On the mechanisms of lysis triggered by perturbations of bacterial cell wall biosynthesis.

Inhibition of bacterial cell wall synthesis by antibiotics such as ß-lactams is thought to cause explosive lysis through loss of cell wall integrity. However, recent studies on a wide range of bacteria have suggested that these antibiotics also perturb central carbon metabolism, contributing to death via oxidative damage. Here, we genetically dissect this connection in Bacillus subtilis perturbed for cell wall synthesis, and identify key enzymatic steps in upstream and downstream pathways that stimulate the generation of reactive oxygen species through cellular respiration. Our results also reveal the critical role of iron homeostasis for the oxidative damage-mediated lethal effects. We show that protection of cells from oxygen radicals via a recently discovered siderophore-like compound uncouples changes in cell morphology normally associated with cell death, from lysis as usually judged by a phase pale microscopic appearance. Phase paling appears to be closely associated with lipid peroxidation.

Genome editing and molecular analyses of an Arabidopsis transcription factor, LATE FLOWERING.

Correct flower organ formation at the right timing is one of the most important strategies for plants to achieve reproductive success. Ectopic overexpression of LATE FLOWERING (LATE) is known to induce late flowering, partly through suppressing expression of the florigen-encoding gene FLOWERING LOCUS T (FT) in Arabidopsis. LATE is one of the C2H2 zinc finger transcription factors, and it has a canonical transcriptional repression domain called the ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif at the end of its C terminus. Therefore, LATE is considered a transcriptional repressor, but its molecular function remains unclear. Our genome-edited late mutants exhibited no distinct phenotype, even in flowering, indicating the presence of redundancy from other factors. To reveal the molecular function of LATE and factors working with it, we investigated its transcriptional activity and interactions with other proteins. Transactivation activity assay showed that LATE possesses transcriptional repression ability, which appears to be attributable to both the EAR motif and other sequences. Yeast two-hybrid assay showed the EAR motif-mediated interaction of LATE with TOPLESS, a transcriptional corepressor. Moreover, LATE could also interact with CRABS CLAW (CRC), one of the most important regulators of floral meristem determinacy, through sequences in LATE other than the EAR motif. Our findings demonstrated the possibility that LATE can form a transcriptional repression complex with CRC for floral meristem determinacy.

Selective triplet exciton formation in a single molecule.

The formation of excitons in organic molecules by charge injection is an essential process in organic light-emitting diodes (OLEDs)1-7. According to a simple model based on spin statistics, the injected charges form spin-singlet (S1) excitons and spin-triplet (T1) excitons in a 1:3 ratio2-4. After the first report of a highly efficient OLED2 based on phosphorescence, which is produced by the decay of T1 excitons, more effective use of these excitons has been the primary strategy for increasing the energy efficiency of OLEDs. Another route to improving OLED energy efficiency is reduction of the operating voltage2-6. Because T1 excitons have lower energy than S1 excitons (owing to the exchange interaction), use of the energy difference could-in principle-enable exclusive production of T1 excitons at low OLED operating voltages. However, a way to achieve such selective and direct formation of these excitons has not yet been established. Here we report a single-molecule investigation of electroluminescence using a scanning tunnelling microscope8-20 and demonstrate a simple method of selective formation of T1 excitons that utilizes a charged molecule. A 3,4,9,10-perylenetetracarboxylicdianhydride (PTCDA) molecule21-25 adsorbed on a three-monolayer NaCl film atop Ag(111) shows both phosphorescence and fluorescence signals at high applied voltage. In contrast, only phosphorescence occurs at low applied voltage, indicating selective formation of T1 excitons without creating their S1 counterparts. The bias voltage dependence of the phosphorescence, combined with differential conductance measurements, reveals that spin-selective electron removal from a negatively charged PTCDA molecule is the dominant formation mechanism of T1 excitons in this system, which can be explained by considering the exchange interaction in the charged molecule. Our findings show that the electron transport process accompanying exciton formation can be controlled by manipulating an electron spin inside a molecule. We anticipate that designing a device taking into account the exchange interaction could realize an OLED with a lower operating voltage.

On-Surface Evolution of meso-Isomerism in Two-Dimensional Supramolecular Assemblies.

Chiral structures created through the adsorption of molecules onto achiral surfaces play pivotal roles in many fields of science and engineering. Here, we present a systematic study of a novel chiral phenomenon on a surface in terms of organizational chirality, that is, meso-isomerism, through coverage-driven hierarchical polymorphic transitions of supramolecular assemblies of highly symmetric π-conjugated molecules. Four coverage-dependent phases of dehydrobenzo[12]annulene were uniformly fabricated on Ag(111), exhibiting unique chiral characteristics from the single-molecule level to two-dimensional supramolecular assemblies. All coverage-driven phase transitions stem from adsorption-induced pseudo-diastereomerism, and our observation of a lemniscate-type (∞) supramolecular configuration clearly reveals a drastic chiral phase transition from an enantiomeric chiral domain to a meso-isomeric achiral domain. These findings provide new insights into controlling two-dimensional chiral architectures on surfaces.

Quasiparticle scattering in type-II Weyl semimetal MoTe2.

The electronic structure of type-II Weyl semimetal molybdenum ditelluride (MoTe2) is studied by using scanning tunneling microscopy and density functional theory calculations. Through measuring energy-dependent quasiparticle interference (QPI) patterns with a cryogenic scanning tunneling microscope, several characteristic features are found in the QPI patterns. Two of them arise from the Weyl semimetal nature; one is the topological Fermi arc surface state and the other can be assigned to be a Weyl point. The remaining structures are derived from the scatterings relevant to the bulk electronic states. The findings lead to further understanding of the topological electronic structure of type-II Weyl semimetal MoTe2.

Visualizing Type-II Weyl Points in Tungsten Ditelluride by Quasiparticle Interference.

Weyl semimetals (WSMs) are classified into two types, type I and II, according to the topology of the Weyl point, where the electron and hole pockets touch each other. Tungsten ditelluride (WTe2) has garnered a great deal of attention as a strong candidate to be a type-II WSM. However, the Weyl points for WTe2 are located above the Fermi level, which has prevented us from identifying the locations and the connection to the Fermi arc surface states by using angle-resolved photoemission spectroscopy. Here, we present experimental proof that WTe2 is a type-II WSM. We measured energy-dependent quasiparticle interference patterns with a cryogenic scanning tunneling microscope, revealing the position of the Weyl point and its connection with the Fermi arc surface states, in agreement with prior theoretical predictions. Our results provide an answer to this crucial question and stimulate further exploration of the characteristics of WSMs.

Transport characteristics of a silicene nanoribbon on Ag(110).

We present the transport characteristics of individual silicene nanoribbons (SiNRs) grown on Ag(110). By lifting up a single SiNR with a low-temperature scanning tunneling microscope tip, a nanojunction consisting of tip, SiNR and Ag is fabricated. In the differential conductance spectra of the nanojunctions fabricated by this methodology, a peak appears at the Fermi level which is not observed in the spectra measured either for the SiNRs before being lifted up or the clean Ag substrate. We discuss the origin of the peak as it relates to the SiNR.

In Situ STM and Vibrational Study of Nanometer-Scale Reorganization of a Phospholipid Monolayer Accompanied by Potential-Driven Headgroup Digestion.

In situ dynamic observation of model biological cell membranes, formed on a water/gold substrate interface, has been performed by the combination of electrochemical scanning tunneling microscopy and reflection infrared absorption vibrational spectroscopy. Monolayers of 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) were formed on alkanethiol-modified gold surfaces in a buffer solution, and the microscopic phase transitions driven by electrochemical potential control were observed more in detail than our previous study on the same system [Electrochem. Commun. 2007, 9, 645-650]. This time the transitions were associated with the chemistry of DHPC by the aid of vibrational spectroscopy and the utilization of deuterium-labeled DHPC molecules. A negative potential shift solidifies the fluidic lipid layers into static striped or grainy features without notable chemical reactions. The first positive potential shift over the virginal DHPC monolayer breaks DHPC into choline and the corresponding phosphatidic acid (DHPA). This is the first case of a phospholipid electrochemical reaction microscopically detected at the solid surface.

Single-Molecule Dynamics in the Presence of Strong Intermolecular Interactions.

In contrast to conventional spectroscopic studies of adsorbates at high coverage that provide only spatially averaged information, we have characterized the laterally confined shuttling dynamics of a single molecule under the influence of intermolecular interactions by vibrational spectroscopy using a scanning tunneling microscope. The bridge sites on Pt(111) are only occupied by a CO molecule that is surrounded by four other CO molecules at on-top sites. The bridge-site CO undergoes laterally confined shuttling toward an adjacent on-top site to transiently occupy a metastable site, which is slightly displaced from the center of an on-top site through repulsive interaction with adjacent on-top CO molecules. Analysis of action spectra for the shuttling events reveals the C-O stretch frequency of the metastable CO. We also constructed a modified potential energy surface incorporating the intermolecular interaction, which reveals the underlying mechanism and provides a new way to experimentally determine detailed information on the energetics of the metastable state.

Formation of Ordered Phospholipid Monolayer on a Hydrophilically Modified Au(111) Substrate.

The molecular arrangement of phospholipid molecules was investigated on a hydrophilically modified gold surface within an aqueous solution by scanning tunneling microscopy. By suspending phospholipid (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, POPC) nanoparticles in the aqueous electrolyte surrounding a hydrophilically modified gold (111) substrate with 3-mercaptopropionic acid (SH-C2H4-COOH, 3-MPA), well-ordered adlattices of POPC were observed. Traces of particle fusion were visualized before formation of the adlattice. Addition of cholesterol to the suspension seems to facilitate accommodation of POPC on this surface. The observed unit cells of POPC adlattices had dimensions of 0.5 nm × 1.9-2.5 nm. By high-resolution imaging, each unit cell was discerned to be occupied by one upright POPC molecule. The POPC + cholesterol suspension also leads to formation of a flat integrated POPC layer, which may be a lipid bilayer covering the surface.

Lewis Basicity of Nitrogen-Doped Graphite Observed by CO2 Chemisorption.

The characteristics of CO2 adsorption sites on a nitrogen-doped graphite model system (N-HOPG) were investigated by X-ray photoelectron and absorption spectroscopy and infrared reflection absorption spectroscopy. Adsorbed CO2 was observed lying flat on N-HOPG, stabilized by a charge transfer from the substrate. This demonstrated that Lewis base sites were formed by the incorporation of nitrogen via low-energy nitrogen-ion sputtering. The possible roles of twofold coordinated pyridinic N and threefold coordinated valley N (graphitic N) sites in Lewis base site formation on N-HOPG are discussed. The presence of these nitrogen species focused on the appropriate interaction strength of CO2 indicates the potential to fine-tune the Lewis basicity of carbon-based catalysts.

Lateral Hopping of CO on Ag(110) by Multiple Overtone Excitation.

A novel type of action spectrum representing multiple overtone excitations of the v(M-C) mode was observed for lateral hopping of a CO molecule on Ag(110) induced by inelastically tunneled electrons from the tip of a scanning tunneling microscope. The yield of CO hopping shows sharp increases at 261±4 mV, corresponding to the C-O internal stretching mode, and at 61±2, 90±2, and 148±7 mV, even in the absence of corresponding fundamental vibrational modes. The mechanism of lateral CO hopping on Ag(110) was explained by the multistep excitation of overtone modes of v(M-C) based on the numerical fitting of the action spectra, the nonlinear dependence of the hopping rate on the tunneling current, and the hopping barrier obtained from thermal diffusion experiments.

Impact of reduced symmetry on magnetic anisotropy of a single iron phthalocyanine molecule on a Cu substrate.

We study the magnetic anisotropy of a single iron phthalocyanine (FePc) molecule on a Cu(110) (2 × 1)-O by using inelastic electron tunneling spectroscopy (IETS) with low-temperature scanning tunneling microscopy. Two inelastic excitations derived from the splitting of the molecular triplet spin state appear as two pairs of steps symmetrically with respect to zero sample voltage. We measured IETS spectra with external magnetic fields perpendicular and parallel to the molecular plane, and we analyzed the spectral evolution with the effective spin Hamiltonian approach. We determined all parameters related with magnetic anisotropy at a single-molecule level, both the easy- and hard-magnetization directions, zero-field splitting constant, D = - 4.0 meV and E = 1.1 meV, the Lande g-tensor gxx, gyy, gzz=(1.82, 2.02, 2.34), and the constant of spin-orbit coupling λ = - 19.1 meV. We stress that the symmetry breaking caused by the adsorption of FePc on the oxidized Cu(110) significantly impacts the magnetic anisotropy.

Seamless growth of a supramolecular carpet.

Organic/metal interfaces play crucial roles in the formation of intermolecular networks on metal surfaces and the performance of organic devices. Although their purity and uniformity have profound effects on the operation of organic devices, the formation of organic thin films with high interfacial uniformity on metal surfaces has suffered from the intrinsic limitation of molecular ordering imposed by irregular surface structures. Here we demonstrate a supramolecular carpet with widely uniform interfacial structure and high adaptability on a metal surface via a one-step process. The high uniformity is achieved with well-balanced interfacial interactions and site-specific molecular rearrangements, even on a pre-annealed amorphous gold surface. Co-existing electronic structures show selective availability corresponding to the energy region and the local position of the system. These findings provide not only a deeper insight into organic thin films with high structural integrity, but also a new way to tailor interfacial geometric and electronic structures.

Characterization of nitrogen species incorporated into graphite using low energy nitrogen ion sputtering.

The electronic structures of nitrogen species incorporated into highly oriented pyrolytic graphite (HOPG), prepared by low energy (200 eV) nitrogen ion sputtering and subsequent annealing at 1000 K, were investigated by X-ray photoelectron spectroscopy (XPS), angle-dependent X-ray absorption spectroscopy (XAS), and Raman spectroscopy. An additional peak was observed at higher binding energy of 401.9 eV than 400.9 eV for graphitic1 N (graphitic N in the basal plane) in N 1s XPS, where graphitic2 N (graphitic N in the zigzag edge and/or vacancy sites) has been theoretically expected to appear. N 1s XPS showed that graphitic1 N and graphitic2 N were preferably incorporated under low nitrogen content doping conditions (8 × 10(13) ions cm(-2)), while pyridinic N and graphitic1 N were dominantly observed under high nitrogen content doping conditions. In addition, angle-dependent N 1s XAS showed that the graphitic N and pyridinic N atoms were incorporated into the basal plane of HOPG and thus were highly oriented. Furthermore, Raman spectroscopy revealed that low energy sputtering resulted in almost no fraction of the disturbed graphite surface layers under the lowest nitrogen doping condition. The suitable nitrogen doping condition was discovered for realizing the well-controlled nitrogen doped HOPG. The electrochemical properties for the oxygen reduction reaction of these samples in acidic solution were examined and discussed.

Tunneling Desorption of Single Hydrogen on the Surface of Titanium Dioxide.

We investigated the reaction mechanism of the desorption of single hydrogen from a titanium dioxide surface excited by the tip of a scanning tunneling microscope (STM). Analysis of the desorption yield, in combination with theoretical calculations, indicates the crucial role played by the applied electric field. Instead of facilitating desorption by reducing the barrier height, the applied electric field causes a reduction in the barrier width, which, when coupled with the electron excitation induced by the STM tip, leads to the tunneling desorption of the hydrogen. A significant reduction in the desorption yield was observed when deuterium was used instead of hydrogen, providing further support for the tunneling-desorption mechanism.

Scanning tunneling microscope observation of the phosphatidylserine domains in the phosphatidylcholine monolayer.

A mixed monolayer of 1,2-dihexanoyl-sn-glycero-3-phospho-l-serine (DHPS) and 1,2-dihexanoyl-sn-glycero-3-phosphocholine (DHPC) on an 1-octanethiol-modified gold substrate was visualized on the nanometer scale using in situ scanning tunneling microscopy (STM) in aqueous solution. DHPS clusters were evident as spotty domains. STM enabled us to distinguish DHPS molecules from DHPC molecules depending on their electronic structures. The signal of the DHPS domains was abolished by neutralization with Ca(2+). The addition of the PS + Ca(2+)-binding protein of annexin V to the Ca(2+)-treated monolayer gave a number of spots corresponding to a single annexin V molecule.

Adsorption of water dimer on platinum(111): identification of the -OH···Pt hydrogen bond.

The fundamental structure of an isolated water dimer on Pt(111) was determined by means of a spectroscopic method using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. Two water molecules on adjacent atop sites form a dimer through a hydrogen bond, and they rotate even at a substrate temperature of 5 K. Action spectroscopy using STM (STM-AS) for water dimer hopping allows us to obtain the vibrational spectrum of a single water dimer on Pt(111). Comparisons between the experiments and theory show that one of the OH groups of the acceptor water molecule points toward the surface to form an -OH···Pt hydrogen bond.

Controlling orbital-selective Kondo effects in a single molecule through coordination chemistry.

Iron(II) phthalocyanine (FePc) molecule causes novel Kondo effects derived from the unique electronic structure of multi-spins and multi-orbitals when attached to Au(111). Two unpaired electrons in the d(z)(2) and the degenerate dπ orbitals are screened stepwise, resulting in spin and spin+orbital Kondo effects, respectively. We investigated the impact on the Kondo effects of the coordination of CO and NO molecules to the Fe(2+) ion as chemical stimuli by using scanning tunneling microscopy (STM) and density functional theory calculations. The impacts of the two diatomic molecules are different from each other as a result of the different electronic configurations. The coordination of CO converts the spin state from triplet to singlet, and then the Kondo effects completely disappear. In contrast, an unpaired electron survives in the molecular orbital composed of Fe d(z)(2) and NO 5σ and 2π* orbitals for the coordination of NO, causing a sharp Kondo resonance. The isotropic magnetic response of the peak indicates the origin is the spin Kondo effect. The diatomic molecules attached to the Fe(2+) ion were easily detached by applying a pulsed voltage at the STM junction. These results demonstrate that the single molecule chemistry enables us to switch and control the spin and the many-body quantum states reversibly.