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 thèse 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 modèle atomique pour simuler les dispositifsexpérimentaux? (ii) comment déterminer avec précisionles propriétés de transport quantique sans l'utilisation deparamètres 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 reàlises 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 systèmespintronique 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 décroîtrapidement avecune augmentation du potentiel électrique, et ce, de manière 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 système spintronique.Nous avons étudié le rôle 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 moléculescontrôle très sensiblement la conduction de charge.Il a été trouvé, pour les jonctions Au/BDT/Au, quel'atome d'hydrogène dans les groupes -SHpréfère énergétiquement la non-dissociation après 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'hydrogène non-dissocié (HND) donnentdes valeurs de conductances à l'équilibre de 0.054G$_0$ (structure d'équilibre) à0.020G$_0$ (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 modèle HND réduit de manière significative l'écart entrela théorie et les expériences. Pour terminer, une conséquence de ce travail estle regroupement d'une base de données complète 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 precipitation–terrain 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.625 T > 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 C–I 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 carbon–halogen 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, 320−324)

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 ‘ballistic’ motion that causes the molecule to leave the ab initio slab of the surface traveling 3–8 Å above it out of range of its roughness, and thereafter skipping-stone ‘bounces’ 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 carbon–iodine either <i>along</i> the rows of Cu(110), “A”, or <i>perpendicular</i>, “P”. Electron-induced dissociative attachment with the C–I bond initially along “A” gave a chemisorbed I atom and chemisorbed <i>vertical</i> pyridyl, singly surface-bound, whereas that with C–I along “P” 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 C–I, accounted for the different product surface binding in terms of closer Cu···Cu atomic spacing along “A” accommodating only one binding site of the pyridyl ring recoiling from I and wider spacing along “P” accommodating simultaneously both binding sites, N–Cu and C–Cu, 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 C₁ fragments at surfaces, en route to higher hydrocarbons. Here scanning tunneling microscopy was employed to examine the interaction of diiodomethane, CH₂I₂, 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 C–I bonds, yielding pairs of I atoms recoiling in opposite directions. Approximately 65% of the carbene, CH₂, product from this highly exothermic (4.1 eV) thermal reaction remained chemisorbed. Two stable physisorbed configurations of diiodomethane were found, “vertical” (75%) and “horizontal” (25%). Electron-induced reaction of these intact adsorbates led to single-electron dissociation of both the C–I bonds, with a minor path leading to single bond breaking to form CH₂I. 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 C–I bond, due to vibrational excitation of the CH₂I radical product. Theory and experiment agreed in evidencing long-range recoil for the CH₂ along the [11̅0] direction of the copper. This recoiling diradical was shown by the I2S model to undergo migration by a novel process of “walking” along a pair of adjacent copper rows