Neutral Polar Molecules Research Articles

Water‐Soluble Aryl‐ and Super Aryl‐Extended Calix[4]pyrroles

AbstractThe study of molecular recognition processes in water using biomimetic synthetic receptors provides valuable information for understanding more complex biological processes. In the last decade, our group focused on the use of aryl‐extended calix[4]pyrrole (AE−C[4]P) scaffolds for the binding of small polar molecules in water. The cone conformation of tetra‐α isomers of aryl‐extended calix[4]pyrroles defines a deep hydrophobic cavity with an open end and functionalized with converging hydrogen‐bond donor groups in its closed end. In this sense, AE−C[4]Ps can be considered as simple biomimetic analogs of enzyme binding sites. In this account, we describe the synthetic strategies used for the preparation of water‐soluble AE‐ and super aryl‐extended (SAE−) C[4]Ps. We review and rationalize the results of their molecular recognition studies in water using pyridyl‐N‐oxide derivatives and a series of small and neutral polar molecules as guests and comment on their applications as supramolecular and sequestering protective groups.

Guiding neutral polar molecules by electromagnetic vortex field

ABSTRACT It is shown, within classical mechanics, that the field of an electromagnetic vortex is capable of capturing and guiding neutral molecules endowed with a permanent electric dipole moment (PEDM). Similarly as in the case of the magnetic field applied to elementary particles or atoms, this effect turns out to be very delicate because of the small values of PEDM observed in real molecules. They amount to (electron charge × fermi) or less, which requires the use of very strong electric fields (reaching ). It has also been observed that there exists a threshold in field strength above which the particles are ejected from the trap. Trajectories of guided particles are usually quite chaotic, which is a consequence of non-linearity of the equations of motion. With a very special and precise adjustment of parameters, a regular (i.e. circular, in the transverse plane) trajectory can be obtained. The presence of an additional constant electric field pointing along the direction of the wave propagation might help to achieve the necessary tuning and realize such trajectories.

Spontaneous Polarization of Cryo-Deposited Films for Five Normal Saturated Monohydroxy Alcohols, CnH2n+1OH, n = 1-5.

Vapor-deposited films of neutral polar molecules on cold surfaces exhibit spontaneous electric polarization across the faces of the film. We deposited known amounts of the first five members of the normal monohydroxy alcohols at substrate temperatures in the range of 30-130 K. It is known that voltages measured are proportional to film thickness and that the effect is substrate-independent. The main trend observed was that the voltage per molecule surface density grows with molecule size and drops with deposition temperature. With the exception of some high-temperature methanol depositions, the films had a negative voltage on the vacuum side. Furthermore, the heavier members (1-butanol and 1-pentanol) showed reduced voltages for the lowest temperatures, suggesting that all members of the series could follow this pattern at temperatures below what was experimentally accessible. After deposition, film voltage was monitored during a temperature ramp showing first an increase in the voltage measured, then gradual decay before film evaporation. Initial film voltages are in general agreement with the concept of surface mobility of vapor-deposited molecules and indicate a negative correlation with dipole moment size.

A structural preview of aquaporin 8 via homology modeling of seven vertebrate isoforms

BackgroundAquaporins (AQPs) facilitate the passage of small neutral polar molecules across membranes of the cell. In animals there are four distinct AQP subfamilies, whereof AQP8 homologues constitute one of the smallest subfamilies with just one member in man. AQP8 conducts water, ammonia, urea, glycerol and H2O2 through various membranes of animal cells. This passive channel has been connected to a number of phenomena, such as volume change of mitochondria, ammonia neurotoxicity, and mitochondrial dysfunction related to oxidative stress. Currently, there is no experimentally determined structure of an AQP8, hence the structural understanding of this subfamily is limited. The recently solved structure of the plant AQP, AtTIP2;1, which has structural and functional features in common with AQP8s, has opened up for construction of homology models that are likely to be more accurate than previous models.ResultsHere we present homology models of seven vertebrate AQP8s. Modeling based on the AtTIP2;1 structure alone resulted in reasonable models except for the pore being blocked by a phenylalanine that is not present in AtTIP2;1. To achieve an open pore, these models were supplemented with models based on the bacterial water specific AQP, EcAqpZ, creating a chimeric monomeric model for each AQP8 isoform. The selectivity filter (also named the aromatic/arginine region), which defines the permeant substrate profile, comprises five amino acid residues in AtTIP2;1, including a histidine coming from loop C. Compared to AtTIP2;1, the selectivity filters of modelled AQP8s only deviates in that they are slightly more narrow and more hydrophobic due to a phenylalanine replacing the histidine from loop C. Interestingly, the models do not exclude the existence of a side pore beneath loop C similar to that described in the structure of AtTIP2;1.ConclusionsOur models concur that AQP8s are likely to have an AtTIP2;1-like selectivity filter. The detailed description of the expected configuration of residues in the selectivity filters of AQP8s provides an excellent starting point for planning of as well as rationalizing the outcome of mutational studies. Our strategy to compile hybrid models based on several templates may prove useful also for other AQPs for which structural information is limited.

3D-Printed Beam Splitter for Polar Neutral Molecules

We describe a macroscopic beam splitter for polar neutral molecules. A complex electrode structure is required for the beam splitter which would be very difficult to produce with traditional manufacturing methods. Instead, we make use of a nascent manufacturing technique: 3D printing of a plastic piece, followed by electroplating. This fabrication method opens a plethora of avenues for research, since 3D printing imposes practically no limitations on possible shapes, and the plating produces chemically robust, conductive construction elements with an almost free choice of surface material; it has the added advantage of dramatically reduced production cost and time. Our beam splitter is an electrostatic hexapole guide that smoothly transforms into two bent quadrupoles. We demonstrate the correct functioning of this device by separating a supersonic molecular beam of ND3 into two correlated fractions. It is shown that this device can be used to implement experiments with differential detection wherein one of the fractions serves as a probe and the other as a reference. Reverse operation would allow to merging of two beams of neutral polar molecules.

Decelerating and Trapping Large Polar Molecules

Manipulating the motion of large polyatomic molecules, such as benzonitrile (C6 H5 CN), presents significant difficulties compared to the manipulation of diatomic molecules. Although recent impressive results have demonstrated manipulation, trapping, and cooling of molecules as large as CH3 F, no general technique for trapping such molecules has been demonstrated, and cold neutral molecules larger than 5 atoms have not been trapped (M. Zeppenfeld, B. G. U. Englert, R. Glöckner, A. Prehn, M. Mielenz, C. Sommer, L. D. van Buuren, M. Motsch, G. Rempe, Nature 2012, 491, 570-573). In particular, extending Stark deceleration and electrostatic trapping to such species remains challenging. Here, we propose to combine a novel "asymmetric doublet state" Stark decelerator with recently demonstrated slow, cold, buffer-gas-cooled beams of closed-shell volatile molecules to realize a general system for decelerating and trapping samples of a broad range of volatile neutral polar prolate asymmetric top molecules. The technique is applicable to most stable volatile molecules in the 100-500 AMU range, and would be capable of producing trapped samples in a single rotational state and at a motional temperature of hundreds of mK. Such samples would immediately allow for spectroscopy of unprecedented resolution, and extensions would allow for further cooling and direct observation of slow intramolecular processes such as vibrational relaxation and Hertz-level tunneling dynamics.

Lopsided Benzene’s Big Moment

Chemists have made a new set of hexasubstituted benzenes in which electron-withdrawing cyano groups on one side of the ring and electron-donating amino groups on the other combine to pull and push the molecule’s electron density in the same direction. These compounds are remarkable for being the most polar neutral molecules now known to exist (Angew. Chem. Int. Ed. 2016, DOI: 10.1002/anie.201508249). Organic molecules with large dipole moments are desirable for their ability to enhance the efficiency of polymer films in electronic devices such as lasers, microchips for smart cards, and solar cells. Multisubstituted benzenes have long been synthetic targets, but chemists have been limited in their ability to prepare them using standard electrophilic substitutions. A research team led by Klaus Müllen of the Max Planck Institute for Polymer Research has now devised a new synthesis of hexasubstituted benzenes and dialkyldihydrobenzimidazoles via a new dibromo intermediate they prepared. The most

Accurate evaluation of charge asymmetry in aqueous solvation.

Charge hydration asymmetry (CHA)-a characteristic dependence of hydration free energy on the sign of the solute charge-quantifies the asymmetric response of water to electric field at microscopic level. Accurate estimates of CHA are critical for understanding hydration effects ubiquitous in chemistry and biology. However, measuring hydration energies of charged species is fraught with significant difficulties, which lead to unacceptably large (up to 300%) variation in the available estimates of the CHA effect. We circumvent these difficulties by developing a framework which allows us to extract and accurately estimate the intrinsic propensity of water to exhibit CHA from accurate experimental hydration free energies of neutral polar molecules. Specifically, from a set of 504 small molecules we identify two pairs that are analogous, with respect to CHA, to the K(+) /F(-) pair-a classical probe for the effect. We use these "CHA-conjugate" molecule pairs to quantify the intrinsic charge-asymmetric response of water to the microscopic charge perturbations: the asymmetry of the response is strong, ∼50% of the average hydration free energy of these molecules. The ability of widely used classical water models to predict hydration energies of small molecules correlates with their ability to predict CHA.

Do identical polar diatomic molecules form stacked or linear dimers?

The interaction of two identical polar neutral molecules is modeled by two equal but oppositely charged point particles at a fixed distance of separation. The total Coulomb potential energy of this system is calculated as a function of this distance, x, and the distance, y, between their centers of mass. We find that when the y/x ratio is less than about 3.1619, the linear configuration has the lower energy, whereas when this ratio exceeds 3.1619, a stacked structure is more stable. Interestingly, when two real polar molecules, such as HF interact, neither of these structures are formed. It is ‘hydrogen bonded’. The NaF dimer on the other hand, has a global minimum as stacked structure at a y/x ratio of about 1, significantly smaller than 3.1619!

Spatial Separation of Molecular Conformers and Clusters

Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold molecular beams. However, these beams often contain multiple conformers and clusters, even at low rotational temperatures. We present an experimental methodology that allows the spatial separation of these constituent parts of a molecular beam expansion. Using an electric deflector the beam is separated by its mass-to-dipole moment ratio, analogous to a bender or an electric sector mass spectrometer spatially dispersing charged molecules on the basis of their mass-to-charge ratio. This deflector exploits the Stark effect in an inhomogeneous electric field and allows the separation of individual species of polar neutral molecules and clusters. It furthermore allows the selection of the coldest part of a molecular beam, as low-energy rotational quantum states generally experience the largest deflection. Different structural isomers (conformers) of a species can be separated due to the different arrangement of functional groups, which leads to distinct dipole moments. These are exploited by the electrostatic deflector for the production of a conformationally pure sample from a molecular beam. Similarly, specific cluster stoichiometries can be selected, as the mass and dipole moment of a given cluster depends on the degree of solvation around the parent molecule. This allows experiments on specific cluster sizes and structures, enabling the systematic study of solvation of neutral molecules.

Spatial Separation of Molecular Conformers and Clusters

Gas-phase molecular physics and physical chemistry experiments commonly use supersonic expansions through pulsed valves for the production of cold molecular beams. However, these beams often contain multiple conformers and clusters, even at low rotational temperatures. We present an experimental methodology that allows the spatial separation of these constituent parts of a molecular beam expansion. Using an electric deflector the beam is separated by its mass-to-dipole moment ratio, analogous to a bender or an electric sector mass spectrometer spatially dispersing charged molecules on the basis of their mass-to-charge ratio. This deflector exploits the Stark effect in an inhomogeneous electric field and allows the separation of individual species of polar neutral molecules and clusters. It furthermore allows the selection of the coldest part of a molecular beam, as low-energy rotational quantum states generally experience the largest deflection. Different structural isomers (conformers) of a species can be separated due to the different arrangement of functional groups, which leads to distinct dipole moments. These are exploited by the electrostatic deflector for the production of a conformationally pure sample from a molecular beam. Similarly, specific cluster stoichiometries can be selected, as the mass and dipole moment of a given cluster depends on the degree of solvation around the parent molecule. This allows experiments on specific cluster sizes and structures, enabling the systematic study of solvation of neutral molecules.

The electrostatic response of water to neutral polar solutes: implications for continuum solvent modeling.

Continuum solvation models are widely used to estimate the hydration free energies of small molecules and proteins, in applications ranging from drug design to protein engineering, and most such models are based on the approximation of a linear dielectric response by the solvent. We used explicit-water molecular dynamics simulations with the TIP3P water model to probe this linear response approximation in the case of neutral polar molecules, using miniature cucurbituril and cyclodextrin receptors and protein side-chain analogs as model systems. We observe supralinear electrostatic solvent responses, and this nonlinearity is found to result primarily from waters' being drawn closer and closer to the solutes with increased solute-solvent electrostatic interactions; i.e., from solute electrostriction. Dielectric saturation and changes in the water-water hydrogen bonding network, on the other hand, play little role. Thus, accounting for solute electrostriction may be a productive approach to improving the accuracy of continuum solvation models.

Polypyrrole derivatives as solvent vapor sensors

Quantum mechanical calculations have been carried out to investigate the affinity of polypyrrole (PPy) and poly[N-(2-cyanoethyl)pyrrole] (PNCEPy) towards molecules from vapors of different solvents (i.e. water, methanol, acetonitrile and chloroform). Results show that neutral cyano-containing polymers interact more favorably with both water and methanol than neutral PPy, whereas these affinities are the opposite for materials in the oxidized state. Moreover, addition of the geometric distortion contributions and the thermodynamic corrections to the interaction energies allow us to conclude that the binding affinities between the two neutral polymers and small polar molecules in the vapor phase are similar, in excellent agreement with experimental information. On the other hand, the affinity of the two conducting polymers towards chloroform is relatively poor independently of the oxidation state, while acetonitrile interacts more favorably with the N–H of PPy than with the cyano group. The influence of both the vapor molecules and the solvent on the geometric parameters (i.e. dihedral angles, inter-ring bond lengths and bond length alternation pattern) and electronic properties (i.e. ionization potential and π–π* lowest transition energy) have been evaluated using different approaches, which include time-dependent density functional theory calculations.

Decelerating molecules with microwave fields

We here report on the experimental realization of a microwave decelerator for neutral polar molecules, suitable for decelerating and focusing molecules in high-field-seeking states. The multi-stage decelerator consists of a cylindrical microwave cavity oscillating on the TE 11n mode, with n=12 electric field maxima along the symmetry axis. By switching the microwave field on and off at the appropriate times, a beam of state-selected ammonia molecules with an incident mean velocity of 25 m/s is guided while being spatially focussed in the transverse direction and bunched in the forward direction. Deceleration from 20.0 m/s to 16.9 m/s and acceleration from 20.0 m/s to 22.7 m/s is demonstrated.

Cluster-state generation using van der Waals and dipole-dipole interactions in optical lattices

We present a scalable method for generation of a cluster state for measurement-based quantum computing using van der Waals or dipole-dipole interactions between neutral atoms or polar molecules in an optical lattice. Nearest neighbor entanglement is accomplished by performing a phase gate using interaction of atoms in Rydberg states or molecules in large dipole moment states. All nearest neighbors are sequentially entangled in a finite number of operations, independent of the number of qubits, producing a 1D cluster state. A universal 2D cluster state can be generated in several ms in a two-dimensional optical lattice by producing a series of 1D cluster states in one lattice direction, followed by application of the entangling operations in another lattice direction. We discuss the viability of the scheme with Rb Rydberg atoms.

Quantum computing implementations with neutral particles

We review quantum information processing with cold neutral particles, that is, atoms or polar molecules. First, we analyze the best suited degrees of freedom of these particles for storing quantum information, and then we discuss both single- and two-qubit gate implementations. We focus our discussion mainly on collisional quantum gates, which are best suited for atom-chip-like devices, as well as on gate proposals conceived for optical lattices. Additionally, we analyze schemes both for cold atoms confined in optical cavities and hybrid approaches to entanglement generation, and we show how optimal control theory might be a powerful tool to enhance the speed up of the gate operations as well as to achieve high fidelities required for fault tolerant quantum computation.

A traveling wave decelerator for neutral polar molecules

Recently, a decelerator for neutral polar molecules has been presented that operates on the basis of macroscopic, three-dimensional, traveling electrostatic traps [A. Osterwalder, S. A. Meek, G. Hammer, H. Haak, and G. Meijer, Phys. Rev. A 81, 051401 (2010)]. In the present paper, a complete description of this decelerator is given, with emphasis on the electronics and the mechanical design. Experimental results showing the transverse velocity distributions of guided molecules are shown and compared to trajectory simulations. An assessment of non-adiabatic losses is made by comparing the deceleration signals from (13)CO with those from (12)CO and with simulated signals.

Cold heteromolecular dipolar collisions

Cold molecules promise to reveal a rich set of novel collision dynamics in the low-energy regime. By combining for the first time the techniques of Stark deceleration, magnetic trapping, and cryogenic buffer gas cooling, we present the first experimental observation of cold collisions between two different species of state-selected neutral polar molecules. This has enabled an absolute measurement of the total trap loss cross sections between OH and ND(3) at a mean collision energy of 3.6 cm(-1) (5 K). Due to the dipolar interaction, the total cross section increases upon application of an external polarizing electric field. Cross sections computed from ab initio potential energy surfaces are in agreement with the measured value at zero external electric field. The theory presented here represents the first such analysis of collisions between a (2)Π radical and a closed-shell polyatomic molecule.

Cold chemistry with electronically excited Ca+ Coulomb crystals

Rate constants for chemical reactions of laser-cooled Ca(+) ions and neutral polar molecules (CH(3)F, CH(2)F(2), or CH(3)Cl) have been measured at low collision energies (<E(coll)>/k(B)=5-243 K). Low kinetic energy ensembles of (40)Ca(+) ions are prepared through Doppler laser cooling to form "Coulomb crystals" in which the ions form a latticelike arrangement in the trapping potential. The trapped ions react with translationally cold beams of polar molecules produced by a quadrupole guide velocity selector or with room-temperature gas admitted into the vacuum chamber. Imaging of the Ca(+) ion fluorescence allows the progress of the reaction to be monitored. Product ions are sympathetically cooled into the crystal structure and are unambiguously identified through resonance-excitation mass spectrometry using just two trapped ions. Variations of the laser-cooling parameters are shown to result in different steady-state populations of the electronic states of (40)Ca(+) involved in the laser-cooling cycle, and these are modeled by solving the optical Bloch equations for the eight-level system. Systematic variation of the steady-state populations over a series of reaction experiments allows the extraction of bimolecular rate constants for reactions of the ground state ((2)S(1/2)) and the combined excited states ((2)D(3/2) and (2)P(1/2)) of (40)Ca(+). These results are analyzed in the context of capture theories and ab initio electronic structure calculations of the reaction profiles. In each case, suppression of the ground state rate constant is explained by the presence of a submerged or real barrier on the ground state potential surface. Rate constants for the excited states are generally found to be in line with capture theories.

Microwave Lens for Polar Molecules

We here report on the implementation of a microwave lens for neutral polar molecules suitable to focus molecules in both low-field-seeking and high-field-seeking states. By using the TE{11m} modes of a 12 cm long cylindrically symmetric microwave resonator, Stark-decelerated ammonia molecules are transversally confined. We investigate the focusing properties of this microwave lens as a function of the molecules' velocity, the microwave power, and the frequency detuning Δ from the molecular resonance. Such a microwave lens can be seen as a first important step towards further microwave devices, such as decelerators and traps.