Site / 2016  
AG Paulus Archive
AG Paulus Website

and triple bonds'', Mol. Phys. 114, 13561364 (2016) DOI: 10.1080/00268976.2015.1122843
ORBKIT is a toolbox for postprocessing electronic structure calculations based on a highly modular and portable Python architecture. The program allows computing a multitude of electronic properties of molecular systems on arbitrary spatial grids from the basis set representation of its electronic wavefunction, as well as several gridindependent properties. The required data can be extracted directly from the standard output of a large number of quantum chemistry programs. ORBKIT can be used as a standalone program to determine standard quantities, for example, the electron density, molecular orbitals, and derivatives thereof. The cornerstone of ORBKIT is its modular structure. The existing basic functions can be arranged in an individual way and can be easily extended by userwritten modules to determine any other derived quantity. ORBKIT offers multiple output formats that can be processed by common visualization tools (VMD, Molden, etc.). Additionally, ORBKIT possesses routines to order molecular orbitals computed at different nuclear configurations according to their electronic character and to interpolate the wavefunction between these configurations. The program is opensource under GNULGPLv3 license and freely available at https://github.com/orbkit/orbkit/. This article provides an overview of ORBKIT with particular focus on its capabilities and applicability, and includes several example calculations.
Due to the importance of both static and dynamical correlation in the bond formation, lowdimensional beryllium systems constitute interesting case studies to test correlation methods. Aiming to describe the whole dissociation curve of extended Be systems we chose to apply the method of increments (MoI) in its multireference (MR) formalism. To gain insight into the main characteristics of the wave function, we started by focusing on the description of small Be chains using standard quantum chemical methods. In a next step we applied the MoI to larger beryllium systems, starting from the Be6 ring. The complete active space formalism was employed and the results were used as reference for local MR calculations of the whole dissociation curve. Although this is a wellestablished approach for systems with limited multireference character, its application regarding the description of whole dissociation curves requires further testing. Subsequent to the discussion of the role of the basis set, the method was finally applied to larger rings and extrapolated to an infinite chain.
Using both DFT as well as G0W0 calculations, we investigate static and dynamic effects on the phosphorene band gap upon deposition and encapsulation on/in BN multilayers. We demonstrate how competing long and shortrange effects cause the phosphorene band gap to increase at low PBN interlayer spacings, while the band gap is found to drop below that of isolated phosphorene in the BN/P bilayer at intermediate distances around 4 A. Subsequent stacking of BN layers, i.e., BN/BN/P and BN/BN/BN/P is found to have a negligible effect at the DFT level while at the G0W0 level, increased screening lowers the band gap as compared to the BN/P bilayer. Encapsulation between two BN layers, on the other hand, is found to further increase the phosphorene band gap with respect to the BN/P bilayer. Lastly we investigate the use of the GLLBSC functional as a starting point for G0W0 calculations showing it to, in the case of phosphorene, yield results close to those obtained from GW0@PBE.
While halogenation of graphene presents a fascinating avenue to the construction of a chemically and physically diverse class of systems, their application in photovoltaics has been hindered by often prohibitively large optical gaps. Herein we study the effects of partial bromination and chlorination on the structure and optoelectronic properties of both graphane and fluorographene. We find brominated and chlorinated fluorographene derivatives to be as stable as graphane with a detailed investigation of the systems band structure revealing significant 1D localization of the charge carriers as well as strongly electron–hole asymmetric effective masses. Lastly using G0W0 and BSE, we investigate the optical adsorption spectra of the aforementioned materials whose first adsorption peak is shown to lie close to the optimal peak position for photovoltaic applications (≈1.5 eV).
The polybromide salts [BrC(NMe2)2]2[Br8] and [BrC(NMe2)2][Br3] were synthesized in the ionic liquid [BMP][OTf] (1butyl1methylpyrrolidinium triflate). The compounds were characterized by Raman, NMR, and Xray single crystal structure determination as well as quantumchemical calculations. The polybromide dianion [Br8]2– structure shows similarities to the very recently reported structure of the first octachloride [Cl8]2–.
Tetramethylammonium tetraiodopentabromide [NMe4][I4Br5] was the first iodobromide to be synthesized and crystallized in an ionic liquid as well as in dichloromethane. The new iodobromides show different structure motives yet are unknown from other nonahalides and can be better described as [(I2Br3)−⋅2 IBr]. The additional IBr units are connected by halogen–halogen interactions on the central Vshaped [I2Br3]−. The characterization was performed by Raman spectroscopy and single crystal Xray structure determination. Conductivity measurements, thermogravimetric analysis and quantumchemical calculations completed the structural discussion.
The polychloride salt [CCl(NMe2)2]+2[Cl8]2− was synthesized and crystallized in the ionic liquid [BMP]OTf. The compound was fully characterized by Raman spectroscopy as well as Xray singlecrystal structure determination, and represents the first example of a polychloride dianion to be described. Detailed gasphase and solidstate calculations concerning the nature of the bonding situation were also performed.
Coinage metal diatomic molecules are building blocks for nanostructured materials, electronic devices, and catalytically or photochemically active systems that are currently receiving lively interest in both fundamental and applied research. The theoretical study presented here elucidates the electronic structure in the ground and several lowlying excited states of the diatomic molecule CuAu that result from the combination of the atoms in their ground states nd10(n + 1)s1 2S and lowest excited dhole states nd9(n + 1)s2 2D (n = 3 for Cu, n = 5 for Au). Full and smooth potential energy curves, obtained at the multireference configuration interaction (MRCI) level of theory, are presented for the complete set of the thus resulting 44 Λ–S terms and 86 Ω terms. Our approach is based on a scalar relativistic description using the Douglas–Kroll–Hess (DKH) Hamiltonian, with subsequent perturbative inclusion of spin−orbit (SO) coupling via the spin–orbit terms of the Breit–Pauli (BP) Hamiltonian. The Ω terms span an energy interval of about 7 eV at the ground state’s equilibrium distance. Spectroscopic constants, calculated for all terms, are shown to accurately reproduce the observation for those nine terms that are experimentally known.
Polyethylene glycol (PEG) is a structurally simple and nontoxic watersoluble polymer that is widely used in medical and pharmaceutical applications as molecular linker and spacer. In such applications, PEG’s elastic response against conformational deformations is key to its function. According to textbook knowledge, a polymer reacts to the stretching of its endtoend separation by a decrease in entropy that is due to the reduction of available conformations, which is why polymers are commonly called entropic springs. By a combination of singlemolecule force spectroscopy experiments with molecular dynamics simulations in explicit water, we show that entropic hydration effects almost exactly compensate the chain conformational entropy loss at high stretching. Our simulations reveal that this entropic compensation is due to the stretchinginduced release of water molecules that in the relaxed state form double hydrogen bonds with PEG. As a consequence, the stretching response of PEG is predominantly of energetic, not of entropic, origin at high forces and caused by hydration effects, while PEG backbone deformations only play a minor role. These findings demonstrate the importance of hydration for the mechanics of macromolecules and constitute a case example that sheds light on the antagonistic interplay of conformational and hydration degrees of freedom.
In this work, fullerene has been functionalized with cyanuric chloride at room temperature by a nitrene mediated [2 + 1] cycloaddition reaction. The adduct after functionalization is inherently in the form of azafulleroid and shows broad UV absorption in the wavelength range of 200–800 nm, as well as photothermal conversion and fluorescence with a high quantum yield.
Rigidity and preorganisation are believed to be required for high affinity in multiply bonded supramolecular complexes as they help reducing the entropic penalty of the binding event. This comes at the price that such rigid complexes are sensitive to small geometric mismatches. In marked contrast, nature uses more flexible building blocks. Thus, one might consider putting the rigidityhigh affinity notion to the test. Multivalent crown/ammonium complexes are ideal for this purpose as the monovalent interaction is well understood. A series of divalent complexes with different spacer lengths and rigidities has thus been analysed to correlate chelate cooperativities and spacer properties. Too long spacers reduce chelate cooperativity compared to exactly matching ones. However, in contrast to expectation, flexible guests bind with chelate cooperativities clearly exceeding those of rigid structures. Flexible spacers adapt to small geometric host/guest mismatches. Spacerspacer interactions help overcoming the entropic penalty of conformational fixation during binding and a delicate balance of preorganisation and adaptability is at play in multivalent complexes.
A thorough thermodynamic analysis by isothermal titration calorimetry of allosteric and chelate cooperativity effects in divalent crown ether/ammonium complexes is combined with DFT calculations including implicit solvent on the one hand and largescale molecular dynamics simulations with explicit solvent molecules on the other. The complexes studied exhibit binding constants up to 2×106 m−1 with large multivalent binding enhancements and thus strong chelate cooperativity effects. Slight structural changes in the spacers, that is, the exchange of two ether oxygen atoms by two isoelectronic methylene groups, cause significantly stronger binding and substantially increased chelate cooperativity. The analysis is complemented by the examination of solvent effects and allosteric cooperativity. Such a detailed understanding of the binding processes will help to efficiently design and construct larger supramolecular architectures with multiple multivalent building blocks.
The predissociation of the N2+ molecular ion in the C 2Σu+ electronic state through the nonadiabatic coupling with the B 2Σu+ electronic state is studied by solving the Schrödinger equation. The predissociation rates are calculated using Fermi's golden rule and compared with experimental results. We characterize the dynamics by calculating the nuclear probability density ρ(R,t), the nuclear flux density j(R,t), and the twoelectron flux density j(r1,r2,t). It is found that at the early dynamics, t≤100 fs, Fermi's golden rule breaks down, while a strong correlation between the electronic and nuclear dynamics is observed. Fourier analyses of the probability and flux densities are also presented and yield insight in their frequency dependency.
Fluorination of the hydroxylated αAl2O3 (0001) surface is studied using periodic density functional theory calculations. On the basis of a hypothetical reaction substituting surface hydroxyl groups with fluorine atoms, we find surface fluorination to be strongly exergonic but kinetically hindered. Fluorinated surface areas turn out to be rather hydrophobic as compared to hydroxylated areas, suggesting fluorination as a potential route for tuning oxide surface properties such as hydrophilicity.
Recently, adiabatic attosecond charge migration (AACM) has been monitored and simulated for the first time, with application to the oriented iodoacetylene cation where AACM starts from the initial superposition of the ground state (φ0) and an electronic excited state (φ1). Here, we develop the theory for electronic fluxes during AACM in ringshaped molecules, with application to oriented benzene prepared in the superposition of the ground and first excited singlet states. The initial state and its time evolution are analogous to coherent tunneling where φ0 and φ1 have different meanings; however, they denote the wave functions of the lowest tunneling doublet. This analogy suggests to transfer the theory of electronic fluxes during coherent tunneling to AACM, with suitable modifications which account for (i) the different time scales and (ii) the different electronic states, and which make use of (iii) the preparation of the initial state for AACM by a linearly polarized laser pulse. Application to benzene yields the multidirectional angular electronic flux with a pincermotion type pattern during AACM: this unequivocal result confirms a previous working hypothesis. Moreover, the theory of AACM allows quantification of the electronic flux; that is, the maximum number of electrons (out of 42) which flow concertedly during AACM in benzene is 6 × 0.08 = 0.48.
The quantum theory of concerted electronic and nuclear fluxes (CENFs) during coherent periodic tunnelling from reactants (R) to products (P) and back to R in molecules with asymmetric doublewell potentials is developed. The results are deduced from the solution of the timedependent Schrödinger equation as a coherent superposition of two eigenstates; here, these are the two states of the lowest tunnelling doublet. This allows the periodic time evolutions of the resulting electronic and nuclear probability densities (EPDs and NPDs) as well as the CENFs to be expressed in terms of simple sinusodial functions. These analytical results reveal various phenomena during coherent tunnelling in asymmetric doublewell potentials, e.g., all EPDs and NPDs as well as all CENFs are synchronous. Distortion of the symmetric reference to a system with an asymmetric doublewell potential breaks the spatial symmetry of the EPDs and NPDs, but, surprisingly, the symmetry of the CENFs is conserved. Exemplary application to the Cope rearrangement of semibullvalene shows that tunnelling of the ideal symmetric system can be suppressed by asymmetries induced by rather small external electric fields. The amplitude for the half tunnelling, half nontunnelling border is as low as 0.218 × 10–8 V/cm. At the same time, the delocalized eigenstates of the symmetric reference, which can be regarded as Schrödinger’s cattype states representing R and P with equal probabilities, get localized at one or the other minima of the asymmetric doublewell potential, representing either R or P.
The curvature dependence of the physisorption properties of a water molecule inside and outside an armchair carbon nanotube (CNT) is investigated by an incremental densityfitting local coupled cluster treatment with single and double excitations and perturbative triples (DFLCCSD(T)) study. Our results show that a water molecule outside and inside (n, n) CNTs (n = 4, 5, 6, 7, 8, 10) is stabilized by electron correlation. The adsorption energy of water inside CNTs decreases quickly with the decrease of curvature (increase of radius) and the configuration with the oxygen pointing toward the CNT wall is the most stable one. However, when the water molecule is adsorbed outside the CNT, the adsorption energy varies only slightly with the curvature and the configuration with hydrogens pointing toward the CNT wall is the most stable one. We also use the DFLCCSD(T) results to parameterize LennardJones (LJ) force fields for the interaction of water both with the inner and outer sides of CNTs and with graphene representing the zero curvature limit. It is not possible to reproduce all DFLCCSD(T) results for water inside and outside CNTs of different curvature by a single set of LJ parameters, but two sets have to be used instead. Each of the two resulting sets can reproduce three out of four minima of the effective potential curves reasonably well. These LJ models are then used to calculate the water adsorption energies of larger CNTs, approaching the graphene limit, thus bridging the gap between CNTs of increasing radius and flat graphene sheets.
The method of increments is applied to investigate the adsorption of a single water molecule inside and outside armchair carbon nanotubes with different curvature using densityfitting local coupled cluster with single and double excitations and perturbative triples treatment (DFLCCSD(T)). The correlation contribution to the adsorption energy is expanded in terms of localized orbitals of both the water molecule and the nanotube. Results of this investigation show that the simultaneous correlation of groups of localized orbitals of the water molecule and of the carbon nanotube (i. e. interfragment twobody increments) is the major contribution to the attractive interaction. In contrast the individual correlation energy of localized orbitals of water molecule or carbon nanotube (i. e. onebody increments) is negligible. A detailed balance between the repulsive Hartree–Fock contribution and the attractive correlation contribution to the adsorption energy determines the groundstate structure of the water molecule inside the carbon nanotube. To elucidate this behavior benzenebased model systems are investigated with the same methods.
We investigate the electronic properties of graphene nanoflakes on Ag(111) and Au(111) surfaces by means of scanning tunneling microscopy and spectroscopy as well as density functional theory calculations. Quasiparticle interference mapping allows for the clear distinction of substratederived contributions in scattering and those originating from graphene nanoflakes. Our analysis shows that the parabolic dispersion of Au(111) and Ag(111) surface states remains unchanged with the band minimum shifted to higher energies for the regions of the metal surface covered by graphene, reflecting a rather weak interaction between graphene and the metal surface. The analysis of graphenerelated scattering on single nanoflakes yields a linear dispersion relation E(k), with a slight pdoping for graphene/Au(111) and a larger ndoping for graphene/Ag(111). The obtained experimental data (doping level, band dispersions around E_{F}, and Fermi velocity) are very well reproduced within DFTD2/D3 approaches, which provide a detailed insight into the sitespecific interaction between graphene and the underlying substrate.
The Gibbs energies of association ΔG_{sol}^{T} between primary alkyl ammonium ions and crown ethers in solution are measured and calculated. Measurements are performed by isothermal titration calorimetry and revealed a strong solventdependent ion pair effect. Calculations are performed with density functional theory including Grimme's dispersion correction D3(BJ). The translational, rotational, and vibrational contributions to the Gibbs energy of association ΔG_{sol}^{T} are taken into account by a rigidrotorharmonicoscillator approximation with a freerotor approximation for low lying vibrational modes. Solvation effects δG_{sol}^{T} are taken into account by applying the continuum solvation model COSMORS. Our study aims at finding a suitable theoretical method for the evaluation of the host guest interaction in crown/ammonium complexes as well as the observed ion pair effects. A good agreement of theory and experiment is only achieved, when solvation and the effects of the counterions are explicitly taken into account.
Tunneling isomerization of molecules with symmetric double well potentials are associated with periodic nuclear fluxes, from the reactant R to the product P and back to R. Halfway between R and P the fluxes achieve their maximum values at the potential barrier. For molecules in the lowest tunneling doublet (v = 0) the rises and falls to and from the maximum alues are approximately bellshaped. Upon excitation to higher tunneling doublets v = 1, 2, etc., however, this shape is eplaced by symmetric ‘‘staircase patterns’’ of the fluxes, with v + 1 stepping up and down in the domains of R and P, respectively. The quantum derivation of the phenomenon is universal. It is demonstrated here for a simple model of nuclear fluxes during tunneling isomerization of ammonia along the umbrella inversion mode, with application to separation of isotopomers.
At the hand of the adsorption of the metal atoms Zn, Cd and Hg on a graphene sheet, we propose a combination of rangeseparated hybrid densityfunctional theory in combination with the incremental scheme in localised orbitals and extrapolation procedures for the description of this type of extended systems. Using only dispersion terms for the longrange part, we were able to obtain results comparable to incremental coupledcluster calculations with singles, doubles and perturbative triples (CCSD(T)). Repulsive threecentre increments reduce the overall correlation contribution to the binding energy by 20 %. 
↑ Top
View
Edit
Attributes
History
Attach
Print
This page was last modified on July 13, 2017, at 12:35 PM 