An official website of the United States government
Abstract We report the first conductance measurements of [n]staffane (bicyclopentane) oligomers in single‐molecule junctions. Our studies reveal two quantum transport characteristics unique to staffanes that emerge from their strained bicyclic structure. First, though staffanes are composed of weakly conjugated C−Cσ‐bonds, staffanes carry a shallower conductance decay value (β=0.84±0.02 n−1) than alkane chain analogs (β=0.96±0.03 n−1) when measured with the scanning tunneling microscopy break junction (STM‐BJ) technique. Staffanes are thus more conductive than otherσ‐bonded organic backbones reported in the literature on a per atom basis. Density functional theory (DFT) calculations suggest staffane backbones are more effective conduits for charge transport because their significant bicyclic ring strain destabilizes the HOMO‐2 energy, aligning it more closely with the Fermi energy of gold electrodes as oligomer order increases. Second, the monostaffane is significantly lower conducting than expected. DFT calculations suggest that short monostaffanes sterically enforce insulating gauche interelectrode orientations over syn orientations; these steric effects are alleviated in longer staffanes. Moreover, we find that [2‐5]staffane wires may accommodate axial mechanical strain by “rod‐bending”. These findings show for the first time how bicyclic ring strain can enhance charge transmission in saturated molecular wires. These studies showcase the STM‐BJ technique as a valuable tool for uncovering the stereoelectronic proclivities of molecules at material interfaces.
more »
« less
Strain visualization for strained macrocycles
Strain has a unique and sometimes unpredictable impact on the properties and reactivity of molecules. To thoroughly describe strain in molecules, a computational tool that relates strain energy to reactivity by localizing and quantifying strain was developed. Strain energy is calculated local to every coordinate in the molecule and areas of higher strain are shown experimentally to be more reactive. Not only does this tool directly compare strain energy in parts of the same molecule, but it also computes total strain to give a full picture of molecular strain energy. It is freely available to the public on GitHub under the name StrainViz and much of the workflow is automated to simplify use for non-experts. Unique insight into the reactivity of curved aromatic molecules and strained alkyne bioorthogonal reagents is described within.
more »
« less
- Award ID(s):
- 1800586
- PAR ID:
- 10176811
- Date Published:
- Journal Name:
- Chemical Science
- Volume:
- 11
- Issue:
- 15
- ISSN:
- 2041-6520
- Page Range / eLocation ID:
- 3923 to 3930
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Intermolecular interactions between radicals and closed-shell molecules are ubiquitous in chemical processes, ranging from the benchtop to the atmosphere and extraterrestrial space. While energy decomposition analysis (EDA) schemes for closed-shell molecules can be generalized for studying radical–molecule interactions, they face challenges arising from the unique characteristics of the electronic structure of open-shell species. In this work, we introduce additional steps that are necessary for the proper treatment of radical–molecule interactions to our previously developed unrestricted Absolutely Localized Molecular Orbital (uALMO)-EDA based on density functional theory calculations. A “polarize-then-depolarize” (PtD) scheme is used to remove arbitrariness in the definition of the frozen wavefunction, rendering the ALMO-EDA results independent of the orientation of the unpaired electron obtained from isolated fragment calculations. The contribution of radical rehybridization to polarization energies is evaluated. It is also valuable to monitor the wavefunction stability of each intermediate state, as well as their associated spin density profiles, to ensure the EDA results correspond to a desired electronic state. These radical extensions are incorporated into the “vertical” and “adiabatic” variants of uALMO-EDA for studies of energy changes and property shifts upon complexation. The EDA is validated on two model complexes, H 2 O⋯˙F and FH⋯˙OH. It is then applied to several chemically interesting radical–molecule complexes, including the sandwiched and T-shaped benzene dimer radical cation, complexes of pyridine with benzene and naphthalene radical cations, binary and ternary complexes of the hydroxyl radical with water (˙OH(H 2 O) and ˙OH(H 2 O) 2 ), and the pre-reactive complexes and transition states in the ˙OH + HCHO and ˙OH + CH 3 CHO reactions. These examples suggest that this second generation uALMO-EDA is a useful tool for furthering one's understanding of both energetic and property changes associated with radical–molecule interactions.more » « less
-
The phenalene (triangulene) and olympicene molecules belong to the polycyclic aromatic hydrocarbons (PAHs) class, which attracted substantial technological interest due to their unique electronic properties. Electronic structure calculations serve as a valuable tool in investigating the stability and reactivity of these molecular systems. In the present work, the multireference calculations, namely the complete active space second-order perturbation theory (CASPT2) and multireference averaged quadratic coupled cluster (MR-AQCC), were employed to study the reactivity and stability of phenalene and olympicene isomers, as well as their modified structures where the sp3-carbon at the borders were removed. The harmonic oscillator model of aromaticity (HOMA) and the nucleus-independent chemical shift (NICS) as geometric and magnetic indexes calculated with density functional theory were utilized to assess the aromaticity of the studied molecules. These indexes were compared with properties such as the excitation energy and natural orbitals occupation. The reactivity analyzed using the HOMA index combined with MR-AQCC revealed the radical character of certain structures, as well as the weakening of their aromaticity. Moreover, the results suggest that the removal of sp3-carbon atoms and the addition of hydrogen atoms did not alter the π network and the excitation energies of the phenalene molecules.more » « less
-
Abstract Chemical reactions conducted in the solid phase (specifically, crystalline) are much less numerous than solution reactions, primarily due to reduced motion, flexibility, and reactivity. The main advantage of crystalline‐state transformations is that reactant molecules can be designed to self‐assemble into specific spatial arrangements, often leading to high control over product regiochemistry and/or stereochemistry. In crystalline‐phase transformations, typically only one type of reaction occurs, and a sacrificial template molecule is frequently used to facilitate self‐assembly, similar to a catalyst or enzyme. Here, we demonstrate the first system designed to undergo two chemically unique and orthogonal cycloaddition reactions simultaneously within a single crystalline solid. Well‐controlled supramolecular self‐assembly of two molecules containing different reactive moieties affords orthogonal reactivity without use of a sacrificial template. Using only UV light, the simultaneous [2+2] and [4+4] cycloadditions are achieved regiospecifically, stereospecifically, and products are obtained in high yield, whereas a simultaneous solution‐state reaction affords a mixture of isomers in low yield. Application of dually‐reactive systems toward (supra)molecular solar thermal storage materials is also discussed. This work demonstrates fundamental chemical approaches for orthogonal reactivity in the crystalline state and highlights the complexity and reversibility that can be achieved with supramolecular design.more » « less
-
Quantum mechanics is central to our understanding of chemistry both qualitatively and quantitatively. Modern electronic structure calculations can yield energies and structures of small to medium size molecules to chemical accuracy, thereby providing a computational model for chemistry. A potential energy surface describes the energy of a molecule as a function of its geometric parameters. The features of potential energy surfaces provide the connections between quantum mechanics and the traditional chemical concepts such as structure, bonding and reactivity. This brief perspective presents an overview of tools for exploring potential energy surfaces such as optimizing equilibrium geometries, finding transition states, following reaction paths and simulating molecular dynamics.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1039/D0SC00629G
