Molecular electronic structures : an introduction

The present book is an introduction to molecular electronic structural theory. It is aimed at students who have reasonable familiarity with differential and integral calculus and are beginning a study of the physical description of chemical systems. We have decided to concentrate on the description of ground state electronic structures, or, in other words, the principles of chemical bonding in molecules. In this important respect the present volume differs from our earlier book "Molecular Orbital Theory" (Benjamin, 1964), which included a strong emphasis on the description of electronic excited states. In our treatment of molecular wave functions we make use of "symmetry operators", the latter being operators that leave the Hamiltonian unchanged. By using such symmetry operators, it is possible to characterize the electronic structures of molecules. In our opinion, this approach provides good preparation for later studies that may be undertaken in which formal group theory is employed. The heart of the book is Chapter 4, where we discuss in some detail the bonding in several selected molecules. Examples from both organic and inorganic chemistry are included in an attempt to make the coverage as general as possible. Our objective here is to provide an introduction to molecular bonding that will serve as a foundation for more advanced study of electronic structures. Suggested reading and problems are included in each chapter. Some of the problems are challenging, but working them will give the student a much better feeling for the principles involved. The suggested reading is of two types, books (and reviews) and original papers. And we urge students to examine at least some of the older papers in the field, as muck can be learned from them

Hydrogen Generation Catalyzed by Fluorinated Diglyoxime−Iron Complexes at Low Overpotentials

Fe^(II) complexes containing the fluorinated ligand 1,2-bis(perfluorophenyl)ethane-1,2-dionedioxime (dAr^FgH_2; H = dissociable proton) exhibit relatively positive Fe^(II/I) reduction potentials. The air-stable difluoroborated species [(dAr^FgBF_2)_2Fe(py)_2] (2) electrocatalyzes H_2 generation at −0.9 V vs SCE with i_(cat)/i_p ≈ 4, corresponding to a turnover frequency (TOF) of ~ 20 s^(–1) [Faradaic yield (FY) = 82 ± 13%]. The corresponding monofluoroborated, proton-bridged complex [(dArFg2H-BF2)Fe(py)2] (3) exhibits an improved TOF of ~ 200 s^(–1) (i_(cat)/i_p ≈ 8; FY = 68 ± 14%) at −0.8 V with an overpotential of 300 mV. Simulations of the electrocatalytic cyclic voltammograms of 2 suggest rate-limiting protonation of an Fe“0” intermediate (k_(RLS) ≈ 200 M^(–1) s^(–1)) that undergoes hydride protonation to form H_2. Complex 3 likely reacts via protonation of an Fe^I intermediate that subsequently forms H_2 via a bimetallic mechanism (k_(RLS) ≈ 2000 M^(–1) s^(–1)). 3 catalyzes production at relatively positive potentials compared with other iron complexes

Funneled angle landscapes for helical proteins

We use crystallographic data for four helical iron proteins (cytochrome c-b₅₆₂, cytochrome c′, sperm whale myoglobin, human cytoglobin) to calculate radial and angular signatures as each unfolds from the native state stepwise though four unfolded states. From these data we construct an angle phase diagram to display the evolution of each protein from its native state; and, in turn, the phase diagram is used to construct a funneled angle landscape for comparison with the topography of its folding energy landscape. We quantify the departure of individual helical and turning regions from the areal, angular profile of corresponding regions of the native state. This procedure allows us to identify the similarities and differences among individual helical and turning regions in the early stages of unfolding of the four helical heme proteins

Bioinorganic Chemistry

This book covers material that could be included in a one-quarter or one-semester course in bioinorganic chemistry for graduate students and advanced undergraduate students in chemistry or biochemistry. We believe that such a course should provide students with the background required to follow the research literature in the field. The topics were chosen to represent those areas of bioinorganic chemistry that are mature enough for textbook presentation. Although each chapter presents material at a more advanced level than that of bioinorganic textbooks published previously, the chapters are not specialized review articles. What we have attempted to do in each chapter is to teach the underlying principles of bioinorganic chemistry as well as outlining the state of knowledge in selected areas. We have chosen not to include abbreviated summaries of the inorganic chemistry, biochemistry, and spectroscopy that students may need as background in order to master the material presented. We instead assume that the instructor using this book will assign reading from relevant sources that is appropriate to the background of the students taking the course. For the convenience of the instructors, students, and other readers of this book, we have included an appendix that lists references to reviews of the research literature that we have found to be particularly useful in our courses on bioinorganic chemistry

Detection of bacterial spores with lanthanide-macrocycle binary complexes

The detection of bacterial spores via dipicolinate-triggered lanthanide luminescence has been improved in terms of detection limit, stability, and susceptibility to interferents by use of lanthanide−macrocycle binary complexes. Specifically, we compared the effectiveness of Sm, Eu, Tb, and Dy complexes with the macrocycle 1,4,7,10-tetraazacyclododecane-1,7-diacetate (DO2A) to the corresponding lanthanide aquo ions. The Ln(DO2A)^+ binary complexes bind dipicolinic acid (DPA), a major constituent of bacterial spores, with greater affinity and demonstrate significant improvement in bacterial spore detection. Of the four luminescent lanthanides studied, the terbium complex exhibits the greatest dipicolinate binding affinity (100-fold greater than Tb^(3+) alone, and 10-fold greater than other Ln(DO2A)^+ complexes) and highest quantum yield. Moreover, the inclusion of DO2A extends the pH range over which Tb−DPA coordination is stable, reduces the interference of calcium ions nearly 5-fold, and mitigates phosphate interference 1000-fold compared to free terbium alone. In addition, detection of Bacillus atrophaeus bacterial spores was improved by the use of Tb(DO2A)^+, yielding a 3-fold increase in the signal-to-noise ratio over Tb^(3+). Out of the eight cases investigated, the Tb(DO2A)^+ binary complex is best for the detection of bacterial spores

Long-range electron transfer in structurally engineered pentaammineruthenium (histidine-62) cytochrome c

In many biological processes, long-range electron transfer (ET) plays a key role. When the three-dimensional structures of proteins are accurately known, use of modified proteins and protein-protein complexes provides an experimental approach to study ET rates between two metal centers. For Ru(His)- modified proteins, the introduction of histidine residues at any desired surface location by site-directed mutagenesis opens the way for systematic investigations of ET pathways

Electron Paramagnetic Resonance and Optical Spectra of Pentacyanocobaltate(II)

Electron paramagnetic resonance (EPR) and optical spectral studies have been carried out on the pentacyanocobaltate(II) ion in ethylene glycol–water solutions, and in electron-irradiated powder samples of K3Co(CN)6. Both EPR and optical spectra observed for the ion in the powder samples are essentially similar to those obtained from the ethylene glycol–water solutions. There was no observable linewidth variation with nuclear spin states MI, no dependence on the different solvent media used, and no dependence on the concentration ratio Co2+/CN–, in both X-band and K-band spectra. The results indicate that the structure of Co(CN)53 - in solutions and in polycrystalline media is a slightly distorted square pyramid with no solvent bound in the sixth coordination site. The two strong hyperfine components with exceptionally large spacings occurring at the low-field end of the X-band spectrum are identified as the so-called angular anomalies. An effective method of simulation of the first-derivative EPR spectra of polycrystalline samples has also been developed

A Monodentate 1,3-Diphenyl-2-triazeno Terpyridineplatinum(II) Complex

The compound (l,3-diphenyl-2-triazeno )(2,2',2"- terpyridine)platinum(II) perchlorate dimethylformamide solvate (1) is formed by reaction of dpt (dptH = 1,3-diphenyltriazene) and [Pt(tpy)Cl]Cl (tpy = terpyridine) in the presence of excess base (NEt3). There are two independent cations in the asymmetric unit. The platinum centers have a monodentate triazeno ligand with the remaining coordination sites occupied by the terpyridine group. The crystal packing is dominated by π-π stacking interactions, and metal-metal interactions are conspicuously absent

Geometrical Description of Protein Structural Motifs

We present a geometrical method that can identify secondary structural motifs in proteins via angular correlations. The method uses crystal structure coordinates to calculate angular and radial signatures of each residue relative to an external reference point as the number of nearest-neighbor residues increases. We apply our approach to the blue copper protein amicyanin using the copper cofactor as the external reference point. We define a signature termed Δβ which describes the change in angular correlation as the span of nearest neighbor residues increases. We find that three turn regions of amicyanin harbor residues with Δβ near zero, while residues in other secondary structures have Δβ greater than zero: for β-strands, Δβ changes gradually residue by residue along the strand. Extension of our analysis to other blue copper proteins demonstrated that the noted structural trends are general. Importantly, our geometrical description of the folded protein accounts for all forces holding the structure together. Through this analysis, we identified some of the turns in amicyanin as symmetrical anchor points

Hopping maps for photosynthetic reaction centers

Photosynthetic reaction centers (PRCs) employ multiple-step tunneling (hopping) to separate electrons and holes that ultimately drive the chemistry required for metabolism. We recently developed hopping maps that can be used to interpret the rates and energetics of electron/hole hopping in three-site (donor–intermediate–acceptor) tunneling reactions, including those in PRCs. Here we analyze several key ET reactions in PRCs, including forward ET in the L-branch, and hopping that could involve thermodynamically uphill intermediates in the M-branch, which is ET-inactive in vivo. We also explore charge recombination reactions, which could involve hopping. Our hopping maps support the view that electron flow in PRCs involves strong electronic coupling between cofactors and reorganization energies that are among the lowest in biology (≤0.4 eV)