bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling Metalloenzymes with Density Functional and Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) Calculations: Progress and Challenges
Authors: Friesner Richard A. 
Published: December 2011

AbstractWe discuss the application of density functional theory (DFT)‐based quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods to the modeling of metalloenzyme chemistry. The state of the art of current approaches in terms of accuracy and reliability is considered, primarily in the context of two example systems, methane monooxygenase (MMO) and cytochrome P450. Key issues include the intrinsic accuracy of current DFT functionals for metal‐containing systems, modeling of conformational changes in protein structure, treatment of environmental electrostatic effects, use of spectroscopic calculations to help in identifying the structures of intermediates, and the validity of standard transition state theory approximations using a small number of optimized structures, as opposed to performing full statistical mechanical sampling with methods such as free energy perturbation theory. Considerable insight into the catalytic cycles of both MMO and P450 have been obtained over the past decade using existing computational methods, in close coupling with experimental efforts. However, significant challenges remain, both for the two systems that we consider here and for the modeling of metalloenzyme chemistry in the general case. A number of the most important of these challenges are identified and prospects for addressing them via improvements of the theoretical methodology are discussed.
Electronic Structure Calculations: Dinitrogen Reduction in Nitrogenase and Synthetic Model Systems
Authors: Tuczek Felix 
Published: December 2011

Abstract

Theoretical studies on the binding and reduction of dinitrogen and alternative substrates at the iron‐molybdenum cofactor (FeMoco) of nitrogenase are reviewed. Before considering the enzymatic pathways, the available mechanistic scenarios for N
2
reduction in small‐molecule model systems are discussed. These systems are divided into those involving an end‐on terminal (Sections 2.1 and 2.2) and those involving a bridging coordination of N
2
(Section 2.3). For the enzyme, calculations of Noodleman
et al
., Nørskov
et al
., Blöchl
et al
., Dance, and others are reviewed and compared to each other. Conclusions are drawn with respect to the most probable scenario of N
2
reduction at the FeMoco and the open mechanistic questions in this research area.
Electronic Structure of Metal—Metal Bonds
Authors: McGrady John E. 
Published: December 2011

Abstract
The nature of bonding between two metal centres is extremely variable, spanning formal bond orders from 1 to 6, and this leads to a great diversity of chemical properties in metal cluster compounds. The bonds themselves have components with σ, π, δ, and ϕ symmetry, each of which has its own distinct properties. This article reviews the key features of these different bonding components.
Computational Studies: Boranes
Authors: Shameema Oottikkal , Jemmis Eluvathingal D. 
Published: December 2011

Abstract

Computational studies on boranes, in recent years, are summarized with the special emphasis on the macropolyhedral boranes. Computational studies to understand the energetics, geometry, aromaticity, and reactivity of boranes and substituted boranes are reviewed. There is a recent interest in macropolyhedral boranes because of their uses in boron neutron capture therapy (BNCT) of cancer, ionic liquids, weakly coordinating ions, and materials chemistry. The
mno
rule, which is the electronic counting rule for the macropolyhedral boranes, is explained. Even though the electron counting rule explains the electronic structure of macropolyhedra, it cannot explain the relative stability of isomers since different structures are possible with the same electron count. There have been many computational studies to explain the relative stability of various structural patterns in macropolyhedral boranes. We have used the concept of orbital compatibility to explain the relative energies of different macropolyhedral structural patterns. Computations on the
closo
‐
closo
macropolyhedral boranes show that a large polyhedral borane prefers to condense with a smaller polyhedron owing orbital compatibility. Even though only a few
closo
‐
closo
macropolyhedral structures have been synthesized experimentally, calculations suggest optimism for the synthesis of many condensation products. A brief discussion about the use of the computational methods for the rearrangement of the B
20
H
16
skeleton reacting with ligands is also provided.
Molecular Mechanics in Bioinorganic Chemistry
Authors: Deeth Robert J. 
Published: December 2011

Abstract
Molecular mechanics (MM) in bioinorganic chemistry separates into applications involving s‐block cations and those involving the d‐block elements. The former behave essentially as hard, charged spheres and can be treated efficiently and accurately with conventional force fields with little or no additional parameterization. The d‐block elements are significantly more challenging. The apparently complex electronic structures associated with the open d shell, the challenges of modeling reaction pathways within empirical methods, the lack of suitable software and MM parameters, and the rise of hybrid quantum mechanics/molecular mechanics (QM/MM) have all contributed to MM for transition metal systems being relatively underdeveloped. Given that metal‐ligand binding in coordination complexes and metalloenzyme active sites is essentially identical, this has significant consequences for bioinorganic applications. However, a critical handicap of any QM‐based method, including QM/MM, is that it is computationally expensive to carry out the configurational sampling or molecular dynamics necessary to get an accurate structure or reaction pathway. In contrast, MM is orders of magnitude faster and therefore has the potential to make a significant impact in bioinorganic chemistry. Encouraging progress is being made, especially with respect to d electron effects where ligand field molecular mechanics has demonstrated QM‐like performance at MM‐like speeds.
Gaussian Basis Sets for Quantum Mechanical (
QM
) Calculations
Authors: Peterson Kirk A. 
Published: December 2011

Abstract
In addition to the selection of a particular electronic structure method, the choice of basis set to use in an ab initio calculation can also strongly influence the accuracy of the results. The possibility of decoupling the errors associated with the chosen method and basis set is central to any systematic treatment of electronic structure. With this in mind, the availability, characteristics, and use of accurate Gaussian basis sets across the entire periodic table are reviewed with special emphasis to series of basis sets that improve in quality in a systematic fashion toward the complete basis set limit.
Theoretical Aspects of Main Group Multiple Bonded Systems
Authors: Silaghi‐Dumitrescu Ioan , Petrar Petronela , Nemeş Gabriela , Bruce King R. 
Published: December 2011

Abstract

Computational data on homonuclear multiple bonding between elements of group 13 and heavier elements of group 14 are reviewed. For R

n

EER

n

, there is an increased tendency of bending the RER planes (
n
= 2) or the RE bonds (
n
= 1) toward the EE axis upon descending a group. This is related to the mixing of the valence σ–π orbitals reflecting the tendency of the heavier elements to retain nonbonding character for their
n
s
2
orbital. As a result, the bond orders are also reduced and the EE interaction weakened.
Radionuclides: Anthropogenic
Authors: Mietelski Jerzy W. 
Published: December 2011

AbstractFollowing the definition of anthropogenic radioactivity, the main discoveries in this field made in the 1930s are briefly presented. The main facts about radioisotopes classification, radioactive decay, and artificial radionuclide production are then described. The article then provides a general overview on anthropogenic sources of radioactivity such as nuclear explosions, nuclear accidents, routine releases from nuclear reactors, releases due to nuclear weapon production programs or nuclear fuel reprocessing installations, and nuclear medicine. A description of modern techniques applied in determining radioactivity in the environment as well as a very general introduction to the concept of radioecology and some basic information on environmental remediation are presented.
Speciation: Radionuclides
Authors: Salbu Brit 
Published: December 2011

AbstractTo assess the environmental impact of radioactive contamination of different ecosystems, information on source terms, mobility, biological uptake, and associated effects is needed. However, naturally occurring and artificially produced radionuclides can be present in different physicochemical forms (ions, colloids, nanoparticles, pseudocolloids, particles) influencing the mobility and biological uptake. Following severe nuclear events associated with the nuclear weapon or fuel cycles, a major fraction of refractory radionuclides will be present as radioactive particles; radionuclides are also present as colloids or low molecular mass (LMM) ionic species in effluents from nuclear installations. Thus, the distribution of radionuclide species depends on the source and release scenarios. LMM radionuclide species are believed to be mobile and potentially bioavailable, while high molecular mass (HMM) species such as nanoparticles, colloids, polymers, and pseudocolloids are mobile in water. Radioactive particles are considered biologically inert, but can be retained in filtering organisms as well as in soils and sediments. If mobile species are present, ecosystem transfer is relatively fast, whereas the ecosystem transfer is delayed if particles are present. Owing to time‐dependent transformation processes such as interactions of mobile and reactive radionuclide species with components in soils and sediments or particle weathering and subsequent remobilization of associated radionuclide species, the original distribution of radionuclides deposited in ecosystems will change over time. Therefore, information on radionuclide species released and deposited, as well as on time‐dependent transformation processes influencing the distribution of radionuclide species, is essential for the assessment of the environmental impact and risk associated with radionuclide contamination. This article summarizes available speciation techniques that should be utilized within radioecology, including fractionation and solid‐state speciation, to characterize radionuclide species in waters, soils, and sediments.
Potassium: Radonuclides
Authors: Jun Taehong , Tsay Olga G. , Churchill David G. 
Published: December 2011

Abstract

There are currently 28 known nuclides of potassium (K). Three of these are naturally occurring:
39
K,
40
K, and
41
K of which potassium‐40 is the only naturally occurring radionuclide. With its long half‐life of 1.28 × 10
9
years and an abundance of 0.012%,
40
K is a discrete source of natural radiation. Thus, in potassium‐rich foods, minerals, etc., a distinct natural dose is unavoidable for humans and all living creatures on Earth. Thus, it may be quantified in soil, plants, and animals and allows for various studies. Potassium‐40 may decay to calcium‐40 (89% probability) or may undergo electron capture (EC) to give argon‐40 (11% probability). The
biological
half‐life (excretion time decay) of
40
K, however, is 30 days. As it is often found in many mineral forms, potassium‐40 is a common constituent of soil and water, but not air. There are various reports in which
40
K is tracked migrating from soil(s) into various plants. In countries such as Europe and Brazil, drinking water was also scrutinized and found to contain
abnormal
levels of
40
K. The abundance of
40
K in human diet and foods from places such as China, Pakistan, and Ukraine has also been studied.
Sulfur: Radionuclides
Authors: Tsay Olga G. , Churchill David G. 
Published: December 2011

Abstract35S is a radionuclide with a half‐life of 87.5 days and it decays via β‐emission. It is available from natural and anthropogenic sources. It is cosmogenic, that is, it is produced by the collision of atmospheric argon with cosmic rays. Anthropogenic molecular sources of35S include carbonyl sulfide (CO35S) and hydrogen sulfide (H235S), which are released from nuclear reactors. The impact of the incorporation of these compounds into plants and animals is of particular interest and concern with regard to the accumulation of35S in human food. Radioisotopes of sulfur can be detected by a Geiger–Müller counter and liquid scintillation counting techniques.
Indium: Radionuclides
Authors: Wehmschulte Rudolf J. 
Published: December 2011

Abstract

Although the major isotope
115
indium (95.7% abundance) is a β‐emitter, it has a very long half‐life at 6 × 10
14
(600 trillion) years and hence can be considered practically nonradioactive. Other radioactive indium isotopes are short‐lived and are either part of the decay processes of other radioactive nuclei or are prepared artificially for medicinal and analytical purposes in very small amounts. The environmental impact of radioactive indium isotopes is very minor and standard safety procedures for low‐level wastes are sufficient.
Polonium: Radionuclides
Authors: Alam Lubna , Rahim Mohamed Che Abd 
Published: December 2011

Abstract

All polonium isotopes are radioactive with only three having appreciable half‐lives:
208
Po,
209
Po, and
210
Po. It is a highly toxic element and is a health hazard if taken into the body. Polonium is a naturally occurring radionuclide and is present in the environment and in people at very low concentrations. Polonium concentrations in the environment can vary by orders of magnitude.
210
Po concentration in soil varies according to soil strata, depth, sedimentation and biological processes, fertilization and pH. Incomplete burning of fuels of coal loading plays an important role in the concentration of
210
Po in air. Usually, the activity concentration of
210
Po in surface air is low. Polonium can be separated by irradiating stable bismuth‐209 with thermal neutrons resulting in the formation of radioactive
210
Bi, which decays into
210
Po.
Chlorine: Radionuclides
Authors: Ashworth Daniel , Shaw George 
Published: December 2011

Abstract

Chlorine is ubiquitous in the environment and is an essential element for higher plants and animals. The primary radioactive isotope is
36
Cl, which has a half‐life of 3.01 × 10
5
years and which is produced both naturally and as a result of anthropogenic nuclear activity. This article considers the important sources of
36
Cl in the environment and the subsequent behavior of the radionuclide. The chemistry of radio‐ and stable chlorine is discussed with particular emphasis on its ability to not only exist as the chloride ion but also as organic chlorine. Procedures for the fractionation/speciation and analytical determination of
36
Cl in environmental samples are also reported. Owing to the high solubility of the chloride ion, the potential for a large degree of
36
Cl migration within soils, and from soils into plants is described. The most significant source of
36
Cl is likely to be nuclear waste buried in underground rock repositories. Over extended time periods, if such a repository were to leak,
36
Cl has the potential to move upward with the flow of water into soils and plants. The article describes risk modeling that assesses this important pathway by which humans may become exposed to
36
Cl. Such modeling suggests that
36
Cl leaked from a buried nuclear waste repository has the potential to eventually contaminate soils, plants, well water, and surface waters. However, the radioactive dose associated with this contamination would apparently be relatively low.
Xenon: Radionuclides
Authors: Saey Paul R.J. 
Published: December 2011

Abstract

Radioxenon isotopes are noble gases mainly produced in nuclear fission e.g., uranium‐235. In nuclear medicine, xenon‐133 isotopes are used for measuring the physiological parameters of lung ventilation and to image the lungs. They are further used in isotonic solutions to image blood flow, particularly cerebral blood flow. Most radioactive isotopes of this element are produced by a nuclear fission reaction of uranium‐235, uranium‐238, or plutonium‐239. Xenon‐133 is the most abundant radioxenons observed in environmental samples, although contributions of
131m
Xe and
135
Xe can be determined down to a few percent of the total β‐activity. The minimum detectable concentration (MDC) for
133
Xe in routine samples is about 1 mBq m
−3
. This article will describe the production, applications, occurrence, and measurement of the various xenon isotopes.
Radon: Radionuclides
Authors: Tracy Bliss L. 
Published: December 2011

AbstractRadon is a naturally occurring radioactive gas formed by the decay of uranium and thorium in the Earth's crust. At atomic number 86, it is the heaviest member of the noble or inert gas family, which also includes helium, neon, argon, krypton, and xenon. Unlike the other members of the family, radon has no stable isotopes. Of the 34 known radioactive isotopes of radon, only three are supported by the decay of primordial radionuclides, and only two occur with any significant abundance in nature. The three isotopes, along with their half‐lives, are222Rn (3.8235 days),220Rn (55.6 s), and219Rn (3.96 s). Both222Rn and220Rn decay by the emission of α‐particles and give rise to a number of short‐lived progeny.222Rn and220Rn are the only ones regarded as having any health impacts and this is due to their short‐lived progeny—218Po,214Pb,214Bi, and214Po from222Rn;216Po,212Pb,212Bi,212Po, and208Tl from220Rn. Being a gas, radon diffuses readily into the atmosphere and may build up to hazardous concentrations in confined spaces in homes and underground mines. Radon is the largest single contributor to natural background radiation exposure worldwide. Radon is now recognized as the second leading cause of lung cancer, following tobacco smoking, and is responsible for up to 20 000 deaths per year in the United States and 1900 deaths per year in Canada. Many countries have now established programs to reduce radon exposures to the population.
Protactinium: Radionuclides
Authors: Hasan Asamuddin Abu , Rahim Mohamed Che Abd 
Published: December 2011

Abstract

Protactinium (Pa) is one of the rarest elements that can be found or extracted from the natural source. Protactinium can be found in soil, rocks, water, plants, and animals, but in a very low concentration. There are no uses outside of basic and experimental scientific research and no commercial applications for protactinium.
231
Pa is the most important natural isotope, while
223
Pa is the only artificial isotope.
231
Pa has become important to the scientists because
231
Pa/
230
Th in the ocean can perform as an ocean circulation proxy. Because of its low concentrations, measurement of protactinium using thermal ionization mass spectrometry (TIMS) has become the finest and most promising technique.
Uranium: Radionuclides
Authors: Vandenhove Hildegarde , Hurtgen Christian , Payne Timothy E. 
Published: December 2011

AbstractThis article describes the occurrence, chemistry, and bioavailability of uranium (U) in terrestrial and aquatic environments, its analysis in environmental samples, and remedial measures applicable to uranium‐contaminated water and soil. Uranium is widely distributed throughout the world. There are three main isotopes present in natural uranium, which comprises234U (0.0055%),235U (0.72%), and238U (99.27%). Uranium can occur either in its reduced state (U(IV)), which is generally highly immobile, or in its more soluble and mobile (U(VI)) state. Uranium mobility and bioavailability are governed by oxidation state, complexation by organic and inorganic ligands, pH, sorption by minerals including clays and hydroxides, and interactions with organic matter. In uncontaminated surface waters uranium content is generally low (<1 ppb). Most groundwaters are low in uranium but the concentration range is large (<0.001–2600 ppb), resulting from the interaction of groundwater with naturally occurring uranium‐bearing materials or anthropogenic contamination sources. Since groundwater is a major source for drinking water, various methods have been developed to remove uranium from potable water. Similar methods are applied in wastewater treatment. Extraction and processing of uranium ore or minerals containing natural radionuclides has resulted in the generation of waste streams. The major challenge associated with these contaminated waste streams, residues, or sites is typically the larger volumes of material and the relatively low specific activities.
Neptunium: Radionuclides
Authors: Runde Wolfgang , Goff George S. 
Published: December 2011

AbstractFollowing the element uranium, neptunium is the fourth element in the actinide series. Although primordial neptunium isotopes formed during the creation of the solar system billions of years ago have long since decayed away, neptunium continues to be formed by the nuclear reactions in naturally occurring uranium deposits. Currently, trace amounts of neptunium isotopes can be isolated from uranium ore minerals. Most of present‐day inventory of neptunium originates from human activities, such as nuclear weapons testing, nuclear accidents, or irradiation of uranium fuel for producing nuclear energy. All neptunium isotopes are highly radioactive and pose extreme health hazards to humans when ingested or inhaled. Neptunium exhibits five oxidation states (III–VII) in solution and solid state, but only the IV and V oxidation states are relevant under most environmental conditions. In the +IV state, neptunium is insoluble and forms stable complexes with ligands abundant in natural environments (such as hydroxide, carbonate, or humic substances), and can adsorb onto mobile colloidal matter. In contrast, neptunium(V) forms a soluble dioxo‐cation in solution (NpO$_{2}^{+}$), which exhibits an increased solubility, weaker complex formation, and higher stability in the aqueous phases of aquatic systems. Thus, neptunium(V) is mostly characterized as the dominant solution species, while Np(IV) is found to be adsorbed on sediments, minerals, and colloidal particles. There is no large‐scale use of neptunium in industrial applications.
Plutonium: Radionuclides
Authors: Neu Mary P. , Goff George S. , Runde Wolfgang 
Published: December 2011

AbstractPlutonium is the most debated actinide element because of its dual use in devastating nuclear weapons and beneficial generation of nuclear energy. Plutonium metal exists in several allotropic phases and plutonium in solution exhibits a rich and complex chemistry. The ability to exist in up to four oxidation states makes plutonium unique among all elements. Pu(III) and Pu(VI) form only under reducing or oxidizing conditions, respectively; whereas Pu(IV) and Pu(V) have broad stability ranges within the geochemical bounds of environmental systems. When Pu(IV) is above trace concentration and particulate matter is present, then solids or suspended colloids are the predominant chemical forms. In contrast, Pu(V), as PuO$_{2}^{+}$, has relatively higher solubility as an aquo species or a monomeric complex of natural ligands (hydroxide, chloride, sulfate, etc.). Stronger complexing, polydentate ligands, such as carbonate and organics, tend to increase plutonium solubility by forming very stable Pu(IV) complexes. Minerals, high molecular weight organic matter, and bacteria can either increase or decrease the solubility of plutonium, depending upon their chemical properties, mechanisms of interaction, and the geochemical conditions of the surrounding environment. Plutonium generally has very low solubility, low mobility, and few health consequences from environmental forms, and therefore poses little risk to living systems under nearly all conditions. This article provides a brief overview of the chemistry and behavior of plutonium in aqueous solutions and in the environment.