pioneer Posted August 4, 2007 Share Posted August 4, 2007 It is possible to model the cell in terms of one variable, i.e., hydrogen bonding. To make this possible, hydrogen bonding needs to be revised. To build some background for this revision, consider the two bases Cl- and OH-. Both have one extra negative charge, but OH- is a stronger base. The reason this is so, is that charge alone is not sufficient to explain relative basicity. One also needs to include the affect of the magnetic fields around the atoms to get the entire electromagnetic affect. A magnetic field is generated by a charge in motion. Writing these anions, in the simple way above, does not give one a good feel for the fact that this extra negative charge or electron is moving about 1/14 the speed of light. At that speed it is giving off a magnetic field as it circulates within these anions. With the electomagnetic force, a unified force composed of both electo-static (charge) and magnetic (charge in motion) aspects, the relative basicity implies that although both give off the same electro-static forces, i.e., both have an extra electron, the Cl- is more stabilized because of its extra magnetic stability lowering the affect of the negative charge. Or its has a lower electromagnetic potential and therefore lower basicity. This electromagnetic (EM) affect is the basis for electronegativity. Atoms with the highest electronegativity have better magnetic addition, which in turn, lowers the impact of the electro-static repulsion between electrons. When Cl- gains its extra electron the octet is full allowing extra magnetic addtion that allows the Cl to compensate for the extra charge. That being said, let us look at the most important molecule of life, i.e., water. Because the O atom is more electronegative than H (offers much better magnetic addition), the water molecule will develop a slight dipole, with the O becoming negative and the H becoming positive. Although the charges are equal and opposite, the EM force fields coming from each side are not the same. The H carries more EM potential than the O. It has to, since O is more electonegative and stabilzed the extra charge. An easier way to see this is consider the molecule HCl or hydrochloric acid. This molecule is a strong acid with a very weak conjugate base. That means that the H side has far more potential than the Cl side even though the dipole charge is equal and opposite. It is not the charge dipole that is causing this disparity in potential, but the magnetic addition. With respect to H2O, a similar affect occurs due to the much higher electronegativity of the oxygen. The O has excellent magnetic addition which diminishes the EM potential of the slight negative charge. The H is left holding the primary burden of the potential since it has both positive charge exposed and has lost magnetic additon to the O. When a H bond forms, the H has more to gain than the O, or else O would not have taken the extra charge in the first place within the single H2O molecule. As such, when looking at H-bonds one only needs to consider how much residual potential is left in the H since it is the one carrying the burden. A hydrogen bond will minimize potential if the H-bond is linear at a critical bond length. Any deviation away from this optimum will mean the hydrogen is carrying some residual potential. The reason this is so is that hydrogen bonds have partial covalent character. The straight bond angle of 180 degrees is needed to optimize magnetic addition. It is due to the magnetic force following the right hand rule of perpendicular affect. If the angle is off one can't get the magnetic fields to add perfectly. The result is that the H will retain some of its residual EM potential. If you look at the average run of the mill enzyme, a large proportion of the H-bonds are not at 180 degrees. This stores H potential, which amount to electrophilic potential within the structure of the enzyme. One way the enzyme tries to lower this is to pull the reactant into an excited state in an attempt to feed electron density to the hungry H. This mechanism is very generic with enzymes developing lock-key specificity so the generic need of the H can lead to very specific results. If we look at ice. The hydrogen bonds are all, more or less, formed in the perfect way with the vast majority at minimum potential. Even though the prefect ice crystal, as a system, is at minimum energy, because the O still has the highest electronegativity, the H are still not at their minimum potential. The ice is at minimum potential with respect to the system of H and O, and with respect to the hydrogen bonds, but the hydrogen still has potential. As an analogy, picture two lionesses sharing a piece of meat. The stronger lioness will get more of the meat. The two lioness system will end up at minimum potential, even thought the stronger lioness will get more. As such, even though the system is at minimum potential, this does not mean the weaker lioness is as full as the dominant lioness. In this case, minimum system potential will still leave the weaker lioness hungry. If H was the only atom in the universe, H2 would be closer to minimum potential relative to the EM needs of H. It is not competing with the highly electronegative oxygen but with a similar lioness that will share equally. The relatively low electronegativity of C, which is close to H, offers H the best way to reach a state of minimal potential. Again, I am not talking about system potential in our environment with the hungry O, but I am talking about, if the goal was to lower H potential to a minimum using the ideal system for the H. The sun, by helping to make reduce C or C-H, i.e, photosynthesis, essentially helps the H get about as low in potential as possible, inspite of the needs of the O system. The O wants to increase the H potential so it becomes part of H2O with much higher potential. If we look at the H in cells, they have a wide range of potential relative to the ideal EM needs of H in its own perfect system. The perfect hydrogen bond is in the middle at minimum system potential but will leave the ideal H with some potential relative to the ideal. A free H+ is at the highest potential and will lower its potential as the hydrogen bond get more and more perfect in distance and angle. While reduce H, such as C-H ,is a state where the hydrogen drops below system potential to where it its own potential is much close to the ideal minimum. Unfortunately for H this creates a potential to be oxidized so hydrogen can carry the burden. When modelling the cell in terms of one variable H, is it easier in one thinks in terms of needs or potential in H instead of the usual O. It makes things much easier to conceptualize and model. I am not suggesting converting all of chemistry to H normalization, only the life sciences. Link to comment Share on other sites More sharing options...
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