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Concept: Molecular geometry


Cholesterol has been suggested to play a role in stable vesicle formation by adjusting the molecular packing of the vesicular bilayer. To explore the mechanisms involved in adjusting the bilayer structure by cholesterol, the molecular packing behavior in a mimic outer layer of cationic dialkyldimethylammonium bromide (DXDAB)/cholesterol vesicular bilayer was investigated by the Langmuir monolayer approach with infrared reflection-absorption spectroscopy (IRRAS). The results indicated that the addition of cholesterol in the DXDAB Langmuir monolayers not only restrained the desorption of the DXDAB with short hydrocarbon chains, such as ditetradecyldimethylammonium bromide or dihexadecyldimethylammonium bromide, into the aqueous phase but also induced a condensing effect on the DXDAB monolayers. At a liquid-expanded (LE) state, the ordering effect of cholesterol accompanying the condensing effect occurred in the mixed DXDAB/cholesterol monolayers due to the tendency of maximizing hydrocarbon chain contact between cholesterol and the neighboring hydrocarbon chains. However, for the mixed monolayers containing the DXDAB with long hydrocarbon chains, such as dioctadecyldimethylammonium bromide (DODAB), the disordering effect of cholesterol took place at a liquid-condensed (LC) state. This was related to the molecular structure of cholesterol and hydrocarbon chain length of DODAB. The rigid sterol ring of cholesterol hindered the portion of neighboring hydrocarbon chains from motion. However, the flexible alkyl side-chain of cholesterol along with the corresponding portion of neighboring hydrocarbon chains formed a fluidic region, counteracting the enhanced conformational order induced by the sterol ring of cholesterol. Furthermore, the long hydrocarbon chains of DODAB possessed a more pronounced motion freedom, resulting in a more disordered packing of the monolayers.

Concepts: Hydrocarbon, Physical chemistry, Steroid, Molecular geometry, Lipid bilayer, Infrared spectroscopy, Monolayer, Langmuir


Polymer and life science applications of a technique that combines atomic force microscopy (AFM) and infrared (IR) spectroscopy to obtain nanoscale IR spectra and images are reviewed. The AFM-IR spectra generated from this technique contain the same information with respect to molecular structure as conventional IR spectroscopy measurements, allowing significant leverage of existing expertise in IR spectroscopy. The AFM-IR technique can be used to acquire IR absorption spectra and absorption images with spatial resolution on the 50 to 100 nm scale, versus the scale of many micrometers or more for conventional IR spectroscopy. In the life sciences, experiments have demonstrated the capacity to perform chemical spectroscopy at the sub-cellular level. Specifically, the AFM-IR technique provides a label-free method for mapping IR-absorbing species in biological materials. On the polymer side, AFM-IR was used to map the IR absorption properties of polymer blends, multilayer films, thin films for active devices such as organic photovoltaics, microdomains in a semicrystalline polyhydroxyalkanoate copolymer, as well as model pharmaceutical blend systems. The ability to obtain spatially resolved IR spectra as well as high-resolution chemical images collected at specific IR wavenumbers was demonstrated. Complementary measurements mapping variations in sample stiffness were also obtained by tracking changes in the cantilever contact resonance frequency. Finally, it was shown that by taking advantage of the ability to arbitrarily control the polarization direction of the IR excitation laser, it is possible to obtain important information regarding molecular orientation in electrospun nanofibers.

Concepts: Spectroscopy, Molecular geometry, Absorption spectroscopy, Infrared spectroscopy, Infrared, Near infrared spectroscopy, Rotational spectroscopy, Photothermal microspectroscopy


The first terbium (Tb)-monometallic cyanide clusterfullerene (CYCF), TbCN@C82, has been successfully synthesized and isolated, whose molecular structure was determined unambiguously as TbCN@C2(5)-C82 by single crystal X-ray diffraction. The C2(5)-C82 isomeric cage represents a new cage capable of encapsulating a monometallic cyanide cluster. The C-N bond length within the encaged TbCN cluster is determined to be 0.94(5) Å, which is smaller by at least 0.17 Å than those of the reported C-N triplet bonds in traditional cyanide/nitrile compounds and cyano coordination complexes. An electronic configuration of [Tb(3+)(CN)(-)](2+)@[C82](2-) was proposed for TbCN@C82.

Concepts: Diffraction, X-ray, Molecule, Atom, Carbon, Ligand, Molecular geometry, Bond length


Laser cooling and trapping are central to modern atomic physics. The most used technique in cold-atom physics is the magneto-optical trap (MOT), which combines laser cooling with a restoring force from radiation pressure. For a variety of atomic species, MOTs can capture and cool large numbers of particles to ultracold temperatures (less than ∼1 millikelvin); this has enabled advances in areas that range from optical clocks to the study of ultracold collisions, while also serving as the ubiquitous starting point for further cooling into the regime of quantum degeneracy. Magneto-optical trapping of molecules could provide a similarly powerful starting point for the study and manipulation of ultracold molecular gases. The additional degrees of freedom associated with the vibration and rotation of molecules, particularly their permanent electric dipole moments, allow a broad array of applications not possible with ultracold atoms. Spurred by these ideas, a variety of methods has been developed to create ultracold molecules. Temperatures below 1 microkelvin have been demonstrated for diatomic molecules assembled from pre-cooled alkali atoms, but for the wider range of species amenable to direct cooling and trapping, only recently have temperatures below 100 millikelvin been achieved. The complex internal structure of molecules complicates magneto-optical trapping. However, ideas and methods necessary for creating a molecular MOT have been developed recently. Here we demonstrate three-dimensional magneto-optical trapping of a diatomic molecule, strontium monofluoride (SrF), at a temperature of approximately 2.5 millikelvin, the lowest yet achieved by direct cooling of a molecule. This method is a straightforward extension of atomic techniques and is expected to be viable for a significant number of diatomic species. With further development, we anticipate that this technique may be employed in any number of existing and proposed molecular experiments, in applications ranging from precision measurement to quantum simulation and quantum information to ultracold chemistry.

Concepts: Oxygen, Quantum mechanics, Matter, Chemistry, Atom, Chemical bond, Molecular geometry, Molecules


The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In the molecular sciences, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists? This approach points to an extension of open computer programs, not only providing access to the source code, but also delivering an easily modifiable and extensible scientific research tool. In this work, we will explore these questions using the Unity3D game engine to develop and prototype a biological network and molecular visualization application for subsequent use in research or education. We have compared several routines to represent spheres and links between them, using either built-in Unity3D features or our own implementation. These developments resulted in a stand-alone viewer capable of displaying molecular structures, surfaces, animated electrostatic field lines and biological networks with powerful, artistic and illustrative rendering methods. We consider this work as a proof of principle demonstrating that the functionalities of classical viewers and more advanced novel features could be implemented in substantially less time and with less development effort. Our prototype is easily modifiable and extensible and may serve others as starting point and platform for their developments. A webserver example, standalone versions for MacOS X, Linux and Windows, source code, screen shots, videos and documentation are available at the address:

Concepts: Computer graphics, Computer program, Molecular geometry, Source code, Source, Video game, Proof of concept, Video game industry


For more than half a century, high-resolution infrared spectroscopy has played a crucial role in probing molecular structure and dynamics. Such studies have so far been largely restricted to relatively small and simple systems, because at room temperature even molecules of modest size already occupy many millions of rotational/vibrational states, yielding highly congested spectra that are difficult to assign. Targeting more complex molecules requires methods that can record broadband infrared spectra (that is, spanning multiple vibrational bands) with both high resolution and high sensitivity. However, infrared spectroscopic techniques have hitherto been limited either by narrow bandwidth and long acquisition time, or by low sensitivity and resolution. Cavity-enhanced direct frequency comb spectroscopy (CE-DFCS) combines the inherent broad bandwidth and high resolution of an optical frequency comb with the high detection sensitivity provided by a high-finesse enhancement cavity, but it still suffers from spectral congestion. Here we show that this problem can be overcome by using buffer gas cooling to produce continuous, cold samples of molecules that are then subjected to CE-DFCS. This integration allows us to acquire a rotationally resolved direct absorption spectrum in the C-H stretching region of nitromethane, a model system that challenges our understanding of large-amplitude vibrational motion. We have also used this technique on several large organic molecules that are of fundamental spectroscopic and astrochemical relevance, including naphthalene, adamantane and hexamethylenetetramine. These findings establish the value of our approach for studying much larger and more complex molecules than have been probed so far, enabling complex molecules and their kinetics to be studied with orders-of-magnitude improvements in efficiency, spectral resolution and specificity.

Concepts: Spectroscopy, Electromagnetic radiation, Molecular geometry, Absorption spectroscopy, Infrared spectroscopy, Infrared, Near infrared spectroscopy, Rotational spectroscopy


We present the first high-resolution rotational spectrum of an ar- tificial molecular rotary motor. By combining chirped-pulse Fourier transform microwave spectroscopy and supersonic expansions we capture the vibronic ground state conformation of a second-generation motor based on chiral overcrowded alkenes. The rotational constants have been accurately determined by fitting more than two hundred rotational transitions in the 2-4 GHz frequency range. Evidence for dissociation products allows for the unambiguous identification and characterisation of the isolated rotor components. Experiment and complementary quantum chemical calculations provide accurate geometrical parameters of the C27H20 molecular motor, the largest molecule investigated to date using high-resolution microwave spectroscopy.

Concepts: Spectroscopy, Chemistry, Chemical bond, Frequency, Molecular geometry, Rotation, Infrared spectroscopy, Rotational spectroscopy


In this study, we have developed a method to create Co6Se8 superatoms in which we program the metal-ligand bonds. We exclusively form the Co6Se8 core under simple reaction conditions with a facile separation of products that contain differential substitution of the core. The combination of Co2(CO)8 and PR3 with excess Se gives the differentially and directionally substituted superatoms, Co6Se8(CO)x(PR3)(6-x). The CO groups on the superatom can be exchanged quantitatively with phosphines and isonitriles. Substitution of the CO allows us to manipulate the type and length of chemical bridge between two redox-active superatomic centers in order to modulate intersuperatomic coupling. Linking two superatoms together allows us to form the simplest superatom molecule: a diatomic molecule. We extend the superatom molecule concept to link three superatoms together in a linear arrangement to form acyclic triatomic molecules. These superatom molecules have a rich electrochemical profile and chart a clear path to a whole family of superatom molecules with new and unusual collective properties.

Concepts: Oxygen, Hydrogen, Chemistry, Atom, Chlorine, Molecular geometry, Molecules


Conformational flexibility is intrinsically related to the functionality of biomolecules. Elucidation of the potential energy surface is thus a necessary step towards understanding the mechanisms for molecular recognition such as docking of small organic molecules to larger macromolecular systems. In this work, we use broadband rotational spectroscopy in a molecular jet experiment to unravel the complex conformational space of citronellal. We observe fifteen conformations in the experimental conditions of the molecular jet, the highest number of conformers reported to date for a chiral molecule of this size using microwave spectroscopy. Studies of relative stability using different carrier gases in the supersonic expansion reveal conformational relaxation pathways that strongly favour ground-state structures with globular conformations. This study provides a blueprint of the complex conformational space of an important biosynthetic precursor and gives insights on the relation between its structure and biological functionality.

Concepts: DNA, Oxygen, Molecule, Chemistry, Atom, Chemical bond, Molecular geometry, Molecules


Synthetic light-driven rotary molecular motors show complicated structural dynamics during the rotation process. A combination of DFT calculations and various spectroscopic techniques is employed to study the effect of the bridging group in the lower half of the molecule on the conformational dynamics. It was found that the extent to which the bridging group can accommodate the increased folding in the transition state is the main factor in rationalizing the differences in barrier height and as a consequence, the rotary speed. These findings will be essential in designing future rotary molecular motors.

Concepts: DNA, Spectroscopy, Molecule, Transition state, Molecular geometry, Rotary International, Evanston, Illinois