bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantum‐Chemistry‐Centered Normal Coordinate Analysis (
QCC
‐
NCA
): Application of
NCA
for the Simulation of the Vibrational Spectra of Large Molecules
Authors: Lehnert Nicolai 
Published: September 2009

Abstract

Vibrational spectroscopy is a powerful spectroscopic method that provides detailed information about the geometric and electronic structural properties of materials, compounds, and biomolecules. In the case of transition‐metal complexes, for example, vibrational spectra allow for the determination of the oxidation and spin state of the metal. In addition, vibrational spectroscopy is of great value in monitoring the binding and activation of small molecules, especially diatomics X–Y (O
2
, N
2
, CO, NO, etc.) and their derivatives, by transition‐metal complexes. Here, the coordination, reduction, protonation, derivatization, etc., of the diatomic can be monitored via the X–Y and metal‐XY bond strengths. Usually, the corresponding X–Y and metal‐XY vibrational frequencies are used for such correlations. This, however, is problematic because the energies of normal modes in general do not correlate directly with bond strengths, as they also depend on mode mixing and atomic masses. Because of this, it is much better to compare the X–Y and metal‐XY force constants along a reaction coordinate or between different species to identify chemically important changes/differences in bond strengths. This poses one problem: force constants are obtained from normal coordinate analysis (NCA), but how can this type of analysis be performed routinely for large molecules with many vibrational degrees of freedom, especially if the interest is focused on a small subunit of the molecule (the metal‐XY bond), whereas the other organic ligands L of the metal are of limited interest? The quantum chemistry centered normal coordinate analysis (QCC‐NCA) provides a solution to this problem by using density functional theory (DFT) calculations to generate an initial force field, followed by refinement of the limited number of force constants of the metal‐XY subunit only, whereas all other force constants remain unchanged. The available QCC‐NCA software allows one to perform this kind of analysis with minimal effort. This article provides a general introduction to the QCC‐NCA method and the underlying principles of vibrational analysis, combined with illustrative examples for applications from the area of the transition‐metal mediated activation of N
2
, O
2
, and NO. Special focus is put on the electronic structures and reactivities of ferrous‐heme nitrosyls, where the Fe–NO and N–O force constants have provided key insight into the activation of NO as a function of the trans ligand. The latest development with respect to the QCC‐NCA method is the calculation of nuclear resonance vibrational spectroscopy (NRVS) intensities, which is described in the final sections of this article.
Quantum Mechanical/Molecular Mechanical (
QM
/
MM
) Methods and Applictions in Bioinorganic Chemistry
Authors: Ryde Ulf 
Published: September 2009

Abstract
The combination of quantum mechanics and molecular mechanics (QM/MM) methods is a promising approach to study the structure, function, and properties of proteins. The number of QM/MM applications on metalloproteins has been steadily increasing and it is the method of choice to study the influence of the protein onto the structure, spectroscopy, and energetics of an active site. In particular, it has been shown that QM/MM calculations can provide geometries of metal sites in proteins with an accuracy that is better than in low‐ and medium‐resolution crystal structures. However, it is quite hard to obtain reliable and converged energies. Therefore, QM/MM is still an area of method development and no consensus of the best treatment of a protein has yet been reached. This review covers various aspects of QM/MM studies of metalloproteins, including methods to incorporate experimental data in the calculations, methods to obtain reliable energies, as well as some examples of typical applications.
Multiconfigurational Quantum Mechanics (QM) for Heavy Element Compounds
Authors: Roos Björn O. 
Published: September 2009

AbstractOne frequently used quantum chemical approach for the studies of transition metal and other heavy element compounds is the complete active space self consistent field (CASSCF) method in combination with multiconfigurational second‐order perturbation theory (CASPT2). Here, we describe this method and some of its typical applications. The basic idea is to construct a wave function that gives a qualitatively correct description of the electronic structure already at the lowest level of theory. This should be possible for all sorts of electronic states independent of spin multiplicity and excitation level. Strong mixing of configurations makes it necessary to use a multiconfigurational approach in such cases. It should also be possible to use for all atoms of the periodic system. The CASSCF wave function fulfills, in principle, this requirement because it is full configuration interaction (CI), albeit in a limited space of active orbitals. The addition of dynamic electron correlation is necessary to give quantitative results. The suggested solution is to compute this energy using second‐order perturbation theory (CASPT2) because it is relatively simple and allows applications to a wide variety of systems and many electrons. Relativistic corrections are included using a Douglas‐Kroll‐Hess Hamiltonian. The method is scrutinized and illustrated by some applications in transition metal and actinide chemistry.
Structural Origins of Noninnocent Coordination Chemistry
Authors: Szilagyi Robert K. 
Published: September 2009

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.
Electronic Structure of Metal—Metal Bonds
Authors: McGrady John E. 
Published: September 2009

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.
Molecular Mechanics in Bioinorganic Chemistry
Authors: Deeth Robert J. 
Published: September 2009

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.
Spin‐Orbit Coupling: Effects in Heavy Element Chemistry
Authors: Kaltsoyannis Nikolas 
Published: September 2009

Abstract

Starting from the premise that the chemical consequences of scalar relativistic effects are by now largely understood, and may be incorporated more or less routinely into quantum chemical calculations, this contribution focuses on the historically less widely investigated part that spin‐orbit coupling plays in heavy element electronic structure. The effects of relativity are first summarized, followed by a discussion of the principal approaches to the calculation of molecular electronic structure and how relativistic effects may be incorporated into them. Two approaches for the calculation of spin‐orbit coupling effects are then presented; namely, the spin‐orbit coupled time‐dependent density functional theory technique of Wang
et al
. [Wang, F.; Ziegler, T.; van Lenthe, E.; van Gisbergen, S.; Baerends, E. J.
J. Chem. Phys.
2005
,
122
, 204103] and the spin‐orbit restricted active space state interaction method of Roos and coworkers [Roos, B. O.; Malmqvist, P. A.
Phys. Chem. Chem. Phys.
2004
,
6
, 2919]. Recent applications of both approaches to the electronic structure of p, d, and f block systems are then discussed, with emphasis on the improved understanding and agreement with experiment that these methods yield.
Algal Photosynthesis
Authors: Moroney James V , Ynalvez Ruby A 
Published: September 2009

AbstractAlgae are a very diverse group of predominantly aquatic photosynthetic organisms that account for almost 50% of the photosynthesis that takes place on Earth. Algae have a wide range of antenna pigments to harvest light energy for photosynthesis giving different types of algae their characteristic colour. Early work done with algae contributed much to what is presently known about the carbon dioxide fixation pathway and the light harvesting reactions. The processes of photosynthesis in algae and higher plants are very similar. From among the three types of carbon dioxide‐concentrating mechanisms known in photosynthetic organisms, two types are found in different types of algae. Algae are proposed to play a role in the global carbon cycle by helping remove excess carbon dioxide from the environment. Recently, algae are recognized as a promising biodiesel source due to its efficient absorption and conversion of solar energy into chemical energy.Key Concepts:Algal photosynthesis account for almost half of the photosynthetic carbon fixed every year.Scientists have utilized different algal species including algal mutants to study different aspects of photosynthesis.Algae's efficiency at pulling inorganic carbon out of the environment is dependent on growth condition which implies the presence of an inducible carbon dioxide‐concentrating mechanism in algal cells.The proposed mechanism for carbon dioxide acquisition in algae includes active HCO3−accumulation, Rubisco packaging in specialized structures and the presence of a carbonic anhydrase near the location of Rubisco.Carbonic anhydrase is an enzyme that interconverts carbon dioxide and hydrogencarbonate which supply Rubisco with carbon dioxide from the pool of HCO3−.The major antenna pigments in algae include chlorophylls, phycobiliproteins and carotenoids and the variation in the composition and relative abundance of these pigments give algae their distinctive colour.Antenna complexes are proteins with many bound antenna pigments which are important in absorbing light energy.Algal photosynthesis is thought to increase with increase in nutrient, that is, N, P and Fe availability.If the algal photosynthesis would increase more carbon dioxide would be removed from the environment.Algae grow faster and are very efficient in absorbing and converting solar energy into chemical energy which is mainly in the form of triacylglycerols.
Aminoacyl‐t
RNA
Synthetases
Authors: Arnez John G , Moras Dino 
Published: September 2009

Abstract

Aminoacyl‐tRNA synthetases
catalyse a key reaction in protein biosynthesis. They match the 20 amino acids to the genetic code by specifically attaching them to their adaptors, transfer
ribonucleic acid
(tRNA) molecules. The reaction proceeds in two steps: the amino acid is first activated by adenosine triphosphate (ATP) to form aminoacyl adenylate, and then the aminoacyl group is transferred to the terminal ribose of tRNA. This family of enzymes is divided into two classes, based on the similarities in primary structure and architecture of the active site domains; the two architectures are characterized by two modes of binding of ATP, the intermediate aminoacyl adenylate and the acceptor end of tRNA, which result in two regioselectivities of amino acid attachment to the terminal ribose of the tRNA.
Aminoacyl‐tRNA synthetases
are modular enzymes; to the central active site module are attached various domains with diverse functions such as tRNA‐binding and amino acid editing. The primary subject of this article are structural and functional aspects of these enzymes.

Key Concepts

Aminoacylation is a key reaction in protein biosynthesis, as it matches the standard 20 amino acids to the genetic code.

Aminoacylation is generally catalysed by aminoacyl‐tRNA synthetases, a family of 20 enzymes, one for each standard amino acid and a set of corresponding (cognate isoacceptor) tRNAs.

Aminoacylation proceeds in two steps, where the amino acid is first activated by ATP to form aminoacyl adenylate, a mixed anhydride, and then transferred to form an ester bond with the terminal ribose of tRNA.

Aminoacyl‐tRNA synthetases are divided into two classes, based on the similarities in primary structure (sequence) and architecture of their active site domains.

Aminoacyl‐tRNA synthetases are modular enzymes; to the central active site module are attached various domains with diverse functions such as tRNA‐binding and amino acid editing.

Aminoacyl‐tRNA synthetases are highly specific enzymes, attaching the correct amino acids to the corresponding tRNAs with high fidelity.

Aminoacyl‐tRNA synthetases of the two classes generally bind the acceptor arm of tRNA in two ways that constitute mirror images of each other, resulting in two different regioselectivities of amino acid attachment to the tRNA.
Lectins
Authors: Sharon Nathan 
Published: September 2009

Abstract

Lectins, a class of sugar‐specific and cell‐agglutinating proteins of nonimmune origin that are devoid of enzymatic activity, are ubiquitous in nature. Plant lectins are invaluable tools for the study of carbohydrates, in solution and on cells, and are also employed for purging of bone marrow for transplantation into ‘bubble children’. Bacterial cell surface lectins mediate the attachment of the organisms to host cell surfaces in the initiation of infection; their blocking by suitable sugars can serve as a basis of antiadhesion therapy of bacterial diseases. Those of animals control the biosynthesis of glycoproteins, play key roles in cell interactions in the immune system and serve as innate immunity agents against microbial pathogens. They also monitor the migration of leucocytes in blood vessels and contribute to proliferation and metastasis of tumour cells.

Key concepts:

Antiadhesion therapy

Carbohydrate specificity

Cell recognition

Circular homology

Glycoarrays; lectin arrays

Lectin replacement therapy

Surface carbohydrates

Multisubunit proteins
Protein‐Coding Segments: Evolution of Exon–Intron Gene Structure
Authors: Rogozin Igor B 
Published: September 2009

Abstract

Many eukaryotic genes are disrupted by noncoding regions of
deoxyribonucleic acid
(DNA) of variable sizes called introns, giving the genes an exon–intron structure. Origin and evolution of introns is an important, long‐standing problem. The availability of multiple, complete genome sequences allows one to address many fundamental evolutionary questions. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes between animals, fungi, plants and protists. The data on intron positions were used as the starting point for evolutionary reconstruction with various phylogenetic methods. These methods reconstructed intron‐rich ancestors but in many cases inferred lineage‐specific high levels of intron loss and gain. These results indicate that numerous introns were present already at the earliest stages of evolution of eukaryotes and are compatible with the hypothesis that the original, catastrophic intron invasion accompanied the emergence of the eukaryotic cells.

Key concepts:

The exon–intron gene structure is highly dynamic.

Orthologous genes from distant eukaryotic species share up to 25–30% intron positions.

Intron gains and losses might occur during limited time spans.

The Last Eukaryotic Common Ancestor was intron‐rich.

In the course of evolution, the splice signal shifts from exons to introns.

The scenario of the origin and evolution of introns that is best compatible with the results of comparative genomics goes as follows: self‐splicing introns since the earliest stages of life's evolution followed by numerous spliceosomal introns invading genes of the emerging eukaryotes and subsequent lineage‐specific loss and gain of spliceosomal introns.
Hypersensitivity: Immunological
Authors: Thomas Wayne R , Cunningham Paula T 
Published: September 2009

Abstract

Immunological hypersensitivity reactions are immune responses that produce tissue damage. In 1963, a classification system was introduced by Gell and Coombs based on how immune reactions produced the damage, and to this day it has provided a framework for the understanding of immune effector mechanisms produced directly by antigen‐specific responses or by the activation of innate immune mechanisms. It was updated in 2001 to introduce type subcategories of the type IV delayed hypersensitivity to describe cell‐mediated allergy in the light of the recent knowledge of T‐cell function. Although the classification system remains useful for describing mechanisms of tissue damage, the damage produced in an individual hypersensitivity reaction is usually produced by a mixture of mechanisms. The type I hypersensitivity mediated by IgE antibody to allergens in asthma and hay fever is, for example, typically accompanied by eosinophils from the Th2 type IVb responses.

Key Concepts

Type I hypersensitivity consists of the IgE‐mediated immediate hypersensitivity responses found in anaphylaxis and asthma attacks and slower responses caused by inflammatory cascades triggered by mediators released in the immediate reaction and by accompanying Th2 responses.

Type II hypersensitivity is mediated by the direct effects of antibody and complement‐mediated killing or opsonization.

Type III hypersensitivity is mediated by the formation of antigen–antibody complexes that either activate complement for direct toxic effects or attract inflammatory cells, especially neutrophils that bind the complexes by Fc receptors and cause tissue damage.

Type IV hypersensitivity can be subdivided depending on the type of T cell activated by the immune response.

Type IVa corresponds to the classical monocytic tuberculin‐type delayed hypersensitivity mediated by Th1 cells.

Type IVb corresponds to the eosinophilic inflammation produced by Th2 cells.

Type IVc corresponds to tissue damage produced by cytotoxic T cells and can have either granzyme B/perforin or Fas/FasL killing mechanisms.

Type IVd hypersensitivity produces tissue damage by the infiltration of neutrophils attracted by T cells producing IL‐8.

Type V hypersensitivity categorizes the damage caused by agonist effects of antibodies binding to endocrine receptors.

The tissue damage in individual hypersensitivity reactions is often caused by a mixture of the types of hypersensitivity reaction, for example, a combination of types I and IVa. IVb and IVc in contact hypersensitivity.
Arenaviruses
Authors: Kunz Stefan 
Published: September 2009

Abstract

The arenaviruses are a large and diverse group of enveloped
ribonucleic acid
(RNA) viruses that merit significant attention as powerful experimental models and important human pathogens. The prototypic arenavirus lymphocytic choriomeningitis virus (LCMV) has been instrumental in many landmark studies on virus–host interaction and antiviral immunity. Several arenaviruses, including

Lassa virus

in Africa and the South American arenaviruses such as

Junin virus

,

Guanarito virus

,

Machupo virus

and

Sabia virus

cause severe viral haemorrhagic fevers in humans and represent serious public health problems. Arenavirus haemorrhagic fevers are among the most devastating emerging human diseases with high fatality rates in hospitalized patients and a limited therapeutic repertoire available. Moreover, compelling evidence indicates that the worldwide‐distributed LCMV is a neglected human pathogen of clinical significance, especially in cases of congenital infection and immunocompromised individuals, as tragically illustrated by recent fatal cases of transplant‐associated infections.

Key concepts
Arenaviruses are zoonotic pathogens that are carried in nature by persistent infection of rodent hosts. The interaction of prototypic arenavirus LCMV with its host species, the mouse, provided fundamental concepts in virology and immunology. The current diversity of arenaviruses is the result of a remarkable long‐term co‐evolution between the viruses and their rodent hosts. When infecting humans as accidental hosts, some arenaviruses cause severe haemorrhagic fevers with high mortality. Arenavirus haemorrhagic fevers belong to the worst human diseases and represent important public health problems in many regions of the developing world. The epidemiology, clinical disease, diagnostics and current treatment for these diseases will be discussed. During the past decade much has been learned about the molecular and cell biology of the arenavirus life cycle. Cellular receptors for all major human pathogenic arenaviruses have been identified and first light has been shed on their mechanisms of cell entry. The advent of a powerful reverse genetic system for arenaviruses has allowed to elucidate the mechanisms of arenavirus replication, gene expression and assembly and release of progeny virions from infected cells. The investigation of the fundamental virology of arenaviruses will likely provide novel avenues for the development of efficacious therapeutic strategies against these important human pathogens.