bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inorganic Nanomaterials Synthesis Using Ionic Liquids
Authors: Taubert Andreas 
Published: December 2011

AbstractIonic 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

AbstractEssential 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

AbstractMetallopharmaceuticals 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

AbstractThe 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

Abstract

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

AbstractThis 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

Abstract
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

Abstract
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

AbstractAlmost 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

Abstract

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

AbstractCisplatin 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

AbstractComputation 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

Abstract

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

Abstract
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

Abstract
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

AbstractThe 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

AbstractCluster 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

AbstractThe 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

AbstractRadionulcides 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

AbstractThe 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

AbstractThe 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.