17 research outputs found
First-principles calculation on the transport properties of molecular wires between Au clusters under equilibrium
Based on the matrix Green's function method combined with hybrid
tight-binding / density functional theory, we calculate the conductances of a
series of gold-dithiol molecule-gold junctions including benzenedithiol (BDT),
benzenedimethanethiol (BDMT), hexanedithiol (HDT), octanedithiol (ODT) and
decanedithiol (DDT). An atomically-contacted extended molecule model is used in
our calculation. As an important procedure, we determine the position of the
Fermi level by the energy reference according to the results from ultraviolet
photoelectron spectroscopy (UPS) experiments. After considering the
experimental uncertainty in UPS measurement, the calculated results of
molecular conductances near the Fermi level qualitatively agree with the
experimental values measured by Tao et. al. [{\it Science} 301, 1221 (2003);
{\it J. Am. Chem. Soc.} 125, 16164 (2003); {\it Nano. Lett.} 4, 267 (2004).]Comment: 12 pages,8 figure
First principles quantitative modeling of molecular devices
In this thesis, we report theoretical investigations ofnonlinear and nonequilibrium quantum electronic transport propertiesof molecular transport junctions from atomistic first principles.The aim is to seek not only qualitative but alsoquantitative understanding of the correspondingexperimental data. At present, the challenges to quantitativetheoretical work in molecular electronics include two most importantquestions: (i) what is the proper atomic model for the experimentaldevices? (ii) how to accurately determine quantum transportproperties without any phenomenological parameters? Our research iscentered on these questions. We have systematically calculatedatomic structures of the molecular transport junctions by performingtotal energy structural relaxation using density functional theory(DFT). Our quantum transport calculations were carried out byimplementing DFT within the framework of Keldysh non-equilibriumGreen's functions (NEGF). The calculated data are directly comparedwith the corresponding experimental measurements. Our generalconclusion is that quantitative comparison with experimental datacan be made if the device contacts are correctly determined.We calculated properties of nonequilibrium spin injection from Nicontacts to octane-thiolate films which form a molecular spintronicsystem. The first principles results allow us to establish a clearphysical picture of how spins are injected from the Ni contactsthrough the Ni-molecule linkage to the molecule, why tunnelmagnetoresistance is rapidly reduced by the applied bias in anasymmetric manner, and to what extent ab initio transporttheory can make quantitative comparisons to the correspondingexperimental data. We found that extremely careful sampling of thetwo-dimensional Brillouin zone of the Ni surface is crucial foraccurate results in such a spintronic system.We investigated the role of contact formation and its resultingstructures to quantum transport in several molecular wires and showthat interface contacts critically control charge conduction. It wasfound, for Au/BDT/Au junctions, the H atom in -SH groupsenergetically prefers to be non-dissociative after the contactformation, which was supported by comparison between computed andmeasured break-down forces and bonding energies. TheH-non-dissociated (HND) junctions give equilibrium conductances from0.054G0 (equilibrium structure) to 0.020G0 (stretchedstructure) which is within a factor of 2-5 of the measureddata. On the other hand, for all H-dissociated contact structures - whichwere the assumed structures in the literature, the conductance is atleast more than an order of magnitude larger that the experimentalvalue. The HND-model significantly narrows down thetheory/experiment discrepancy. Finally, a by-product of this work isa comprehensive pseudopotential and atomic orbital basis setdatabase that has been carefully calibrated and can be used by theDFT community at large.Cette thÚse présentera nos recherches théoriquessur les propriétés quantiques de transport électroniquedes jonctions de transport moléculaire. Cette analyse a été effectuéeà l'aide de méthodes ab initio atomiques qui sont validesdans les régimes non-linéaire et hors-équilibre.L'objectif est de rechercher non seulement une compréhensionqualitative des données expérimentales mais aussi quantitative. Les deux questions les plus importantesquant au travail théorique en électronique moléculaire sont:(i) quel est le bon modÚle atomique pour simuler les dispositifsexpérimentaux? (ii) comment déterminer avec précisionles propriétés de transport quantique sans l'utilisation deparamÚtres phénoménologiques?Nos recherches sont centrées sur ces questions. Nous avonssystématiquement calculéles structures atomiques de jonctions moléculaires en effectuantla relaxation structurelle dans le cadre de la théorie de la fonctionnelle de la densité (DFT).Les calculs de transport quantique ont été reà lises encombinant la DFT avec les fonctions de Green hors-équilibre deKeldysh (NEGF).Les calculs sont directement comparésaux données expérimentales correspondantes. Notre conclusiongénérale est qu'un accord quantitatif entre les valeurs théoriqueset empiriques est possible si la structure atomique du contact estcorrectement déterminée.Nous avons calculé les propriétés hors-équilibred'injection de spin à travers un film d'octane-thiole en contactavec des électrodes en Ni, formant ainsi un systÚmespintronique moléculaire.Les résultats obtenus par premiers principes nous fournissentune compréhension claire sur la façon dont les spins sontinjectés à partir des électrodes en Ni à la molécule par la liaisonNi-molécule. De plus, nous expliquonspourquoi la magnéto-résistance à effet tunnel décroßtrapidement avecune augmentation du potentiel électrique, et ce, de maniÚre asymétrique.Finalement, nous démontrons que la théorie ab initiodu transport électronique est en mesure d'effectuer des comparaisonsquantitatives avec les données expérimentales.Nous avons constaté qu'un échantillonnage minutieux de la zonede Brillouin 2D de la surface du Ni est crucial afin d'obtenir desrésultats précis dans un tel systÚme spintronique.Nous avons étudié le rÎle de la formation du contact,ainsi que la structure atomique associée sur l'influence dutransport quantique dans le cas de plusieurs jonctions moléculaires.Nous démontrons que l'interface reliant les électrodes aux moléculescontrÎle trÚs sensiblement la conduction de charge.Il a été trouvé, pour les jonctions Au/BDT/Au, quel'atome d'hydrogÚne dans les groupes -SHpréfÚre énergétiquement la non-dissociation aprÚs la formationdu contact. En effet, ceci a été corroboré par la comparaison entreles donnéees calculées et mesurées des forces de rupture et desénergies de liaison.Les jonctions avec l'hydrogÚne non-dissocié (HND) donnentdes valeurs de conductances à l'équilibre de 0.054G (structure d'équilibre) à 0.020G (structure étirée). Ces valeurs sontà l'intérieur d'un facteur de 2-5 aux données expérimentales actuelles.D'autre part, toutes les structures de contact H-dissociées --- quiont été les structures supposées dans la littérature --- résultenten des valeurs de conductancescalculées au moins un ordre de grandeur plus élevé que lesvaleurs empiriques.Le modÚle HND réduit de maniÚre significative l'écart entrela théorie et les expériences. Pour terminer, une conséquence de ce travail estle regroupement d'une base de données complÚte incluant des pseudo-potentielset des orbitales atomiques. Celle-ci a été soigneusement calibrée et est disponibleà toute la communauté DFT
Topographic Effects on Stratiform Precipitation Observed by Vertically Pointing Micro Rain Radars at Ridge and Valley Sites in the Liupan Mountains Area, Northwest China
To investigate the topographic effects on precipitation in the Liupan Mountains Area of Northwest China, three micro rain radars, located at a ridge, west valley, and east valley in the area, respectively, were used to observe precipitation processes. By comparing the characteristics of stratiform precipitation at three sites, it was found that (i) the effective radar reflectivity and characteristic falling velocity of hydrometeors at the ridge and east valley were larger than those at the west valley; (ii) the diameter and density of solid hydrometeors at the ridge and east valley were slightly larger than those at the west valley; and (iii) there was also a higher occurrence frequency of larger graupel at the ridge. It is inferred that the precipitable water vapor at the ridge and east valley is richer than at the west valley, which leads to a larger aggregation efficiency and degrees of riming at the former than the latter. Besides, forced uplifting of water vapor over the mountain area around the ridge may play a part in topographic supercooling, which leads to enhanced riming of supercooled liquid water. The conclusions will contribute to a better understanding of the mechanisms of precipitationâterrain interactions in the area
Generation of an induced pluripotent stem cell line from patient with atrial fibrillation with KCNQ1 p.Ser209Pro mutation
Gain-of-function mutations in the KCNQ1 gene can cause atrial fibrillation. In this study, we generated an induced stem cell line (GRCHJUi001) from one member of an atrial fibrillation family line, whom had heterozygous mutation in the KCNQ1 gene c.625Â TÂ >Â C (p.Ser209Pro), and the cell line showed maintenance of stem cells characterized by morphology, normal karyotype, and pluripotency
Single-Electron Induces Double-Reaction by Charge Delocalization
Injecting
an electron by scanning tunneling microscope into a molecule physisorbed
at a surface can induce dissociative reaction of one adsorbate bond.
Here we show experimentally that a single low-energy electron incident
on ortho-diiodobenzene physisorbed on Cu(110) preferentially induces
reaction of both of the CâI bonds in the adsorbate, with an
order-of-magnitude greater efficiency than for comparable cases of
single bond breaking. A two-electronic-state model was used to follow
the dynamics, first on an anionic potential-energy surface (pes*)
and subsequently on the ground state pes. The model led to the conclusion
that the two-bond reaction was due to the delocalization of added
charge between adjacent halogen-atoms of ortho-diiodobenzene through
overlapping antibonding orbitals, in contrast to the cases of para-dihalobenzenes,
studied earlier, for which electron-induced reaction severed exclusively
a single carbonâhalogen bond. The finding that charge delocalization
within a single molecule can readily cause concerted two-bond breaking
suggests the more general possibility of intra- and also intermolecular
charge delocalization resulting in multisite reaction. Intermolecular
charge delocalization has recently been proposed by this laboratory
to account for reaction in physisorbed molecular chains (Ning, Z.; Polanyi, J. C. Angew.
Chem., Int. Ed. 2013, 52, 320â324)
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Repulsion-induced surface-migration, by ballistics and bounce
The motion of adsorbate molecules across surfaces is fundamental to self-assembly, material growth, and heterogeneous catalysis. Recent Scanning Tunneling Microscopy studies have demonstrated the electron-induced long-range surface-migration of ethylene, benzene, and related molecules, moving tens of Angstroms across Si(100). We present a model of the previously unexplained long-range recoil of chemisorbed ethylene across the surface of silicon. The molecular dynamics reveal two key elements for directed long-range migration: first âballisticâ motion that causes the molecule to leave the ab initio slab of the surface traveling 3â8 Ă
above it out of range of its roughness, and thereafter skipping-stone âbouncesâ that transport it further to the observed long distances. Using a previously tested Impulsive Two-State model, we predict comparable long-range recoil of atomic chlorine following electron-induced dissociation of chlorophenyl chemisorbed at Cu(110
How Adsorbate Alignment Leads to Selective Reaction
There has been much interest in the effect of adsorbate alignment in a surface reaction. Here we show its significance for an electron-induced reaction occurring along preferred axes of the asymmetric Cu(110) surface, characterized by directional copper rows. By scanning tunneling microscopy (STM), we found that the heterocyclic aromatic reagent, physisorbed <i>meta</i>-iodopyridine, lay with its carbonâiodine either <i>along</i> the rows of Cu(110), âAâ, or <i>perpendicular</i>, âPâ. Electron-induced dissociative attachment with the CâI bond initially along âAâ gave a chemisorbed I atom and chemisorbed <i>vertical</i> pyridyl, singly surface-bound, whereas that with CâI along âPâ gave a chemisorbed I atom and a <i>horizontal</i> pyridyl, doubly bound. An impulsive two-state model, involving a short-lived antibonding state of CâI, accounted for the different product surface binding in terms of closer Cu···Cu atomic spacing along âAâ accommodating only one binding site of the pyridyl ring recoiling from I and wider spacing along âPâ accommodating simultaneously both binding sites, NâCu and CâCu, in the meta-position on the recoiling pyridyl ring. STM studies combined with dynamical modeling can be seen as a way to improve understanding of the role of surface alignment in determining reactive outcomes in induced reaction at asymmetric crystalline surfaces
Molecular Dynamics of the Electron-Induced Reaction of Diiodomethane on Cu(110)
Diiodomethane
is used to generate C<sub>1</sub> fragments at surfaces,
en route to higher hydrocarbons. Here scanning tunneling microscopy
was employed to examine the interaction of diiodomethane, CH<sub>2</sub>I<sub>2</sub>, with a Cu(110) surface, from 4.6 to 8.8 K. In this
temperature range unexpectedly rapid thermal reaction resulted in
the rupture of two CâI bonds, yielding pairs of I atoms recoiling
in opposite directions. Approximately 65% of the carbene, CH<sub>2</sub>, product from this highly exothermic (4.1 eV) thermal reaction remained
chemisorbed. Two stable physisorbed configurations of diiodomethane
were found, âverticalâ (75%) and âhorizontalâ
(25%). Electron-induced reaction of these intact adsorbates led to
single-electron dissociation of both the CâI bonds, with a
minor path leading to single bond breaking to form CH<sub>2</sub>I.
Directed recoil of chemisorbed carbene was observed in approximately
half the electron-induced reactive events. Simulation of the electron-induced
reaction by the impulsive two-state (I2S) model consistently predicted
delayed dissociation of the second CâI bond, due to vibrational
excitation of the CH<sub>2</sub>I radical product. Theory and experiment
agreed in evidencing long-range recoil for the CH<sub>2</sub> along
the [11Ì
0] direction of the copper. This recoiling diradical
was shown by the I2S model to undergo migration by a novel process
of âwalkingâ along a pair of adjacent copper rows