82 research outputs found
Calculation Of Non-Adiabatic Coupling Vectors In A Local-Orbital Basis Set
The following article appeared in Journal of Chemical Physics 138.15 (2013): 154106 and may be found at http://scitation.aip.org/content/aip/journal/jcp/138/15/10.1063/1.4801511Most of today's molecular-dynamics simulations of materials are based on the Born-Oppenheimer approximation. There are many cases, however, in which the coupling of the electrons and nuclei is important and it is necessary to go beyond the Born-Oppenheimer approximation. In these methods, the non-adiabatic coupling vectors are fundamental since they represent the link between the classical atomic motion of the nuclei and the time evolution of the quantum electronic state. In this paper we analyze the calculation of non-adiabatic coupling vectors in a basis set of local orbitals and derive an expression to calculate them in a practical and computationally efficient way. Some examples of the application of this expression using a local-orbital density functional theory approach are presented for a few simple molecules: H3, formaldimine, and azobenzene. These results show that the approach presented here, using the Slater transition-state density, is a very promising way for the practical calculation of non-adiabatic coupling vectors for large systems.This work was partially supported by Spanish Ministerio de EconomĂa y Competitividad (Contract No.FIS2010-16046), the Comunidad de Madrid (Contract No.S2009/MAT-1467), the Office of Science, Basic Energy Sciences in the US Department of Energy (Grant No. DEFG02-10ER16164), the Czech Science Foundation (GAÄŚR)(Project No. 204/10/0952), the Grant of the MĹ MT of the Czech Republic (Grant No. ME 09048), and COST-CMTS
Action CM1002 (CODECS). J.O. gratefully acknowledges support from the Spanish Ministerio de Ciencia e InnovaciĂłn (PR2008-0027). E.A. gratefully acknowledges financial support by the ConsejerĂa de EducaciĂłn de la Comunidad de Madrid and Fondo Social Europeo
Automated structure discovery in atomic force microscopy
Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar aromatic molecules due to difficulties with interpretation of highly distorted AFM images originating from nonplanar molecules. Here, we develop a deep learning infrastructure that matches a set of AFM images with a unique descriptor characterizing the molecular configuration, allowing us to predict the molecular structure directly. We apply this methodology to resolve several distinct adsorption configurations of 1S-camphor on Cu(111) based on low-temperature AFM measurements. This approach will open the door to applying high-resolution AFM to a large variety of systems, for which routine atomic and chemical structural resolution on the level of individual objects/molecules would be a major breakthrough
Terminology of bioanalytical methods (IUPAC Recommendations 2018)
Recommendations are given concerning the terminology of methods of bioanalytical chemistry. With respect to dynamic development particularly in the analysis and investigation of biomacromolecules, terms related to bioanalytical samples, enzymatic methods, immunoanalytical methods, methods used in genomics and nucleic acid analysis, proteomics, metabolomics, glycomics, lipidomics, and biomolecules interaction studies are introduced
Terminology of bioanalytical methods (IUPAC Recommendations 2018)
free accessRecommendations are given concerning the terminology of methods of bioanalytical chemistry. With respect to dynamic development particularly in the analysis and investigation of biomacromolecules, terms related to bioanalytical samples, enzymatic methods, immunoanalytical methods, methods used in genomics and nucleic acid analysis, proteomics, metabolomics, glycomics, lipidomics, and biomolecules interaction studies are introduced.Peer reviewe
Visualizing the orientational dependence of an intermolecular potential
Scanning probe microscopy can now be used to map the properties of single molecules with intramolecular precision by functionalization of the apex of the scanning probe tip with a single atom or molecule. Here we report on the mapping of the three-dimensional potential between fullerene (C₆₀) molecules in different relative orientations, with sub-Angstrom resolution, using dynamic force microscopy (DFM). We introduce a visualization method which is capable of directly imaging the variation in equilibrium binding energy of different molecular orientations. We model the interaction using both a simple approach based around analytical Lennard–Jones potentials, and with dispersion-force-corrected density functional theory (DFT), and show that the positional variation in the binding energy between the molecules is dominated by the onset of repulsive interactions. Our modelling suggests that variations in the dispersion interaction are masked by repulsive interactions even at displacements significantly larger than the equilibrium intermolecular separation
Interplay of Conductance, Force, and Structural Change in Metallic Point Contacts
The coupling between two atomically sharp nanocontacts provides tunable access to a fundamental underlying interaction: the formation of the bond between two atoms as they are brought into contact. Here we report a detailed experimental and theoretical analysis of the relation between the chemical force and the tunneling current during bond formation in atom-scale metallic junctions and their dependence on distance, junction structure, and material. We found that the short-range force as well as the conductance in two prototypical metal junctions depend exponentially on the distance and that they have essentially the same exponents. In the transition regime between tunneling and point contact, large short-range forces generate structural relaxations which are concomitant with modifications of the surface electronic structure and the collapse of the tunneling barrier
Believe in the force
Nearly a decade after discovering molecular chirality in 1848, Louis Pasteur changed research direction and began investigating fermentations. Conflicting explanations have been given for this switch to microbiology, but the evidence strongly suggests that Pasteur’s appointment in 1854 to the University of Lille—an agricultural- industrial region where fermentation-based manufacturing was of great importance— and an appeal for help in 1856 by a local manufacturer experiencing problems in his beetroot-fermentation-based alcohol production played a significant role. Thus began, in late 1856, Pasteur’s pioneering studies of lactic and alcoholic fermentations. In 1857, reportedly as a result of a laboratory mishap, he found that in incubations of ammonium (6)-tartrate with unidentified microorganisms (1)-tartaric acid was consumed with con- siderable preference over (2)-tartaric acid. In 1860, he demonstrated a similar enantio- selectivity in the metabolism of tartaric acid by Penicillium glaucum, a common mold. Chance likely played a significant role both in Pasteur’s shift to microbiology and his discovery of enantioselective tartrate fermentations, but he rejected pure serendipity as a significant factor in experimental science and in his own career. Pasteur’s mile- stone discovery of biological enantioselectivity began the process that in the long run established the fundamental importance of molecular chirality in biology. Chiralit
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