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PubMed1980

Ultraviolet photoelectron spectroscopy of cyclic amidines. 2. Electronic structure of clonidine and some related 2-(phenylimino)imidazolidines with alpha-adrenergic activity.

Ultraviolet photoelectron spectroscopy (UV PES) and CNDO/s molecular orbital calculations have been employed to investigate the electronic structure of clonidine and some other 2-(phenylimino)imidazolidines. The assignment of the bands in the spectra to particular molecular orbitals is based on the CNDO/s results in conjunction with Koopmans' theorem, substituent effects, and differences in intensity between the He (I) and He(II) spectra. The location of the energy levels of orbitals with mainly nN and delta character is not correctly estimated estimated by CNDO/s, while the pi orbital energy levels are satisfactorally predicted. The UV PES and CNDO/s results indicate in contrast investigated 2-(phenylimino)imidazolidines, which may indicate that differences in hypotensive activity cannot be ascribed to variations in steric hindrance within the molecules. The first ionization energies of the pharmacologically active 20-(phenylimino)imidazolidines do not correlate with hypotensive activity based on dosage data after intravenous administration to rats.

Adrenergic alpha-Antagonists↗
PubMed2006

Analysis of conformational polymorphism in pharmaceutical solids using solid-state NMR and electronic structure calculations.

A detailed analysis of molecular structure in three polymorphic forms of 5-methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile is made using a combination of multidimensional solid-state NMR (SSNMR) experiments and molecular modeling via electronic structure calculations. These compounds, collectively referred to as ROY because of their red, orange, and yellow colors, share a similar molecular structure with the exception of the dihedral angle between the phenyl and thiophene rings. The ROY materials make it possible to study the influence of nearly a single degree of freedom on the associated NMR spectra. Using the 2D PASS (Antzutkin et al. J. Magn. Reson. A 1995, 115, 7) experiment, spectral editing techniques, and DFT-based calculations of the local fields, an analysis is made of the sensitivity of all carbon and nitrogen sites to changing molecular conformation. Chemical shift and dipolar coupling information obtained from these experiments vary noticeably between forms and are subsequently used to quantitatively determine aspects of molecular structure in these materials, including the coplanar angle between the phenyl and thiophene rings. The influence of motion on the methyl and nitro chemical shifts is also investigated. The accuracy of the information obtained from local field analysis and the model structure calculation demonstrates the capabilities of SSNMR as a quantitative structural method.

Algorithms↗
PubMed1993

The electronic structure of [Fe4S4]3+ clusters in proteins. An investigation of the oxidized high-potential iron-sulfur protein II from Ectothiorhodospira vacuolata.

Within the framework of an investigation of the electronic structure of oxidized high-potential iron-sulfur proteins (HiPIP), we have studied the HiPIP II from Ectothiorhodospira vacuolata, which was known to have a peculiar temperature dependence of the 1H NMR isotropic hyperfine shifts. The signals of the cysteine ligand protons have been sequence specifically assigned through NOE, NOESY, and TOCSY experiments. Nine hyperfine-shifted signals are observed: seven in the downfield and two in the upfield region. They have been assigned to the eight beta-CH2 protons of the four coordinated cysteines and to one alpha-CH cysteine proton. The two most downfield-shifted signals belong to the beta-CH2 protons of Cys 63 (Chromatium vinosum numbering) and the two upfield protons to those of Cys 43. These two pairs of protons show a Curie-type temperature dependence of the hyperfine shifts. Among the remaining five downfield-shifted signals, three show a Curie-type temperature dependence and two have an anti-Curie temperature dependence. The former are assigned to the beta-CH2 and alpha-CH protons of Cys 77 and the latter to the beta-CH2 protons of Cys 46. The shift patterns are thus similar, in a sequence-specific sense, to those of the analogous proteins from C. vinosum and Rhodocyclus gelatinosus, whereas they differ from those of Rhodocyclus globiformis HiPIP and even more from those of Ectothiorhodospira halophila HiPIP II. Oxidized HiPIPs can be formally viewed as containing a cluster of four ferric ions plus one extra electron. We present here a model based on a chemical equilibrium, fast on the NMR time scale, between two species, both of which contain a pair of iron(III) ions and a mixed-valence pair but are differently oriented within the protein frame. The EPR data are also discussed in the light of the debate on the nature of the different species detected at low temperature. The interpretation of the whole set of data on HiPIPs in the light of the present model is compared with that based on previous models.

Bacteria↗
PubMed2000

Probing the electronic structures of coordination compounds by transient spectral hole-burning. Applications to specifically deuterated [Ru(bpy)3]2+ complexes.

Transient spectral hole-burning (THB), a powerful technique for probing the electronic structures of coordination compounds, is applied to the lowest excited 3MLCT states of specifically deuterated [Ru(bpy)3]2+ complexes doped into crystals of racemic [Zn(bpy)3](ClO4)2. Results are consistent with and complementary to conclusions reached from excitation-line-narrowing experiments. Two sets of 3MLCT transitions are observed in conventional spectroscopy of [Ru(bpy-d(n))(3-x)(bpy-d(m))x]2+ (x = 1, 2; n = 0, 2; m = 2, 8; n not = m) complexes doped into [Zn(bpy)3](ClO4)2. The two sets coincide with the 3MLCT transitions observed for the homoleptic [Ru(bpy-d(m))3]2+ and [Ru(bpy-d(n))3]2+ complexes and can thus be assigned to localized 3MLCT transitions to the bpy-d(m) and bpy-d(n) ligands. The THB experiments presented in this paper exclude a two-site hypothesis. When spectral holes are burnt at 1.8 K into 3MLCT transitions associated with the bpy and bpy-d2 ligands in [Ru(bpy)(bpy-d8)2]2+, [Ru(bpy)2(bpy-d8)]2+, and [Ru(bpy-d2)2(bpy-d8)]2+, side holes appear in the 3MLCT transitions associated with the bpy-d8 ligands approximately 40 and approximately 30 cm(-1) higher in energy. Since energy transfer to sites 40 or 30 cm(-1) higher in energy cannot occur at 1.8 K, the experiments unequivocally establish that the two sets of 3MLCT transitions observed for [Ru(bpy-d(n))(3-x)(bpy-d(m))x]2+ (x = 1, 2) complexes in [Zn(bpy)3](ClO4)2 occur on one molecular cation.

Journal Article↗
PubMed2004

Thermal stability and electronic structure of atomically uniform Pb films on Si(111).

Atomically uniform Pb films are successfully prepared on Si(111), despite a large lattice mismatch. Angle-resolved photoemission measurements of the electronic structure show layer-resolved quantum well states which can be correlated with dramatic variations in thermal stability. The odd film thicknesses N = 5, 7, and 9 monolayers show sharp quantum well states. The even film thicknesses N = 6 and 8 do not, but are much more stable than the odd film thicknesses. This correlation is discussed in terms of a total energy calculation and Friedel-like oscillations in properties.

Journal Article↗
PubMed1998

Bonding in Mo(3)M'S(4) Cubane-Type Clusters: Variations in Electronic Structure When M' Is a Main Group or Transition Metal.

The results of Fenske-Hall molecular orbital calculations for cubane-type clusters having Mo(3)M'S(4) cores show that the electronic structures of the clusters depend on the nature of M'. When M' is a main group metal, as in [Mo(3)(SnCl(3))S(4)(NCS)(9)](6)(-), Mo(3)SnS(4)(S(2)PEt(2))(6), or [Sn(Mo(3)S(4)(H(2)O)(9))(2)](8+), the heterometal is oxidized upon incorporation into the cluster; no M'-Mo bonds are formed, and electrons are transferred from M' to an orbital localized on the Mo(3)S(4) incomplete cubane core. When M' is a transition metal, as in [Mo(3)NiS(4)(CO)(H(2)O)(9)](4+), [Mo(3)PdS(4)(CO)(tacn)(3)](4+) (tacn = 1,4,7-triazacyclononane), or Mo(3)CoS(4)(CO)(Cp')(3) (Cp' = methylcyclopentadiene), M' is not oxidized but instead shares electron density with the Mo(3)S(4) core through the formation of metal-metal bonds with the Mo(3) triangle. The relatively high stretching frequencies observed for CO ligands bound to the Ni and Pd centers in the Mo(3)NiS(4) and Mo(3)PdS(4) clusters arise from the nature of the bonding in the clusters, not from the oxidation of the Ni and Pd atoms. Since the same heterometal orbitals are used both to form the M'-Mo bonds and to back-donate to the CO ligand, the Mo(3) orbitals and the CO pi orbitals compete for M' electron density. The CO orbitals do not compete effectively for metal electron density in the Ni and Pd clusters, and this results in weak back-donation to the CO pi orbitals and relatively high CO stretching frequencies. Although it has been proposed that the Mo(3)NiS(4) cluster may serve as a model for NiMoS hydrodesulfurization (HDS) catalysts, the fact that the Ni center in this cluster is not electron rich suggests that it may not provide a suitable model. The electron density at the heterometal can be increased slightly by increasing the donor ability of the ligands attached to the Mo atoms.

Journal Article↗
PubMed2003

Investigation of the reduced high-potential iron-sulfur protein from chromatium vinosum and relevant model compounds: a unified picture of the electronic structure of [Fe(4)S(4)](2+) systems through magnetic and optical studies.

Magnetization measurements and variable temperature optical spectroscopy have been used to investigate, within the 4-300 K temperature range, the electronic structure of the reduced high-potential iron protein (HiPIP) from Chromatium vinosum and the model compounds (Cat)(2)[Fe(4)S(4)(SR)(4)], where RS(-) = 2,4,6-triisopropylphenylthiolate (1), 2,6-diphenylphenylthiolate (2), diphenylmethylthiolate (3), 2,4,6-triisopropylbenzylthiolate (4, 4'), 2,4,6-triphenylbenzylthiolate (5, 5'), 2,4,6-tri-tert-butylbenzylthiolate (6), and Cat(+) = (+)NEt(4) (1, 2, 3, 4', 5', 6), (+)PPh(4) (4, 5). The newly synthesized 2(2)(-), 3(2)(-), 5(2)(-), and 6(2)(-) complexes are, as 1(2)(-) and 4(2)(-), excellent models of the reduced HiPIPs: they exhibit the [Fe(4)S(4)](3+/2+) redox couple, because of the presence of bulky ligands which stabilize the [Fe(4)S(4)](3+) oxidized core. Moreover, the presence of SCH(2) groups in 4(2)(-), 5(2)(-), and 6(2)(-), as in the [Fe(4)S(4)] protein cores, makes them good biomimetic models of the HiPIPs. The X-ray structure of 2 is reported: it crystallizes in the orthorhombic space group Pcca with no imposed symmetry and a D(2)(d)()-distorted geometry of the [Fe(4)S(4)](2+) core. Fit of the magnetization data of the reduced HiPIP and of the 1, 2, 3, 4, 5, and 6 compounds within the exchange and double exchange theoretical framework leads to exchange coupling parameters J = 261-397 cm(-)(1). A firm determination of the double exchange parameters B or, equivalently, the transfer integrals beta = 5B could not be achieved that way. The obtained |B| values remain however high, attesting thus to the strength of the spin-dependent electronic delocalization which is responsible for lowest lying electronic states being characterized by delocalized mixed-valence pairs of maximum spin (9)/(2). Electronic properties of these systems are then accounted for by the population of a diamagnetic ground level and excited paramagnetic triplet and quintet levels, which are respectively J and 3J above the ground level. Optical studies of 1, 2, 4', 5', and 6 but also of (NEt(4))(2)[Fe(4)S(4)(SCH(2)C(6)H(5))(4)] and the isomorph (NEt(4))(2)[Fe(4)S(4)(S-t-Bu)(4)] and (NEt(4))(2)[Fe(4)Se(4)(S-t-Bu)(4)] compounds reveal two absorption bands in the near infrared region, at 705-760 nm and 1270-1430 nm, which appear to be characteristic of valence-delocalized and ferromagnetically coupled [Fe(2)X(2)](+) (X = S, Se) units. The |B| and |beta| values can be directly determined from the location at 10|B| of the low-energy band, and are respectively of 699-787 and 3497-3937 cm(-)(1). Both absorption bands are also present in the 77 K spectrum of the reduced HiPIP, at 700 and 1040 nm (Cerdonio, M.; Wang, R.-H.; Rawlings, J.; Gray, H. B. J. Am. Chem. Soc. 1974, 96, 6534-6535). The blue shift of the low-energy band is attributed to the inequivalent environments of the Fe sites in the protein, rather than to an increase of |beta| when going from the models to the HiPIP. The small differences observed in known geometries of [Fe(4)S(4)](2+) clusters, especially in the Fe-Fe distances, cannot probably lead to drastic changes in the direct Fe-Fe interactions (parameter beta) responsible for the delocalization phenomenon. These differences are however magnetostructurally significant as shown by the 261-397 cm(-)(1) range spanned by J. The cluster's geometry, hence the efficiency of the Femicro(3)-S-Fe superexchange pathways, is proposed to be controlled by the more or less tight fit of the cluster within the cavity provided by its environment.

Journal Article↗
PubMed2006

Local atomic and electronic structure in nanocrystalline Sn-doped anatase TiO2.

Tin-doped anatase TiO(2) nanopowders and nanoceramics with particle sizes between 12 and 30 nm are investigated by X-ray absorption fine-structure (EXAFS) and Mössbauer spectroscopies. Furthermore, ab initio calculations based on the density functional theory are performed to analyze changes in the electronic structure due to Sn doping. The three approaches consistently show that Sn is dissolved on substitutional bulk sites with a slight increase of the bond lengths of the inner coordination shells. The Debye-Waller factors show that the nanocrystallites are highly ordered. There is no indication of defect states or bandgap changes with Sn doping.

Journal Article↗
PubMed2006

Electronic structure of four-coordinate C3v nickel(II) scorpionate complexes: investigation by high-frequency and -field electron paramagnetic resonance and electronic absorption spectroscopies.

A series of complexes of formula TpNiX, where Tp*- = hydrotris(3,5-dimethylpyrazole)borate and X = Cl, Br, I, has been characterized by electronic absorption spectroscopy in the visible and near-infrared (NIR) region and by high-frequency and -field electron paramagnetic resonance (HFEPR) spectroscopy. The crystal structure of TpNiCl has been previously reported; that for TpNiBr is given here: space group = Pmc2(1), a = 13.209(2) A, b = 8.082(2) A, c = 17.639(4) A, alpha = beta = gamma = 90 degrees , Z = 4. TpNiX contains a four-coordinate nickel(II) ion (3d8) with approximate C3v point group symmetry about the metal and a resulting S = 1 high-spin ground state. As a consequence of sizable zero-field splitting (zfs), TpNiX complexes are "EPR silent" with use of conventional EPR; however, HFEPR allows observation of multiple transitions. Analysis of the resonance field versus the frequency dependence of these transitions allows extraction of the full set of spin Hamiltonian parameters. The axial zfs parameter for TpNiX displays pronounced halogen contributions down the series: D = +3.93(2), -11.43(3), -22.81(1) cm(-1), for X = Cl, Br, I, respectively. The magnitude and change in sign of D observed for TpNiX reflects the increasing bromine and iodine spin-orbit contributions facilitated by strong covalent interactions with nickel(II). These spin Hamiltonian parameters are combined with estimates of 3d energy levels based on the visible-NIR spectra to yield ligand-field parameters for these complexes following the angular overlap model (AOM). This description of electronic structure and bonding in a pseudotetrahedral nickel(II) complex can enhance the understanding of similar sites in metalloproteins, both native nickel enzymes and nickel-substituted zinc enzymes.

Journal Article↗
PubMed2002

Electronic structure and nature of the ground state of the mixed-valence binuclear tetra(mu-1,8-naphthyridine-N,N')-bis(halogenonickel) tetraphenylborate complexes: experimental and DFT characterization.

The ground state electronic structure of the mixed-valence systems [Ni(2)(napy)(4)X(2)](BPh(4)) (napy=1,8-naphthyridine; X=Cl, Br, I) was studied with combined experimental (X-ray diffraction, temperature dependence of the magnetic susceptibility, and high-field EPR spectroscopy) and theoretical (DFT) methods. The zero-field splitting (zfs) ground S=3/2 spin state is axial with /D/ approximately 3 cm(-1). The iodide derivative was found to be isostructural with the previously reported bromide complex, but not isomorphous. The compound crystallizes in the monoclinic system, space group P2(1)/n, with a=17.240(5), b=26.200(5), c=11.340(5) A, beta=101.320(5) degrees. DFT calculations were performed on the S=3/2 state to characterize the ground state potential energy surface as a function of the nuclear displacements. The molecules can thus be classified as Class III mixed-valence compounds with a computed delocalization parameter, B=3716, 3583, and 3261 cm(-1) for the Cl, Br, and I derivatives, respectively.

Journal Article↗
PubMed1979

Geometric and electronic structure of oxyhemocyanin: spectral and chemical correlations to met apo, half met, met, and dimer active sites.

The chemical and spectral properties of a series of hemocyanin derivatives were systematically compared to provide insight into the geometric and electronic structure of the oxyhemocyanin active site. The binuclear copper site is characterized as two tetragonal Cu(II) atoms bridged by both an endogenous protein ligand and the exogenous ligand (i.e., peroxide), with the lack of an electron paramagnetic resonance signal being the result of antiferromagnetic exchange via the endogenous bridge. A transition dipole-vector coupling model is used to assign the unique absorption spectral properties of oxyhemocyanin: the bands at 570 and 486 nm are assigned as components of the peroxide pi v* to copper dx2-y2 charge transfer. The 345-nm band is one component of the pi sigma* leads to dx2-y2 charge transfer. The model also predicts an end-to-end bridging geometry for the peroxide in oxyhemocyanin.

Animals↗
PubMed2001

Electronic structure investigation of Mg(1-x)Fe(x)S solid solution: X-ray absorption study.

X-ray absorption fine structure at the sulfur K edge in Mg(1-x)Fe(x)S solid solution (0 < or = x < or = 0.68) has been measured at the Canadian Synchrotron Radiation Facility. It was shown that the S K-edge in MgS was formed by the multiple scattering of the photoelectron wave within a cluster of large size (containing 27 atoms and having radius about 4.5 A). Comparison of experimental data with theoretical results allows study of the electronic structure of this system. The analysis of partial electronic density of s-, p- and d- states makes it possible to investigate the mutual influence of sulfur s-, p- and metal d- states in the conduction band. The study of changes in experimental S K-edges XANES of Mg(1-x)Fe(x)S solid solution with variation of relative Fe-Mg concentration allows the extraction of the hypothetical cubic phase (B1) of FeS, and this is supported by theoretical simulation.

Journal Article↗
PubMed1989

A nuclear Overhauser effect investigation of the molecular and electronic structure of the heme crevice in lactoperoxidase.

The proton homonuclear nuclear Overhauser effect, NOE, in conjunction with paramagnetic-induced dipolar relaxation, is utilized to assign resonances and to probe the molecular and electronic structures of the heme cavity in the low-spin cyanide complex of resting-state bovine lactoperoxidase, LPO-CN. Predominantly primary NOEs were detected in spite of the large molecular weight (approximately 78 x 10(3)) of the enzyme, which demonstrates again the advantage of paramagnetism suppressing spin diffusion in large proteins. Both of the nonlabile ring protons of a coordinated histidine are located at resonance positions consistent with a deprotonated imidazole. Several methylene proton pairs are identified, of which the most strongly hyperfine-shifted pair is assigned to the unusual chemically functionalized 8-(mercaptomethylene) group of the prosthetic group [Nichol, A. W., Angel, L. A., Moon, T., & Clezy, P. S. (1987) Biochem. J. 247, 147-150]. The large 8-(mercaptomethylene) proton contact shifts relative to that of the only resolved heme methyl signal are rationalized by the additive perturbations on the rhombic asymmetry of the functionalization of the 8-position and the alignment of the axial histidyl imidazole projection along a vector passing through pyrrole A and C of the prosthetic group. Such a stereochemistry is consistent with the resolution of only a single heme methyl group, 3-CH3, as observed.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed2001

Unique [(1)infinityNi(8)Bi(8)S] metallic wires in a novel quasi-1D compound. Synthesis, crystal and electronic structure, and properties of Ni(8)Bi(8)SI.

A new quasi-one-dimensional compound Ni(8)Bi(8)SI has been synthesized and its crystal structure determined from single-crystal X-ray diffraction data. The structure of Ni(8)Bi(8)SI consists of [(1)infinityNi(8)Bi(8)S] columns separated by iodine atoms. Conductivity and magnetic susceptibility measurements (down to 4.2 K) show that Ni(8)Bi(8)SI is a one-dimensional metal and exhibits Pauli paramagnetic properties. These observations are in good agreement with the results from electronic structure calculations. An analysis of the chemical bonding employing difference electron charge density maps reveals strong multicenter Ni-Bi bonds and pair Ni-S interactions within the [(1)infinityNi(8)Bi(8)S] columns. Only electrostatic interactions are inferred between the columns and iodine atoms.

Journal Article↗
PubMed2003

Electronic structure of oxovanadium IV complexes of alpha-hydroxycarboxylic acids.

A series of V(IV)O bis chelated complexes of alpha-hydroxycarboxylic acids with a 2(COO(-), O(-)) coordination set was analyzed by electronic absorption and EPR spectroscopy in aqueous solution. All the complexes exhibit a square-pyramidal geometry distorted toward trigonal bipyramid. The influence of the distortion of the geometry, as deduced from the steric hindrance produced by the substituents at the alpha-carbon atom of the ligands, on the spectroscopic parameters has been studied. The observed trends were related to the electronic structure of the metal ion in the distorted geometry.

Journal Article↗
PubMed2001

Quasi-three-dimensional network of molecular interactions and electronic structure of a new organic semiconductor, ET(NCS)0.77.

The radical cation salt ET(NCS)0.77 [bis(ethylenedithio)tetrathiafulvalene thiocyanate (1/0.77)] has been prepared for the first time by electrocrystallization and its crystal and electronic structure at 110 K was investigated. The unit-cell dimensions are orthorhombic, a = 6.638 (1), b = 8.309 (2), c = 28.776 (6) A, V = 1587.1 (6) A3, space group Pbcm, Z = 4. The compound has a layered structure. The ET radical cations of the conducting cationic layer build stacks. In the anionic layer the thiocyanate groups form polymeric chains where they are oriented in a 'head-to-tail' mode. The structure has short intermolecular contacts of the cation-cation, anion-anion and cation-anion types, which leads to the formation of a three-dimensional structure of intermolecular interactions. This phenomenon is very rare in molecular conductors. Tight binding band structure calculations suggest, however, that the interlayer interactions through the anions are weak and that the incomplete occupation of the anion sites is the reason for the activated conductivity of the salt.

Journal Article↗
PubMed1998

Effect of Protonation on Peroxo-Copper Bonding: Spectroscopic and Electronic Structure Study of [Cu(2)((UN-O-)(OOH)](2+).

Spectroscopic studies of a &mgr;-1,1-hydroperoxo-bridged copper dimer are combined with SCF-Xalpha-SW molecular orbital calculations to describe the vibrational and electronic structure of the hydroperoxo-copper complex and compare it to that of previously studied peroxo-copper species. Four vibrational modes of the Cu(2)OOH unit in the resonance Raman and infrared spectra are assigned on the basis of isotope shifts: nu(O-O) = 892 cm(-)(1), nu(as)(Cu-O) = 506 cm(-)(1), nu(s)(Cu-O) = 322 cm(-)(1), and nu(O-H) = 3495 cm(-)(1). The 892 cm(-)(1) O-O stretch of the &mgr;-1,1-hydroperoxo-bridged copper dimer is 89 cm(-)(1) higher than that of the unprotonated complex. Resonance Raman profiles of the 892 cm(-)(1) O-O stretch are used to assign an electronic absorption band at 25 200 cm(-)(1) (epsilon = 6700 M(-)(1) cm(-)(1)) to a hydroperoxide pi-to-Cu charge transfer (CT) transition. This band is approximately 5000 cm(-)(1) higher in energy than the corresponding transition in the unprotonated complex. The pi-to-Cu CT transition intensity defines the degree of hydroperoxide-to-copper charge donation, which is lower than in the unprotonated complex due to the increased electronegativity of the peroxide with protonation. The lower Cu-O covalency of this hydroperoxo-copper complex shows that the high O-O stretching frequency is not due to increased pi-to-Cu charge donation but rather reflects the direct effect of protonation on intra-peroxide bonding. Density functional calculations are used to describe changes in intra-peroxide and Cu-O bonding upon protonation of the peroxo-copper complex and to relate these changes to changes in reactivity.

Journal Article↗
PubMed2004

Indirect adsorbate-adsorbate interactions mediated through the surface electronic structure of the Si(100) surface.

Indirect adsorbate-adsorbate interactions between adsorbed ammonia (NH3) molecules on the Si(100) surface are investigated using density functional theory. Two different nonlocal effects mediated through the surface electronic structure are observed: "poisoning" and hydrogen bonding. We find that adsorbed NH3 "poisons" adsorption of NH3 on neighboring Si dimers on the same side of the dimer row whereas neighboring NH2(a) groups favor this configuration. Adsorption of NH3 involves charge transfer to the surface that localizes on neighboring Si dimer atoms, preventing adsorption of NH3 at these sites. These indirect interactions are similar to Friedel-type interactions observed on metal surfaces with an estimated range of less than 7.8 A on the Si(100) surface. These interactions may be manipulated to construct local ordering of the adsorbates on the surface.

Journal Article↗