Recent achievements in ab initio modelling of liquid water

The application of newly developed first-principle modeling techniques to liquid water deepens our understanding of the microscopic origins of its unusual macroscopic properties and behaviour. Here, we review two novel ab initio computational methods: second-generation Car-Parrinello molecular dynamics and decomposition analysis based on absolutely localized molecular orbitals. We show that these two methods in combination not only enable ab initio molecular dynamics simulations on previously inaccessible time and length scales, but also provide unprecedented insights into the nature of hydrogen bonding between water molecules. We discuss recent applications of these methods to water clusters and bulk water.Comment: 23 pages, 17 figure

From ab initio quantum chemistry to molecular dynamics: The delicate case of hydrogen bonding in ammonia

The ammonia dimer (NH3)2 has been investigated using high--level ab initio quantum chemistry methods and density functional theory (DFT). The structure and energetics of important isomers is obtained to unprecedented accuracy without resorting to experiment. The global minimum of eclipsed C_s symmetry is characterized by a significantly bent hydrogen bond which deviates from linearity by about 20 degrees. In addition, the so-called cyclic C_{2h} structure is extremely close in energy on an overall flat potential energy surface. It is demonstrated that none of the currently available (GGA, meta--GGA, and hybrid) density functionals satisfactorily describe the structure and relative energies of this nonlinear hydrogen bond. We present a novel density functional, HCTH/407+, designed to describe this sort of hydrogen bond quantitatively on the level of the dimer, contrary to e.g. the widely used BLYP functional. This improved functional is employed in Car-Parrinello ab initio molecular dynamics simulations of liquid ammonia to judge its performance in describing the associated liquid. Both the HCTH/407+ and BLYP functionals describe the properties of the liquid well as judged by analysis of radial distribution functions, hydrogen bonding structure and dynamics, translational diffusion, and orientational relaxation processes. It is demonstrated that the solvation shell of the ammonia molecule in the liquid phase is dominated by steric packing effects and not so much by directional hydrogen bonding interactions. In addition, the propensity of ammonia molecules to form bifurcated and multifurcated hydrogen bonds in the liquid phase is found to be negligibly small.Comment: Journal of Chemical Physics, in press (305335JCP

Halogen Bonding with Phosphine: Evidence for Mulliken Inner Complexes and the Importance of Relaxation Energy

Intermolecular halogen bonding in complexes of phosphine and dihalogens has been theoretically investigated using explicitly correlated coupled cluster methods and symmetry adapted perturbation theory. The complexes H3P· · · ClF, H3P· · · BrF and H3P· · ·IF are demonstrated to possess unusually strong interactions that are accompanied by an increase in the induction component of the interaction energy and significant elongation of the X–Y halogen distance on complex formation. The combination of these factors is indicative of Mulliken inner complexes and criteria for identifying this classification are further developed. The importance of choosing an electronic structure method that describes both dispersion and longer range interactions is demonstrated, along with the need to account for the change in geometry on complexation formation via relaxation energy and overall stabilisation energies

Entrance Channel X-HF (X=Cl, Br, and I) Complexes studied by High-Resolution Infrared Laser Spectroscopy in Helium Nanodroplets

Rotationally resolved infrared spectra are reported for halogen atom - HF free radical complexes formed in helium nanodroplets. An effusive pyrolysis source is used to dope helium droplets with Cl, Br and I atoms, formed by thermal dissociation of Cl$_2$, Br$_2$ and I$_2$. A single hydrogen fluoride molecule is then added to the droplets, resulting in the formation of the X-HF complexes of interest. Analysis of the resulting spectra confirms that the observed species have $^2\Pi_{3/2}$ ground electronic states, consistent with the linear hydrogen bound structures predicted from theory. Stark spectra are also reported for these species, from which the permanent electric dipole moments are determined.Comment: 41 pages, 16 figures, 5 table

Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP

Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identify techniques, the code is designed specifically for non-periodic systems. Application to the small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2-8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a bi-nucleobase CT exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments

Ab initio calculation of intermolecular potentials, prediction of second virial coefficients for dimers H2-H2, H2-O2, F2-F2 and H2-F2, and Monte Carlo simulations of the vapor-liquid equilibria for hydrogen and fluorine

Die reinen Elemente Wasserstoff, Fluor und Sauerstoff sowie die Mischungen Wasser-stoff-Sauerstoff und Wasserstoff-Fluor besitzen zahlreiche industrielle Anwendungen. Wasserstoff koennte ein erneuerbarer Energietraeger bei Brennstoffzellen-Technologien werden und koennte die anderen wichtigen Brennstoffe verdraengen. Daher ist die Berechnung der thermodynamischen Daten der oben genannten Systeme ein wichtiges Anliegen fuer die praktische Anwendung. Diese Arbeit enthaelt die Ergebnisse der Berechnungen der vier Ab-initio-Paarpoten-tiale fuer die Dimere H2-H2, H2-O2, F2-F2 und H2-F2 der daraus abgeleiteten zweiten Virialkoeffizienten einschliesslich der Quantenkorrekturen 1. Ordnung sowie der thermodynamischen Phasengleichgewichtsdaten der Reinstoffe Wasserstoff und Fluor, wobei letztere mit der Gibbs-Ensemble-Monte-Carlo-Methode (GEMC) berechnet wurden. Die neuen intermolekularen Wechselwirkungspotentiale der Dimere H2-H2, H2-O2, F2-F2 und H2-F2 wurden mit quantenmechanischen Methoden berechnet, und zwar mit Hilfe der Coupled-cluster-Theorie CCSD(T) und unter Verwendung korrelations-konsistenter Basissaetze aug-cc-pVmZ (m = 2, 3, 4); die Ergebnisse wurden zum Basissatzlimit extrapoliert (hier mit aug-cc-pV23Z bezeichnet) und bezueglich des ``basis set superposition error" (BSSE) korrigiert. Die so erhaltene Potentialhyperflaeche fuer das H2-H2-Dimer stimmt gut mit der von Diep und Johnson [25] vorgeschlagenen Hyperflaecheueberein. Zum Vergleich wurden auch stoerungstheoretische Rechnungen mit der Moller-Plesset-Theorie zweiter und vierter Ordnung angestellt sowie Rechnungen mit den Basissaetzen 6-31G und 6-311G, aber die Ergebnisse waren schlechter. Fuer die Abschaetzung der Genauigkeiten der theoretischen Methoden und der Basissaetze wurden verschiedene molekulare Parameter berechnet. Die quantenmechanischen Ergebnisse wurden fuer die Erstellung von vier neuen ana-lytischen Paarpotential-Funktionen verwendet. Die anpassbaren Parameter dieser Funktionen wurden durch Anpassung an die Ab-initio - Wechselwirkungsenergien durch eine globale Minimierung der Fehlerquadrate bestimmt, und zwar durch eine Kombination des Levenberg-Marquardt-Verfahrens und eines genetischen Algorithmus. Aus diesen Funktionen wurden die zweiten Virialkoeffizienten von Wasserstoff und Fluor sowie die Kreuz-Virialkoeffizienten der Systeme Wasserstoff-Sauerstoff und Wasserstoff-Fluor durch Integration ermittelt; dabei wurden Quantenkorrekturen beruecksichtigt. Die Ergebnisse stimmen mit experimentellen Daten-soweit vorhan-den-oder mit empirischen Korrelationen ueberein. Monte-Carlo-Simulationen unter Verwendung der Gibbs-Ensemble-Technik (GEMC) wurden eingesetzt, um mit Hilfe der analytischen Paarpotentiale den Dampfdruck von Wasserstoff und Fluor, die Dichten der koexistierenden fluessigen und gasfoermigen Phasen, die Verdampfungsenthalpie und -entropie im Temperaturbereich 18-32 K fuer Wasserstoff und 60-140~K fuer Fluor zu berechnen. Diese Temperaturintervalle reichen nahe an die kritischen Gebiete der Substanzen heran. Aus den berechneten orthobaren Dichten konnten die kritische Temperatur, der kritische Druck und das kritische Molvolumen abgeschaetzt werden. Die Ergebnisse stimmen gut mit experimentellen Daten sowie mit Berechnungen mit Hilfe von Zustandsgleichungen ueberein. Ferner wurden zur Charakterisierung der Strukturen von Wasserstoff und Fluor die Site-site-Paarkorrelationsfunktionen g(r) ermittelt

Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns

The partitioning of the energy in ab initio quantum mechanical calculations into its chemical origins (e.g., electrostatics, exchange-repulsion, polarization, and charge transfer) is a relatively recent development; such concepts of isolating chemically meaningful energy components from the interaction energy have been demonstrated by variational and perturbation based energy decomposition analysis approaches. The variational methods are typically derived from the early energy decomposition analysis of Morokuma [Morokuma, J. Chem. Phys., 1971, 55, 1236], and the perturbation approaches from the popular symmetry-adapted perturbation theory scheme [Jeziorski et al., Methods and Techniques in Computational Chemistry: METECC-94, 1993, ch. 13, p. 79]. Since these early works, many developments have taken place aiming to overcome limitations of the original schemes and provide more chemical significance to the energy components, which are not uniquely defined. In this review, after a brief overview of the origins of these methods we examine the theory behind the currently popular variational and perturbation based methods from the point of view of biochemical applications. We also compare and discuss the chemical relevance of energy components produced by these methods on six test sets that comprise model systems that display interactions typical of biomolecules (such as hydrogen bonding and pi-pi stacking interactions) including various treatments of the dispersion energy

Proton transfer, electron binding and electronegativity in ammonium-containing systems

Using modern electronic structure methods, the ammonia-hydrogen halide complexes and their anions are characterised to determine the number, type, and properties of their minima, and their electron binding energies. Methodological issues of determining the potential energy surfaces of reactive monomers are addressed in the course of this investigation. The energetic origins of the hydrogen-bonded minima are determined by evaluation of the one-body and two-body terms composing the total energy of the complexes, and a rationale for the drive to proton transfer is presented. It is concluded that the systems have qualitatively similar potential surfaces, and that the balance of the one-body and two-body forces determines the number and depth of minima, while the electron acts as a perturbing agent on the one- or two-body energy, depending upon the nature of the minimum encountered. The halogen-bonded structures of ammonia-hydrogen bromide, iodide, and astatide complexes are shown to be stable, and one may perhaps bind an electron. The concept of the ammonium radical as a pseudo-atom is presented and tested. It is found to show competing pseudo-atomic and molecular properties.Engineering and Physical Sciences Research Council (EPSRC

High quality electron densities as a tool in Kohn-Sham theory

In this thesis high quality electron densities are used to provide insight into density functional theory (DFT) and to improve the quality of DFT calculations. Chapter 1 provides an introduction to ab initio molecular wavefunction calculations with particular emphasis on the Hartree-Fock method. Chapter 2 outlines important concepts in density functional theory (DFT). This includes a discussion of the Zhao, Morrison and Parr (ZMP) method, which is the key to calculating DFT quantities from high quality densities. In Chapter 3, high quality densities are used to gain an understanding of dispersion interactions in the helium dimer. The investigation seeks to understand the correlation potentials associated with a density distortion that gives rise to the correct dispersion forces. Chapter 4 presents a study of response properties using orbitals and eigenvalues determined from high quality densities. Both magnetic and electric properties are considered and comparisons are made with conventional DFT functionals and wavefunction methods. Chapter 5 makes a comparison between Kohn-Sham eigenvalues and related properties, generated both by conventional functionals and from densities. The influence on NMR shielding constants is considered and two approaches to correcting LUMO eigenvalues are presented. In chapter 6, a DFT exchange-correlation functional determined from a lit to high quality densities is applied to study the gauche effect in 2-fluoroethylamine, 2-fluoroethanol and their protonated analogues. Conclusions are presented in Chapter 7