arXiv subjects

Eiichi Nakamura

Publications and source records attributed to Eiichi Nakamura.

5 recordsLinked to original sources

arXiv2024

Unveiling a crystal's entropy of disorder via electron diffraction. A statistical mechanics approach

Upon melting, the molecules in the crystal explore numerous configurations, reflecting an increase in disorder. The molar entropy of disorder can be defined by Bolzmann's formula dSd = Rln(Wd) where Wd is the increase in the number of microscopic states, so far inaccessible experimentally. We found that the Arrhenius frequency factor A of the electron diffraction signal decay provides Wd via an experimental equation A = AINTWd where AINT is an inelastic scattering cross-section. The method connects Clausius and Boltzmann experimentally and supplements the Clausius approach, being applicable to a femtogram quantity of thermally unstable and biomolecular crystals. The data also showed that crystal disordering and crystallization of melt are reciprocal, both governed by the entropy change, but manifesting in opposite directions.

physics.chem-ph↗

arXiv2023

Atomically precise incorporation of BN doped rubicene into graphene nanoribbons

Substituting heteroatoms and non-benzenoid carbons into nanographene structure offers an unique opportunity for atomic engineering of electronic properties. Here we show the bottom-up synthesis of graphene nanoribbons (GNRs) with embedded fused BN-doped rubicene components on a Au(111) surface using on-surface chemistry. Structural and electronic properties of the BN-GNRs are characterized by scanning tunneling microscopy (STM) and atomic force microscopy (AFM) with CO-terminated tips supported by numerical calculations. The periodic incorporation of BN heteroatoms in the GNR leads to an increase of the electronic band gap as compared to its undoped counterpart. This opens avenues for the rational design of semiconducting GNRs with optoelectronic properties.

cond-mat.mtrl-sci↗

arXiv2022

Time-resolved Imaging of Stochastic Cascade Reactions over a Submillisecond to Second Time Range at the Angstrom Level

Most chemical reactions are cascade reactions in which a series of transient intermediates appear and disappear stochastically over an extended period. The mechanisms of such reactions are challenging to study, even in ultrafast pump-probe experiments. The dimerization of a van der Waals dimer of [60]fullerene producing a short carbon nanotube is a typical cascade reaction and is probably the most frequently studied in carbon materials chemistry. As many as 23 intermediates were predicted by theory, but only the first stable one has been verified experimentally. With the aid of fast electron microscopy, we obtained cinematographic recordings of individual molecules at a maximum frame rate of 1600 frames per second. Using Chambolle total variation algorithm processing and automated cross-correlation image matching analysis, we report on the identification of several metastable intermediates by their shape and size. Although the reaction events occurred stochastically, varying the lifetime of each intermediate accordingly, the average lifetime for each intermediate structure could be obtained from statistical analysis of many cinematographic images for the cascade reaction. Among the shortest-living intermediates, we detected one that lasted for less than 3 ms in three independent cascade reactions. We anticipate that the rapid technological development of microscopy and image processing will soon initiate an era of cinematographic studies of chemical reactions.

cond-mat.mtrl-sci↗

arXiv2022

Ionization and electron excitation of fullerene molecules in a carbon nanotube. A variable temperature/voltage transmission electron microscopic study

There is increasing attention to chemical applications of transmission electron microscopy, which is often plagued by radiation damage. The damage in organic matter predominantly occurs via ionization (radiolysis). Although radiolysis is highly important, previous studies on radiolysis have largely been descriptive and qualitative, lacking in such fundamental information as the product structure, the influence of the energy of the electrons, and the reaction kinetics. We need a chemically well-defined system to obtain such data, and have chosen as a model a variable-temperature and variable-voltage (VT/VV) study of the dimerization of a van der Waals dimer [60]fullerene (C60) to C120 in a carbon nanotube (CNT) as studied for individual reaction events at atomic resolution. We report here the identification of five reaction pathways that serve as mechanistic models of radiolysis damage. Two of them occur via a radical cation of the specimen generated by specimen ionization, and three involve singlet or triplet excited states of the specimen, as initiated by electron excitation of the CNT followed by energy transfer to the specimen. The pathways were distinguished by the pre-exponential factor and the Arrhenius activation energy. The prototypal reaction path is the radical cation reaction that we saw at <200 K, but, at >350 K, the excited-state reactions dominate. The results illustrate the importance of VT/VV kinetic analysis in the studies of radiation damage, and show that chemical ionization and electron excitation are inseparable but different mechanisms of radiation damage, which has so far been classified loosely under the single term "ionization."

physics.chem-ph↗

arXiv2021

Atomic-Number (Z)-Correlated Atomic Sizes for Deciphering Electron Microscopic Molecular Images

With the advent of atomic-resolution transmission electron microscopy (AR-TEM) achieving sub-Ångstrom image resolution and submillisecond time resolution, an era of visual molecular science where chemists can visually study the time evolution of molecular motions and reactions at atomistic precision has arrived. However, the appearance of experimental TEM images often differs greatly from that of conventional molecular models, and the images are difficult to decipher unless we know in advance the structure of the specimen molecules. The difference arises from the fundamental design of the molecular models that represent atomic connectivity and/or the electronic properties of molecules rather than the nuclear charge of atoms and electrostatic potentials that are felt by the e-beam in TEM imaging. We found a good correlation between the atomic number (Z) and the atomic size seen in TEM images when we consider shot noise in digital images. We propose here Z-correlated (ZC) atomic radii for modeling AR-TEM images of single molecules and ultrathin crystals, with which we can develop a good estimate of the molecular structure from the TEM image much more easily than with conventional molecular models. Two parameter sets were developed for TEM images recorded under high-noise (ZCHN) and low-noise (ZCLN) conditions. The new molecular models will stimulate the imaginations of chemists planning to use AR-TEM for their research.

cond-mat.mtrl-sci↗