Biochemical forces, effect

The fourth and perhaps the most important message of this book is that contrary to the almost universal belief that hydrophobic interactions are the most important driving forces in biochemical forces, I believe that hydrophilic interactions are far more important in biochemistry. In a sense what I am proposing is an inversion of the Hydrophobic/Hydrophilic paradigm. This proposal is similar to but not exactly the same as the side-chain/backbone paradigm inversion proposed by Rose et al. (2006). As will be shown in Chapter 4, hydrophilic groups exhibit a richer and a more powerful repertoire of effects than... 

How relevant are these phenomena First, many oscillating reactions exist and play an important role in living matter. Biochemical oscillations and also the inorganic oscillatory Belousov-Zhabotinsky system are very complex reaction networks. Oscillating surface reactions though are much simpler and so offer convenient model systems to investigate the realm of non-equilibrium reactions on a fundamental level. Secondly, as mentioned above, the conditions under which nonlinear effects such as those caused by autocatalytic steps lead to uncontrollable situations, which should be avoided in practice. Hence, some knowledge about the subject is desired. Finally, the application of forced oscillations in some reactions may lead to better performance in favorable situations for example, when a catalytic system alternates between conditions where the catalyst deactivates due to carbon deposition and conditions where this deposit is reacted away. 

Zhang ZQ, Li Y, Ming Y, Luo ZP, Zhao YM. The effect of Morinda officinalis How, a Chinese traditional medicinal plant, on the DRL 72-s schedule in rats and the forced swimming test in mice. Pharmacol Biochem Behav 2002 72 39-43. 

When addressing problems in computational chemistry, the choice of computational scheme depends on the applicability of the method (i.e. the types of atoms and/or molecules, and the type of property, that can be treated satisfactorily) and the size of the system to be investigated. In biochemical applications the method of choice - if we are interested in the dynamics and effects of temperature on an entire protein with, say, 10,000 atoms - will be to run a classical molecular dynamics (MD) simulation. The key problem then becomes that of choosing a relevant force field in which the different atomic interactions are described. If, on the other hand, we are interested in electronic and/or spectroscopic properties or explicit bond breaking and bond formation in an enzymatic active site, we must resort to a quantum chemical methodology in which electrons are treated explicitly. These phenomena are usually highly localized, and thus only involve a small number of chemical groups compared with the complete macromolecule. 

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Khisti RT, Chopde CT, Jain SP (2000) Antidepressant-like effect of the nemosteroid 3a-hydroxy-5a-pregnan-20-one in mice forced swim test. Pharmacol Biochem Behav 67 137-143... 

Cummings JL, Miller B, Hill MA, et al Neuropsychiatric aspects of multi-infarct dementia and dementia of the Alzheimer type. Arch Neurol 44 389-393, 1987 Cundall RL, Brooks PW, Murray LG A controlled evaluation of lithium prophylaxis in affective disorders. Psychol Med 2 308-311, 1972 Cutler NR, Haxy J, Kay AD, et al Evaluation of zimeldine in Alzheimer s disease cognitive and biochemical measures. Arch Neurol 42 744-748, 1985 Czyrak A The effect of chronic nifedipine and ECS in the forced swimming test in rats. PolJ Pharmacol 45 191-195, 1993... 

From its inception, the combined Quantum Mechanics/Molecular Mechanics (QM/MM) method [1-3] has played an important roll in the explicit modeling of solvent [4], Whereas Molecular Mechanics (MM) methods on their own are generally only able to describe the effect of solvent on classical properties, QM/MM methods allow one to examine the effect of the solvent on solute properties that require a quantum mechanical (QM) description. In most cases, the solute, sometimes together with a few solvent molecules, is treated at the QM level of theory. The solvent molecules, except for those included in the QM region, are then treated with an MM force field. The resulting potential can be explored using Monte Carlo (MC) or Molecular Dynamics (MD) simulations. Besides the modeling of solvent, QM/MM methods have been particularly successful in the study of biochemical systems [5] and catalysis [6],... 

We are cognizant that the structural data on hydrogen bonds derived from crystal structure analyses refer particularly to the hydrogen bond in the solid state. These data are subject to crystal field effects caused by other intermolecular forces. Just as with any discussion of covalent or ionic bonds observed in crystals, these crystal field effects have to be taken into consideration when extrapolating from the precise data available from the crystalline state to the imprecise data that applies to the liquid state in which most chemical and biochemical reactions take place. 

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