Showing papers in "Chemical Reviews in 2006"

Synthesis of transportation fuels from biomass: chemistry, catalysts, and engineering.

Abstract: 1.0. Introduction 4044 2.0. Biomass Chemistry and Growth Rates 4047 2.1. Lignocellulose and Starch-Based Plants 4047 2.2. Triglyceride-Producing Plants 4049 2.3. Algae 4050 2.4. Terpenes and Rubber-Producing Plants 4052 3.0. Biomass Gasification 4052 3.1. Gasification Chemistry 4052 3.2. Gasification Reactors 4054 3.3. Supercritical Gasification 4054 3.4. Solar Gasification 4055 3.5. Gas Conditioning 4055 4.0. Syn-Gas Utilization 4056 4.1. Hydrogen Production by Water−Gas Shift Reaction 4056

Chemistry of Carbon Nanotubes

Abstract: Department of Materials Science, University of Patras, 26504 Rio Patras, Greece, Theoretical and Physical Chemistry Institute, National Hellenic Research Foundation, 48 Vass. Constantinou Avenue, 116 35 Athens, Greece, Institut de Biologie Moleculaire et Cellulaire, UPR9021 CNRS, Immunologie et Chimie Therapeutiques, 67084 Strasbourg, France, and Dipartimento di Scienze Farmaceutiche, Universita di Trieste, Piazzale Europa 1, 34127 Trieste, Italy

Water-splitting chemistry of photosystem II.

Abstract: Life on earth is almost entirely solar-powered. We can get some idea of the enormous quantity of energy received from the sun by noting that during daylight hours, the sun provides several thousand times more power to the surface of the U.S.A. than is produced by all of the nation’s electrical power stations. 1,2 Around 50% of the radiation that reaches the earth’s surface, roughly the visible region, is of a frequency useful to photosynthetic organisms. Oxygenic photosynthetic organisms convert this radiation into chemical energy, in the form of carbohydrate and dioxygen, at an optimal efficiency of something like 25%. 3 These products together sustain the rest of aerobic life, with carbohydrate acting as a source of high-energy electrons and dioxygen providing a lower-energy destination for these electrons. The overall equation of oxygenic photosynthesis is given in eq 1, where (CH2O) represents carbohydrate:

Assembly-line enzymology for polyketide and nonribosomal Peptide antibiotics: logic, machinery, and mechanisms.

Abstract: biotics of the penicillin and cephalosporin families, 3,4 as well as the glycopeptides of the vancomycin family 5 (Figure 1a). * To whom correspondence should be addressed: christopher_walsh@ hms.harvard.edu. † Harvard Medical School. ‡ Harvard University. Christopher T. Walsh is the Hamilton Kuhn Professor of Biological Chemistry and Molecular Pharmacology (BCMP) at Harvard Medical School. He has had extensive experience in academic administration, including Chairmanship of the MIT Chemistry Department (1982−1987) and the HMS Biological Chemistry & Molecular Pharmacology Department (1987−1995) as well as serving as President and CEO of the Dana Farber Cancer Institute (1992−1995). His research has focused on enzymes and enzyme inhibitors, with recent specialization on antibiotics. He and his group have authored over 590 research papers, a text (Enzymatic Reaction Mechanisms), and two books (Antibiotics: Origins, Actions, Resistance and Posttranslational Modification of Proteins: Expanding Nature’s Inventory). He is a member of the National Academy of Sciences, the Institute of Medicine, and the American Philosophical Society.

Specific ion effects at the air/water interface.

Abstract: Aqueous ion-containing interfaces are ubiquitous and play a key role in a plethora of physical, chemical, atmospheric, and biological processes, from which we mention just a few illustrative examples: (i) Ions at the air/water interface are important for atmospheric chemistry involving ocean surfaces and seawater aerosols, 1-5 as well as that of the Arctic snowpack covered by sea spray. 6,7 (ii) Many salts (such as NaCl) tend to inhibit bubble coalescence, 8-12 which is one of the reasons why foam is formed when waves break in the ocean but not in freshwater lakes. (iii) Brine rejection occurring at the seawater/ice interface has profound climatic effects in polar regions. 13 (iv) The aqueous electrolyte/metal interface is involved in electrode and corrosion processes. 14,15

Molecular dynamics: survey of methods for simulating the activity of proteins.

Abstract: The term molecular mechanics (MM) refers to the use of simple potential-energy functions (e.g., harmonic oscillator or Coulombic potentials) to model molecular systems. Molecular mechanics approaches are widely applied in molecular structure refinement, molecular dynamics (MD) simulations, Monte Carlo (MC) simulations, and ligand-docking simulations. Typically, molecular mechanics models consist of spherical atoms connected by springs which represent bonds. Internal forces experienced in the model structure are described using simple mathematical functions. For example, Hooke’s law is commonly used to describe bonded interactions, and the nonbonded atoms might be treated as inelastic hard spheres or may interact according to a Lennard-Jones potential. Using these simple models, a molecular dynamics simulation numerically solves Newton’s equations of motion, thus allowing structural fluctuations to be observed with respect to time. Dynamic simulation methods are widely used to obtain information on the time evolution of conformations of proteins and other biological macromolecules1–4 and also kinetic and thermodynamic information. Simulations can provide fine detail concerning the motions of individual particles as a function of time. They can be utilized to quantify the properties of a system at a precision and on a time scale that is otherwise inaccessible, and simulation is, therefore, a valuable tool in extending our understanding of model systems. Theoretical consideration of a system additionally allows one to investigate the specific contributions to a property through “computational alchemy”,5 that is, modifying the simulation in a way that is nonphysical but nonetheless allows a model’s characteristics to be probed. One particular example is the artificial conversion of the energy function from that representing one system to that of another during a simulation. This is an important technique in free-energy calculations.6 Thus, molecular dynamics simulations, along with a range of complementary computational approaches, have become valuable tools for investigating the basis of protein structure and function. This review offers an outline of the origin of molecular dynamics simulation for protein systems and how it has developed into a robust and trusted tool. This review then covers more recent advances in theory and an illustrative selection of practical studies in which it played a central role. The range of studies in which MD has played a considerable or pivotal role is immense, and this review cannot do justice to them; MD simulations of biomedical importance were recently reviewed.4 Particular emphasis will be placed on the study of dynamic aspects of protein recognition, an area where molecular dynamics has scope to provide broad and far-ranging insights. This review concludes with a brief discussion of the future potential offered to advancement of the biological and biochemical sciences and the remaining issues that must be overcome to allow the full extent of this potential to be realized. 1.1. Historical Background MD methods were originally conceived within the theoretical physics community during the 1950s. In 1957, Alder and Wainwright7 performed the earliest MD simulation using the so-called hard-sphere model, in which the atoms interacted only through perfect collisions. Rahman8 subsequently applied a smooth, continuous potential to mimic real atomic interactions. During the 1970s, as computers became more widespread, MD simulations were developed for more complex systems, culminating in 1976 with the first simulation of a protein9,10 using an empirical energy function constructed using physics-based first-principles assumptions. MD simulations are now widely and routinely applied and especially popular in the fields of materials science11,12 and biophysics. As will be discussed later in this review, a variety of experimental conditions may be simulated with modern theories and algorithms. The initial simulations only considered single molecules in vacuo. Over time, more realistic or at least biologically relevant simulations could be performed. This trend is continuing today. The initial protein MD simulation, of the small bovine pancreatic trypsin inhibitor (BPTI), covered only 9.2 ps of simulation time. Modern simulations routinely have so-called equilibration periods much longer than that, and production simulations of tens of nanoseconds are routine, with the first microsecond MD simulation being reported in 1998.13 In addition, the original BPTI simulation included only about 500 atoms rather than the 104-106 atoms that are common today. While much of this advancement results from an immense increase in availability of computing power, major theoretical and methodological developments also contribute significantly. The number of publications regarding MD theory and application of MD to biological systems is growing at an extraordinary pace. A single review cannot do justice to the recent applications of MD. Using data from ISI Web of Science, the authors estimate that during 2005 at least 800 articles will be published that discuss molecular dynamics and proteins. The historical counts are shown in Figure 1. Open in a separate window Figure 1 Articles matching ISI Web of Science query “TS=(protein) AND TS=(molecular dynamics)”.

Hyaluronidases: their genomics, structures, and mechanisms of action.

Abstract: 1.1 Overview of the hyaluronidases The hyaluronidases (Hyals) are classes of enzymes that degrade predominantly hyaluronan (HA). The term “hyaluronidase” is somewhat of a misnomer since they have the limited ability to degrade chondroitin (Ch) and chondroitin sulfates (ChS), albeit at a slower rate. It is a common misconception that the bacterial Hyals have absolute specificity for HA. This is incorrect. Both bacterial 1 and vertebrate enzymes degrade Ch and ChS, albeit at a slower rate. The plausible reason for this broader specificity is that chondroitins preceded HA in evolution. For example, the nematode, Caenorhabditis elegans, contains only Ch and no HA, with only one Hyal-like sequence (unpublished observations). This is most likely a chondroitinase. It is plausible, therefore, that the vertebrate Hyals evolved originally from pre-existing chondroitinases 1. This may explain why Hyals, recognizing their ancestral substrate, retain limited ability to also degrade Ch and ChS. The Hyals from bacteria have been well characterized, and much information is available (for representative publications see 2–5). The Hyals in vertebrate tissues, on the other-hand, have not been studied extensively, however, due to the lack of structural information. Such studies were more difficult and, therefore, more limited. In addition, vertebrate Hyals are present at exceedingly low concentrations. In human serum, e.g., Hyal1 is present at 60 ng/ml 6. They have high specific activities that are unstable during the course of purification, requiring the constant presence of detergents and protease inhibitors for their isolation. Many of such difficulties have been overcome, and a great deal of information is now available, facilitated in part by the Human Genome Project 7. Six Hyal sequences occur in the human genome, constituting a newly recognized family of enzymes. They have similar catalytic mechanisms that contrast markedly with the bacterial Hyals. There is growing interest in these enzymes as their HA substrate is achieving much attention. An outstanding review of the hyaluronidases was published 50 years ago by Karl Meyer, who was also the first to describe the chemical structure of HA 8. Interestingly, a chapter on mucopolysaccharidases, the former name for the hyaluronidases, was included in Volume 1 of Methods in Enzymology 9. The most recent overview of all of the Hyals appeared in 1971 10. Since that time, no comprehensive review has appeared. Karl Meyer classified the Hyals into three distinct classes of enzymes 8, based entirely on the biochemical analyses available at the time. With the advent of sequence and structural data, we can now appreciate how remarkably accurate Karl Meyer’s classification scheme was. No modification of his formulation is necessary. There are three major groups of Hyals, based on their mechanisms of action. Two of the groups are endo-β-N-acetyl-hexosaminidases. One group includes the vertebrate enzymes that utilize substrate hydrolysis 11,12. The second group, which is predominantly bacterial, includes the eliminases that function by β-elimination of the glycosidic linkage with introduction of an unsaturated bond 2–4,13–17. As these enzymes catalyze the breaking of chemical bond by means other than hydrolysis or oxidation, and with the forming a new double bond they are also termed lyases. Both terms, the eliminase (or β-eliminase) and the lyase, are used in the review interchangeably. The third group are the endo-β-glucuronidases. These are found in leeches, which are annelids 18, and in certain crustaceans 19. No sequence data are available, and little is known about this potentially interesting class of enzymes. However, their mechanism of action resembles that of the eukaryotic or vertebrate enzymes more closely than the bacterial enzymes. Sequence data for vertebrate Hyals now provide opportunities to formulate structure-function relationships, to examine probable mechanisms of catalysis, to identify putative substrate binding sites, and to consider the additional non-enzymatic functions of this family of multifunctional enzymes for two of the three groups, for the hydrolase and lyase types of Hyals, respectively 2. Such a review is presented here, documenting some of the common and some of the unusual features that distinguish each of these families of enzymes. The primary objective of this review is to clarify what is known about the structure and mode of action of all the Hyals. Since so little is known of the leech-type of Hyals, the β-endoglucuronidases, the emphasis will, by necessity, be upon two of the three classes of enzymes. Other aspects of these enzymes, such as their physiological activities, their dependence on reaction conditions, their role in cell biology and involvement in metabolism, and their use as reagents or as therapeutics, are not the concern presently. A review of these other aspects of the Hyals will appear separately (Stern and Jedrzejas, in preparation). High levels of HA turnover occur in vertebrate tissues. Tight regulation of catabolism is crucial for modulating steady state levels, important for normal homeostasis, and for embryonic development, wound healing, regeneration, and repair. Under pathological conditions, as in severe stress, shock, septicemia, in burn patients, following major surgery, massive injury, circulating HA levels increases rapidly. HA also increases in association with aggressive malignancies. Determining the mechanism of action of the Hyals is critical for understanding their controls over such a wide range of functions (for reviews, see 20,21).

Diazonium salts as substrates in palladium-catalyzed cross-coupling reactions.

Abstract: 2.1.4. Effect of Bases and Other Additives 4628 2.1.5. Improved Catalytic Systems 4629 2.1.6. Applications in Synthesis 4630 2.1.7. Mechanistic Studies 4632 2.1.8. Related Matsuda−Heck Reactions 4633 2.2. Suzuki−Miyaura Reaction 4634 2.2.1. Early Studies 4634 2.2.2. Modification of the Boronic Counterpart 4635 2.2.3. Improved Catalytic Systems 4637 2.2.4. Superior Reactivity of N2 as the Nucleofuge 4637