on a water subphase

We have investigated the surface ordering of a synthetic, asymmetric, fan-shaped dendrimer containing a carboxyl core and perfluorinated tails which was obtained by the esterification of the intermediary. X-ray diffraction patterns and transmission electron microscopy (TEM) images show the molecules self-assemble into a hexagonal, cylindrical mesophase. Surface pressure-area isotherms and Brewster angle microscopy measurements show the molecule forms a stable monolayer at the air-water interface with a single phase transition. As a condensed monolayer, the perfluorinated tails are well-packed with hexagonal symmetry with (10) spacing of approximately 0.5 nm from molecular-scale atomic force microscopy (AFM) images. Such dense molecular-scale packing has not been observed in other dendritic molecules thus far. Compared to the case of conventional dendritic molecules with alkyl tails, these molecules occupy a much smaller molecular area due to the strong microphase separation between the carboxylic core and perfluorinated tails at the air-water interface. After monolayer collapse, the irregular islands with terrace morphology are observed in contrast with conventional alkyl-terminated self-assembled dendritic molecules where irregular islands do not appear. The interfacial and internal structure of every terrace shows planar columnar morphology from AFM and TEM imaging. From these results, we discuss the stability of perfluorinated, self-assembled dendrimers on water, as well as how to generate planar morphology on a hydrophilic surface.     

Synthesis, loading, and application of individual nanocapsules for probing single-cell signaling

This paper describes the synthesis and loading of silica and polystyrene-acrylic based nanocapsules with small molecules. The nanocapsules are used for delivering defined packages of stimuli to single cells with both high spatial and temporal resolutions. To introduce molecules into the capsules, we characterized two approaches. The first approach is based on a base-swell process in which the shell of the capsule is swelled so small molecules can diffuse into the interior of the capsule and be trapped inside once the capsules are de-swelled. The second approach is based on a dry-swell-dry process in which the solution containing the molecules of interest and the nanocapsules is physically dried to promote more molecules to enter into the interior of the capsule. We characterized both methods by monitoring the content of and the release from individual capsules with confocal microscopy and wide-field imaging. To illustrate the biological applications of such nanocapsules, we used optical trapping to position a single carbachol-loaded capsule adjacent to a single CHO cell that has been transfected with muscarinic acetylcholine (M1) receptors, released the carbachol from the capsule with a single 3-ns N2 laser pulse, and then monitored the subsequent intracellular signaling triggered by the binding of carbachol to the M1 receptors.     

Density, distribution, and orientation of water molecules inside and outside carbon nanotubes

The behavior of water molecules inside and outside 1.1, 2.8, 6.9, and 10.4 nm diameter armchair carbon nanotubes (CNTs) is predicted using molecular dynamics simulations. The effects of CNT diameter on mass density, molecular distribution, and molecular orientation are identified for both the confined and unconfined fluids. Within 1 nm of the CNT surface, unconfined water molecules assume a spatially varying density profile. The molecules distribute nonuniformly around the carbon surface and have preferred orientations. The behavior of the unconfined water molecules is invariant with CNT diameter. The behavior of the confined water, however, can be correlated to tube diameter. Inside the 10.4 nm CNT, the molecular behavior is indistinguishable from that of the unconfined fluid. Within the smaller CNTs, surface curvature effects reduce the equilibrium water density and force water molecules away from the surface. This effect changes both the molecular distribution and preferred molecular orientations.     

Generation, characterisation, and applications of atomic and molecular alignment and orientation

The gas phase is generally defined as a state of matter in which atoms or molecules are in constant, rapid, random Brownian motion. However, a range of techniques exist for preparing distributions of gas phase atoms and molecules whose motion is far from random, and whose orientation in space is well defined. In this Perspective, we will explore the nature of atomic and molecular alignment and orientation, the various techniques by which samples of spatially oriented species may be prepared and characterised, and some of the ways in which oriented molecules are being exploited to further our knowledge of molecular structure and dynamics.     

Hydration forces: Observations, explanations, expectations, questions

The hydration force between large molecules or large surfaces is built on weak perturbation of many solvent molecules. The structure of the surface sets boundary conditions on solvent while structural forces within the solvent set the range. For this collection of essays, we focused on forces between surfaces at nanometer separations. It is instructive to distinguish primary hydration, the binding of water and perturbation within a few layers, from secondary hydration related to redistribution of solutes. The subject is still basically empirical, lacking satisfactory theory and sufficient measurement.