Point-charge Description of some Molecular Properties

The notion of formal atomic charges in molecules is probably the most debated issue in quantum chemistry. Although atomic charge can not be rigorously defined in a unique way, conclusive evidence is given here which shows that it provides semiquantitative information about a number of molecular properties in a very simple and transparent way. In particular, the calculations of ESCA chemical shifts, diamagnetic shielding of nuclei and diamagnetic part of the molecular magnetic susceptibility are well described and thoroughly discussed. Finally, a relation between the effective atomic charges and total molecular SCF energies is illustrated by numerical examples. The point-charge description of the mentioned molecular properties is particularly useful if it is employed within the framework of semiempirical theories .because the computational costs are then negligible. The most successful semiempirical scheme in this respect seems to be the SCC- MO (self-consistent charge MO) method

Point-charge Description of some Molecular Properties

The notion of formal atomic charges in molecules is probably the most debated issue in quantum chemistry. Although atomic charge can not be rigorously defined in a unique way, conclusive evidence is given here which shows that it provides semiquantitative information about a number of molecular properties in a very simple and transparent way. In particular, the calculations of ESCA chemical shifts, diamagnetic shielding of nuclei and diamagnetic part of the molecular magnetic susceptibility are well described and thoroughly discussed. Finally, a relation between the effective atomic charges and total molecular SCF energies is illustrated by numerical examples. The point-charge description of the mentioned molecular properties is particularly useful if it is employed within the framework of semiempirical theories .because the computational costs are then negligible. The most successful semiempirical scheme in this respect seems to be the SCC- MO (self-consistent charge MO) method

Model Description of Some Molecular Properties by the Modified-Atom-in-Molecule (MAM) Approach

Conclusive evidence is presented whlch shows that the concept of modified atoms in molecule (MAM) is a viable model for a good description of numerous molecular properties. Atomic modification . can be decomposed to isotropic and anisotropic components. The isotropic change caused by molecular formation is given by the electric monopoles of atoms. It is a consequence of the charge drift accompanying chemical bonding. Atomic monopoles reproduce diamagneticshielding of the nuclei rJAd, diamagnetic susceptibility xd and ESCA shifts with an intriguing success. The atomic monopole model is easily extended to include higher local multipoles (i. e. anisotropic contribution), thus yielding satisfactory total molecular multipoles and extramolecular electrostatic potentials. Salient directional properties of covalent bonds are well described by the use of polarized atomic orbitals. It was shown that hybridization is the underlying concept which explains interrelations between steric features and local bond properties. Hybridization rationalizes in a natural and simple way the electron pair (Lewis) bond which is one of the corner stones of chemistry being particularly important for the first row atoms. It was concluded that the high information content of hybrid AOs can be ascribed to the fact that they conform to the local symmetry of the immediate molecular environment. Thus the HAOs are local wavefunctions of the zeroth order which describe atomic angular distortions. Although atoms can not be uniquely defined within molecules, the MAM model has high interpretative power yielding reasonable results. Special attention deserves a picture of charged atoms immersed in the »sea« of mixed electron density, because it is free of any arbitrariness in the slicing of molecular volume of partitioning of overlap charge. Finally, the definition of pseudo-observables is given. It was concluded that atomic monopoles and hybridization indices are pseudo-observables par exceHence. A.pparently there is colour, apparently sweetness, apparently bitterness; actuaUy there are only atoms and the void. Democritus, 420 B. C

Model Description of Some Molecular Properties by the Modified-Atom-in-Molecule (MAM) Approach

Conclusive evidence is presented whlch shows that the concept of modified atoms in molecule (MAM) is a viable model for a good description of numerous molecular properties. Atomic modification . can be decomposed to isotropic and anisotropic components. The isotropic change caused by molecular formation is given by the electric monopoles of atoms. It is a consequence of the charge drift accompanying chemical bonding. Atomic monopoles reproduce diamagneticshielding of the nuclei rJAd, diamagnetic susceptibility xd and ESCA shifts with an intriguing success. The atomic monopole model is easily extended to include higher local multipoles (i. e. anisotropic contribution), thus yielding satisfactory total molecular multipoles and extramolecular electrostatic potentials. Salient directional properties of covalent bonds are well described by the use of polarized atomic orbitals. It was shown that hybridization is the underlying concept which explains interrelations between steric features and local bond properties. Hybridization rationalizes in a natural and simple way the electron pair (Lewis) bond which is one of the corner stones of chemistry being particularly important for the first row atoms. It was concluded that the high information content of hybrid AOs can be ascribed to the fact that they conform to the local symmetry of the immediate molecular environment. Thus the HAOs are local wavefunctions of the zeroth order which describe atomic angular distortions. Although atoms can not be uniquely defined within molecules, the MAM model has high interpretative power yielding reasonable results. Special attention deserves a picture of charged atoms immersed in the »sea« of mixed electron density, because it is free of any arbitrariness in the slicing of molecular volume of partitioning of overlap charge. Finally, the definition of pseudo-observables is given. It was concluded that atomic monopoles and hybridization indices are pseudo-observables par exceHence. A.pparently there is colour, apparently sweetness, apparently bitterness; actuaUy there are only atoms and the void. Democritus, 420 B. C

An overview of nonadiabatic dynamics simulations methods, with focus on the direct approach versus the fitting of potential energy surfaces

We review state-of-the-art nonadiabatic molecular dynamics methods, with focus on the comparison of two general strategies: the "direct" one, in which the potential energy surfaces (PES) and the couplings between electronic states are computed during the integration of the dynamics equations; and the "PES-fitting" one, whereby the PES and couplings are preliminarily computed and represented as functions of the nuclear coordinates. Both quantum wavepacket dynamics (QWD) and classical trajectory approaches are considered, but we concentrate on methods for which the direct strategy is viable: among the QWD ones, we focus on those based on traveling basis functions. We present several topics in which recent progress has been made: quantum decoherence corrections in trajectory methods, the use of quasi-diabatic representations, the sampling of initial conditions and the inclusion of field-molecule interactions and of spin-orbit couplings in the dynamics. Concerning the electronic structure calculations, we discuss the use of ab initio, density functional and semiempirical methods, and their combination with molecular mechanics (QM/MM approaches). Within the semiempirical framework, we provide a concise but updated description of our own method, based on configuration interaction with floating occupation molecular orbitals. We discuss the ability of different approaches to provide observables directly comparable with experimental results and to simulate a variety of photochemical and photophysical processes. In the concluding remarks, we stress how the border between direct and PES-fitting methods is not so sharp, and we briefly discuss recent trends that go beyond this traditional distinction

Machine Learning methodology for the study of a disulfide exchange reaction

Die Thiol-Disulfid-Austauschreaktion ist eine nukleophile Substitution, die in einer großen Klasse von Proteinen stattfindet. Sie spielt eine wichtige Rolle für die dritt- und viertdimensionale Struktur von Proteinen und die Katalyse biologischer Reaktionen. Außerdem kann der Thiol-Disulfid-Austausch die Aktivität bestimmter Proteine regulieren. In dieser Arbeit werden die strukturellen und Umgebungsfaktoren, die diese Reaktion beeinflussen, diskutiert. Aufgrund ihrer Recheneffizienz hat sich die Density-Functional based Tight-binding (DFTB) Methode als beliebte und zuverlässige quantenmechanische Methode für Anwendungen in kondensierter Phase positioniert. Mit DFTB ist es möglich die freie Energiefläche komplexer Reaktionen zu erzeugen, da der Phasenraum usreichen abgetastet werden kann. Diese Einsparungen bei den Rechenkosten können jedoch auf Kosten einer geringeren Genauigkeit gehen. Beim Thiol-Disulfid-Austausch zum Beispiel weisen die Übergangszustände eine fehlerhate Struktur und Energie auf. Die Literaturrecherche zeigt, dass für eine korrekte Beschreibung dieser Reaktion sehr genaue ab initio Methoden verwendet werden müssen. Daher bestand die Motivation dieser Arbeit darin, die DFTB-Fehler mit einem maschinellen Lernansatz zu korrigieren. Um dies zu erreichen, haben wir ein neuronales Netzwerk vom Typ Behler-Parrinello verwendet, das die Energiewertdifferenzen zwischen der ab initio und DFTB Methode füreine gegebene Molekülstruktur erlernt. Die maschinell erlernte Energiekorrektur wurde dann in die DFTB+ Software implementiert. Mit diesem neuen Ansatz konnten wir hybride Quantum Mechanics/Molecular Mechanics (QM/MM)-Simulationen des Thiol-Disulfid-Austauschs mit Coupled Cluster und B3LYP-Genauigkeit mit einem Rechenaufwand durchführen, der mit DFTB vergleichbar ist. Dieser Korrekturalgorithmus ist auch in einer Pipeline mit grafischer Schnittstelle implementiert, die dem Benutzer hilft, Trainingsdaten zu generieren und zu arrangieren sowie das maschinelle Lernmodell in DFTB+ zu exportieren, um es in QM/MM-Simulationen weiter zu verwenden. Die Einführung dieser Pipeline soll die Anwendungsmöglichkeiten des Codes für neuronale Netze erweitern, indem das Wissen über Quantenmodellierung gegenüber einem Programmierhintergrund bevorzugt wird. Darüber hinaus stellen wir erste Arbeiten an einem maschinell erlernten Kraftfeld zur Beschreibung der Disulfid-Austauschreaktion unter Verwendung von Coupled Cluster-Referenzdaten vor

Semiempirical vs. Ab Initio Calculations of Molecular Properties. Part 3. Electric Field Gradients at 14N Nuclei in some Small Molecules

Electric field gradients (EFG) at nitrogen nuclei in some small and medium size molecules are calculated by the semiempirical CND0/2D and SCC-MO methods. A salient feature of our procedure is accurate evaluation of matrix elements ot the EFG operator. Hence, comparison of EFG values with the results or more sophisticated ab initio procedures obtained by suitable basis sets indicates flaws and shortcomings of the semiempirical schemes