Efficient Elimination of the Basis Set Superposition Error

The basis set superposition error (BSSE) is one of the major obstacle occuring in quantum chemical calculations which aim at a accurately prediction of interaction energies. The importance of a BSSE elimination procedure is among other things manifasted by the fact, that the magnitude of the BSSE can be as large as the interaction energy itself, affecting the accuracy of the calculated interaction energies therefore significantly. In this work new approaches to eliminate the BSSE efficiently from wavefunction based quantum chemical calculations on large molecular clusters are presented. The applicability of these schemes is studied in great detail among others on a water cluster series ranging in size from a water dimer up to even a (H2O)20 water cluster. An overview of the correction schemes known from the literature is also given and the newly developed schemes are compared with the literature ones. The presented schemes allow to account with only small loss in accuracy very efficiently for BSSE corrected interaction energies, which are partly no more feasible to calculate with standard methods due to the large system size

Explicit influence of water microsolvation on charge transfer and dynamics in ground and excited electronic states of molecular systems

Modern computational molecular quantum chemical studies, such as the present one, typically employ a wide range of theoretical techniques. The latter are often rather complicated and one should not generally expect that an experimental scientist in the area of physical chemistry, a potential reader of this work, should be familiar with all these techniques. To simplify the reading of the Thesis and to make it self-sufficient, it is supplied with an overview of the employed theoretical methodologies (Chapter 1). The overview explains basic quantum-chemical terminology referred to throughout the Thesis, introduces theoretical foundations of the methods and outlines their properties and limitations. In Part 1.1 of Chapter 1, methods for the solution of the molecular Schrödinger equation are introduced, while in the subsequent Parts 1.2 and 1.3 methods for the solution of the electronic Schrödinger equation are presented to find the ground and excited states, respectively. Part 1.4 is dedicated to basis-set effects which are omnipresent in electronic-structure calculations. It contains a number of unusual insights and concepts proposed by the author and, thus, may be insightful also to experts in quantum chemistry. In Chapter 2, the phenomenon of acetone-water proton exchange catalyzed by tubular as well as amorphous aggregates of calix[4]hydroquinone (CHQ) macromolecules, which has been observed previously in NMR experiments (Ref. D1D), is investigated by means of correlated quantum-chemical methods. The first part of the study (Section 2.3-2.7) considers concerted proton transfer, assisted by several initially neutral OH-groups in the hydrogen-bonded networks of CHQ aggregates. The second part of the study (Section 2.8-2.13) is dedicated to a second mechanism of proton exchange: step-wise proton transfer via formation of ionic intermediates resulting from CHQ pre-dissociation. CHQ application-specific as well as general conclusions, relevant to the main topic of the Thesis (i.e. influence of specific microsolvation on the considered proton transfer processes), are presented in Section 2.14. The phenomenon of dual fluorescence observed in clusters of methyl 4-N,N-dimethylaminobenzoate ester (DMABME) and two water molecules in the gas phase, is studied in Chapter 3. Experimentally, the dual fluorescence was detected in experiments combining optical and ground-state ion-depletion infrared spectroscopies in ultracold molecular beams (Ref. D2D). In Section 3.3, calculated ground-state infrared spectra are presented that allow to identify the structures of those isomers, which are present in the gas-phase, as well as the structure of the isomer responsible for dual fluorescence. To further understand the reaction mechanism of dual fluorescence, excited-state potential energy surfaces of the identified isomers were computed along the relevant twisted intermolecular charge-transfer formation coordinate and the mechanism of energy dissipation in these complexes was investigated (Section 3.4-3.5) (Ref. D3D). A brief summary of the main results of this chapter and conclusions are given in Section 3.6. Finally, in Section 3.7 a complementary benchmark study of the quality of ground-state potential energy surfaces of prototypical hydrogen-bonded systems (ammonia-water and formic acid-water dimers) obtained at the level of BSSE-corrected MP2 combined with moderate basis sets, has been conducted. The quality of potential energy surfaces was tested with respect to basis-set size, level of electron correlation and anharmonicity effects and the applied methodology to identify the IR spectrum of hydrated DMABME complexes (Section 3.3) has been found to be sufficient to uniquely assign the IR spectra.Moderne computergestützte molekulare quantenchemische Studien, wie die vorliegende, verwenden in der Regel ein breites Spektrum theoretischer Methoden. Die letzteren sind oft sehr komplex und man sollte generell nicht erwarten, dass ein praxisorientierter Wissenschaftler im Bereich der physikalischen Chemie – ein potentieller Leser dieser Arbeit – mit all diesen Methoden vertraut sein muß. Um das Lesen dieser Dissertation in einem solchen Fall zu vereinfachen, und sie autark zu machen, ist sie mit einem Überblick über die verwendeten theoretischen Methodologien versehen (Kapitel 1). In diesem Überblick werden quantenchemische Grundbegriffe erläutert, auf die in der gesamten Arbeit immer wieder verwiesen wird, die theoretischen Grundlagen verwendeter Methoden dargelegt und deren Eigenschaften und Beschränkungen skizziert. Im Abschnitt 1.1 werden allgemeine Ansätze zur Lösung der molekularen Schrödingergleichung eingeführt, und in den Teilen 1.2 und 1.3 werden spezifische Ansätze zur Lösung der elektronischen Schrödingergleichung zur Bestimmung des elektronischen Grundzustands und angeregter Zustände präsentiert. Teil 1.4 ist der Beschreibung von Basissatzeffekten, die in Elektronenstrukturrechnungen im Allgemeinen auftreten, gewidmet. Dieser Abschnitt enthält eine Reihe von verschiedenen Einblicken und Konzepten, die im Rahmen dieser Arbeit vorgeschlagen werden, und welche den Experten in der Quantenchemie aufschlußreich sein können. Im Kapitel 2 wird das Phänomen der Katalyse von Aceton-Wasser Protonenaustausch durch selbstaggregierende Calix[4]hydrochinon (CHQ)-Nanotubes sowie durch amorphe Aggregate von CHQ, welche in NMR-Versuchen (Ref. X1X) beobachtet wurde, mit Hilfe von modernen quantenchemischen Methoden untersucht. Der erste Teil dieser Studie (Abschnitt 2.3-2.7) betrachtet den konzertierten Protonentransfer, unterstützt von mehreren ursprünglich neutralen OH-Gruppen innerhalb der wasserstoffgebundenen Netzwerke der CHQ-Aggregate. Der zweite Teil der Studie (Abschnitt 2.8-2.13) ist dem dem schrittweisen Protonentransfer mittels Bildung von ionischen Zwischenprodukten infolge der CHQ- Prädissoziation gewidmet. CHQ-anwendungsspezifische Schlußfolgerungen, sowie allgemeine Aspekte, die für das Hauptthema dieser Dissertation relevant sind (i.e. Einfluß spezifischer Mikrosolvatation auf die betrachteten Protonentransferprozesse), werden im Abschnitt 2.1.4 zusammengefasst. Das Phänomen der dualen Fluoreszenz, das in Komplexen von 4-N,N-Dimethylaminobenzoesäuremethylester (DMABME) und zwei Wassermolekülen in der Gasphase beobachtet wurde, wird im Kapitel 3 untersucht. Im Abschnitt 3.3 werden zunächst berechnete Grundzustandsinfrarotspektren verschiedener DMABME*2H2O Isomere präsentiert, die zum einen die Identifikation aller in der Gasphase vorliegenden Isomeren erlauben, und zum anderen vor allem die Charakterisierung des für das Auftreten der dualen Fluoreszenz verantwortlichen Isomer ermöglichen. Um weiter den Reaktionsmechanismus der dualen Fluoreszenz zu verstehen, wurden die Potentialenergieflächen der relevanten Isomere im angeregten Zustand entlang der sogenannten TICT-Koordinate (TICT: engl. twisted intramolecular charge transfer) berechnet und der Mechanismus der Energierelaxation dieser Komplexe erforscht (Abschnitt 3.4-3.5) (Ref. X3X). Eine kurze Zusammenfassung der wichtigsten Ergebnisse dieses Kapitels und die wichtigsten Schlußfolgerungen finden sich in Abschnitt 3.6. Zum Abschluß wird im Abschnitt 3.7 eine Vergleichsstudie der Qualität der Potentialenergieflächen von prototypischen wasserstoffgebundenen Systemen im elektronischen Grundzustand (Ammoniak-Wasser und Ameisensäure-Wasser) zusammengefasst, in der die Qualität der Potentialenergieflächen hinsichtlich des verwendeten atomaren Basissatzes, der Behandlung der Elektronenkorrelation und der Anharmonizität der Potentialflächen getestet werden. Vor allem wurde festgestellt, dass die zum Studium der IR-Spektren der hydratisierten DMABME-Komplexe verwendete Methode hinreichend genau ist, um die einzelnen Isomere zu unterscheiden und die experimentellen Spektren eindeutig zuzuordnen (Abschnitt 3.3)

Accurate Computation Of Molecular Properties From Novel Applications Of Quantum Mechanical Wavefunction Methods

High-accuracy quantum mechanical (qm) wavefunction methods have been applied to compute molecular properties of weakly-bound clusters. This work focuses on both extending the applicability of robust theoretical methods to larger systems and also determining the inherent accuracy of ab initio methods when compared to experimentally measured properties. Described here is the development of an efficient many-body approach that offers the ability to reduce both the time and the computational resources normally required to compute these properties reliably. The n-body:many-body qm:qm technique has been extended to compute harmonic vibrational frequencies of clusters. Applying this methodology to small hydrogen-bonded clusters demonstrates that this approach yields both optimized geometries and harmonic vibrational frequencies in excellent agreement with the gold standard of correlated wavefunction methods, the ccsd(t) method, but with much greater efficiency. In addition, this work includes careful calibration studies to examine the basis set convergence of harmonic frequencies to determine which basis sets can be employed to obtain ab initio frequencies lying near the complete basis set (cbs) limit. These benchmark values are used to calibrate more efficient methods including ab initio methods, various density functional approximations and water potentials. Lastly, anharmonic vibrational frequencies and dissociation energies have been computed for small hydrogen-bonded dimers, allowing for a direct comparison to experiment

Nekovalentní interakce v základních biologických procesech

Charles University in Prague Faculty of Science Department of Physical and Macromolecular Chemistry Non-covalent interactions in fundamental biological processes Doctoral Thesis Abstract Mgr. Vojtěch Klusák Supervisor: Mgr. Lubomír Rulíšek, CSc. Institute of Organic Chemistry and Biochemistry AS CR Center for Biomolecules and Complex Molecular Systems Praha 2010 2 3 Universita Karlova v Praze Přírodovědecká fakulta Katedra fyzikální a makromolekulární chemie Nekovalentní interakce v základních biologických procesech Souhrn disertační práce Mgr. Vojtěch Klusák Školitel: Mgr. Lubomír Rulíšek, CSc. Ústav organické chemie a biochemie AV ČR Centrum biomolekul a komplexních molekulárních systémů Praha 2010 4 5 Introduction Understanding inter- and intra-molecular interactions is the key for our insight into the properties of the biomolecular systems which, in turn, maintain and govern virtually all the processes in biology. Attempts to draw the structure-function relationship at the atomistic or electronic level bring us quite often beyond experimental resolution and capabilities. Modern tools of computational chemistry enable us to focus with satisfactory degree of reliability on the details of the studied process, gather additional (often complementary) information and ascribe particular structural features to...Charles University in Prague Faculty of Science Department of Physical and Macromolecular Chemistry Non-covalent interactions in fundamental biological processes Doctoral Thesis Abstract Mgr. Vojtěch Klusák Supervisor: Mgr. Lubomír Rulíšek, CSc. Institute of Organic Chemistry and Biochemistry AS CR Center for Biomolecules and Complex Molecular Systems Praha 2010 10 Úvod Klíčem k pochopení vlastností a chování biomolekul je porozumění jejich vzájemným interakcím, ať už jde o interakce mezi nimi jako celky či mezi jejich jednotlivými částmi, (např. funkčními skupinami) .Snaha o pochopení vztahu mezi strukturou a funkcí na úrovni atomů či elektronů nás často dovádí za hranice možností či rozlišení experimentálních metod. Moderní nástroje výpočetní chemie nám však často s dostatečnou mírou přesnosti a spolehlivosti umožňují popsat tyto detaily studovaných procesů a doplnit tak naše znalosti a přiřadit k měřitelným veličinám určité strukturní vlastnosti. Za normálních podmínek, za kterých se biomolekuly při buněčných procesech přeskupují a seskupují (například při sbalování proteinů, formování a přeskupování membrán, při buněčné signalizaci) nedochází ke vzniku a zániku kovalentních vazeb. Takovéto procesy jsou z velké míry řízeny nekovalentními interakcemi. Tyto interakce jsou sice poměrně slabé, jejich celkový...Department of Physical and Macromolecular ChemistryKatedra fyzikální a makromol. chemieFaculty of SciencePřírodovědecká fakult

GAS PHASE ION/MOLECULE REACTIONS BETWEEN MONOCATIONIC METAL-BIPYRIDYL (METAL = CU, AG, AU) COMPLEXES AND SMALL GAS MOLECULES USING ION TRAP MASS SPECTROMETER

Ion/molecule reactions happens in the very diluted low-pressure environment provided by mass spectrometer. Studying ion/molecule reactions in gas phase may reveal novel chemistries of the pertinent reactants and products. The convenience of isolating target reactant ions with multistage MS in the gas phase eliminates the involvement of solvent or counterions which could add unnecessary complexity for interpreting novel chemistry. A lot of research has been applied to the metal-bipyridine system in the solution phase, but not too much research reported in the gas phase.In this work, the study of metal-bipyridine system has been extended to the gas phase with aid of Mass Spectrometer. Monocationic metal-bipyridyl [M-bpy]+ complexes (Metal = Cu, Ag, Au) were produced in the gas phase with electrospray coupled with MS/MS, reactions with water gas and nitrogen gas were performed inside the Linear Quadrupole Ion Trap, and the full reaction process was detected by Mass Spectrometer synchronously. Product peaks for water adduct ([H2OM-bpy]+) and nitrogen adduct ([N2M-bpy]+) are observed on the mass spectrum. Kinetic study shows the gas phase reaction follows pseudo-first order with respect to [M-bpy]+ for Cu and Au. The attributes of products were further investigated with Density Functional Theory (DFT) at PBE0/cc-pVTZ/cc-pVTZ-PP level, including the geometry optimization and IR prediction. Thermo stability was calculated for the dissociation process. For a given gas, gold complex has the highest binding ability followed by copper and silver complexes. For the dissociation process from the respective bound complexes, they are all indicated as endothermic processes under vacuum and at room temperature. The metal complexes are also found to act as mild bond activation reagents for small gas molecules, with gold complex being the best candidate for O-H activation of water and copper complex being the best for nitrogen bond activation of N2. Compared with the bond length in free gases, the bond lengths of O-H and N≡N get elongated in the complexes with the optimized structures. In addition, the IR spectra predict a major red-shift in correspond to the stretch frequency of O-H and N≡N in the complexes. Ligands effects are also predicted with calculations, and the results show that phenanthroline perform similar ability binding with water and nitrogen gas molecules as bipyridine

An alternative methodology to assess the quality of empirical potentials for small gold clusters

We present a methodology based on local comparisons of potential energy surfaces (PES) in order to assess the quality of empirical potentials. We compare five typical empirical potentials using a criterion that shows which of these potentials resembles better a PES obtained with a high-level electronic structure method. The methodology relies on a many-body expansion in terms of normal coordinates of both the empirical and high-level theory PES. Then we investigate in a systematical way, how the features of the reference high-level theory PES are reproduced by each empirical potential in the vicinity of a given minimum energy structure. We use plane-wave density functional theory (DFT) as a reference, in particular the Perdew–Burke–Ernzerhof (PBE) exchange–correlation functional and an ultrasoft Vanderbilt pseudo potential. This study is carried out on neutral gold clusters with up to five atoms

Computational simulation of the excited states dynamics of azobenzene in solution

Azobenzene and its derivatives are molecules very often used to construct photomodulable materials and molecular devices. The main characteristic of this kind of molecules is the efficient and reversible trans → cis photoisomerization, that occurs in either sense, without secondary processes. Using the appropriate wavelength, one can convert either isomer into the other one. The photoisomerization mechanism of azobenzene has been debated, during the last decades, because of the peculiar wavelength dependence of the quantum yields and because at least two standard possibilities exist: N=N double bond torsion and N inversion. Our research group has performed simulations of the photodynamics of azobenzene molecule by mixed quantum-classical methods. Such simulations have been successful in explaining the dependence of the quantum yield on the excitation wavelength. However, these simulations have been conducted on the isolated azobenzene molecule, while almost all the experimental data have been obtained in condensed phase. In particular, Diau's group, from Taiwan, has shown a strong dependence of the excited states dynamics on the solvent viscosity. The general aim of this work is to study the excited state dynamics of azobenzene in solution, in order to obtain its transient spectra and to produce data directly comparable with the experiments. In particular, we have studied the quantum yields, the isomerization mechanism and the reorientation of the transition dipole moment during the excited state relaxation, in order to understand the time resolved fluorescence anisotropy measurements obtained by Diau and collaborators. This research will also permit to study the reorientation of the whole molecule, which leads to alignment of an azobenzene sample in a polarized laser field. A basic issue for the interpretation of the fluorescence anisotropy and of the orientation of azobenzene samples in polarized light is related with the direction of the transition dipole vector for the forbidden n-π* transition of trans-azobenzene. Therefore, we have carried out a preliminary ab initio study of the n-π* transition dipole moment, considering the vibrational motions that contribute to the oscillator strength, and focusing on the most effective ones, i.e. those of lowest frequency. The most effective coordinate in promoting this transition is the symmetric torsion of the phenyl groups. Other important coordinates are the antisymmetric phenyl torsion and the torsion of the N=N double bond. The transition dipole vector turns out to lie essentially in the molecular plane, almost parallel to the N-C bonds and to the longest axis of the molecule. Semiempirical calculations are in sufficiently good agreement with those obtained by ab initio methods. The main part of the thesis work has been devoted to the simulation of the dynamics of the photoisomerization process of azobenzene in solution. We have made use of a mixed quantum-classical method of the surface hopping family. The electronic energies and wavefunctions are computed on the fly, by a semiempirical method modified by our group. A reparameterization of the semiempirical AM1 Hamiltonian has been carried out, considering new ab initio results used as reference values, in order to improve the accuracy of the semiempirical PES. The solvent effects have been introduced in a preliminary way by brownian dynamics, simulating two different solvent viscosities, and then explicitly, with a QM/MM approach. In this approach, the solvent itself is represented by a Molecular Mechanics force-field (OPLS) and the QM/MM interactions are made of electrostatic and Lennard-Jones terms. We have first determined, by ab initio calculations, the solute-solvent interaction potential between azobenzene and two simple molecules, methane and methanol (representatives of non-polar and of protic compounds). In this way we have obtained the necessary QM/MM interaction parameters, and we have run simulations with two solvents used in the experiments, methanol and ethylene glycol (simulations with n-hexane are in progress). We obtain very good results for the dependence of the quantum yields on the solvent viscosity, and in this way we can confirm that the photoisomerization mechanism is dominated by the torsion of the N=N double bond. The simulations also provide the necessary information to compute the time-resolved fluorescence spectra and anisotropy, i.e. for a complete reproduction of the experimental results. We have obtained a good agreement with the measured time-dependent intensities and anisotropies, but our explanation of the mechanism partly differs from that put forward in the experimental work

First-principles calculations of hybrid inorganic–organic interfaces : from state-of-the-art to best practice

This work highlights the challenges and problems when modelling inorganic–organic interfaces and provides practical tips and suggestions for efficient calculations

INVESTIGATION OF HALOGEN BONDING BY EXPERIMENTAL CHARGE DENSITY STUDIES AND THEORETICAL METHODS

In this thesis the results obtained during the three years of doctorate (2015-2018) will be illustrated. Although several different computational and crystallographic techniques have been exploited throughout my research activity, almost all projects were linked by a common thread: halogen bond (XB), a non-covalent interaction the nature of which will be briefly illustrated in the introduction section of the thesis together with a brief description of the state of art of the research on this interaction. Among XB project present in my PhD thesis, it is worth mentioning the presence of an experimental and theoretical charge density study of crystals containing XB interacting molecules, the development of a new method to treat chlorine XB by means of classical force field and a valence bond study of bromine XB. Beside halogen bonding, a brand new method (the X-Ray Constrained Spin-Coupled, XCSC) has been developed in the framework of quantum crystallography