E-Book, Englisch, Band Volume 62, 536 Seiten
E-Book, Englisch, Band Volume 62, 536 Seiten
Reihe: Advances in Inorganic Chemistry
ISBN: 978-0-12-380875-2
Verlag: Elsevier Science & Techn.
Format: EPUB
Kopierschutz: 6 - ePub Watermark
Autoren/Hrsg.
Weitere Infos & Material
1;Cover;1
2;Advances in Inorganic Chemistry;2
3;Copyright;5
4;Contents;6
5;List of Contributors;10
6;Preface;12
7;Molecular Mechanics for Transition Metal Centers:From Coordination Complexes to Metalloproteins;14
7.1;I. Introduction;14
7.2;II. Conventional Molecular Mechanics;15
7.3;III. Shortcomings of MM for TM Systems: Angular Potentials;17
7.4;IV. Effects from d Electrons;18
7.5;V. Ligand Field Molecular Mechanics;21
7.6;VI. LFMM Parameterization;23
7.7;VII. Simple Metal, Simple Ligand: Ga(III) Hydroxamates;24
7.8;VIII. Simple Metal, Complex Ligand: Mn(II) Carboxylates;26
7.9;IX. Difficult Metals: Jahn–Teller Effects in Cu(II) and the transInfluence in Pt(II);29
7.10;X. Spin States;33
7.11;XI. Metalloproteins and Molecular Dynamics: Copper Proteins;35
7.12;XII. Bond Energies and Reaction Mechanisms: Water Exchange;41
7.13;XIII. Effects of M-L p Bonding;46
7.14;XIV. Conclusions;49
7.15;Summary;50
7.16;References;50
8;Calculation of Magnetic Circular Dichroism SpectraWith Time-Dependent Density Functional Theory;54
8.1;I. Introduction;54
8.2;II. Theory;60
8.3;III. Applications;87
8.4;IV. Concluding Remarks;113
8.5;List of Symbols;114
8.6;Acknowledgments;116
8.7;References;117
9;Theoretical Investigation of Solvent Effects and Complex Systems: Towardthe calculations of bioinorganic systems from ab initio molecular dynamicssimulations and static quantum chemistry;124
9.1;I. Introduction;124
9.2;II. AIMD Simulations;126
9.3;III. Static Quantum Chemical Calculations;146
9.4;IV. Conclusion;149
9.5;Acknowledgment;150
9.6;References;150
10;Simulations of Liquids and Solutions Basedon Quantum Mechanical Forces;156
10.1;I. Introduction;156
10.2;II. Methodology of the QMCF Approach;160
10.3;III. Applications of the QMCF MD Methodology;172
10.4;IV. Conclusions;185
10.5;Acknowledgment;185
10.6;References;186
11;Spin Interactions in Cluster Chemistry;190
11.1;I. Introduction;190
11.2;II. Theoretical Foundations;192
11.3;III. From Dirac–Breit to Breit–Pauli Hamiltonians;202
11.4;IV. Phenomenological Spin Hamiltonians;216
11.5;V. Concept of Local Electronic Spins;216
11.6;VI. Technical Issues: Optimization of Broken-Symmetry Determinants;226
11.7;VII. Studies on Open-Shell Polynuclear Transition-Metal Clusters;229
11.8;VIII. Conclusions;237
11.9;Acknowledgments;238
11.10;References;238
12;Inner- and Outer-Sphere Hydrogenation Mechanisms:A Computational Perspective;244
12.1;I. Introduction;244
12.2;II. Reaction Mechanisms for Hydrogenation Reactions:The Substrate Viewpoint;246
12.3;III. Computational Investigation of Hydrogenation Mechanisms;253
12.4;IV. Concluding Remarks;268
12.5;Acknowledgements;270
12.6;References;270
13;Computational Studies on Properties, Formation, and Complexationof M(II)-Porphyrins;274
13.1;I. Introduction;274
13.2;II. Models and Methods;277
13.3;III. Geometries and Electronic States of Metalloporphyrins;279
13.4;IV. Metalation of Porphyrins;282
13.5;V. Binding of Small Molecules;292
13.6;VI. Summary and Conclusions;305
13.7;Acknowledgements;306
13.8;References;306
14;Dealing with Complexity in Open-Shell Transition Metal Chemistryfrom a Theoretical Perspective: Reaction Pathways, Bonding,Spectroscopy, and Magnetic Properties;314
14.1;I. Introduction;314
14.2;II. Calculation of Reaction Pathways;316
14.3;III. EPR of Degenerate Systems;326
14.4;IV. Metal Radical Interactions;337
14.5;V. Magnetic Properties of Oligonuclear Clusters;346
14.6;VI. Concluding Remarks;357
14.7;References;358
15;Vibronic Coupling in Inorganic Systems: Photochemistry,Conical Intersections, and the Jahn–Teller andPseudo-Jahn–Teller Effects;364
15.1;I. Introduction;364
15.2;II. Theoretical and Computational Background;367
15.3;III. Important Computational Results in Inorganic Photochemistry;375
15.4;IV. Case Studies;378
15.5;V. Conclusions and Outlook;399
15.6;Acknowledgments;399
15.7;References;399
16;Elementary Reactions in Polynuclear Ionsand Aqueous–Mineral Interfaces: A New Geology;404
16.1;I. Molecular Geology;404
16.2;II. Modeling Tools for Geochemical Systems;406
16.3;III. Example Systems;415
16.4;IV. Geological Problems with Molecular Level Solutions;441
16.5;References;446
17;The Aromatic Amino Acid Hydroxylase Mechanism:A Perspective from Computational Chemistry;450
17.1;I. Introduction;450
17.2;II. Structural Information;462
17.3;III. The Cluster Model Approach to Quantum Chemical Studiesof Enzyme Reactions;465
17.4;IV. DFT Investigations of the AAH Mechanism;469
17.5;V. Conclusions;504
17.6;Acknowledgment;508
17.7;References;508
18;Index;514
19;Contents of Previous Volumes;528
Molecular Mechanics for Transition Metal Centers: From Coordination Complexes To Metalloproteins
Robert J. Deeth Inorganic Computational Chemistry Group, Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom Abstract
Computer modeling of transition metal centers presents many challenges. Whether in relatively small complexes or attached to large biomolecules, the electronic structure arising from the open-shell dn configuration can be complicated. Most workers therefore resort to quantum mechanical (QM) methods, notably density functional theory (DFT). However, many problems require large numbers of calculations: e.g., high-throughput screening, comprehensive conformational searching, and molecular dynamics. In these cases, all forms of QM, including DFT, are prohibitively expensive and impractical. In contrast, classical molecular mechanics (MM) is fast enough and has for many years been used for such large-scale computations. Unfortunately, while MM works well for “organic” systems, it is not well suited to TM systems since it misses many important d-electron effects which are implicit in QM methods. However, since we cannot make QM methods much faster, the only option is to make MM smarter. We have combined ligand field theory (LFT), in its angular overlap model (AOM) form, with “normal” MM to give ligand field molecular mechanics (LFMM). LFMM has a sophisticated AOM description of metal–ligand bonding which can be designed to emulate DFT. However, since LFT is empirical, LFMM is up to four orders of magnitude faster than DFT. Illustrative applications are presented which span the structural chemistry of Ga(III) and Mn(II) complexes, Jahn–Teller effects in Cu(II) and Fe(II) systems, the trans-influence in Pt(II) chemistry, spin-state changes in Ni(II) and Co(III) species, transition states for water exchange at first-row M(II) centers, through to 16 ns molecular dynamics simulations of copper proteins. Provided the necessary investment in parameter development is justifiable, LFMM provides DFT-like accuracy at a MM cost and represents a powerful, general tool for modeling TM centers in coordination complexes and metalloproteins. Keywords Ligand field theory molecular mechanics Jahn–Teller effect spin states copper enzymes I Introduction
Transition metal (TM) systems present a fundamental dilemma for computational chemists. On the one hand, TM centers are often associated with relatively complicated electronic structures which appear to demand some form of quantum mechanical (QM) approach (1). On the other hand, all forms of QM are relatively compute intensive and are impractical for conformational searching, virtual high-throughput screening, or dynamics simulations since all these approaches may require many hundreds of thousands of individual calculations. Consequently, TM computational chemists tend to restrict themselves to smaller “model” systems with limited conformational freedom. This is particularly marked in bioinorganic chemistry where the calculation focuses on the “important” active site region but the bulk of the protein is not treated explicitly (2,3). In contrast, those interested in purely “organic” systems have long enjoyed the advantages of “cheap,” classical molecular mechanics (MM) and molecular dynamics (MD) to study the entire molecular system including the surrounding solvent. However, conventional MM is not well suited to TM systems since it does not provide a general way of accounting for the important effects arising from the d electrons (4,5). In response, hybrid QM/MM methods have appeared (6). The metal center and its immediate environment is handled by a “high level” QM method, typically based on Density Functional Theory (DFT), with the rest of the system treated by MM. As the many technical difficulties of QM/MM have progressively been solved—most importantly how to couple the quantum region to the classical region—QM/MM has grown in popularity. However, the inclusion of any QM, even on a relatively small piece of the whole system, soon exacts a huge cost in execution time. Just a few minutes per calculation soon equates to years of CPU time. The only options are either to use thousands of computers or to develop a method which is as accurate as QM, but many orders of magnitude more efficient. We have taken the second path by augmenting MM with additional terms designed to provide a physically meaningful description of metal–ligand bonding and thus be able to emulate the behavior of more sophisticated, but expensive, QM methods. However, in order to put our model into perspective, we must first appreciate the nature of “conventional” MM and its shortcomings when applied to TM systems. II Conventional Molecular Mechanics
Molecular mechanics in its simplest form expresses the total potential energy, Etot, as a sum of terms describing bond stretching, Estr, angle bending, Ebend, torsional twisting, Etor, and nonbonding interactions, Enb(1). The latter can include both van der Waals (vdW) interactions and, by assigning to each atom a partial atomic charge, electrostatics. tot=?Estr+?Ebend+?Etor+?Enb (1) Each term in (1) is represented by a simple mathematical expression as exemplified in (2), where the k are appropriate force constants, ? are bond angles, t are torsion angles, n is the torsional periodicity parameter, ? is the torsion offset, ? are partial atomic charge, e is the dielectric constant, A and B are Lennard-Jones vdW parameters, and the summations run over bonded atom pairs (ij), angle triples (ijk) and torsional quadruples (ijkl). The nonbonded terms are summed over the distances, dij, between unique atom pairs excluding bonded pairs and the atoms at either end of an angle triple. For the atoms at the ends of a torsion quadruple, the nonbonded term may be omitted or scaled. tot=?i,jkij(rij-r0,ij)2+?i,j,kkijk(?ijk-?0,ijk)2+?i,j,k,lkijkl[1+cos(nijklt-?ijkl)]+[?i
