Focus On. .. Molecular Mechanics

Computer simulations of electron transfer proteins often entail a variety of calculation techniques electronic structure calculations, molecular mechanics, and electrostatic calculations. In this section, general considerations for calculations of metalloproteins are outlined in subsequent sections, details for studying specific redox properties are given. Quantum chemistry electronic structure calculations of the redox site are important in the calculation of the energetics of the redox site and in obtaining parameters and are discussed in Sections III.A and III.B. Both molecular mechanics and electrostatic calculations of the protein are important in understanding the outer shell energetics and are discussed in Section III.C, with a focus on molecular mechanics. 

Ramaswamy K (1999) Intestinal absorption of water-soluble vitamins focus on molecular mechanism ofthe intestinal biotin titLnspottprocess. AmericanJournalofPhysiology 277, C603-4. 

Unlike traditional textbooks of tribology, in this book we regard boundary lubrication as a limit state of hydrodynamic lubrication when film thickness is down to molecular dimension and independent of the velocity of relative motion. The discussions are based on the existing results, some from literatures but mostly from the authors own work. The topics are mainly focused on the mechanical properties of boundary films, including rheology transitions, molecular ordering, and shear responses. Ordered molecule films, such as L-B films and SAM, are discussed, with emphasis on the frictional performance, energy dissipation and the effects from structural features. Boundary films can be modeled either as a confined substance, or an adsorbed/reacted layer on the... 

Various endeavors have been undertaken to get insight into the 3D selector-selectand complex structures and to elucidate chiral recognition mechanisms of cinchonan carbamate selectors for a few model selectands (in particular, DNB-Leu). Such studies comprised NMR [92-94], ET-IR [94-96], X-ray diffraction [33,59,92,94], and molecular modeling investigations (the latter focusing on molecular dynamics [92,93,97], and 3D-QSAR CoMFA studies [98]). 

Studies on artificial ion channels are expected to provide important information on molecular mechanisms and to deepen our understanding of natural ion channels through the establishment of a detailed structure-function relationship. At the same time, the research will contribute to the fascinating area of nanoscale transducers, and may eventually lead to the development of so-called molecular ionics. Here, the author would like to describe the basic concept for the molecular design of various artificial ion channels and to compare their characteristics in the hope of stimulating a future explosion of this research field. Special attention is focused on non-peptidic approaches. Helical bundle approaches " and studies on modified antibiotics " are beyond the scope of this review. 

This chapter describes some of the principles and mechanisms underlying the primary processes of olfactory signaling, the chemo-electrical signal transduction. We will focus on molecular events that follow the interaction of odorants with olfactory sensory neurons, and leave aside perireceptor events including odorant... 

Theoretical studies published since 1993 reporting computationally optimized structures for four-membered boracycles and metallacycles are listed in Table 1. Many of these investigations, however, maintain a specific focus on molecular transformations (i.e., reaction mechanisms) and no longer explicitly consider the details of metallacyclobutane structure. The most significant theoretical investigations of boracyclobutene derivatives were conducted sufficiently long ago to have been reviewed in CHEC-II(1996) <1996CHEC-II(lb)887> and are not discussed further. 

It is not in the scope of this chapter to focus on the mechanism of this reaction, which is reviewed extensively in the literature127,136. However, it must be pointed out that these routes are well known in organosilicon chemistry. Moreover, the final material s texture is highly dependent on the experimental conditions and therefore on the chemistry at the molecular level4,8. This suggests a strong kinetic control in the preparation of the solid however, the precise relation between the chemical processes and the texture remains difficult to precisely define and this is certainly also the case for the hybrid material presented in Section IV. 

The consequences of product accumulation on the structural and chemical properties of a reacting crystal have been examined by several authors. These can be analyzed from a perspective that focuses on molecular changes or from a crystal phase point of view. A molecular analysis focuses on local structural properties that affect the reaction mechanism [55,57,58]. A solid-phase analysis focuses on how a crystalline ensemble reacts to the changes in composition that occur as the reaction proceeds [59-61]. However, as suggested in Scheme 5, a separation... 

However, the most important driving force for performing in vitro toxicity studies is a scientific one if one wishes to study the toxicity mechanisms of action of a compound, it is no longer appropriate to rely on the apical endpoints for toxicity that are the commonly measured parameters in an animal study. A focus on these mechanisms, in relation to the events following the molecular initiating event, eventually leading to an adverse outcome gives... 

The majority of sorption kinetic stndies have ntilized either batch or flow-through methods coupled with aqueous measurements for determination of the concentrations of species of interest. More recent work has focused on molecular-scale approaches, including spectroscopic and microscopic techniques that allow for observations at increased spatial and temporal resolution to be made, often in situ and in real time. Complementary to both macroscopic and molecular-scale observations has been the utilization of theoretical techniques, such as molecular mechanics and quantum mechanics, to model surface complexes computationally. It has been through the integration of macroscopic, molecular-scale, and theoretical approaches that some of the most profound observations of sorption-desorption phenomena over the past decades have been made. 

It is apparent that the upstream signals have, in some cases, been identified and the molecular mechanism by which ZP3 produces these intracellular ionic messengers is perceived with some degree of resolution. It is equally apparent that the specific components of the signaling cascade as well as their relationship to the secretory machinery are not well understood. In partieular, recent studies have characterized the upstream elements of the cascade, focusing on the mechanisms that mediate the rise in Ca +j. The next objective may be to identify the Ca +-reg-ulated downstream targets and to tie these target proteins to secretion. 

NMR observations basically contain spin relaxation processes which are associated with molecular motions with different specific frequencies in a given system. For quantitative measurements to determine the compositions of the system or selective measurements of particular components with different relaxation parameters, it is essential, therefore, to understand the principle of the relaxation mechanism. When our interest is focused on molecular motions, spin relaxation parameters such as spin-lattice relaxation time T, spin-spin relaxation time T2, and the nuclear Overhauser enhancement (NOE), are directly measured as a function of temperature or field frequency by using appropriate pulse sequences. Such temperature or frequency dependencies of the spin relaxation parameters are analyzed in terms of appropriate models to obtain detailed information of molecular motions with frequencies of Hz in the system. In this chapter, the basic theories and analyses... 

Roberto Contestabile was educated at tbe Sapienza University of Rome, were be graduated in biological sciences. He received bis Pb.D. in biochemistry from tbe School of Molecular and Medical Biosciences of the University of Wales, Cardiff, UK. His research interests focuses on the mechanism, structure, and folding of enzymes using pyridoxal 5 -phosphate as a cofactor. 

Even though this chapter has largely focused on the mechanism of correct dNTP incorporation and the molecular origin of fidelity, the computational approaches described here can also be utilized to study the effects of modified substrates in the active site of polymerases,as well as the effect of interacting proteins on catalysis. Overall, computational methods will continue to be a valuable tool for DNA polymerase mechanism studies. A complete understanding of polymerase mechanism and fidelity will surely be facilitated by future advancements in computational methodology, as well as the availability of new complex structures. 

In recent years, the development of biosensor configurations has been concentrated largely around the design of the transducer used. Further researchers attention, however, should be focused on the mechanism of molecular recognition and catalysis. The fundamental properties of the device must be better understood in order to optimize critical factors such as response time, selectivity, and stability. Immobilization technologies and new membrane materials may basically change the present performance of biosensors. 

The electrodes of supercapacitors, in particular carbon-based electrodes, have very complex microstructure. Consequently, many types of EDLs can exist in a supercapacitor. For example, some EDLs are formed near open surfaces that can be planar (e.g., flat graphene sheet), cylindrical (e.g., CNT), or spherical (e.g., OLC) some EDLs appear inside narrow pores (e.g., sUt-shaped and cylindrical (Mies). By taking each EDL as a separate capacitor, a supercapacitor can be considered as many capacitiM s connected in series and/or in parallel. Thus, it is reasonable to study some of these capacitors (i.e., EDLs) to gain insights into the charge storage mechanism in a real supercapacitor. Many different techniques can be used to model the EDLs, and here we focus on molecular simulations and density functional theory (DFT) calculations. 

In this book we have provided an overview of the physical chemistry of catalytic systems with a focus on molecular mechanistic aspects. Theories, concepts and techniques to describe the relevant chemistry have advanced to a state that the reaction mechanism in heterogeneous catalysis is becoming well understood. Clearly, similar advances relevant to the practice of catalyst synthesis and design are now on the near horizon. The foundation of theoretical molecular heterogeneous catalysis provides a firm basis towards these future endeavors. 

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