bluuebunny/crossref_metadata_2025 huggingface dataset:
Perturbed Angular Correlations of γ‐rays (PAC) Spectroscopy
Authors: Hemmingsen Lars , Butz Tilman
Published: December 2011

In this article, we give an elementary introduction to the theory and applications of perturbed angular correlation of γ‐rays (PAC) spectroscopy. In most applications in bioinorganic and inorganic chemistry the nuclear quadrupole interaction (NQI) is measured, providing a spectroscopic fingerprint of the local electronic and molecular structure and dynamics at the PAC probe site. The focus is on selected illustrative applications of PAC spectroscopy in bioinorganic chemistry: (i) local structure at metal ion binding sites in the bacterial mercury sensor MerR; de novo designed proteins; alcohol dehydrogenase–pH dependence; carboxypeptidase A—crystalline state versus solution; and carboxypeptidase A–during the hydrolysis of substrate; (ii) trapping intermediates in reactions using rapid freeze quenching; (iii) in vivo experiments on Cd(II) binding to biomolecules in cyanobacteria; (iv) cooperativity of metal ion binding in multinuclear sites; (v) dynamics of protein folding; (vi) rotational diffusion of biomolecules as a tool to monitor protein–protein interactions; (vii) exchange dynamics; and (viii) internal dynamics in proteins.

Examples from inorganic chemistry and solid state physics are included for cases where the information derived is different from that already presented in the examples from bioinorganic chemistry: (i) magnetic properties of metals; (ii) defects trapped by the impurity PAC probe atom; (iii) temperature and pressure dependence of the EFG in metals; (iv) amorphous metals, alloys and internal oxidation; (v) metal surfaces and interfaces; (vi) semiconductors; (vii) phase transitions; (viii) charge density waves in transition metal dichalcogenides; (ix) intercalation reactions in 2H‐TaS2; (x) structure and bonding; (xi) single crystal experiments.
Vibrational Spectroscopy
Authors: Dyer R. Brian , Woodruff William H.
Published: December 2011

The application of vibrational spectroscopy to the study of inorganic and bioinorganic structures and dynamics has a rich history. Recent advances in vibrational spectroscopic techniques have increased the utility of these methods. Time‐resolved methods in particular have benefited from advances in lasers and other enabling technologies. In this chapter we describe the application of both Raman and infrared methods to problems in inorganic chemistry, with a focus on bioinorganic systems. We also describe difference vibrational spectroscopy methods for the analysis of metal active sites within complex protein structures. We develop quantitative rules for the relationships between force constants and bond distances. Such relationships are useful for predicting bond distances for cases where it is difficult to measure them otherwise, such as for excited states of molecules. Finally, we review time‐resolved Raman and IR methods and their application to the study of the structures and dynamics of excited states and chemical reactions of inorganic systems.
Electronic Spectroscopy
Authors: Hughes Joseph L. , Krausz Elmars
Published: December 2011

Developments in the ability of electronic spectroscopy to provide insights into the fundamental electronic structure, photophysical and/or photochemical processes in inorganic and bioinorganic systems are outlined. These are highlighted by a number of examples across a range of chemical and biochemical systems. Some fundamental constraints regarding the application of electronic spectroscopy to a wider range of chemical questions are identified, as well as both practical and intrinsic limitations associated with the processes of measurement. The ubiquitous phenomenon of spectral broadening in optical and UV spectroscopy is given particular attention and the important concept of homogeneous versus inhomogeneous broadening is highlighted. The overall focus is on absorption‐based spectroscopies of chromophores at variable and low temperatures in either glassy, crystalline, or protein environments. The utilization of some of the powerful emerging technologies such as tuneable laser sources or synchrotron sources, along with the very high efficiency charge coupled device (CCD) and semiconductor diode detectors that are now available, allows the rapid accumulation of high quality spectra of small samples as well as measurements in minimal actinic fluences.
Biomineralization: Peptide‐Mediated Synthesis of Materials
Authors: Rutledge Ryan D. , Wright David W.
Published: December 2011

Biomineralization provides many examples of the ambient synthesis of materials. Often associated with these systems are peptide templates. Synthetically, these templates offer tunable entities that can be altered in ways that affect the resulting composition, size, and morphology of the desired material. The development of peptide‐display methods has aided in the expansion of this approach to include many types of abiological substances. Accordingly, this review focuses on the identification and use of peptides involved in the syntheses of a number of different types of materials (metal oxides, calcium carbonate, metallic nanostructures). Covering only the most recent of advances (2004–2007), we examine the control exhibited by peptides free in solution and the ability of researchers to address and alter that control. The effects demonstrated as a result of immobilizing the peptide on a nanostructured or biological surface are discussed. Finally, the future of biomimetic synthesis of nanomaterials is considered in an attempt to gauge where biomineralization is headed and what possibilities it might offer down the road.
Carbon Nanotubes and Nanocomposites for Electrical and Thermal Applications
Authors: Wang Wei , Lu Fushen , Veca Lucia Monica , Meziani Mohammed J. , Wang Xin , Cao Li , Gu Lingrong , Sun Ya‐Ping
Published: December 2011

The extraordinary electrical and thermal properties of individual carbon nanotubes have prompted predictions on their potentials for ultimately forming polymeric nanocomposites. A significant barrier for the predicted nanocomposites is the severe bundling and insolubility of carbon nanotubes. Chemical modification and functionalization have been demonstrated as being effective in the debundling and solubilization of carbon nanotubes for their homogeneous dispersion into polymer matrices for desired high‐quality nanocomposites. More elegant is the approach to use polymers that are structurally identical or maximally similar to the matrix polymers in the nanotube functionalization to ensure full compatibility of the functionalized nanotubes with the corresponding polymer matrix. Several representative examples are presented, along with discussion on the benefits and issues concerning the polymeric nanocomposites thus obtained. For superior electrical properties, there is experimental evidence suggesting that the nanotube dispersion in the polymer matrix plays an important role. More promising is the use of separated metallic carbon nanotubes for a much enhanced performance in conductive nanocomposites and in related applications, such as transparent conductive films. For highly thermal conductive polymeric nanocomposites, on the other hand, the feasibility of using carbon nanotubes to achieve the desired performance has yet to be convincingly demonstrated experimentally. Nevertheless, the available results do suggest significant effects of the nanotube dispersion and alignment on thermal conductivities of the nanocomposites.
Carbon Nanotubes, Single‐Walled: Functionalization by Intercalation
Authors: Shiozawa Hidetsugu , Pichler Thomas , Pfeiffer Rudolf , Kuzmany Hans
Published: December 2011

The article reviews recent progresses in functionalization of single‐walled carbon nanotubes (SWCNT). Detailed studies of electronic, chemical, and structural properties of intercalated and filled carbon nanotubes using state‐of‐the‐art spectroscopic and microscopic techniques are described. Intercalation with alkali metal allows one to fine tuned the electron‐doping level of SWCNT. A photoemission study of potassium intercalation compounds of SWCNT bundles unveils a transition of the metallic ground state of a SWCNT bundle from Tomonaga–Luttinger liquid state to Fermi liquid state. In turn, the filling of single‐walled carbon nanotubes with fullerenes and organic molecules facilitates a reality of nanochemistry using carbon nanotubes as a nanoreactor. A combined spectroscopic and microscopic investigation of the interconversion of encapsulated fullerenes and organic molecules unveils either a catalytic or a noncatalytic process for the inner‐tube growth from different filler precursors. Such encapsulated reactions vary the chemical status of filling material which eventually leads to a modulation of the doping level of the carbon nanotube host.
Carbon Nanotubes: Fluorinated Derivatives
Authors: Khabashesku Valery N. , Kuznetsov Oleksandr V. , Pulikkathara Merlyn X.
Published: December 2011

Ongoing extensive research on carbon nanotubes (CNTs) has been facilitated by unique physicochemical properties and wide opportunities the CNTs offer for the new field of nanotechnology. Recent studies have shown that for efficient use of the remarkable properties of CNTs, particularly in the design of multifunctional materials for engineering and biomedical applications, they need to be surface modified by attachment of functional groups for improving solubility, processing, and compatability with host materials. It has been shown that fluorination is an efficient way to modify and control the surface properties of CNTs. For instance, fluorine functional groups on the sidewalls of CNTs effectively assist in unroping the nanotube bundles and in dispersion in alcohols and other polar solvents. Weakness of the CF bond and solubility of fluorinated nanotubes (fluoronanotubes) provide an opportunity for the synthesis of a variety of nanotube derivatives by substitution of fluorine through wet chemistry methods. This approach has been applied to preparation of a series of amino, amide, hydroxyl, thiol, and carboxyl group‐terminated derivatives. The activated sidewall CC π bonds in fluoronanotubes also permit a solution‐phase chemistry leading to addition reactions of free radicals, carbenes, dienes, and other reactive molecules. Functional groups chemically attached to the CNTs effectively assist in the dispersion of CNTs in polymer matrices, crucial for nanocomposites fabrication. “Tailored” chemical modifications are particularly useful for creating multiple sites for covalent bonding of nanotubes to polymer matrices for the enhancement of mechanical properties of epoxy, polyethylene, polypropylene, and nylon. Fluorinated CNTs represent a new family of nanoscale fluorocarbon materials. They enable various applications of functionalized CNTs, derived from fluoronanotubes, particularly in nanocomposites, sensors, nanoelectronic devices, nanoengineered drug delivery systems, and nanolubricants.
Inorganic Nanotubes
Authors: Remškar Maja
Published: December 2011

The first synthetic inorganic nanotubes were reported in 1992, but owing to the simultaneous discovery of carbon nanotubes they attracted wide international attention only recently. They are distinguished by important peculiarities, from growth mechanisms to the various physical and chemical properties and possible applications. Further analogies to carbon nanotubes, fullerenes, nanobuds, and peapods are presented as the first hybrid inorganic nanotube structures, i.e., nanobuds and “mama” tubes. Their structural and morphological properties determining chemical stability and activity, transport properties, mechanics and interaction with other building blocks in composites are discussed in this article.
Nanocomposite Materials: Polyhedral Silsesquioxanes
Authors: Seifalian Alexander M. , Kannan Ruben Y. , Ghanbari Hossein , Bakhshi Raheleh
Published: December 2011

The unique properties of nanocomposites have revolutionized the field of materials science. Polyhedral oligomeric silsesquioxane (POSS) is one of the widely used nanostructured materials for the synthesis of hybrid nanocomposites. POSS nanocrystals have been incorporated as building blocks of controllable shapes into polymers to form hybrid materials exhibiting improved properties. A variety of polymerization techniques have been used in the preparation of POSS‐containing hybrids. Incorporation of POSS into polymers can result in substantial improvement in physical properties of the polymers, such as low dielectric constants, increased glass‐transition temperatures, low coefficient of thermal expansion, enhanced thermal stability, mechanical strength, as well as improved oxidation resistance and reduction in flammability, oxygen permeability, heat evolution, and viscosity during processing. The most interesting POSS‐polymer has been the development of POSS–poly(carbonate‐urea)urethane that is used in medical applications owing to its enhanced biocompatibility and antithrombogenesity. These composites are materials of choice in the fabrication of various cardiovascular devices, such as artificial heart valves, stent‐grafts, bypass grafts, microvascular beds, and other biomedical devices including breast implants, and as scaffolds for tissue engineering.
Supramolecular Materials: Assemblies Based on Square‐Complexation
Authors: James Stuart L.
Published: December 2011

Square complexation of metal ions has become a remarkably useful construction motif for the self‐assembly of discrete nanoscopic structures and infinite frameworks. This article covers developments in the area since 2004. Interesting new aspects of self‐assembly methodology include solvent and anion dependence, use of three‐coordinate centers, photolabilization, kinetically controlled assembly, heteroligand structures, and the first very large mesoscopic structures (>20 nm). Also, known types of large self‐assembled cages, mainly based on palladium(II) and platinum(II) have been developed as protective reaction nanovessels in which to observe unusual, even unprecedented, chemistry. Internal and external functionalization of known structure types is leading to rich internal and external supramolecular chemistry. For infinite frameworks, square complexation, not only at single metal ions but also dimetallic units, typified by the dimetal‐tetracarboxylate paddle‐wheel motif, has led to a family of structurally versatile and functionalizable microporous pillared‐layer frameworks. In common with all coordination framework types, those based on square complexation are being increasingly studied with regard to their dynamics, sorption behavior, and catalysis.
Nano/Microporous Materials: Metal‐Ion Sorption Materials
Authors: Hobbs David T.
Published: December 2011

This paper provides a literature review from 2004 to the present, summarizing studies evaluating the use of nanomaterials and microporous materials as sorbents for the separation of metal ions from aqueous solutions. Materials such as microporous titanosilicates, mesoporous silicas, metal oxide nanoparticles, and carbon nanotubes exhibit increased loading and removal kinetics for a variety of metal ions compared to conventional sorbent materials. Also, incorporation of functional groups into these materials has shown promise to provide enhanced selectivity for a variety of metal ions.
Gold Nanoparticles as Chemical Catalysts
Authors: Ma Zhen , Overbury Steven H. , Dai Sheng
Published: December 2011

Gold, often known as being
chemically inert
, has rich inorganic and organic chemistry. In particular, gold nanoparticles, either protected by organic ligands or supported on solid surfaces, have attracted wide attention for their applications in catalysis, electronics, nonlinear optics, and biology. In this article, we summarize some recent advances in the synthesis of supported gold catalysts from the perspective of inorganic materials chemistry. These advances include new methods used to load gold, to prepare functionalized supports, and to postdecorate supported gold catalysts. More recent advances in the use of nanoparticle supports and other ordered nanostructures in making supported gold catalysts are also highlighted, and a critical analysis of the status of the field is presented. From this review, it is hoped that the reader will get an impression that inorganic materials chemistry can contribute to the synthesis of novel gold catalysts with good catalytic performance.
Inorganic Nanomaterials Synthesis Using Ionic Liquids
Authors: Taubert Andreas
Published: December 2011

Ionic liquids (ILs) have been studied for a wide range of applications, including organic synthesis, separation and extraction, and electrochemistry. Inorganic nanomaterials synthesis in and with ILs is still a new but rapidly developing research branch. This article gives an overview over recent developments in the field of inorganic materials synthesis in ILs. Furthermore, the article highlights a few promising approaches that add value to inorganic materials science by giving access to hitherto unknown inorganic materials or materials that have so far only been accessible with great experimental effort via more conventional processes.
Medicinal Inorganic Chemistry: Correcting Essential Metal‐Ion Deficiencies
Authors: Thompson Katherine H.
Published: December 2011

Essential metal ions are those for which there is a known requirement for good health in the body. When dietary intake does not, or cannot, maintain adequate tissue stores of an essential trace or ultratrace metal ion, metal‐ion supplementation may be necessary. Simple salts of metal ions are often poorly tolerated, not well absorbed, or too rapidly excreted (or all three of these); therefore, appropriate ligand binding of the particular metal ion can significantly improve the success of supplementation efforts. The most common deficiency disorder, iron‐deficiency anemia, is now treated with a number of iron complexes, e.g., Ferrochel™ and ferrous gluconate, that are superior to simple iron salts such as ferrous sulfate; others, such as ferric maltol, are being proposed as useful substitutes. Marginal deficiencies of trace and ultratrace elements, such as zinc, copper, manganese, and chromium, are purported to have long‐term negative health effects, especially in aging or ill populations. Defining marginal deficiency is difficult, owing to lack of reliable and accurate biomarkers for the determination of trace element status.
Medicinal Inorganic Chemistry: Metal‐containing Diagnostic Compounds
Authors: Thompson Katherine H.
Published: December 2011

Metallopharmaceuticals designed for use in diagnostic compounds cover a broad spectrum of diagnostic modalities, starting with barium sulfate for enhanced X‐ray contrast, to the hugely successful gadolinium‐based magnetic resonance imaging (MRI) contrast agents, to more recent advances in positron emission tomography (PET) and single photon emission computed tomography (SPECT) requiring radiolabeled metal‐based diagnostic agents for image detection. In each case, the pharmacokinetics of tissue distribution and the thermodynamic stability of the metal‐ligand coordination complex are very important to the clinical utility of the particular compound. For radiolabeling, the speed and ease of radiolabel production are also key features of the metallodiagnostic agent's utility.
Medicinal Inorganic Chemistry: Using Toxicity to Advantage
Authors: Thompson Katherine H.
Published: December 2011

The field of metal‐based compounds intended for treatment of cancer has long been dominated by cisplatin, first approved for clinical use in treating testicular cancer, in 1978. By all accounts, cisplatin has been a resounding success. Other platinum‐based compounds have been introduced since then, with carboplatin and oxaliplatin serving to broaden the range of tumors that can be effectively treated. Overcoming tumor cell resistance is an ongoing problem, and the target of many newer platinum‐based anticancer therapeutic agents. More recently, substitution of platinum with other metal ions, such as ruthenium, gallium, lanthanides, and arsenic, has expanded the array of potential metal‐based anticancer agents, with the arsenic trioxide having particular success against acute promyelocytic leukemia (APL).

A key feature of metal‐based anticancer therapeutic agents is that they are toxic by design: without toxicity, the tumor cells could not be eliminated. Similar strategies are useful for diseases such as malaria, Chagas disease, and leishmaniasis, in which the target organisms are parasites. For parasitic diseases, as well as for resistant bacterial infections, or to stop tumor growth, the requirement for appropriate metallotherapeutic design is to minimize contact with healthy tissue, to target particular cells, and to avoid premature release of the metal ion.
Calculation of Reduction Potential and
p

K

a
Authors: Jensen Jan H. , Li Hui
Published: December 2011

Three methods, quantum mechanical and molecular mechanical polarizable continuum model (QM/MM/PCM), QM/PCM, and empirical, were developed and applied to calculate protein reduction potential (
E
0
) and p
K
a
values. In the QM/MM/PCM calculation of Lys55 p
K
a
of turkey ovomucoid third domain (OMTKY3), the MP2/6‐31 + G(2d,p) method was used to describe the QM region consisting of ∼45 atoms; the rest of the protein was modeled either with ab initio‐derived electric multipole points or atomic charges from standard force field methods; and the aqueous solvation effect was described with the polarizable continuum model (PCM). The calculated Lys55 p
K
a
values are in good agreement with experiments. QM/PCM methods were used to calculate p
K
a
values of various proteins and the
E
0
of type‐1 Cu centers. For solvent‐exposed p
K
a
sites, QM/PCM (MP2/6‐31 + G(2d,p) for ∼100 atoms, PCM with dielectric = 78.39 for aqueous solution) methods can often reproduce experimental p
K
a
values. For type‐1 Cu
E
0
, because of protein burial, the desolvation effect becomes significant: it was found that Cu‐ligand interactions and desolvation can potentially change the
E
0
by ∼300 and ∼400 mV, respectively, using the CPCM/B3LYP/6‐311++G(2df,p) method and model molecules of ∼100 atoms. An empirical method, PROPKA, was developed for protein p
K
a
calculation and analysis, which is able to calculate the p
K
a
values of a protein within ∼1 s.
Determining Transition States in Bioinorganic Reactions
Authors: Lundberg Marcus , Morokuma Keiji
Published: December 2011

This article summarizes basic aspects of time‐dependent density functional theory (TD‐DFT) and its applications in inorganic chemistry. Sections titled TD‐DFT and Spectroscopic Properties outline some of the theoretical formalism and explain how excitation energies can be obtained from TD‐DFT linear response theory. Common approximations in density functional theory (DFT) exchange‐correlation (XC) potentials that might have adverse effects on the accuracy of computed results are explained. Sections titled Benchmark Data and Some Case Studies discuss a number of case studies, with emphasis on TD‐DFT excitation spectra computations in coordination chemistry. Computations of spectra and other properties of metals clusters are also discussed. Apart from excitation spectra, this section also describes TD‐DFT computations of Raman intensities (including resonance Raman and surface‐enhanced Raman spectra (SERS)), magnetic circular dichroism, optical rotatory dispersion (CD and ORD), and concludes with some comments on relativistic effects.
Ab
initio
and Semiempirical Methods
Authors: Gorelsky Serge I.
Published: December 2011

Ab initio and semiempirical methods play a very important role in modern computational chemistry. The main advantage of semiempirical methods is a substantial reduction in the required computation time and, consequently, an increase in ability to execute calculations for large molecules. The disadvantages are the loss of the variational principle (one can obtain a total energy that is below the true total energy), the limited applicability (methods can only be applied to molecules containing elements that have been parameterized), and the danger of spurious results (especially for molecular systems that are different from those used for parameterizations). On the other hand, high‐level ab initio techniques enable researchers to obtain very accurate results and act as a reference to lower‐accuracy methods. These ab initio methods play an important role for calculations of small molecular systems and progress is being made to extend the area of application of such methods to bigger systems.
Spin Contamination in Inorganic Chemistry Calculations
Authors: Sonnenberg Jason L. , Schlegel H. Bernhard , Hratchian Hrant P.
Published: December 2011

An overview of spin contamination and its relationship to broken‐symmetry wave functions are presented. Spin operator expectation‐value formulas are developed for use with generalized, unrestricted, and restricted spin orbitals. Current projection techniques are reviewed and illustrated for a variety of current theoretical methods.
Water Oxidation by the Manganese Cluster in Photosynthesis
Authors: Siegbahn Per E. M.
Published: December 2011

Almost all quantum chemical studies performed on enzyme mechanisms have relied on high‐resolution X‐ray structures as starting points. Since no such structure yet exists for photosystem II, a model study of this enzyme is unusually difficult. In this chapter, the approach adopted to obtain the mechanism for OO bond formation in this enzyme is described. Another difficulty, in common with many other enzymatic mechanisms, is that electrons and protons are stepwise removed from the active complex. A method is outlined in which accurate redox potentials and pKavalues can be obtained from rather small models. In this approach, the main effects of the enzyme, homogeneous and inhomogeneous, are included. The most important result is that the OO bond is formed between an oxygen radical and an oxo group. In the S2to S3transition a reconstruction of the oxygen evolving complex takes place due to insertion of a water molecule. Good agreement with most experimental observations is obtained.
Hydrogenases: Theoretical Investigations Towards Bioinspired
H
2
Production and Activation
Authors: Bruschi Maurizio , Zampella Giuseppe , Greco Claudio , Bertini Luca , Fantucci Piercarlo , De Gioia Luca
Published: December 2011

Hydrogenases catalyze the reduction of protons, and have great biotechnological relevance in light of the key role played by H
2
in several industrial processes. Moreover, the industrial and social relevance of H
2
stems also from the observation that dihydrogen could be an efficient and cost‐attractive energy carrier for the future.

Hydrogenases invariably contain a transition metal ion (Fe and in some case Ni) in their active site, and therefore have attracted the attention of experimental and theoretical bioinorganic chemists, which have given fundamental contributions to the elucidation of structure‐activity relationships in this class of enzymes. In addition, the recent elucidation of the X‐ray structure of [NiFe]‐ and [FeFe]‐hydrogenases has prompted synthetic chemists to design and characterize bioinspired coordination compounds, with the aim of obtaining efficient catalysts for H
2
production/activation.

Here, we briefly review the contributions given by quantum chemistry to the characterization of key forms of the enzymes, the elucidation of reaction pathways and catalytic mechanisms, as well as the complementation of experimental data in the investigation of synthetic models. Emphasis is mainly given to underline the kind of insights that can be obtained using quantum chemical methods when investigating coordination compounds related to the hydrogenases active site, and to highlight some strengths and limitations of density functional theory, which currently is the most frequently used quantum chemical method to investigate metalloenzymes.
Computational Studies: Cisplatin
Authors: Mantri Yogita , Baik Mu‐Hyun
Published: December 2011

Cisplatin is one of the most successful anticancer drugs currently in use. Since the discovery of its antitumor activity over three decades ago, intense research has been carried out to uncover the details of its cytotoxic activity and to design analogs with fewer side effects. Computational studies have complemented experimental studies in this research effort. Much of the early computational effort was dedicated to understanding the details of the hydrolysis process of cisplatin that leads to the activated drug. With mounting evidence that DNA was the primary target of the drug and a simultaneous increase in computing power, later theoretical studies aimed to explore the atomistic details of cisplatin–DNA interactions. Currently, both quantum mechanical and molecular mechanical methods are being used to study the thermodynamics and kinetics of not only cisplatin–DNA complexes, but also of other complexes such as Pt(II)‐based cisplatin analogs, other transition metal complexes, and DNA binding organic molecules. Despite these remarkable achievements, much work still remains to be done, both experimentally and computationally, especially in elucidating the role of repair enzymes in modulating the cytotoxic activity of DNA binding agents.
Computational Methods: Modeling of Reactivity in Zn‐Containing Enzymes
Authors: Mujika Jon I. , Mulholland Adrian J. , Harvey Jeremy N.
Published: December 2011

Computation is increasingly well placed to offer insight into a range of structural and spectroscopic properties of Zn‐containing enzymes, as well as into their reactivity. The latter aspect is the focus of this article. Molecular dynamics simulations provide insight into substrate binding and active‐site relaxation around the metal and substrate. A significant challenge in such studies is the representation of the zinc center. Quantum mechanical methods, either on their own using small active‐site models, or for whole enzymes using hybrid techniques, provide insight into reaction paths and hence into transition states and intermediates. Examples of these applications are reviewed for carbonic anhydrase, carboxypeptidase A, thermolysin, type B β‐lactamase, and farnesyltransferase.
Combined Density Functional Theory (
DFT
) and Electrostatics Study of the Proton Pumping Mechanism in Cytochrome

C

Oxidase
Authors: Quenneville Jason , Popović Dragan M. , Stuchebrukhov Alexei A.
Published: December 2011

Cytochrome
c
oxidase is a redox‐driven proton pump which converts atmospheric oxygen to water and couples the oxygen reduction reaction to the creation of a membrane proton gradient. The structure of the enzyme has been solved; however, the mechanism of proton pumping is still poorly understood. Recent calculations from this group indicate that one of the histidine ligands of the enzyme's Cu
B
center, His291, may play the role of the pumping element. Here, we discuss results of calculations that combined first principles density functional theory (DFT) and continuum electrostatics to evaluate the energetics of the key energy generating step—the transfer of the chemical proton to the binuclear center of the enzyme, where the hydroxyl group is converted to water, and the concerted expulsion of the proton from d‐nitrogen of the His291 ligand of the Cu
B
center.
Structural Origins of Noninnocent Coordination Chemistry
Authors: Szilagyi Robert K.
Published: December 2011

A concise synthesis is provided for key electronic and geometric structural features, leading to noninnocent coordination chemistry as manifested by unprecedented reactivity, unusual coordination chemistry, and ligand‐based redox chemistry. These include ligand–ligand repulsion arising from steric rigidity, reduced effective nuclear charge of the ligand‐donor atoms, and increased effective nuclear charge of the metal centers in addition to suitable metal–ligand overlap for efficient intramolecular electron transfer. These features can contribute to considerable deviations from formal oxidation states by leading to effectively low‐valent, reduced metal centers and oxidized ligands that can have very different electronic and geometric structures from their uncoordinated forms. To demonstrate the influence of these structural factors, classical examples of dithiolene complexes are discussed, followed by pincer‐type ligands with late transition metals that show unexpected noninnocent behavior. Combined calibrated density functional theory and multi‐edge X‐ray absorption spectroscopy (XAS) has the potential for uncovering new families of noninnocent ligands that have importance in involving generally redox silent metals in electron‐transfer processes or inducing nucleophilic character for metals due to extreme ligand‐to‐metal electron donation.
Multiple Aromaticity, Multiple Antiaromaticity, and Conflicting Aromaticity in Inorganic Systems
Authors: Zubarev Dmitry Yu. , Boldyrev Alexander I.
Published: December 2011

In recent years there have been significant advances in extending the concepts of aromaticity and antiaromaticity into the realm of inorganic chemistry. These new developments have shown that aromaticity and antiaromaticity in metal systems are frequently multiple in nature. Two new types of aromaticity, namely, δ‐ and ϕ‐aromaticity, were found in transition metal and f‐element cyclic systems in addition to the σ‐ and π‐types already known in organic chemistry. There are also now many examples of inorganic systems with conflicting aromaticity, which refers to the systems with simultaneous presence of aromaticity and antiaromaticity in different electronic (σ‐, π‐, δ‐, or ϕ‐) subsystems. It was shown that the antiaromaticity in any electronic subsystem could be interpreted in terms of formation of small areas of aromaticity leading to the island aromaticity.
Potential Energy Surfaces for Metal‐Assisted Chemical Reactions
Authors: Marino Tiziana , del Carmen Michelini Maria , Russo Nino , Sicilia Emilia , Toscano Marirosa
Published: December 2011

The potential energy surfaces for a series of metal‐assisted reactions have been investigated in the framework of density functional theory (DFT). The reported examples are representative of the difficulties encountered in the construction of reliable potential energy surfaces (PESs) when metal‐containing systems are involved. The results contribute to the elucidation of the elementary mechanisms underlying the activation processes of prototypical bonds in gas phase and in enzymatic environment.
Computational Methods: Transition Metal Clusters
Authors: Gautier Régis , Halet Jean‐François , Saillard Jean‐Yves
Published: December 2011

Cluster chemistry is dominated by structural aspects. Indeed, structure and bonding are strongly related to stability and properties, and cluster structures are particularly diverse and often complex. Thus, electron‐counting rules, which relate structure to electron count, have been the key to the development of cluster chemistry as a distinct area of chemistry. These rules have been set up progressively along time with the help of quantum chemistry. This article deals with the recent progress on transition metal and mixed main group/transition metal cluster chemistry arising from the contribution of modern computational theory to the rationalization of structures. This article focuses on “viable” species, i.e., molecules that are isolable under reasonable conditions and deals with the exploration of the limitations of the classical electron‐counting rules as well as the establishment of new rules for new structural types with the help of quantum chemical calculations.
Radionuclides: Natural
Authors: Larivière Dominic , Guérin Nicolas
Published: December 2011

The natural ionizing radiation present on our planet comes from many sources and generates most of the radioactivity that surrounds us. Primordial radionuclides, defined as radionuclides present since the formation of Earth about 4.6 × 109years ago, play a critical role in our understanding of geological conditions on our planet over its whole history. Radioactivity initiated by the successive decay of232Th,235U, and238U is essentially responsible for the presence of radioisotopes of lead, polonium, bismuth, astatine, radon, francium, radium, and protactinium on Earth. Because of their short half‐lives with respect to Earth's geologic timescale, the decay of these radionuclides is responsible for a significant portion of the doses of natural radioactivity received by humans. Cosmic radiation, originating from both within and beyond our solar system, completes the list of significant modes of production of natural radioactivity in the atmosphere and the lithosphere. Minor sources of natural radioactivity (including radionuclides produced by cosmic neutron bombardments and spontaneous fission in uranium and thorium minerals) are known to generate quantities of transuranium isotopes and fission products, which are generally associated with the development of nuclear power.
Cobalt: Radionuclides
Authors: Lima Enrique
Published: December 2011

Radionulcides of cobalt are generated through nuclear reactions from other stables isotopes. The most common radionuclide of cobalt is60Co, which is generated in nuclear power plants. Medical equipment is also a minor source of radioactive cobalt. Important applications of60Co in the field of medicine, biology, and food are possible because of the powerful emitted γ‐rays (1.17 and 1.33 MeV). However, this kind of radiation may be very dangerous to human beings; serious cellular damage can occur if exposed directly to doses as high as 1000 rad. Thus, discharges of radioactive cobalt to the environment should be minimized, but accidental releases have occurred. The chemical behavior of cobalt in aqueous media is a determinant for the stabilization of cobalt in polluted effluents. Water and soil in several regions in the world are contaminated. The chemical complexity of seawater and soil makes it difficult to remediate60Co. The chemical media determine the stabilization and rate of transport through marine media and soil. Several strategies have been designed to remediate water and soil polluted with cobalt radionuclides. This article describes some of the common uses of cobalt as well as some problems associated with cobalt radionuclides.
Rhenium: Radionuclides
Authors: Tagami Keiko , Uchida Shigeo
Published: December 2011

The occurrence, chemistry, and speciation of rhenium (Re) in environmental components such as soil and water, as well as rhenium separation and analytical characterization techniques in the environment, are summarized. Rhenium has two isotopes: one is stable185Re and the other is radioactive187Re, which has a very long half‐life of 4.35 × 1010years. The decay system,187Re–187Os has been used for dating rocks and meteorites. Artificially made radioisotopes with short half‐lives, such as186Re and188Re have been used in radiopharmaceuticals. Because of similarities in chemistry, rhenium has been used as a chemical analog of technetium.
Oceans and Seas: Radionuclides
Authors: Aoyama Michio
Published: December 2011

The main sources of anthropogenic radioactivity of the world ocean are fallout from atmospheric nuclear weapon testing and the releases from nuclear fuel reprocessing plants and from the Chernobyl accident in 1986. This article summarizes the numbers of tests and the annual fission and fusion yields for the atmospheric weapon tests. The artificial radionuclides137Cs,239, 240Pu,90Sr, and other transuranics are used for monitoring and study by many institutes and organizations in many countries for the following reasons: (i)137Cs and90Sr are conservative in the open sea, the most abundant anthropogenic radionuclides, and the main contributors to biological exposure; and (ii) the very long‐lived239, 240Pu is nonconservative and the most abundant among transuranics. The number of observations of these radionuclides in each sea area is summarized. Global distribution of137Cs decay corrected for accumulative deposition as of January 1, 1970 is described as the initial condition of137Cs inventory in the world ocean. The collective effective dose commitment to the world population from artificial and natural radionulides in the marine food is described. The current radionuclide levels in the world ocean are low and therefore of no concern from the radiological point of view.
Civilian Nuclear Accidents
Authors: Runde Wolfgang , Neu Mary P. , Goff George S.
Published: December 2011

Since the discovery of plutonium and its use for nuclear weapons and nuclear energy radionuclides have been dispersed into the environment and contribute significantly to the global presence of anthropogenic radionuclides. Today, nuclear power plants are controlled by the national radiation protection authorities but are continuously emitting the small amounts of radioactivity permitted by the national health authorities. Other releases originate from the use of radionuclides in medical diagnostic and therapeutic treatments. Although these releases are minor compared to natural radioactivity and anthropogenic radionuclides, they contribute to the current radiation background. The anthropogenic actinides in the northern hemisphere mainly originated during nuclear weapons testing, fallout from the reactor accident at Chernobyl, atmospheric burnup of nuclear satellites, and intentional discharges of liquid waste streams from industrial‐scale nuclear reprocessing facilities. Despite the increasingly sophisticated engineered reactor and processing systems, accidents since the 1950s have resulted in the release of radioactivity to the environment. The most prominent accidents that led to a significant dispersion of radionuclides are the Three Miles Island accident, the Windscale Fire, and the Chernobyl accident. In this article, we discuss these events and other nonweapons related uncontrolled releases of radioactivity into the environment.
Photosynthesis: Energy Conversion
Authors: Ulas Gözde , Brudvig Gary W.
Published: December 2011

The process of water oxidation and carbon dioxide reduction in oxygenic photosynthesis involves a complex series of events that start with light energy capture and end with its storage in the form of the chemical energy in glucose. These reactions provide a solution to efficient solar energy conversion into high‐energy chemicals. The principles revealed by study of natural photosynthetic systems may be used to design artificial systems for solar fuel production. Understanding the light‐driven oxidation of water, in particular, is of high interest, as this half reaction could be used in sustainable solar fuel production by processes of artificial photosynthesis to meet the world's growing energy demand. In this article, we look into the intricate photosynthetic machinery and the various processes that it performs in order to efficiently capture, convert, and store light energy. Our main focus is on the so‐called “light” reactions, where specific processes are driven by direct light absorption. As a result, reducing equivalents are extracted from water and transferred to NADP+, to be used in the carbon‐fixing reactions, which are not directly modulated by sunlight. We describe the characteristic features of each protein in the photosynthetic electron‐transport machinery, and specifically focus on the water‐oxidation catalysis performed as the first step of oxygenic photosynthesis by the metalloenzyme photosystem II, due to its relevance to synthetic biomimetic water‐oxidation catalysts. Several processes that photosystem II employs to couple light energy absorption to catalytic turnover are discussed, including proton and electron transfers, redox leveling, charge accumulation, and proposed catalytic mechanisms.
Energy Research: Computational Challenges
Authors: Batista Victor S.
Published: December 2011

The emergence of photocatalytic solar cells based on semiconductor materials functionalized with earth‐abundant transition metal complexes represent a promising development for the sustainable production of fuel from renewable resources (e.g., water). This article reviews recent advances in studies of nanoporous TiO2 thin films sensitized with manganese catalysts, with emphasis on recent computational work integrated with synthesis, electrochemistry, and spectroscopy. The resulting interdisciplinary approach addresses fundamental aspects that affect the overall efficiency of photocatalytic mechanisms, including proton‐coupled electron transfer, rectification of interfacial electron transfer, and visible light absorption, providing guidelines for the design of novel photocatalytic materials for fuel production.
6‐Pyruvoyl‐Tetrahydropterin Synthase
Authors: Nar Herbert
Published: December 2011

The 6‐pyruvoyl‐tetrahydropterin synthase (PTPS), a zinc‐dependent, heat‐stable, homohexameric protein complex of approximately 90 kDa molecular weight catalyzes the conversion of dihydroneopterin triphosphate to 6‐pyruvoyl‐tetrahydropterin, the second of three enzymatic steps in the synthesis of tetrahydrobiopterin from GTP.

The 6‐pyruvoyl‐tetrahydropterin synthetase monomer forms a compact, single‐domain α + β structure containing a sequential, four‐stranded, antiparallel β‐sheet. Oligomerization occurs through association of monomers via their β‐sheets that form a 12‐stranded β‐barrel structure that is duplicated in the functional hexameric form via a head‐to‐head association of two trimers.

The PTPS active site is a 12‐Å deep cavity that is located on the interface of three monomers, two from one trimer and one subunit from the other trimer. The Zn(II) binding site is located at the center of the cavity. The transition metal is bound to the NE2 atoms of the three histidine residues. The role of the catalytic metal is to correctly position the substrate, to polarize the carbon–oxygen bonds for facile proton release from the substrate, and to prevent cleavage of the C1′‐C2′ substrate side‐chain bond.

In addition, PTPS contains an intersubunit catalytic triad motif composed of the amino acid residues CysA42, HisB89, and AspB88 from two neighboring monomers (A and B) that putatively function as a relay system for proton abstraction from substrate and reaction intermediate. Residue GluA133 may represent the key residue for the stereospecificity of the catalyzed reaction.
E. coli Alkaline Phosphatase
Authors: Kantrowitz Evan R
Published: December 2011

Escherichia colialkaline phosphatase (AP) is a metalloenzyme that catalyzes the nonspecific hydrolysis of phosphomonoesters. Because of the extensive functional and structural studies available on the AP fromE. coli, this enzyme has become the model for all APs. The two active sites of dimeric AP each contain binding sites for two Zn2+and one Mg2+. These metals are critical for dimer formation and catalytic activity. The reaction proceeds via a phosphoseryl intermediate formed by the attack of the hydroxyl oxygen of Ser102 on the phosphorus of the substrate. The substrate is stabilized in the active site by binding to Zn2+. In the second step of the double in‐line displacement mechanism, a hydroxyl bound to Zn2+hydrolyzes the phosphoseryl intermediate. Under basic conditions, the slow step in the mechanism is the release of phosphate from the noncovalent enzyme–phosphate complex. X‐ray structures of the free enzyme, the phosphoseryl intermediate, an enzyme–vanadate complex that mimics the transition state, and the enzyme–phosphate noncovalent complex have been used to delineate molecular details of the catalytic mechanism. Sequence alignments of APs from various species have been used to provide explanations for the enhanced activity of the mammalian APs as compared to the bacterial APs and why certain APs utilize Co2+in place of Zn2+. The molecular details of phosphate hydrolysis ascertained from the study of AP has applications to other enzymes that are involved in phosphate ester hydrolysis.