Xsorb: a software for identifying the most stable adsorption configuration and energy of a molecule on a crystal surface

Molecular adsorption is the first important step of many surface-mediated chemical processes, from catalysis to tribology. This phenomenon is controlled by physical/chemical interactions, which can be accurately described by first principles calculations. In recent years, several computational tools have been developed to study molecular adsorption based on high throughput/automatized approaches. However, these tools can sometimes be over-sophisticated for non-expert users. In this work, we present Xsorb, a Python-based code that automatically generates adsorption configurations, guides the user in the identification the most relevant ones, which are then fully optimized. The code relies on well-established Python libraries, and on an open source package for density functional theory calculations. We show the program capabilities through an example consisting of a hydrocarbon molecule, 1-hexene, adsorbed over the (110) surface of iron. The presented computational tool will help users, even non-expert, to easily identify the most stable adsorption configuration of complex molecules on substrates and obtain accurate adsorption geometries and energies

A comparative study on the functionality of S- and P-based lubricant additives by combined first principles and experimental analysis

Sulfur and phosphorus are key elements for the functionality of lubricant additives used in extreme pressure applications, such as synchronizer systems in cars. To understand their mechanism of action we combine first principles calculations and gas phase lubrication experiments. The surface spectroscopy analysis performed in situ after the tribological test indicates that iron sulfide (phosphide) is formed by rubbing steel-on-steel in the presence of organo-sulfur (-phosphorus) molecules. We, thus, study the effects of elemental sulfur and phosphorus on the interfacial properties of iron by spin-polarized density functional theory calculations. The results show that both the elements are very effective in reducing the adhesion and shear strength of iron. Sulfur is predicted to be more effective than phosphorus, especially at high pressure. Gas phase lubrication experiments confirm these results, indicating that the friction coefficient of iron-sulphide is lower than that of iron-phosphide and both S and P dramatically reduce the friction of steel-on-steel. These results indicate that the release of elemental sulfur and phosphorus may be the key mechanism to controlling the tribological properties of the metal interface and elucidate that the underling microscopic phenomenon is metal passivation. © 2016 The Royal Society of Chemistry.Sulfur and phosphorus are key elements for the functionality of lubricant additives used in extreme pressure applications, such as synchronizer systems in cars. To understand their mechanism of action we combine first principles calculations and gas phase lubrication experiments. The surface spectroscopy analysis performed in situ after the tribological test indicates that iron sulfide (phosphide) is formed by rubbing steel-on-steel in the presence of organo-sulfur (-phosphorus) molecules. We, thus, study the effects of elemental sulfur and phosphorus on the interfacial properties of iron by spin-polarized density functional theory calculations. The results show that both the elements are very effective in reducing the adhesion and shear strength of iron. Sulfur is predicted to be more effective than phosphorus, especially at high pressure. Gas phase lubrication experiments confirm these results, indicating that the friction coefficient of iron-sulphide is lower than that of iron-phosphide and both S and P dramatically reduce the friction of steel-on-steel. These results indicate that the release of elemental sulfur and phosphorus may be the key mechanism to controlling the tribological properties of the metal interface and elucidate that the underling microscopic phenomenon is metal passivation

Tribochemistry of phosphorus additives: Experiments and first-principles calculations

Organophosphorus compounds are common additives included in liquid lubricants for many applications, in particular automotive applications. Typically, organic phosphites function as friction-modifiers whereas phosphates as anti-wear additives. While the antiwear action of phosphates is now well understood, the mechanism by which phosphites reduce friction is still not clear. Here we study the tribochemistry of both phosphites and phosphates using gas phase lubrication (GPL) and elucidate the microscopic mechanisms that lead to the better frictional properties of phosphites. In particular, by in situ spectroscopic analysis we show that the friction reduction is connected to the presence of iron phosphide, which is formed by tribochemical reactions involving phosphites. The functionality of elemental phosphorus in reducing the friction of iron-based interfaces is elucidated by first principle calculations. In particular, we show that the work of separation and shear strength of iron dramatically decrease by increasing the phosphorus concentration at the interface. These results suggest that the functionality of phosphites as friction modifiers may be related to the amount of elemental phosphorus that they can release at the tribological interface

Trimethyl-phosphite dissociative adsorption on iron by combined first-principle calculations and XPS experiments

The reaction of trimethyl-phosphite, TMPi, with a clean Fe(110) surface has been investigated by ab initio calculations. The most stable configurations and energies are identified for both molecular and dissociative adsorption. The calculated reaction energies indicate that dissociation is energetically more favorable than molecular adsorption and we provide a description of the dissociation path and the associated energy barrier. In situ XPS analysis of adsorbed TMPi on metallic iron confirmed molecular chemisorption and dissociation at high temperature. These results shed light on the mechanism of phosphorus release from organophosphites at the iron surface, which is important for the functionality of these phosphorus-based additives, included in lubricants for automotive applications

First-principles insights into the structural and electronic properties of polytetrafluoroethylene in its high-pressure phase (form III)

Polytetrafluoroethylene (PTFE), commercially known as Teflon, is one the most effective insulating polymers for a wide range of applications because of its peculiar electronic, mechanical, and thermal properties. Several studies have attempted to elucidate the structural and electronic properties of PTFE; however, some important aspects of its structural and electronic characteristics are still under debate. To shed light on these fundamental features, we have employed a first-principles approach to optimize the two coexisting PTFE structures (monoclinic and orthorhombic) at high pressure by using the characteristic zigzag planar chain configuration. Our electronic analysis of the optimized structures shows charge transfer from carbons to fluorines, supporting the PTFE electronegative character. In addition, band structure calculations show that the band gap is estimated to be around 5 eV, which correlates with previous studies. Moreover, the analysis of the valence and conduction states reveals an intrachain and an interchain character of the charge distribution, suggesting additional insights into the PTFE electronic properties

Atomic and electronic structure of the cleaved 6H-SiC (11 2̄ 0) surface

We present a combined cross-section scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS) and ab initio simulations study of the nonpolar (11 2̄ 0) cleaved surface of 6H-SiC. The experimental results show an unreconstructed surface in agreement with theory. Upon truncation, two surface bands appear inside the semiconductor band gap: one empty band localized on the Si atoms and one filled band on the C atoms. According to the STS experimental results on n -doped samples, the Fermi energy is pinned at the surface inside the band gap. By comparison of STM filled and empty states topographies we propose that on the fresh cleaved surface the Fermi level lies at the bottom of the Si-like band. The calculated STM images reproduce the experimental contrast of the 6H stacking sequence and its bias dependence very well. © 2007 The American Physical Society

Atomic and electronic structure of the nonpolar GaN (1 1\u304 00) surface

We present a cross-section scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS) and ab initio density-functional theory simulations study of the cleaved nonpolar (1[overline 1]00) surface (m-plane) of n-type HVPE GaN free-standing quasisubstrates. Atomically resolved empty and filled states STM topographies show that no reconstruction occurs upon cleavage, as predicted by theory. STS measurements on clean and atomically flat cleaved surfaces (defect concentration sigmad<=2 710**12 cm 122) show that the Fermi energy is not pinned and the tunneling current flows through Ga-like electronic states lying outside the fundamental band gap. On surface areas with defect concentration sigmad>=3 710**13 cm 122, the Fermi energy is pinned inside the band gap in defect-derived surface states and tunneling through filled (empty) N-like (Ga-like) states takes place.We present a cross-section scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS) and ab initio density-functional theory simulations study of the cleaved nonpolar (1 1\u304 00) surface (m -plane) of n -type HVPE GaN free-standing quasisubstrates. Atomically resolved empty and filled states STM topographies show that no reconstruction occurs upon cleavage, as predicted by theory. STS measurements on clean and atomically flat cleaved surfaces (defect concentration \u3c3d 642 7 1012 cm-2) show that the Fermi energy is not pinned and the tunneling current flows through Ga-like electronic states lying outside the fundamental band gap. On surface areas with defect concentration \u3c3d 3 7 1013 cm-2, the Fermi energy is pinned inside the band gap in defect-derived surface states and tunneling through filled (empty) N-like (Ga-like) states takes place. \ua9 2009 The American Physical Society