J. A. Larsson

A density functional study of Ce@C82: explanation of the Ce preferential bonding site.

Ce has been found experimentally to be preferentially incorporated into the C82 isomer of C2v symmetry as have other lanthanoids in M@C82 (M = La, Pr, Nd, etc.). We have investigated the underlying reason for this preference by calculating structural and electronic properties of Ce@C82 using density functional theory. The ground-state structure of Ce@C82 is found to have the cerium atom attached to the six-membered ring on the C2 axis of the C82-C2v cage, and the encapsulated atom is found to perturb the carbon cage due to chemical bonding. We have found Ce to favor this C2v chemisorption site in C82 by 0.62 eV compared to other positions on the inside wall of the cage. The specific preference of the metal atom to this six-membered ring is explained through electronic structure analysis, which reveals strong hybridization between the d orbitals of cerium and the pi orbitals of the cage that is particularly favorable for this chemisorption site. We propose that this symmetry dictated interaction between the cage and the lanthanide d orbital plays a crucial role when C82 forms in the presence of Ce to produce Ce@C82 and is also more generally applicable for the formation of other lanthanoid M@C82 molecules. Our theoretical computations are the first to explain this well-established fact. Last, the vibrational spectrum of Ce@C82 has been simulated and analyzed to gain insight into the metal-cage vibrations.

Quantification of ink diffusion in microcontact printing with self-assembled monolayers.

Spreading of ink outside the desired printed area is one of the major limitations of microcontact printing (micro-CP) with alkanethiol self-assembled monolayers (SAMs) on gold. We use molecular dynamics (MD) computer simulations to quantify the temperature and concentration dependence of hexadecanethiol (HDT) ink spreading on HDT SAMs, modeling 18 distinct printing conditions using periodic simulation cells of approximately 7 nm edge length and printing conditions ranging from 7 ink molecules per cell at 270 K to 42 ink molecules per cell at 371K. The computed alkanethiol ink diffusion rates on the SAM are of the same order of magnitude as bulk liquid alkanethiol diffusion rates at all but the lowest ink concentrations and highest temperatures, with up to 20-30 times increases in diffusion rates at the lowest concentration-highest temperature conditions. We show that although alkanethiol surfaces are autophobic, autophobicity is not enough to pin the ink solutions on the SAM, and so any overinking of the SAM will lead to spreading of the printed pattern. Comparison of experimental and calculated diffusion data supports an interpretation of pattern broadening as a mixture of spreading on fully and partially formed SAMs, and the calculated spreading rates establish some of the fundamental limitations of mu-CP in terms of stamp contact time and desired pattern width.

Measuring the mechanical properties of molecular conformers

Scanning probe-actuated single molecule manipulation has proven to be an exceptionally powerful tool for the systematic atomic-scale interrogation of molecular adsorbates. To date, however, the extent to which molecular conformation affects the force required to push or pull a single molecule has not been explored. Here we probe the mechanochemical response of two tetra(4-bromophenyl)porphyrin conformers using non-contact atomic force microscopy where we find a large difference between the lateral forces required for manipulation. Remarkably, despite sharing very similar adsorption characteristics, variations in the potential energy surface are capable of prohibiting probe-induced positioning of one conformer, while simultaneously permitting manipulation of the alternative conformational form. Our results are interpreted in the context of dispersion-corrected density functional theory calculations which reveal significant differences in the diffusion barriers for each conformer. These results demonstrate that conformational variation significantly modifies the mechanical response of even simple porpyhrins, potentially affecting many other flexible molecules.

Guanidinium chloride molecular diffusion in aqueous and mixed water-ethanol solutions.

Solutions containing guanidinium chloride (GdmCl), or equivalently guanidine hydrochloride (GdnHCl), are commonly used to denature macromolecules such as proteins and DNA in, for example, microfluidics studies of protein unfolding. To design and study such applications, it is necessary to know the diffusion coefficients for GdmCl in the solution. To this end, we use molecular dynamics simulations to calculate the diffusion coefficients of GdmCl in water and in water-ethanol solutions, for which no direct experimental measurements exist. The fully atomistic simulations show that the guandinium cation Gdm (+) diffusion decreases as the concentration of both Gdm (+) and ethanol in the solution increases. The simulations are validated against available literature data, both transformed measured viscosity values and computed diffusion coefficients, and we show that a prudent choice of water model, namely TIP4P-Ew, gives calculated diffusion coefficients in good agreement with the transformed measured viscosity values. The calculated Gdm (+) diffusion behavior is explained as a dynamic mixture of free cation, stacked cation, and ion-paired species in solution, with weighted contributions to Gdm (+) diffusion from the stacked and paired states helping explain measured viscosity data in terms of atom-scale dynamics.

A basis set study for the calculation of electronic excitations using Monte Carlo configuration interaction

A systematic study of basis sets and many-body correlations for the treatment of electronic excitations is presented. Particular emphasis is placed on the highly accurate treatment of transition energies within a computationally tractable scheme. All calculations have been performed using the Monte Carlo configuration interaction method and correlation-consistent basis sets augmented by diffuse functions constructed for the description of anions, and with the inclusion of additional Rydberg functions. The importance of a balanced description of the excited states and the ground state has been emphasized and the resulting electronic transitions have been compared with experimental values. We have found that the aug-cc-pVTZ basis set further augmented with Rydberg functions constitutes a good choice of basis set for which we report electronic excitations in excellent agreement with experiment.

Band structure engineering of a molecular wire system composed of dimercaptoacetoamidobenzene, its derivatives, and gold clusters

Abstract The properties of molecular devices can be engineered through modification of the conformation of the molecule and through chemical substitution. The following study presents the results of density functional theory studies of the properties of a metal–molecule assembly resulting from the interaction between an organic molecular linker, dimercaptoacetoamidobenzene and thirteen atom “magic number” gold nanoclusters. Bonding between two gold nanoclusters, changing the conformation of the linker molecule and the effect of chemical substitution in the linker are assessed through considering the geometry and electronic structure of the resulting assemblies. Changing the conformation in the molecule leads to significant changes in the electronic structure of the metal–linker–metal complex. Chemical substitution in the molecular wire also has an effect on the electronic structure; however, energy level shifts are larger for conformational changes than for chemical substitution.

The role of ellipticity on the preferential binding site of Ce and La in C78-D3h--a density functional theory study.

Endohedral metallofullerenes that encapsulate one or several atoms, or a cluster of atoms have molecular properties making them useful both in technology and in bio-medical applications. Some fullerenes are found to have two metal atoms incarcerated and it has been recently found that two Ce atoms are incorporated into the C(78)-D(3h) (78 : 5) cage. In this study, we report calculations on the structural and electronic properties of Ce(2)@C(78) using density functional theory (DFT). While Ce(2)@C(80)-I(h) (D(3d)) and La(2)@C(80)-I(h) (D(2h)) have different ground state structures, we have found that Ce(2)@C(78) has a D(3h) ground state structure just as La(2)@C(78). The encapsulated Ce atoms bind strongly to the C(78)-D(3h) cage with a binding energy (BE) of 5.925 eV but not as strong as in Ce@C(82)-C(2v) nor in Ce(2)@C(80)-I(h). The elliptical nature of the cage plays a crucial role and accommodates the two Ce atoms at opposite ends of the C(3) axis with a maximized inter atomic distance (4.078 A). This means that the effect of the additional f-electron repulsion in M(2)@C(78) with M = Ce compared to M = La, is less pronounced than in Ce(2)@C(80) compared to La(2)@C(80). We compare the results to the elliptical M(2)@C(72) (#10611) (M = La, Ce), and with a range of additional Ce and La endohedral fullerenes and explain the role ellipticity has in the preferential binding site of Ce and shed light on the formation mechanism of these nanostructures.

A Physical Compact Model for Electron Transport Across Single Molecules

Prediction of current flow across single molecules requires ab initio electronic structure calculations along with their associated high computational demand, and a means for incorporating open system boundary conditions to describe the voltage sources driving the current. To date, first principle predictions of electron transport across single molecules have not fully achieved a predictive capability. The situation for molecular electronics may be compared to conventional technology computer-aided design (TCAD), whereby various approximations to the Boltzmann transport equation are solved to predict electronic device behavior, but in practice are too time consuming for most circuit design applications. To simplify device models for circuit design, analytical but physically motivated models are introduced to capture the behavior of active and passive devices; however, similar models do not yet exist for molecular electronics. We follow a similar approach by evaluating an analytical model achieved by combining a mesoscopic transport model with parameterizations taken from quantum chemical calculations of the electronic structure of single molecule bonded between two metal contacts. Using the model to describe electron transport across benzene-1,4-dithiol and by comparing to experiment, we are able to extract the coupling strength of the molecule attached to two infinite metal electrodes. The resulting procedure allows for accurate and computationally efficient modeling of the static (dc) characteristics of a single molecule, with the added capability of being able to study the physical model parameter variations across a range of experiments. Such simple physical models are also an important step towards developing a design methodology for molecular electronics

Photo-dissociation of hydrogen passivated dopants in gallium arsenide

A theoretical and experimental study of the photo-dissociation mechanisms of hydrogen passivated n- and p-type dopants in gallium arsenide is presented. The photo-induced dissociation of the SiGa–H complex has been observed for relatively low photon energies (3.48 eV), whereas the photo-dissociation of CAs–H is not observed for photon energies up to 5.58 eV. This fundamental difference in the photo-dissociation behavior between the two dopants is explained in terms of the localized excitation energies about the Si–H and C–H bonds.