In exploring the toxicity of micro- and nanoplastics, molecular simulations of plastic nanoparticles have been gaining traction recently. Modeling of nanoplastics involves the folding of multiple polymeric chains into an entangled particle, which is a challenging process, necessitating thorough optimization of the folding procedure. In this contribution, we use the simulated annealing procedure in a systematic workflow for preparing stable nanoplastic structures for the first time, based on the CHARMM36 force field. On the structures prepared with the fine-tuned protocol, we carry out quantum chemical geometry optimizations with the GFN2-xTB method, followed by benchmarking single-point calculations with GGA and hybrid DFT functionals. We further demonstrate the applicability of this approach through four plastic systems, including polyethylene, polypropylene, polystyrene, and nylon-66. Remarkably, the geometry of the resulting most stable assemblies show similarities to features observed earlier theoretically and experimentally for such systems. For polyethylene, a highly ordered, crystalline structure is obtained, in which the polymer chains possess long sections with all C-C-C-C units in trans configuration. For polypropylene and polystyrene, helical structures are observed, formed by alternating gauche and trans configurations along the backbone. For nylon-66, the structure-directing effect of the hydrogen bonds between amide moieties complicates the folding, resulting in parallelly arranged hydrogen bonding chains throughout the particle. Especially, we make the whole set of optimized structures available for the community in an online repository, with hopes of advancing simulation studies in the field, even making ensemble simulations accessible.

The scaling behavior of ab initio molecular dynamics simulations for the different size bulk systems of liquid methanol is presented and thereby the characteristics of every system performing on either a local compute cluster or a supercomputer are analyzed. Additionally, the influence of different parameters on the quality of the infrared and Raman spectra is investigated using different simulation frameworks, including time step, convergence criteria, density functional approximation, and basis set. Both the maximally localized Wannier functions and the radical Voronoi tessellation approaches are employed to evaluate vibrational spectra from the trajectories. The results of infrared and Raman spectra are classified in two frequency regions, 500 to 1600 cm −1 and 2500 to 4000 cm −1 , in order to compare and discuss the experimental spectra and the results derived from ab initio molecular dynamics simulations comprehensively. The outcome of this study guides future experimental and theoretical researchers in order to acquire a profound perception into vibrational spectra, which evolves the way of elucidating molecular structure.

Flexible molecules and non-idle environments can present severe problems in the prediction of vibrational spectra. This work focuses on infrared and vibrational circular dichroism for which the latter is extremely sensitive to such complicated situations. Here two possible ways to perform spectroscopy calculations for such situations are investigated. The first approach is based on static quantum chemical calculations employing cluster-weighting. The second approach is rooted in ab initio molecular dynamics simulations using the time correlations approach. For the present example ((R)-butan-2-ol), excellent spectra from simulations are obtained for gas and bulk, when the former is averaged over trajectories with all possible starting conformers and these are scaled to match the experimental spectrum. The cluster-weighted approach is inferior to the simulations but still reaches very good results at much less computational cost. A simplified, but computationally less expensive simulation approach is considered by approximating the electric and magnetic moments, which are input quantities in the correlation function, by classical equations and different populations analysis for the required partial charges. The results are inferior to the full simulations but still give satisfying results at the advantage of being much faster to calculate.

The N‐heterocyclic carbene organocatalytic reactivity of the 1‐ethyl‐3‐methylimidazolium acetate ionic liquid was investigated on the model reaction between this solvent and anisaldehyde. The formation of carbenes by a proton transfer from the cation to the anion was compared to a direct reaction mechanism, in which the proton transfer and the C–C bond formation between catalyst and substrate occurs in a single elementary step. Interestingly, the two reaction mechanisms show a much smaller difference in activation energies than those observed for analogous catalytic systems with neutral bases, showing that the mechanism might switch from one to the other at different temperatures or with different substrates. In this particular case, however, the direct reaction mechanism, avoiding free carbenes in the solution, is apparently more feasible. Based on the detailed analysis of this reaction path, the earlier contradictions between theory and experiments can be resolved, resulting in a consistent mechanistic picture for the related processes. Additionally, we show on the example of a platinum surface that introducing metal probes into the liquid may induce carbene‐like reactions, as the formation of a strong coordinative bond between the carbene and a platinum atom at the surface is highly exothermic, shifting the acid‐base equilibrium considerably.

We report on ordered binary monolayer structures consisting of a sulfur-containing pi-conjugated molecule, namely, tetrabenzo thianthrene (TBTA) or tetrathiatetracene (TTT) as a donor, and tetracyano naphtho quinodimethane (TNAP) as an acceptor on the Au(111) surface. The investigations were performed by low-energy electron diffraction (LEED) and scanning tunneling microscopy (STM) and additional density functional theory (DFT) calculations for TTT/TNAP. Both pairs of molecules (TTT/TNAP and TBTA/TNAP) form long-range ordered, commensurate structures on the Au(111) surface with a 1:1 stoichiometry. The structures consist of alternating rows containing only one type of molecule. The TNAP rows are stabilized by hydrogen bonds. Submolecular resolved STM images indicate a net charge transfer from the donor molecules to the TNAP molecules. The reconstruction of the Au(111) surface is modified upon the formation of the ordered binary structures, pointing to a significant surface-molecule interaction. For TTT/TNAP, the surface interaction leads to bonds of the S atoms to the Au atoms. For TBTA/TNAP, there exists an additional porous, TBTA-rich structure in which TBTA builds the framework.

This study investigates the effect of substitution with different functional groups and of molecular flexibility by changing within the axle from a single C–C bond to a double C=C bond. Therefore, we present static quantum chemical calculations at the dispersion-corrected density functional level (DFT-D3) for several Leigh-type rotaxanes. The calculated crystal structure is in close agreement with the experimental X-ray data. Compared to a stiffer axle, a more flexible one results in a stronger binding by 1–3 kcal/mol. Alterations of the binding energy in the range of 5 kcal/mol could be achieved by substitution with different functional groups. The hydrogen bond geometry between the isophtalic unit and the carbonyl oxygen atoms of the axle exhibited distances in the range of 2.1 to 2.4 Å for six contact points, which shows that not solely but to a large amount the circumstances in the investigated rotaxanes are governed by hydrogen bonding. Moreover, the complex with the more flexible axle is usually more unsymmetrical than the one with the stiff axle. The opposite is observed for the experimentally investigated axle with the four phenyl stoppers. Furthermore, we considered an implicit continuum solvation model and found that the complex binding is weakened by approximately 10 kcal/mol, and hydrogen bonds are slightly shortened (by up to 0.2 Å).

The adsorption of benzene on the M(111), M(100) and M(110) surfaces of the coinage metals copper (M = Cu), silver (M = Ag) and gold (M = Au) is studied on the basis of density functional theory (DFT) calculations with an empirical dispersion correction (D3). Variants of the Perdew–Burke–Ernzerhof functionals (PBE, RPBE and RevPBE) in combination with different versions of the dispersion correction (D3 and D3(BJ)) are compared. PBE-D3, PBE-D3(BJ) and RPBE-D3 give similar results which exhibit a good agreement with experimental data. RevPBE-D3 and RevPBE-D3(BJ) tend to overestimate adsorption energies. The inclusion of three-center terms (PBE-D3(ABC)) leads to a slightly better agreement with the experiment in most cases. Vertical adsorbate–substrate distances are calculated and compared to previous theoretical results. The observed trends for the surfaces and metals are consistent with the calculated adsorption energies.

The normal incidence x-ray standing wave (NIXSW) technique is used to determine the adsorption geometry of submonolayer 3,4,9,10-perylene tetracarboxylic dianhydride (PTCDA) adsorbed on the Ag(110) surface. An accurate analysis of both C1$s$ and O1$s$ photoemission (PE) spectra allows the respective adsorption heights of carbon and oxygen atoms in different chemical environments within PTCDA to be distinguished. Due to the intricacy of the PE fitting models, a systematic error analysis of NIXSW structural parameters was developed and employed. Based on the adsorption geometry of PTCDA on Ag(110) a bonding mechanism is discussed.

The particular mechanistic role of halides in the additive-assisted copper electrodeposition is studied by means of combined potential/time transients, in situ STM (scanning tunneling microscopy) experiments, DFT (density functional theory) calculations and ICP-MS (inductively coupled plasma mass spectroscopy) analysis. More specifically, we studied the competitive interaction of bromide and SPS (bis-sodium-sulfopropyl-disulfide). The latter additive is commonly used in the Damascene process as specific antagonist (anti-suppressor, depolarizer) of the polyalkylene glycol (PAG) suppressor additives whereas halides are essential co-additives of the suppressors.Galvanostatic potential transient experiments indicate a substantial stabilization of the PAG suppressor complexes at the copper/electrolyte interface under reaction conditions when the chloride is displaced by the bromide in the formed PAG-Cu(I)-X (X = halide) ensemble. Those bromide containing suppressor complexes reveal substantially improved barrier properties with respect to inter-diffusion of cupric and cuprous ions. Furthermore they are more robust against degradation by the MPS (mercaptopropane sulfonic acid) which is formed under reactive conditions from the SPS as the actual anti-suppressor species in the course of a surface-confined SPS dissociation.Our combined STM and DFT work demonstrates that identical halide/MPS co-adsorption phases are formed when the SPS interacts with either the chloride or the bromide modified copper surfaces. The MPS production gets, however, substantially decelerated when the bromide is present. This effect is discussed as one important reason among others why the antagonistic interaction between the PAG suppressor ensembles and the SPS (MPS) is disturbed when the chloride is displaced by the bromide. We further demonstrate by means of an ICP-MS analysis the capability of the free MPS ligands to dissolve less soluble Cu(I) aggregates. (C) 2012 Elsevier Ltd. All rights reserved.

The competitive interaction of chloride and SPS (bis-(sodium-sulfopropyl)-disulfide) at Cu(1 0 0)/electrolyte model interfaces was studied by means of cyclic voltammetry in combination with in situ STM and DFT. This specific anion/anion interaction is of paramount importance for the suppressor ensemble deactivation in the context of the industrial Cu Damascene process used for the state-of-the-art on-chip metallization. It is the interplay between chemisorbed chloride and SPS which regulates the dissociative SPS adsorption on copper as the key step in the course of the surface-confined MPS (mercaptopropane sulfonic acid) production. The latter species is considered as the actual anti-suppressor (depolarizer) in context of the Cu Damascene process.Under competitive conditions the chloride adsorbs and orders much faster on Cu(1 0 0) than the SPS. The resulting c(2 x 2)-Cl adlayer acts as an effective barrier for the dissociative SPS adsorption, at least under non-reactive conditions. Defect sites within the chloride matrix are identified as crucial pre-requisites for the dissociative SPS adsorption. Defects are generated under reactive conditions during copper dissolution or copper deposition due to rapid anion adsorption/desorption dynamics. As consequence of the SPS dissociation a mixed, defect-rich c(2 x 2)-Cl-MPS co-adsorption phase forms on Cu(1 0 0) where every second chloride species of the pristine c(2 x 2)-Cl adlayer is displaced by MPS units. This co-adsorption phase reveals an apparent p(2 x 2) symmetry in the STM experiment since only the sulfonic head groups of the MPS units are imaged while the S and the Cl species chemisorbed on the copper surface remain invisible at the "buried" interface.The relevance of this surface reaction for the Cu Damascene process is discussed in detail. (C) 2012 Elsevier Ltd. All rights reserved.

A recently developed empirical dispersion correction (Grimme et al., J. Chem. Phys. 2010, 132, 154104) to standard density functional theory (DFT-D3) is implemented in the plane-wave program package VASP. The DFT-D3 implementation is compared with an implementation of the earlier DFT-D2 version (Grimme, J. Comput. Chem. 2004, 25, 1463; Grimme, J. Comput. Chem. 2006, 27, 1787). Summation of empirical pair potential terms is performed over all atom pairs in the reference cell and over atoms in shells of neighboring cells until convergence of the dispersion energy is obtained. For DFT-D3, the definition of coordination numbers has to be modified with respect to the molecular version to ensure convergence. The effect of three-center terms as implemented in the original molecular DFT-D3 version is investigated. The empirical parameters are taken from the original DFT-D3 version where they had been optimized for a reference set of small molecules. As the coordination numbers of atoms in bulk and surfaces are much larger than in the reference compounds, this effect has to be discussed. The results of test calculations for bulk properties of metals, metal oxides, benzene, and graphite indicate that the original parameters are also suitable for solid-state systems. In particular, the interlayer distance in bulk graphite and lattice constants of molecular crystals is considerably improved over standard functionals. With the molecular standard parameters (Grimme et al., J. Chem. Phys. 2010, 132, 154104; Grimme, J. Comput. Chem. 2006, 27, 1787) a slight overbinding is observed for ionic oxides where dispersion should not contribute to the bond. For simple adsorbate systems, such as Xe atoms and benzene on Ag(111), the DFT-D implementations reproduce experimental results with a similar accuracy as more sophisticated approaches based on perturbation theory (Rohlfing and Bredow, Phys. Rev. Lett. 2008, 101, 266106).

The trends in the bonding mechanism of 3,4,9,10-perylenetetracarboxylic acid dianhydride (PTCDA) to the Ag(111), Ag(100), and Ag(110) surfaces were analyzed on the basis of data obtained from x-ray standing waves and dispersion-corrected density functional theory. Of importance are the attractive local O-Ag bonds on the anhydride groups. They are the shorter, the more open the surface is, and lead even to partly repulsive interactions between the perylene core and the surface. In parallel, there is an increasing charge donation from the Ag surface into the pi system of the PTCDA. This synergism explains the out-of-plane distortion of the adsorbed PTCDA and the surface buckling. DOI: 10.1103/PhysRevB.86.235431

Structure and stability of solid formamide are studied theoretically at density-functional level in order to reveal the importance of hydrogen bonds and dispersion forces for intermolecular binding. The PBE-D2 and PBE-D3 functionals which include recent implementations of empirical dispersion corrections describe the crystal structure in good agreement with experimental results, whereas standard PBE fails. From wavefunction analyses and by decomposition of the total sublimation energy we find that weak CH⋯O hydrogen bonds exist between neighboring sheets of formamide molecules. Accordingly, we conclude that the formamide crystal consists of an extended three-dimensional hydrogen bond network.

Dispersion-corrected density functional theory calculations (DFT-D3) were performed for the adsorption of CO on MgO and C(2) H(2) on NaCl surfaces. An extension of our non-empirical scheme for the computation of atom-in-molecules dispersion coefficients is proposed. It is based on electrostatically embedded M(4)X(4) (M=Na, Mg) clusters that are used in TDDFT calculations of dynamic dipole polarizabilities. We find that the C(MM)(6) dispersion coefficients for bulk NaCl and MgO are reduced by factors of about 100 and 35 for Na and Mg, respectively, compared to the values of the free atoms. These are used in periodic DFT calculations with the revPBE semi-local density functional. As demonstrated by calculations of adsorption potential energy curves, the new C(6) coefficients lead to much more accurate energies (E(ads)) and molecule-surface distances than with previous DFT-D schemes. For NaCl/C(2) H(2) we obtained at the revPBE-D3(BJ) level a value of E(ads) =-7.4 kcal mol(-1) in good agreement with experimental data (-5.7 to -7.1 kcal mol(-1)). Dispersion-uncorrected DFT yields an unbound surface state. For the MgO/CO system, the computed revPBE-D3(BJ) value of E(ads) =-4.1 kcal mol(-1) is also in reasonable agreement with experimental results (-3.0 kcal mol(-1)) when thermal corrections are taken into account. Our new dispersion correction also improves computed lattice constants of the bulk systems significantly compared to plain DFT or previous DFT-D results. The extended DFT-D3 scheme also provides accurate non-covalent interactions for ionic systems without empirical adjustments and is suggested as a general tool in surface science.

We present a theoretical investigation of amide pseudorotaxane IR spectra in the harmonic approximation. In particular, we focus on the effect of axle substitution on the hydrogen bonds that are formed between axle and wheel. Two types of pseudorotaxanes are studied: one with the substituent affecting mostly the axle's carbonyl group and one with the effect influencing primarily the amide NH group. Sizeable red shifts are predicted for the carbonyl stretching frequencies, and large red shifts for the NH stretching frequencies. For the wheel amide groups involved in hydrogen bonding merely with their NH hydrogens, a small shift is observed for the carbonyl stretch mode. A clear relation is observed between the NH stretch shifts and individual hydrogen bond energies. This is confirmed by correlations of the shared electron number with the NH stretch shift showing that this quantity can be taken as an indicator for individual hydrogen bond energies. Axle substitution influences the strengths of the individual hydrogen bonds which is again reflected in the NH stretch frequency shifts. A linear relationship of Hammett's substituent parameters with the NH frequency shifts can be established.

The formation of intermolecular complexes of two large molecules-a macrocycle and a semiaxle, which have been used in templated syntheses of amide rotaxanes-was studied by scanning tunneling microscopy (STM) and density functional theory (DFT). These experiments mimic the so-called "threading process", which is based on intermolecular recognition and which is essential for the rotaxane synthesis in solution. First, ordered monolayers of a tetralactam macrocycle (TLM), i.e. the rotaxane wheel, are prepared on a Au(111) surface. Then, semiaxles (SA) are deposited on top of these ordered TLM layers at ca. 140 K. In solution, the SA molecule threads into the TLM cavity by formation of three hydrogen bonds between the amide groups of both molecules. On the Au(111) surface, the scenario is similar, although different in detail due to geometric restrictions given by the underlying An(111) surface and conformational energy barriers due to the confinement of the TLM geometry in the ordered monolayer structure, Three distinct and defined adsorption sites of the SA molecules with respect to the TLM molecules exist. Notably, the population of these sites is assisted by interaction with the STM. tip. Two sites are compatible with a structural model, in which the tail of the SA molecule binds into the TLM cavity, in one case with three H bonds, one to the terminal NH2 group of the SA and two to the central amide group. This SA-TLM adsorption complex formed at low temperatures is metastable and dissociates at higher temperatures. These results demonstrate the possibility to study intermolecular complex formation by STM.

The mass spectrometric characterization of Fréchet-type dendrons is reported. In order to provide the charges necessary for electrospray ionization, dendrons bearing an OH group at the focal point can be deprotonated and observed in the negative ion mode. Alternatively, the corresponding bromides can be converted to quaternary ammonium ions that can easily be detected in the positive mode. If the latter ions are subjected to collision-induced dissociation experiments, a fragmentation cascade begins with the dissociation of the focal amine. The focal benzyl cation quickly decomposes in a fragmentation cascade from the focal point to the periphery until the peripheral benzyl (or naphthylmethyl) cations are formed. Five different mechanisms are discussed in detail, three of which can be excluded based on experimental evidence. The cascade fragmentation is reminiscent of self-immolative dendrimers.