Real-Space Identification of Intermolecular Bonding with Atomic Force Microscopy
01 Nov 2013-Science (American Association for the Advancement of Science)-Vol. 342, Iss: 6158, pp 611-614
TL;DR: The method can image and characterize hydrogen-bonding contacts formed between 8-hydroxyquinoline molecules adsorbed on the (111) surface of copper under cryogenic conditions and indicates the electron density contribution from the hybridized electronic state of the hydrogen bond.
Abstract: We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.
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TL;DR: In this article, a numerical model for high-resolution atomic force microscopy and scanning tunneling microscopy (STM) imaging with functionalized tips is presented, which takes into account the relaxation of the probe due to the tip-sample interaction.
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Cites background or methods from "Real-Space Identification of Interm..."
...On the basis of this finding we suggest that also in the experiments of Zhang et al.13 probe particle relaxation may in fact be the origin of the observed features which the authors identify with hydrogen bonds....
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...To test this conjecture that the observation of apparent bonds is in general mainly driven by the relaxation of the probe particle, we have performed AFM simulations for the 8-hydroxyquinoline tetramer (Fig.5) molecule that was investigated by Zhang et al.13....
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References
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TL;DR: An efficient scheme for calculating the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set is presented and the application of Pulay's DIIS method to the iterative diagonalization of large matrices will be discussed.
Abstract: We present an efficient scheme for calculating the Kohn-Sham ground state of metallic systems using pseudopotentials and a plane-wave basis set. In the first part the application of Pulay's DIIS method (direct inversion in the iterative subspace) to the iterative diagonalization of large matrices will be discussed. Our approach is stable, reliable, and minimizes the number of order ${\mathit{N}}_{\mathrm{atoms}}^{3}$ operations. In the second part, we will discuss an efficient mixing scheme also based on Pulay's scheme. A special ``metric'' and a special ``preconditioning'' optimized for a plane-wave basis set will be introduced. Scaling of the method will be discussed in detail for non-self-consistent and self-consistent calculations. It will be shown that the number of iterations required to obtain a specific precision is almost independent of the system size. Altogether an order ${\mathit{N}}_{\mathrm{atoms}}^{2}$ scaling is found for systems containing up to 1000 electrons. If we take into account that the number of k points can be decreased linearly with the system size, the overall scaling can approach ${\mathit{N}}_{\mathrm{atoms}}$. We have implemented these algorithms within a powerful package called VASP (Vienna ab initio simulation package). The program and the techniques have been used successfully for a large number of different systems (liquid and amorphous semiconductors, liquid simple and transition metals, metallic and semiconducting surfaces, phonons in simple metals, transition metals, and semiconductors) and turned out to be very reliable. \textcopyright{} 1996 The American Physical Society.
81,985 citations
IBM1
TL;DR: An approach for electronic structure calculations is described that generalizes both the pseudopotential method and the linear augmented-plane-wave (LAPW) method in a natural way and can be used to treat first-row and transition-metal elements with affordable effort and provides access to the full wave function.
Abstract: An approach for electronic structure calculations is described that generalizes both the pseudopotential method and the linear augmented-plane-wave (LAPW) method in a natural way. The method allows high-quality first-principles molecular-dynamics calculations to be performed using the original fictitious Lagrangian approach of Car and Parrinello. Like the LAPW method it can be used to treat first-row and transition-metal elements with affordable effort and provides access to the full wave function. The augmentation procedure is generalized in that partial-wave expansions are not determined by the value and the derivative of the envelope function at some muffin-tin radius, but rather by the overlap with localized projector functions. The pseudopotential approach based on generalized separable pseudopotentials can be regained by a simple approximation.
61,450 citations
TL;DR: In this paper, the formal relationship between US Vanderbilt-type pseudopotentials and Blochl's projector augmented wave (PAW) method is derived and the Hamilton operator, the forces, and the stress tensor are derived for this modified PAW functional.
Abstract: The formal relationship between ultrasoft (US) Vanderbilt-type pseudopotentials and Bl\"ochl's projector augmented wave (PAW) method is derived. It is shown that the total energy functional for US pseudopotentials can be obtained by linearization of two terms in a slightly modified PAW total energy functional. The Hamilton operator, the forces, and the stress tensor are derived for this modified PAW functional. A simple way to implement the PAW method in existing plane-wave codes supporting US pseudopotentials is pointed out. In addition, critical tests are presented to compare the accuracy and efficiency of the PAW and the US pseudopotential method with relaxed core all electron methods. These tests include small molecules $({\mathrm{H}}_{2}{,\mathrm{}\mathrm{H}}_{2}{\mathrm{O},\mathrm{}\mathrm{Li}}_{2}{,\mathrm{}\mathrm{N}}_{2}{,\mathrm{}\mathrm{F}}_{2}{,\mathrm{}\mathrm{BF}}_{3}{,\mathrm{}\mathrm{SiF}}_{4})$ and several bulk systems (diamond, Si, V, Li, Ca, ${\mathrm{CaF}}_{2},$ Fe, Co, Ni). Particular attention is paid to the bulk properties and magnetic energies of Fe, Co, and Ni.
57,691 citations
TL;DR: A new density functional of the generalized gradient approximation (GGA) type for general chemistry applications termed B97‐D is proposed, based on Becke's power‐series ansatz from 1997, and is explicitly parameterized by including damped atom‐pairwise dispersion corrections of the form C6 · R−6.
Abstract: A new density functional (DF) of the generalized gradient approximation (GGA) type for general chemistry applications termed B97-D is proposed. It is based on Becke's power-series ansatz from 1997 and is explicitly parameterized by including damped atom-pairwise dispersion corrections of the form C(6) x R(-6). A general computational scheme for the parameters used in this correction has been established and parameters for elements up to xenon and a scaling factor for the dispersion part for several common density functionals (BLYP, PBE, TPSS, B3LYP) are reported. The new functional is tested in comparison with other GGAs and the B3LYP hybrid functional on standard thermochemical benchmark sets, for 40 noncovalently bound complexes, including large stacked aromatic molecules and group II element clusters, and for the computation of molecular geometries. Further cross-validation tests were performed for organometallic reactions and other difficult problems for standard functionals. In summary, it is found that B97-D belongs to one of the most accurate general purpose GGAs, reaching, for example for the G97/2 set of heat of formations, a mean absolute deviation of only 3.8 kcal mol(-1). The performance for noncovalently bound systems including many pure van der Waals complexes is exceptionally good, reaching on the average CCSD(T) accuracy. The basic strategy in the development to restrict the density functional description to shorter electron correlation lengths scales and to describe situations with medium to large interatomic distances by damped C(6) x R(-6) terms seems to be very successful, as demonstrated for some notoriously difficult reactions. As an example, for the isomerization of larger branched to linear alkanes, B97-D is the only DF available that yields the right sign for the energy difference. From a practical point of view, the new functional seems to be quite robust and it is thus suggested as an efficient and accurate quantum chemical method for large systems where dispersion forces are of general importance.
23,058 citations
TL;DR: In this paper, a simple formulation of a generalized gradient approximation for the exchange and correlation energy of electrons has been proposed by Perdew, Burke, and Ernzerhof (PBE), which improves the chemisorption energy of atoms and molecules on transition-metal surfaces.
Abstract: A simple formulation of a generalized gradient approximation for the exchange and correlation energy of electrons has been proposed by Perdew, Burke, and Ernzerhof (PBE) [Phys. Rev. Lett. 77, 3865 (1996)]. Subsequently Zhang and Yang [Phys. Rev. Lett. 80, 890 (1998)] have shown that a slight revision of the PBE functional systematically improves the atomization energies for a large database of small molecules. In the present work, we show that the Zhang and Yang functional (revPBE) also improves the chemisorption energetics of atoms and molecules on transition-metal surfaces. Our test systems comprise atomic and molecular adsorption of oxygen, CO, and NO on Ni(100), Ni(111), Rh(100), Pd(100), and Pd(111) surfaces. As the revPBE functional may locally violate the Lieb-Oxford criterion, we further develop an alternative revision of the PBE functional, RPBE, which gives the same improvement of the chemisorption energies as the revPBE functional at the same time as it fulfills the Lieb-Oxford criterion locally.
5,971 citations