Computational Spectroscopy E-Book

• Herausgeber: Wiley-VCH
• Kategorie: Wissenschaft und neue Technologien
• Sprache: Englisch

Seitenzahl: 804

Veröffentlichungsjahr: 2011

Beschreibung

Unique in its comprehensive coverage of not only theoretical methods but also applications in computational spectroscopy, this ready reference and handbook compiles the developments made over the last few years, from single molecule studies to the simulation of clusters and the solid state, from organic molecules to complex inorganic systems and from basic research to commercial applications in the area of environment relevance.
In so doing, it covers a multitude of apparatus-driven technologies, starting with the common and traditional spectroscopic methods, more recent developments (THz), as well as rather unusual methodologies and systems, such as the prediction of parity violation, rare gas HI complexes or theoretical spectroscopy of the transition state.
With its summarized results of so many different disciplines, this timely book will be of interest to newcomers to this hot topic while equally informing experts about developments in neighboring fields.

Leseprobe

Contents

Preface

List of Contributors

1 Concepts in Computational Spectrometry: the Quantum and ChemistryJ.F. Ogilvie

1.1 Introduction

1.2 Quantum Laws, or the Laws of Discreteness

1.3 Quantum Theories of a Harmonic Oscillator

1.4 Diatomic Molecule as Anharmonic Oscillator

1.5 Quantum Mechanics and Molecular Structure

1.6 Conclusions

2 Computational NMR SpectroscopyIbon Alkorta and Jose Elguero

2.1 Introduction

2.2 NMR Properties

2.3 Chemical Shifts

2.4 NICS and Aromaticity

2.5 Spin-Spin Coupling Constants

2.6 Solvent Effects

2.7 Conclusions

2.8 The Problem of the Error in Theoretical Calculations of Chemical Shifts and Coupling Constants

3 Calculation of Magnetic Tensors and EPR Spectra for Free Radicals in Different EnvironmentsPaola Cimino, Frank Neese, and Vincenco Barone

3.1 Introduction

3.2 The General Model

3.3 Spin Hamiltonian, g-Tensor, Hyperfine Coupling Constants, and Zero-Field Splitting

3.4 Stereoelectronic, Environmental, and Dynamical Effects

3.5 Line Shapes

3.6 Concluding Remarks

4 Generalization of the Badger Rule Based on the Use of Adiabatic Vibrational ModesElf Kraka, John Andreas Larsson, and Dieter Cremer

4.1 Introduction

4.2 Applicability of Badger-Type Relationships in the Case of Diatomic Molecules

4.3 Dissection of a Polyatomic Molecule into a Collection of Quasi-Diatomic Molecules: Local Vibrational Modes

4.4 Local Mode Properties Obtained from Experiment

4.5 Badger-type Relationships for Polyatomic Molecules

4.6 Conclusions

5 The Simulation of UV-Vis Spectroscopy with Computational MethodsBenedetto Mennucci

5.1 Introduction

5.2 Quantum Mechanical Methods

5.3 Modeling Solvent Effects

5.4 Toward the Simulation of UV-Vis Spectra

5.5 Some Numerical Examples

5.6 Conclusions and Perspectives

6 Nonadiabatic Calculation of Dipole MomentsFrancisco M. Fernandez and Julian Echave

6.1 Introduction

6.2 The Molecular Hamiltonian

6.3 Symmetry

6.4 The Hellmann-Feynman Theorem

6.5 The Born-Oppenheimer Approximation

6.6 Interaction between a Molecule and an External Field

6.7 Experimental Measurements of Dipole Moments

6.8 The Born-Oppenheimer Calculations of Dipole Moments

6.9 Nonadiabatic Calculations of Dipole Moments

6.10 Molecule-Fixed Coordinate System

6.11 Perturbation Theory for the Stark Shift

6.12 Conclusions

7 The Search for Parity Violation in Chiral MoleculesPeter Schwerdtfeger

7.1 Introduction

7.2 Experimental Attempts

7.3 Theoretical Predictions

7.4 Conclusions

8 Vibrational Circular Dichroism: Time-Domain ApproachesHanju Rhee, Seongeun Yang, and Minhaeng Cho

8.1 Introduction

8.2 Time-Correlation Function Theory

8.3 Direct Time-Domain Calculation with QM/MM MD Simulation Methods

8.4 Direct Time-Domain Measurement of VOA Free Induction Decay Field

8.5 Summary and a Few Concluding Remarks

9 Electronic Circular DichroismLorenzo Di Bari and Cennaro Pescitelli

9.1 Introduction

9.2 Molecular Anatomy

9.3 Conformational Manifolds and Molecular Structure

9.4 Hybrid Approaches

9.5 The QM Approach

9.6 Conclusions and Perspectives

10 Computational Dielectric Spectroscopy of Charged, Dipolar SystemsChristian Schroder and Othmar Steinhauser

10.1 Methods

10.2 Applications and Experiments

10.3 Summary and Outlook

11 Computational Spectroscopy in Environmental ChemistryJames D. Kubicki and Karl T. Mueller

11.1 Introduction

11.2 Methods

11.3 Examples

11.4 Summary and Future

12 Comparison of Calculated and Observed Vibrational Frequencies of New Molecules from an Experimental PerspectiveLester Andrews

12.1 Introduction

12.2 Experimental and Theoretical Methods

12.3 Aluminum and Hydrogen: First Preparation of Dibridged Dialane, A12H6

12.4 Titanium and Boron Trifluoride Give the Borylene FB=TiF2

12.5 Ti and CH3F Form the Agostic Methylidene Product CH2=TiHF

12.6 Zr and CH4 Form the Agostic Methylidene Product CH2=ZrH2

12.7 Mo and CHCl3 Form the Methylidyne CH≡MOCl3

12.8 Tungsten and Hydrogen Produce the WH4(H2)4 Supercomplex

12.9 Pt and CCl4 Form the Carbene CCl2=PtCl2

12.10 Th and CH4 Yield the Agostic Methylidene Product CH2=ThH2

12.11 U and CHF3 Produce the Methylidyne CH≡UF3

13 Astronomical Molecular SpectroscopyTimothy W. Schmidt

13.1 The Giants’ Shoulders

13.2 The First Spectroscopists and Seeds of Quantum Theory

13.3 Small Molecules

13.4 The Diffuse Interstellar Bands

13.5 The Red Rectangle, HD44179

13.6 The Aromatic Infrared Bands

13.7 The Holy Grail

Index

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The Editor

Dr.Jörg GrunenbergTU BraunschweigInstitut fur Organische ChemieHagenring 3038106 BraunschweigGermany

All books published by Wiley-VCH are carefully produced. Nevertheless, authors, editors, and publisher do not warrant the information contained in these books, including this book, to be free of errors. Readers are advised to keep in mind that statements, data, illustrations, procedural details or other items may inadvertently be inaccurate.

Library of Congress Card No.: applied for

British Library Cataloguing-in-Publication DataA catalogue record for this book is available from the British Library.

Bibliographic information published by the Deutsche NationalbibliothekThe Deutsche Nationalbibliothek lists this publication in the Deutsche Nationalbibliografie; detailed bibliographic data are available on the Internet at http://dnb.d-nb.de.

© 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Boschstrae 12, 69469 Weinheim

All rights reserved (including those of translation into other languages). No part of this book may be reproduced in any form – by photoprinting, microfilm, or any other means – nor transmitted or translated into a machine language without written permission from the publishers. Registered names, trademarks, etc. used in this book, even when not specifically marked as such, are not to be considered unprotected by law.

ISBN: 978-3-527-32649-5

Preface

... with its help, debates can be resolved forever, if they can be settled on the basis of some data; and if one took the pen it would be enough for the two disputing men to say to one another: Let’s calculate.

Leibniz in a letter to P. J. Spener, 1687

Computational chemistry has reached a high degree of maturity and comprehension making it one of the vivid research areas in modern chemical and physical research in general. This is true because an accurate simulation of spectroscopic properties is one of the major challenges and – at the same time – a precious benefit of modern theoretical chemistry. Predictions concerning single molecules, molecular clusters, or even the solid state in combination with detailed information from apparatus-based experiments are therefore providing ingredients to an auspicious revolution in the borderland between theory and experiment: computational spectroscopy. At first sight, the term seems to contradict itself: from the traditional point of view, spectroscopy (or spectrometry) belongs to the realm of the experimentalists, while computational chemistry is allocated to the domain of theory. The frantic developments in both areas during the last years have nevertheless helped build new bridges between both worlds.

This is important because until the end of the last millennium theoretical and experimental chemistry were separated by respectable gaps. Studying chemistry in the 1990s was yet sometimes accompanied by dialectical training: equipped with the sanguine knowledge that molecular orbitals are artifacts (learned from an exciting theoretical chemistry course), one stumbled into an organic chemistry exam being forced to explain the formation of a covalent bond in terms of those very orbitals. Those days are history now for several – in part ambivalent – reasons. The main cause nevertheless is a simple one: modern computational chemistry deals with observable properties and this positivistic shift does not leave too much room for “overinterpretations.” One can always try to find an experiment, which allows either falsification or confirmation of the computer simulation. This is in sharp contrast to the second major application area of computational chemistry: the underpinning of chemical concepts. Led by Coulson’s famous request, “... give us insights, not numbers ...,” more and more chemical perceptions as well as new molecular categories were introduced. It is, however, still unclear whether the addition of those ad hoc concepts is always helpful in characterizing the huge variety of chemical phenomena. On the contrary, many of these early chemical concepts resembled Leibniz’s voces metaphysicae, that means phrases, which we use believing that we understand entities just by pinning names on them. Or, to quote Wolfgang Pauli, many of the earlier concepts deduced from approximate quantum chemistry were so fuzzy that they were not even wrong.

In order to keep pace with new developments in terms of more rigorous solutions for Schrödinger equation, we anyhow may not demand that ideas from the early days of numerical theoretical chemistry persist permanently. The decade-long debate and struggle for a unique definition of aromaticity is only one of the many examples of those fruitless endeavors. The (in part humoristic) suggestion by Heilbronner as early as 1971 at the famous Jerusalem symposium on “Aromaticity, Pseudo-Aroma- ticity, Anti-Aromaticity” to introduce the term “schizo-aromaticity” for molecules, which are aromatic by one definition and nonaromatic by another, illuminates this dilemma quite graphically.

The situation changed dramatically during the last 20 years. Reliable first-principle electronic structure calculations on the one hand and sophisticated molecular dynamic simulations for complex systems on the other hand are nowadays well-established instruments in the toolbox of theoretical chemists, and these rapid developments are paving the way for the study of increasingly large and chemically complex systems. At the same time, experimental molecular spectroscopy is also an extremely active and fast-developing field, which is evolving toward the possibility of performing precise measurements for single molecules and, even more intriguing, for the hub of chemistry itself, the individual covalent bond. The title of this book Computational Spectroscopy states its aim: From basic research to commercial applications in the area of environment relevance, we will compile the major developments during the past 5–10 years. A multitude of apparatus-driven technologies will be covered. Nevertheless, the selection of topics is of course a subjective one. Summarizing the results of so many different disciplines, I hope that this book will on the one hand attract the attention of newcomers and on the other hand inform the experts about developments in scientific areas adjacent to their own expertise.

At Wiley, I would especially like to thank Dr. Elke Maase and Dr. Martin Graf for their guidance through all phases (from the first concept of the book to the final cover design) of this challenging and fascinating project.

July 2010 Jörg Grunenberg

List of Contributors

Ibon Alkorta

Instituto de Química Médica CSIC Juan de la Cierva 3 E-28006 Madrid Spain

Lester Andrews

University of Virginia Department of Chemistry Charlottesville VA 22904-4319 USA

Lorenzo Di Bari

Università degli Studi di Pisa Dipartimento di Chimica e Chimica Industriale Via Risorgimento 35 I-56516 Pisa Italy

Vincenco Barone

Scuola Normale Superiore Piazza dei Cavalieri 7 56126 Pisa Italy

Minhaeng Cho

Korea University Department of Chemistry and Center for Multidimensional Spectroscopy 5-1 Anam-dong Songbuk-ku Seoul 136-701 Korea

and

Korea Basic Science Institute Multidimensional Spectroscopy Laboratory Seoul 136-713 Korea

Paola Cimino

University of Salerno Department of Pharmaceutical Science Via Ponte don Melillo 84084 Fisciano Italy

Dieter Cremer

Southern Methodist University Department of Chemistry 3215 Daniel Ave Dallas TX 75275-0314 USA

Julián Echave

INIFTA (UNLP, CCTLa Plata-CONICET) Diag. 113 y 64 (S/N) Sucursal 4 Casilla de Correo 16 1900 La Plata Argentina

José Elguero

Instituto de Química Médica CSIC Juan de la Cierva 3, E-28006 Madrid Spain

Francisco M. Fernández

INIFTA (UNLP CCTLa Plata-CONICET) Diag. 113 y 64 (S/N) Sucursal 4 Casilla de Correo 16 1900 La Plata Argentina

Elfi Kraka

Southern Methodist University Department of Chemistry 3215 Daniel Ave Dallas TX 75275-0314 USA

James D. Kubicki

The Pennsylvania State University Department of Geosciences University Park PA 16802 USA

J. Andreas Larsson

Southern Methodist University Department of Chemistry 3215 Daniel Ave Dallas TX 75275-0314 USA

Benedetta MennucciUniversity of Pisa Department of Chemistry Via Risorgimento 35 56126 Pisa Italy

Karl T. Mueller

The Pennsylvania State University Department of Chemistry University Park PA 16802 USA

Frank Neese

University of Bonn Institute for Physical and Theoretical Chemistry 53115 Bonn Germany

J.F. Ogilvie

Universidad de Costa Rica Ciudad Universitaria Rodrigo Facio Escuela de Quimica San Pedro de Montes de Oca San Jose 2060 Costa Rica

and

Simon Fraser University Centre for Experimental and Constructive Mathematics Department of Mathematics 8888 University Drive Burnaby British Columbia V5A 1S6 Canada

Gennaro Pescitelli

Università degli Studi di Pisa Dipartimento di Chimica e Chimica Industriale Via Risorgimento 35 I-56516 Pisa Italy

Hanju Rhee

Korea University Department of Chemistry and Center for Multidimensional Spectroscopy 5-1 Anam-dong Songbuk-ku Seoul 136-701 Korea

Timothy W. Schmidt

University of Sydney School of Chemistry NSW 2006 Australia

Christian Schröder

University of Vienna Department of Computational Biological Chemistry Währinger Str. 17 1090 Vienna Austria

Peter Schwerdtfeger

Massey University New Zealand Institute for Advanced Study Centre for Theoretical Chemistry and Physics Auckland Campus Private Bag 102904 North Shore City 0745 Auckland New Zealand

Othmar Steinhauser

University of Vienna Department of Computational Biological Chemistry Währinger Str. 17 1090 Vienna Austria

Seongeun Yang

Korea University Department of Chemistry and Center for Multidimensional Spectroscopy 5-1 Anam-dong Songbuk-ku Seoul 136-701 Korea

Concepts in Computational Spectrometry: the Quantum and Chemistry

J. F. Ogilvie

1.1Introduction

During the nineteenth century and most of the first half of the twentieth century, after Dalton’s recognition of the atomic nature of chemical matter, which is everything tangible, that matter was regarded by most chemists as a material. Even though chemists, following Couper, Kekule, van’t Hoff, and others, drew structural formulae in terms of atoms connected by bonds represented as lines, chemical samples were generally regarded as materials or “stuff”. When, after 1955, molecular spectra, particularly of organic compounds, began to be recorded routinely in the mid-infrared region and with nuclear magnetic resonance, the outlook of chemists shifted from macroscopic properties, such as density, melting point, and refractive index, to purportedly molecular properties, such as the effect of adjacent moieties on the characteristic infrared absorption associated with a carbonyl group or on the chemical shift of a proton. The first “quantum-chemical” calculations, on H2+ by Burrau and on H2 by Heitler and London, all physicists, had as subjects chemical species remote from common laboratory experience, but Pauling’s brilliant insight and evangelical manner stimulated great qualitative interest in a theoretical interpretation of chemical properties, even though a large gap existed between the primitive calculations on methane and other prototypical molecules and molecules of substances of practical interest. This gap was bridged largely through the efforts of Pople and his collaborators during the second half of the twentieth century in developing computer programs that enabled efficient calculation of observable molecular properties; not coincidentally, Pople was also an early exponent of the application of nuclear-magnetic-resonance spectra in the publication in 1959 of an authoritative monograph [1] that was seminally influential in the general application of this spectral method [2].

Chemists concerned with quantitative analysis have always understood the distinction between spectroscopy and spectrometry: spectroscopy implies the use of a human eye as a visual detector with a dispersive optical instrument and hence necessarily qualitative and imprecise observations, whereas spectrometry pertains to an instrument with an electrical detector amenable to quantitative measurement of both frequency and intensity. For spectra throughout the entire accessible range of frequencies from 106 Hz, characteristic of nuclear quadrupole or nuclear magnetic resonance, to radiation in the X-ray region sufficiently energetic to cause ionization, a significant use of the numerical results of computations based nominally on quantum mechanics, such as of molecular electronic structure and properties, is to assist that spectral analysis. Pople’s programs were based, to an increasing extent over the years, on selected quantum-mechanical principles that arose from quantum theories. During the past century, the practice of chemistry has thus evolved much, from being a largely empirical science essentially involving operations in a laboratory and their discussion, to having – allegedly – an underpinning based on quantum theories.

During the nineteenth century, a standard paradigm for most chemical operations was that both matter and energy are continuous; following a philosophical point of view of Greek savants and concrete ideas of Bacon and Newton, Dalton’s contention that matter is particulate provided a basis to explain chemical composition, but Ostwald remained skeptical of the existence of atoms until 1909 [3]. The essence of the quantum concept is that both energy and matter ultimately comprise small packets, or chunks, not further divisible retaining the same properties. In Latin, quantum means how much?. A descriptor more enlightening than quantum is discrete, so we refer to the ultimate prospective discreteness of matter and energy. (In a mathematical context, integers take discrete values, even though they number uncountably, and have a constant unit increment, whereas real numbers 1.1, 1.11, 1.111,... vary continuously, with an increment between adjacent representatives as small as desired.) One accordingly distinguishes between the laws of discreteness, based on experiment, and various theories that have been devised to encompass or to reproduce those discrete properties. The distinctions between physical laws and theories or mathematical treatments are poorly appreciated by chemists; our objective is thus to clarify the nature of both quantum laws and quantum theories, thereby to propose an improved understanding of the purported mathematical and physical basis of chemistry and the application of computational spectrometry. After distinguishing between quantum laws and quantum theories, we apply to a prototypical problem three distinct quantum-mechanical methods that nevertheless conform to the fundamental postulate of quantum mechanics; we then consider molecular structure in relation to quantum-mechanical principles and their implications for the practice of chemistry aided by computational spectrometry.

For many chemists, the problem so called the particle in a box is the only purportedly quantum-mechanical calculation that they are ever required to undertake as a manual exercise, but its conventional solution is at least problematic. Any or all treatments of a harmonic oscillator in Section 1.3 serve as a viable alternative to that deficient model. The connection between quantum mechanics and chemistry might be based on a notion that “quantum mechanics governs the behavior of electrons and atoms in molecules,” which is merely supposition. While Dirac and Einstein had, to the ends of their lives, grave misgivings about fundamental aspects of quantum mechanics [4], and even Born was never satisfied with a separate – and thereby inconsistent – treatment of the motions of electrons and atomic nuclei that underpins common quantum-chemical calculations, almost all chemists accept, as recipes, these highly mathematical theories, in a mostly qualitative manner embodied in orbitals – “for fools rush in where angels fear to tread” (Pope). For those chemists who undertake calculations, typically with standard computer programs developed by mathematically knowledgeable specialists who have no qualms about producing more or less efficient coding but who might refrain from questioning the underlying fundamental aspects, the emphasis is placed on the credibility of the results. For the molecular structures of stable species that have been established by essentially experimental methods, although a theoretical component is invariably present, the empirical nature of the computer coding – its parameters are invariably set to reproduce, approximately, various selected properties of selected calibration species – reduces its effect to a sophisticated interpolation scheme; for the molecular structures of such fabulous species as as these are inherently impossible to verify, the results of the calculations merely reinforce preconceived notions of those undertaking such calculations. We trust that reconsideration of the current paradigm in chemistry that abides such questionable content will motivate an improved understanding of the mathematical and physical bases of chemistry and a reorientation of chemistry as an experimental and logical science ofboth molecules and materials. For this purpose, computational spectrometry has a substantial role to play in a fertile production of information about the structure and properties of molecules and materials.