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Jinlong Yang

Publications and source records attributed to Jinlong Yang.

At least 19 recordsLinked to original sources
PubMed2026

Exploring the hypothetical role of Bacteroides species in depression progression: insights from metagenomic analysis.

Depression, a psychiatric disorder with significant morbidity and mortality, has a complex etiology. Recent advances in microbiome research have highlighted the potential role of fecal microbiota in depression pathogenesis. This study utilized shotgun metagenomic sequencing to compare the fecal microbiota of 28 depression patients and 26 healthy individuals. Significant differences in fecal microbiota composition were observed between the two groups. We generated 350 non-redundant high-quality metagenome-assembled genomes (MAGs) by binning and conducted comparisons between the depression and control groups. Notably, we found that the MAGs enriched in people with depression mostly belonged to Bacteroides, indicating a close link between Bacteroides abundance and the development of depression, suggesting that Bacteroides might be a potential culprit for depression. In the depression group, we found that the module of nitric oxide synthesis was remarkably enriched, and all Bacteroides MAGs contained genes annotated as nitric oxide synthase, suggesting that increased levels of Bacteroides may contribute to elevated nitric oxide synthesis. A distinct microbial signature consisting of Arthrobacter sp._U41, Bacillus cereus, Campylobacter rectus, and Pasteurella dagmatis accurately discriminates between depressed individuals and healthy controls, achieving an average area under the receiver operating characteristic curve of 0.950. This research sheds light on the potential role of fecal microbiota in depression and highlights specific metabolic pathways and microbial markers for further investigation.IMPORTANCEThis research highlighted significant differences in the composition and function of fecal microbiota between individuals with depression and healthy individuals, particularly the enrichment of Bacteroides metagenome-assembled genomes (MAGs) in depression patients. The upregulation of the nitric oxide synthesis pathway associated with these MAGs belonging to Bacteroides in the gut of depression patients had also been observed. The selected bacterial biomarkers reliably differentiate depression cases from healthy controls with high diagnostic accuracy (mean area under the receiver operating characteristic curve = 0.950). Our results suggest the importance of exploring microbial markers as potential diagnostic and therapeutic targets in managing depression.

Humans↗
PubMed2007

Driving Energies of Hydrogen Scrambling Motions in CH5+.

A comprehensive quantum chemistry study with natural bond orbital analysis is performed to reveal the intrinsic properties of the floppy potential energy surface of the smallest methonium ion CH5+. In contrast to the low-energy barriers of Cs(I)-->Cs(II)-->Cs(I) and Cs(I)-->C2v-->Cs(I) that correspond to the H2 rotation and H-flip motions, the remarkably larger intramolecular interaction energies are the driving power to mimic the hydrogen scrambling in CH5+. As for the H2 rotation and H-flip motions, the hyperconjugative and electrostatic interactions compete strongly. They together with other interactions compensate for each other and lead to the floppy potential energy surface.

Journal Article↗
PubMed2006

Conduction mechanism of Aviram-Ratner rectifiers with single pyridine-sigma-C(60) oligomers.

We present the electron transport of pyridyl aza[60]fulleroid oligomers, abbreviated as C(60)NPy, which is based on the donor-barrier-acceptor (D-sigma-A) architecture, at a single molecular scale using scanning tunneling microscopy. A rectifying effect is observed in the current-voltage characteristics. The theoretical calculation shows that the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) are well localized either on the Py moiety (donor) or on the C(60) moiety (acceptor), indicating the sigma-bridge decouples the LUMO and the HOMO of the donor and the acceptor, respectively. This structure accords well with the unimolecular rectifying model proposed by Aviram and Ratner [Chem. Phys. Lett. 1974, 29, 277]. The mechanism of the rectifying effect is understood by analyzing in detail the electron transport through energy levels of the donor and the acceptor of the C(60)NPy molecules. By directly comparing the experimental conductance peaks and the calculated density of states of the C(60)NPy, we find that the observed rectification is attributed to the asymmetric positioning of the LUMOs and the HOMOs of both sides of the acceptor and the donor of the C(60)NPy molecules with respect to the Fermi level of the electrodes. When a main voltage drop is over the molecule-electrode vacuum junction but a small fraction over the molecule itself, the shift of the energy levels between the donor and the acceptor will be small. This behavior deviates from the original proposal by Aviram and Ratner in which a large shift of the energy level is expected.

Journal Article↗
PubMed2006

Single quintuple bond [PhCrCrPh] molecule as a possible molecular switch.

The electronic transport properties of a single quintuple bond [PhCrCrPh] molecule sandwiched between two Au(111) surfaces with the trans-bent and linear configurations are studied by a fully self-consistent nonequilibrium Green's function method combined with density functional theory. The calculated transmission spectra of two chemical isomers are remarkably distinctive. Theoretical results suggest that the current through the trans-bent configuration is significantly larger than the corresponding linear one. The predicted on-off ratio of currents ranging from around 50 to 200 in the applied bias window [-1.5 V, 1.5 V] suggests that multiple bond compounds have attractive potential in molecular switch technology.

Journal Article↗
PubMed2006

Geometric and electronic properties of endohedral Si @ C74.

The generalized gradient approximation based on density functional theory is used to analyze the geometric and electronic properties of Si @ C(74). It is found that among the five possible optimized geometries of Si @ C(74), the most favorable endohedral site of Si atom is under the center of a pentagon ring on the sigma(h) plane, i.e., Si @ C(74)-5, which is different from the center stable site for Si in C(74) calculated by the semiempirical molecular orbital calculations and molecular mechanics calculations, and it is also different from the stable site, i.e., under a [6, 6] bond along the C(2) axis on the sigma(h) plane in C(74) for metal atoms Ba, Ca, and Eu. The deformation charge density on the sigma(h) plane reveals that the Si-C bonds in Si @ C(74)-5 have covalent character, while the Mulliken charge analysis together with a longer Si-C bond length reveals that the Si-C bonds in Si @ C(74)-5 have ionic character. Therefore, we infer that Si-C bonds in Si @ C(74)-5 contain both covalent and ionic characters.

Journal Article↗
PubMed2006

Linear scaling calculation of maximally localized Wannier functions with atomic basis set.

We have developed a linear scaling algorithm for calculating maximally localized Wannier functions (MLWFs) using atomic orbital basis. An O(N) ground state calculation is carried out to get the density matrix (DM). Through a projection of the DM onto atomic orbitals and a subsequent O(N) orthogonalization, we obtain initial orthogonal localized orbitals. These orbitals can be maximally localized in linear scaling by simple Jacobi sweeps. Our O(N) method is validated by applying it to water molecule and wurtzite ZnO. The linear scaling behavior of the new method is demonstrated by computing the MLWFs of boron nitride nanotubes.

Journal Article↗
PubMed2006

Electronic excitation of polyfluorenes: a theoretical study.

We present systematic, theoretical investigations on structure-property correlations in polyfluorenes (PFs) derived mainly from the chain morphology, oligomer length, and chemical substitutent. Both the vertical absorptions and the vibrational contributions to electronic absorption and fluorescence spectra have been calculated. The effect of temperature on the nature of photoexcitations of PFs has been demonstrated. It is found that the vibronic (electronic and vibrational) structures of PFs are morphology-dependent. beta-phase oligofluorenes (beta-(FL)(n)) and ladder-type poly(p-phenylene) (LPPP) oligomers show a red shift compared to the spectra of alpha-(FL)(n). The asymmetry of the absorption and fluorescence spectra in alpha-(FL)(n) and the fluorenone (FLO) defect oligofluorenes alpha-(FL)(n)(-)(m)(FLO)(m) is significantly more pronounced than that in planarized beta-(FL)(n) and LPPP oligomers. By properly taking into account the anharmonic torsion potentials resulting from the strong electronic and nuclear coupling in the oligofluorenes, we have reasonably reproduced the experimentally observed spectroscopic features. The low-energy on-chain chemical defect sites such as FLO units act as charge-trapping sites for singlet excitations, are the predominantly lighting-emitting species, and thus alter the blue light-emitting properties of PFs whereas the blue-light-emitting properties of PFs are hardly influenced by the hole-transporting molecules. The optical properties of PFs have been predicted by the finite-size calculations. Energy gaps of PFs are estimated by extrapolations from excitation energies of oligofluorenes up to 21 FL units.

Journal Article↗
PubMed2006

Ultrafast interfacial proton-coupled electron transfer.

The coupling of electron and nuclear motions in ultrafast charge transfer at molecule-semiconductor interfaces is central to many phenomena, including catalysis, photocatalysis, and molecular electronics. By using femtosecond laser excitation, we transferred electrons from a rutile titanium dioxide (110) surface into a CH3OH overlayer state that is 2.3 +/- 0.2 electron volts above the Fermi level. The redistributed charge was stabilized within 30 femtoseconds by the inertial motion of substrate ions (polaron formation) and, more slowly, by adsorbate molecules (solvation). According to a pronounced deuterium isotope effect (CH3OD), this motion of heavy atoms transforms the reverse charge transfer from a purely electronic process (nonadiabatic) to a correlated response of electrons and protons.

Deuterium↗
PubMed2006

One-dimensional transition metal-benzene sandwich polymers: possible ideal conductors for spin transport.

We investigate the electronic and magnetic properties of the proposed one-dimensional transition metal (TM = Sc, Ti, V, Cr, and Mn) -benzene (Bz) sandwich polymers by means of density functional calculations. [V(Bz)](infinity) is found to be a quasi-half-metallic ferromagnet, and half-metallic ferromagnetism is predicted for [Mn(Bz)](infinity). Moreover, we show that stretching the [TM(Bz)](infinity) polymers could have dramatic effects on their electronic and magnetic properties. The elongated [V(Bz)](infinity) displays half-metallic behavior, and [Mn(Bz)](infinity) stretched to a certain degree becomes an antiferromagnetic insulator. The possibilities to stabilize the ferromagnetic order in [V(Bz)](infinity) and [Mn(Bz)](infinity) polymers at finite temperatures are discussed. We suggest that the hexagonal bundles composed by these polymers might display intrachain ferromagnetic order at finite temperatures by introducing interchain exchange coupling.

Journal Article↗
PubMed2006

Single-electron tunneling spectroscopy of single C60 in double-barrier tunnel junction.

The single-electron tunneling (SET) spectroscopy of C(60) molecule in a double-barrier tunnel junction is investigated by combining the scanning tunneling spectroscopy experiment and the theoretical simulation using the modified orthodox theory. The interplay between the SET effect and the discrete energy levels of C(60) molecule is studied. Three types of SET spectroscopies with different characters are obtained, corresponding to different tunneling processes and consistent with the previous theoretical prediction. Both the charging mode and resonance mode can arouse the current increase in the SET spectroscopy. The resonance mode is realized mainly by two mechanisms, including the resonance when the electron spans the second junction after already spanning the first junction. Some previous confused results have been clarified. Our results show that three types of SET spectroscopies can be together examined to quantitatively determine the frontier orbitals of the nanostructure by identifying the modes of various current increases.

Journal Article↗
PubMed2006

Geometric and electronic structures of metal-substitutional fullerene C59Sm and metal-exohedral fullerenes C60Sm.

The geometric and electronic structures of metal-substituted fullerene C59Sm and exohedral fullerenes C60Sm are studied using the density-functional theory. The geometric optimization shows that the replacement of a C atom with a Sm in C60 yields a stable substitutionally doped fullerene C59Sm, and among the five possible optimized geometries for C60Sm, the most favorable exohedral sites are above the center of a hexagon and a pentagon ring. The calculations for electronic structures show that the magnetic moment of Sm is preserved for all the stable structures as tiny hybridization takes place between the orbitals of the Sm atom and those of their neighboring carbons. Because of the small energy gaps and the half occupation of the highest occupied molecular orbitals, all the stable C60Sm isomers are inferred to be conductors.

Journal Article↗
PubMed2006

Defects-enhanced dissociation of H2 on boron nitride nanotubes.

With the density-functional theory and nudged elastic band method, the adsorption and dissociation of the hydrogen molecule on the boron nitride (BN) nanotubes with and without defects are studied theoretically. Hydrogen molecule physically adsorbs on the surface of the BN layer and nanotubes. The dissociation of the hydrogen molecule on the surface of the perfect BN layer and nanotubes is endothermic, and the energy barrier reduces with the decrease of the diameter of the tubes, while it is still larger than 2.0 eV for the (7,0) BN nanotube. Antisite, carbon substitutional, vacancy, and Stone-Wales 5775 defects on the wall of the tube are considered. With the presence of the defects, the dissociation of the hydrogen molecule becomes exothermic and the dissociation barrier can be reduced to about 0.67 eV.

Journal Article↗
PubMed2005

Nonequilibrium electronic transport of 4,4'-bipyridine molecular junction.

The electronic transport properties of a 4,4'-bipyridine molecule sandwiched between two Au(111) surfaces are studied with a fully self-consistent nonequilibrium Green's-function method combined with the density-functional theory. The 4,4'-bipyridine molecule prefers to adsorb near the hollow site of the Au(111) surface and distorts slightly. The modifications on the electronic structure of the molecule due to the presence of the electrodes are described by the renormalized molecular orbitals, which correspond well to the calculated transmission peaks. The average Fermi level lies close to the lowest unoccupied renormalized molecular orbital, which determines the electronic transport property of the molecular junction under a small bias voltage. The total transmission is contributed by a single channel. The transmission peaks shift with the applied bias voltage, and this behavior depends on the spatial distribution of the renormalized molecular orbitals and the voltage drop along the molecular junction. The shape of the calculated conductance curve of the equilibrium geometric configuration reproduces the main feature of the experimental results, but the value is larger than the measured data by about 6 times. Good agreement with the experimental measurements can be obtained by elongating the molecular junction. The electronic transport behaviors depend strongly on the interface configuration.

Journal Article↗
PubMed2005

Spin-unrestricted linear-scaling electronic structure theory and its application to magnetic carbon-doped boron nitride nanotubes.

We present an extension of the density-matrix-based linear-scaling electronic structure theory to incorporate spin degrees of freedom. When the spin multiplicity of the system can be predetermined, the generalization of the existing linear-scaling methods to spin-unrestricted cases is straightforward. However, without calculations it is hard to determine the spin multiplicity of some complex systems, such as many magnetic nanostuctures and some inorganic or bioinorganic molecules. Here we give a general prescription to obtain the spin-unrestricted ground state of open-shell systems. Our methods are implemented into the linear-scaling trace-correcting density-matrix purification algorithm. The numerical atomic-orbital basis, rather than the commonly adopted Gaussian basis functions, is used. The test systems include O2 molecule and magnetic carbon-doped boron nitride (BN)(5,5) and BN(7,6) nanotubes. Using the newly developed method, we find that the magnetic moments in carbon-doped BN nanotubes couple antiferromagnetically with each other. Our results suggest that the linear-scaling spin-unrestricted trace-correcting purification method is very powerful to treat large magnetic systems.

Journal Article↗
PubMed2005

Controlling the Kondo effect of an adsorbed magnetic ion through its chemical bonding.

We report that the Kondo effect exerted by a magnetic ion depends on its chemical environment. A cobalt phthalocyanine molecule adsorbed on an Au111 surface exhibited no Kondo effect. Cutting away eight hydrogen atoms from the molecule with voltage pulses from a scanning tunneling microscope tip allowed the four orbitals of this molecule to chemically bond to the gold substrate. The localized spin was recovered in this artificial molecular structure, and a clear Kondo resonance was observed near the Fermi surface. We attribute the high Kondo temperature (more than 200 kelvin) to the small on-site Coulomb repulsion and the large half-width of the hybridized d-level.

Journal Article↗
PubMed2005

Single C59N molecule as a molecular rectifier.

We report a new kind of experimental realization of a molecular rectifier, which is based on a single azafullerene C59N molecule in a double-barrier tunnel junction via the single electron tunneling effect. An obvious rectifying effect is observed. The positive onset voltage is about 0.5-0.7 V, while the negative onset voltage is about 1.6-1.8 V. Theoretical analyses show that the half-occupied molecular orbital of the C59N molecule and the asymmetric shift of the molecular Fermi level when the molecule is charged are responsible for the molecular rectification.

Journal Article↗
PubMed2005

Wet electrons at the H2O/TiO2(110) surface.

At interfaces of metal oxide and water, partially hydrated or "wet-electron" states represent the lowest energy pathway for electron transfer. We studied the photoinduced electron transfer at the H2O/TiO2(110) interface by means of time-resolved two-photon photoemission spectroscopy and electronic structure theory. At approximately 1-monolayer coverage of water on partially hydroxylated TiO2 surfaces, we found an unoccupied electronic state 2.4 electron volts above the Fermi level. Density functional theory shows this to be a wet-electron state analogous to that reported in water clusters and which is distinct from hydrated electrons observed on water-covered metal surfaces. The decay of electrons from the wet-electron state to the conduction band of TiO2 occurs in </=15 femtoseconds.

Journal Article↗