![]() They appear with two lobes at a distance of 13.0 ± 0.1 Å (Fig. 2) allows individual isolated molecules to be investigated. 1).ĭeconstructing the islands molecule by molecule (Supplementary Fig. 1c) with ordering determined by the dipolar interaction between molecules (Supplementary Fig. Depositing these molecules onto a Ag(111) surface at room temperature, results in highly ordered honeycomb assemblies (Fig. To protect the polar groups from strong adsorption with the surface, DDNB contains two peripheral adamantane groups which allows for facile diffusion and interaction with the electric field 16. 1b) with a resulting net dipole moment of 6.78 Debye in the gas phase (see Supplementary Table 1). This arises from the electron-donating character of the dimethylamine (−N(CH 3) 2) and the electron-withdrawing properties of the nitro (−NO 2) group attached to the central benzene ring (Fig. We have developed the 2,5-di(ethynyladamantanyl)−4-(dimethylamino)nitrobenzene molecule (DDNB) 16 which, at its core, has a strong electric dipole. From these precision manipulation experiments, the electric field-induced motion can be mapped and used to determine the internal dipole moment of a single molecule. Here, we manipulate single dipolar molecules and obtain unidirectional rotation on demand, and thus deterministic behavior. In contrast to non-deterministic processes, we show that the electric field in an STM junction can be used to manipulate polar molecules with absolute precision (Fig. Molecular rotors in double-decker complexes have been rotated in large assemblies, albeit without control over the direction of rotation 15. While rotation is often combined with translation, e.g., along the edge of a molecular island 12, it can also be constrained to a fixed rotational axis 13, 14. Moreover, the STM tip has been used to induce rotation of various molecules 9, 10, 11. Scanning tunneling microscopy (STM) is attractive in this regard as it provides the means to image and manipulate matter at the single-molecule scale and track thermally induced processes like rotation and translation on metallic surfaces 8. Deterministically controlling the direction of molecular rotation and translation remains a challenge because numerous degrees of freedom exist and thermally activated processes offer little selectivity 7. Specifically, the orientation of a molecule or a functional group can affect many processes, for instance, molecular diffusion on a surface 1, 2, the efficiency of a chemical reaction 3, 4, and heterogeneous catalysis 5 or biochemical reactions with enzymes as catalyst 6. The coordinates are rotated 90 degrees around the Z axis. Z can be changed to X and Y to rotate around the X and Y axes, respectively.Controlling the motion and orientation of single molecules is key to the understanding of heterogeneous catalysis, growth and assembly processes as well as to the operation of surface-adsorbed molecular machines. If you want this bond to be parallel to other Cartesian axes, then follow the above method to first make this bond parallel to the X axis and then execute the following code. $sel move Īfter executing the above code, if you want to align bond between atom 3 and 5 to be parallel to the X axis then enter the following codeĪfter that, save the coordinate file. Copy the following code to VMD console and execute. Orient a certain bond parallel to a certain axisįirst load molecule’s structure file (such as. ![]() From Gaussian output file confirm dipole moment oreintation.xyz file to the gaussian input (.gjf) file and do single point energy calculation with the same orignal level of theory as of the optimized structure with an additional keyword nosymm. If the dipole moment vector of the molecule is (-6.5624 -3.2697 -2.1767), enter folowing commands in the VMD console to oreint the dipole moment vector along Z-axis.Then copy molecule coordinates from gaussian input file and paste in the new text file from 3rd line. xyz file format by creating a new text file and in this new file on the first line write the number of atoms in your molecule. Create Gaussian input file (.gjf) from the output file.Open output file in Gaussview and note dipole moment vector from results => charge distribution window).If you have Gaussian Output file of a molecule and want its dipole moment parallel to a certain axis for example Z-axis. Orient dipole moment parallel to a certain axis The easiest way to orient a certain vector or bond of a molecule parallel to Cartesian coordinate axis is to use the commands provided by VMD. Sometimes it is necessary to reorient the molecule to make its dipole moment or any other vector or certain bond of the molecule parallel to a certain Cartesian coordinate axis.
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