Sunday, October 28, 2012

Electronegativity and reactivity of molecules



In general molecules are more stable if there is large difference between electronegativities of their atoms but less stable and more energetically reacting if they are made of atoms with similar electronegativites (EN) excluding those elements with 4 free electrons like carbon that can form strong cubical crystal structure.
For example most metals react with oxygen when they could come in contact with that. Also pure sodium and other alkali metals start burning in water but they lose reactivity after combining with chlorine or other element from opposite side of periodic table. While nitrogen doesn't react easily with organic materials it can react in contact with lithium or magnesium. EN difference of 1,5 or more is usually enough to start energetic (often flaming) chemical reaction without any need to add heat but with smaller differences heat or catalyst are needed like between carbon and oxygen.

Energy releasing metabolism and burning usually create molecules with larger difference of EN between its atoms than before. For example fats and sugars often have mainly carbon and hydrogen connected to each other which have 0,35 difference in EN but after turning them into CO2 (0,89) and water (1,2 difference) this difference grows and resulting molecules need much energy (heat or energetic electric current) to break those up.

Precious metals in middle columns are relatively nonreactive or resistant to most acids, oxygen and other reactive substances compared to other metals. Among the most stable metals are metals with EN at least 2,2 (or more) like gold and those with less EN can rust like silver but others between like Mo usually need heat to start combining with oxygen without visibly rusting in room temperature air.

Many infrared sensors use unstable molecules that create electron flow with even less energy than visible light provides. These are often cooled to 60-100 degrees above absolute zero to avoid detectors from blinding itself by creating electron currents due to room temperature and cooling is commonly needed to see room temperature heat. At the same time these same sensors without cooling are usually only useful for detecting temperatures that are hundreds of degrees above room temperature. As example PbSe has elements with EN differences of 0,2 and can detect infrared with 5-6 micrometer wavelength. Heat from human body is about 10 micrometer infrared radiation.
One of the most sensitive infrared sensor materials is mixture of Hg, Te and Cd which can detect almost 2-3 times less energetic infrared radiation than PbSe and it has about 2 times smaller difference in EN. Due to sensitivity HgTeCd has to be about 77 degrees above absolute zero to detect weaker infrared wavelength (up to ~12 micrometer wavelength for this mixture). 

Thursday, October 18, 2012

Few comments about thiamine (vitamin B1) deficiency

Awareness about thiamine/vitamin B1 (other vitamin B types can run out together with B1) is maybe most important to those who use drugs that influence GABA and acetylcholine levels. GABA influencing drugs include ethanol, GHB and almost all sedatives like benzodiazepines and barbiturates. Acetylcholine is needed to move, remember stuff and to keep many glands working so most drugs that cause dryness in mouth, skin, mucus membranes and eyes probably block acetylcholine activity.


Thiamine is needed for at least 3 enzymes that produce energy from carbohydrates. It usually becomes effective for proteins after it gets 2 phosphate groups added to it. Alcohol stops thiamine absorption from stomach and also slows its activation by slower addition of phosphate groups (that last reaction is slowed because it needs magnesium and ethanol also lowers magnesium levels). While all cells seem to need it, heart and neurons are most sensitive. Serious lack of B1 can cause coma leading to death or deadly heart failure. It is also needed to produce GABA, acetylcholine and building materials to proteins, myelin and DNA plus many other substances. Usually thiamine levels become low if there are problems with absorbing it from intestines due to alcohol and drugs or due to health problems like chronic diarrhea, vomiting, stomach surgery or excessive urination with diuretics. Thiamine requirements are about 0,33 mg for each 1000 kcal of nutrients eaten. Meat is one main source of thiamine like also whole grains and brown rice. White rice on other hand cause lack of thiamine which is often called beriberi. Wernicke-Korsakoff syndrome is common name for this deficiency if caused by chronic alcoholism.  
Common symptoms of thiamine deficiency: weakness, apathy, faster heart rate, weaker reflexes, unwanted eye movements, trouble breathing, possibly fluid in lungs related to heart problems, edema of lower legs and droopy eyelids. In case of Korsakoff syndrome (more extreme deficiency) it can cause problems with remembering past, learning new memories and may lead to memories of events that didn't happen (confabulation). Alcoholic delirium and brain damage are likely to come from thiamine deficiency. These last memory problems are somewhat common if brain is very low on acetylcholine.

Un-cited personal part: i recently noticed that almost all the unwanted side effects my sedative (pregabalin) causes overlapped with thiamine deficiency. I've experienced almost all previously mentioned temporary symptoms with that except serious memory problems. Pregabalin blocks calcium channels and it has mostly weak effect on all neurotransmitters (each is released after calcium triggers release). During minor withdrawal phase ~12 after dosing i often notice weird weakness and changes in posture with very foggy thinking with runny nose. Maybe it was because GABA and acetylcholine were being released too fast after calcium channel normalized and ran low so thiamine was diverted to producing those neurotransmitters and after awhile also run low causing deficiency symptoms. While inside cells neurotransmitters should preserve well but after releasing they get broken up often in split second. For example acetylcholine activates muscles controlled by willpower and this effect on muscles disappears fast because it gets broken up fast outside cells by acetylcholinesterase (each enzyme molecule breaking about 25 000 acetylcholine molecules per second). Acetylcholine is involved in nose mucus gland activation so anything causing that could cause problems with thiamine reserves. After noticing that it could explain why these outwardly visible symptoms happened i almost quit pregabalin overnight after taking it ~300 mg daily for over 3 years and got rid of these symptoms (surprising lack of withdrawals after 24 hour pause). I suspect most antipsychotics and sedatives could cause this effect on small scale but ethanol is still the most obvious cause for thiamine deficiency with worst magnitude that i know about. One nonacademic source listed diuretics, nicotine (binding with nicotinic acetylcholine receptors) and barbiturates (GABA receptor blockers) as substances that can adversely affect thiamine levels.

Tuesday, October 16, 2012

Floating gate transistors


Floating gate MOSFET transistors use relatively high voltage to force few electrons into "floating gate" that is surrounded by non-conductive material like glass. Such memory storage can preserve data for many years without any electricity source and these floating gates are common in memory cards and Flash memory sticks or other chip shaped storages. While good at keeping data for long time they are slow at writing as capacitors have to charge up around 5-12 volt charge to push electrons there and later similar voltage is needed to push that electron out of floating gate. Fast computer memories like DRAM or SRAM read-write fast using about 1-1,5 volts but they lose data fast and DRAM has to rewrite its contents several times each second. These DRAM and other unstabler RAM memories use capacitors to hold charge but they leak their charge and this leaking happens faster with smaller capacitors so future RAMs may need to rewrite increasingly faster. 

Floating gates are filled with the help of control gate with varying charge that can pull or push electron to desired direction depending on if it used for writing, reading or erasing (last 2 are similar at first). Like other static electricity using memories that use electrons they lose their contents every time they are read because electrons get pushed out towards sensor and if data was detected in floating gate then it is usually automatically rewritten.

Wednesday, October 10, 2012

Electronegativity related to acids




Acids, similarly to other chemical reactions, tend to connect atoms that have largest difference between their electronegativities (EN). For example mixing NaOH and HCl in water creates NaCl and extra water. As strong acid HCl breaks up (disassociates) completely in water forming hydrogen and chlorine ions so probably all atoms in them combine into salt or water. 

Strong acids like HCl, HI and HBr disassociate completely creating about same amount of hydrogen ions as there were strong acid molecules added to water. All these 3 simpler examples are pairs of atoms that have smaller difference in EN than H and O so if mixed with water then atoms in these acids tend to combine with water molecules leaving no intact acid molecule.

Weak acid like acetic acid in vinegar don't disassociate completely. Amount of hydrogen ions in vinegar is about 0,4% of the number of acetic acid molecules. This may be due to oxygen atoms so close together to region that loses hydrogen (-OH) like in other carboxylic acids. If hydrogen is released it would be attracted back to oxygen atoms.

Citric acid above. Many weak acids have such part with carbon connected to 2 oxygen atoms. Weak acids have central atoms with with more electronegativity than hydrogen.

Superacids can be over million time more acidic than strong acids. One consistent part of their structure is having many electronegative atoms outside connected to one or few atoms in middle which are less electronegative than hydrogen. Some superbases have opposite relation as they may have electronegative atom surrounded by less electronegative elements.
For example HSbF6 is the strongest known superacid over trillion times more acidic than sulfuric acid. Hydrogen ion is thought to keep moving between fluorine atoms due to very weak connections with main molecule so they are easily released into the mix. 

Triflic acid.


Carborane. Green=chlorine, pink=boron, black=carbon and white is hydrogen.

Target atoms of acids could be predicted to some extent if EN is considered. Many organic molecules like starch and cellulose have ether bonds where oxygen atom is between 2 carbon atoms. EN difference between C and O is smaller than between H and O so in acidic mix these ether bonds break up leaving -OH groups to both carbons that used be connected with same oxygen atoms.

EN related to acid resistance

Hydrofluoric acid doesn't corrode some plastics, gold or silver but it does dissolve ceramics (ingredients include Al and Ca ), glass, iron, nickel, titanium and most other materials. While HF reacts with copper it doesn't react with nickel and many other elements with electronegativity over 1,9 but things are fuzzier around this 1,9 region. Elements with EN closer to EN of fluorine are usually more fluorine resistant.
 HF can be safe(ish)ly held in polyethylene (structure above) bottle while it could dissolve glass. 


Other materials that can tolerate HF are Teflon (left) and neoprene (common synthetic rubber) to right.

Thursday, October 4, 2012

Relation between energy flow and electronegativity

In general materials are more conductive if they are made of same element so elements with same electronegativity are connected but non-conductive if electron current would have to switch from one element to other many times on the way. Also if they conduct electricity then they are probably good conductors of heat like metals. There are some exceptions as diamonds don't conduct electricity well (about 100 times better than glass) while being fast at conducing heat but this may be due to bit chaotic looking crystal structure (lack of straight pathways to flow to). Other pure carbon materials like graphite and nanotubes are good conductors and their simple structure allows more parallel flow of electrons.
Electrons are attracted to more electronegative elements and that could have predictable effect on electrical conductivity.

For example insulating quartz is made of silicon and oxygen connected one after other. If electron flows through it then it is bit attracted to every oxygen atom on the way unlike to silicon atoms around oxygen which lose electrons easily. Electrons could flow relatively easily from silicon to oxygen but not from that oxygen to any neighboring silicon atom so in large scale glass is about as conductive as air or vacuum. That may be the main reason why pure silicon is about billion to trillion times more conductive than glass.

Above are 4 examples of transparent conductive polymers which may be used in transmitting current through transparent materials like touch-screens. They also tend to have one type of element in main chain but there may be other elements in main chain like sulfur which has about 1% higher electronegativity than carbon. Possible that they are transparent while metals are reflective is due to only guiding energy in straight line not in every direction like in piece of metal. If light is polarized parallel to this chain it may more likely absorb but at same time allow light to pass if it is polarized in any other direction.
Many non-conductive polymers have oxygen atoms in main chain like polyester which can easily collect static electricity but there are several non-conductive polymers which don't have anything in main chain beside usual carbon and hydrogen.
Other special feature that these conductive polymers have is lack of charged parts next to main chain.
For example above structure is of non-conductive plexiglass. While main chain is carbon it has side chain that has oxygen atoms which could probably pull to the side any electrons that would move through main chain. Nylon has main chain with carbon and nitrogen but the the side it too has oxygen atoms that may interfere with its conductivity.  

(Diode in above image) Electronegativity is in some ways used in electronics to create predictably routed flow of electrons by doping silicon with some element from group next to silicon. Adding aluminum (or other III A group element) would make it more positive (p-doped) and sulfur or arsenic from more electronegative 5th group can make it more negative (n-doped). 1 n-doped and 1 n-doped material connected together can create one way current in diodes. While electrons easily flow from negative area to more positive area, they may not flow at all in opposite direction or only if some high voltage pushed it against easy direction. Such setup is used in rectifiers to convert alternating current to direct current allowing only one way direction flow. Similar setup was used in cat whisker detectors in early radios that turned alternating current produced by absorbed radio waves in antenna into one way electricity. 
LEDs use such diodes to create light or electricity. If electrons flowing in one direction get at least 1,2 electron volts of energy then they will start to glow. Same LED could create current if it was exposed to energetic enough photons that could get electrons moving (most likely only in one direction due to larger resistance in other direction).

Electrical conductivity is close to thermal conductivity as electrons carry energy/heat about as fast as wires could carry electricity. In this regard electronegativity could be used to predict how well and in what direction will materials carry energy/electricity/heat with the precision close to size of atoms involved. This precision could potentially be further increased by using magnetic fields to align atomic nuclei (and their electron movements) with outside magnetic fields or by smaller magnetic field produced by local groups of atoms. Cooling near absolute zero may further help to keep precision of interactions between atoms.

Tuesday, October 2, 2012

About atomic structure of high-temperature superconductors

In general superconductors work at higher temperatures if they are made of more chemical elements. Superconductors that are made of one metallic element are usually superconductive in temperatures less than 10 degrees above absolute zero while high-temperature superconductors (HTS) working up to over 100 degrees above absolute zero may have 5 different elements. Copper oxides are present in HTSs that work at the highest known superconductive temperatures and for some time all known HTSs had copper although oxygen seems needed in all HTSs. 

Crystal structure of such ceramics or alloys have mirroring layers that keep repeating through material. For example following 3 HTSs all have repeating layers with mirroring order.
TBCCO (thallium barium calcium copper oxide).



YBCO (yttrium barium copper oxide).


BSCCO (bismuth strontium calcium copper oxide).

This ordering may be suitable to create regular flow of electrons. Table of electronegativity can hint from where to where they'll flow. Calcium and barium have the lowest electronegativity among the above ingredients so they are most likely to lose electrons which flow to atoms that attract electrons stronger. Strongest attractors in TBCCO seems to be TlO layers (also labelled as "charge reservoirs" in above image) and BiO in BSCCO. Tl, Bi and O are all strong attractors of electrons although ionized calcium may eventually pull these electrons back. These layers provide somewhat flat few atom thick layers that move electrons easily. As these layers are so close to each others they may increase chances that electrons are always moving between layers due to pull between O and Ca or Ba. Superconductors levitate in magnetic field because they create magnetic field that opposes outside magnetic field. Charged particles in magnetic fields are forced to move circularly around magnetic field lines and in turn they themselves create magnetic field that opposes the outside magnetic field that caused circular movements for electrons and other charged particles. Having many charge reservoir layers every few atoms means that every microscopic part of HTS could locally react to outside magnetic field lines.

Catalase

Catalase is protein that turns H2O2 into water and oxygen molecules. It is present in almost all organisms and bacteria that could survive in oxygen but it is usually missing in species that don't tolerate oxygen like bacteria that live deeper underground or in the bottom of stagnant water.
In university biology class we each had to identify some bacteria by how they reacted to different substances. If bacteria tolerated oxygen then they started to bubble and foam after adding drop of hydrogen peroxide on them but lack of bubbles meant that those species couldn't survive well in oxygen. Same bubbling happens in larger organisms like in mushrooms, plants and animals. If wound is getting cleaned by H2O2 then it starts to bubble (not if it goes on undamaged skin). Likewise broken plant leaves would foam with H2O2 but not if it was added on unbroken leaves. Because body reacts this way to H2O2 it will also form bubbles deeper in body and also clog some small blood vessels near wound with small oxygen bubbles.