Search This Blog

Tuesday, July 26, 2022

Bioinorganic chemistry

From Wikipedia, the free encyclopedia
https://en.wikipedia.org/wiki/Bioinorganic_chemistry

Bioinorganic chemistry is a field that examines the role of metals in biology. Bioinorganic chemistry includes the study of both natural phenomena such as the behavior of metalloproteins as well as artificially introduced metals, including those that are non-essential, in medicine and toxicology. Many biological processes such as respiration depend upon molecules that fall within the realm of inorganic chemistry. The discipline also includes the study of inorganic models or mimics that imitate the behaviour of metalloproteins.

As a mix of biochemistry and inorganic chemistry, bioinorganic chemistry is important in elucidating the implications of electron-transfer proteins, substrate bindings and activation, atom and group transfer chemistry as well as metal properties in biological chemistry. The successful development of truly interdisciplinary work is necessary to advance bioinorganic chemistry.

Composition of living organisms

About 99% of mammals' mass are the elements carbon, nitrogen, calcium, sodium, chlorine, potassium, hydrogen, phosphorus, oxygen and sulfur. The organic compounds (proteins, lipids and carbohydrates) contain the majority of the carbon and nitrogen and most of the oxygen and hydrogen is present as water. The entire collection of metal-containing biomolecules in a cell is called the metallome.

History

Paul Ehrlich used organoarsenic (“arsenicals”) for the treatment of syphilis, demonstrating the relevance of metals, or at least metalloids, to medicine, that blossomed with Rosenberg's discovery of the anti-cancer activity of cisplatin (cis-PtCl2(NH3)2). The first protein ever crystallized (see James B. Sumner) was urease, later shown to contain nickel at its active site. Vitamin B12, the cure for pernicious anemia was shown crystallographically by Dorothy Crowfoot Hodgkin to consist of a cobalt in a corrin macrocycle. The Watson-Crick structure for DNA demonstrated the key structural role played by phosphate-containing polymers.

Themes in bioinorganic chemistry

Several distinct systems are of identifiable in bioinorganic chemistry. Major areas include:

Metal ion transport and storage

A diverse collection of transporters (e.g. the ion pump NaKATPase), vacuoles, storage proteins (e.g. ferritin), and small molecules (e.g. siderophores) are employed to control metal ions concentration and bio-availability in living organisms. Crucially, many essential metals are not readily accessible to downstream proteins owing to low solubility in aqueous solutions or scarcity in the cellular environment. Organisms have developed a number of strategies for collecting and transporting such elements while limiting their cytotoxicity.

Enzymology

Many reactions in life sciences involve water and metal ions are often at the catalytic centers (active sites) for these enzymes, i.e. these are metalloproteins. Often the reacting water is a ligand (see metal aquo complex). Examples of hydrolase enzymes are carbonic anhydrase, metallophosphatases, and metalloproteinases. Bioinorganic chemists seek to understand and replicate the function of these metalloproteins.

Metal-containing electron transfer proteins are also common. They can be organized into three major classes: iron–sulfur proteins (such as rubredoxins, ferredoxins, and Rieske proteins), blue copper proteins, and cytochromes. These electron transport proteins are complementary to the non-metal electron transporters nicotinamide adenine dinucleotide (NAD) and flavin adenine dinucleotide (FAD). The nitrogen cycle make extensive use of metals for the redox interconversions.

4Fe-4S clusters serve as electron-relays in proteins.

Toxicity

Several metal ions are toxic to humans and other animals. The bioinorganic chemistry of lead in the context of its toxicity has been reviewed.

Oxygen transport and activation proteins

Aerobic life make extensive use of metals such as iron, copper, and manganese. Heme is utilized by red blood cells in the form of hemoglobin for oxygen transport and is perhaps the most recognized metal system in biology. Other oxygen transport systems include myoglobin, hemocyanin, and hemerythrin. Oxidases and oxygenases are metal systems found throughout nature that take advantage of oxygen to carry out important reactions such as energy generation in cytochrome c oxidase or small molecule oxidation in cytochrome P450 oxidases or methane monooxygenase. Some metalloproteins are designed to protect a biological system from the potentially harmful effects of oxygen and other reactive oxygen-containing molecules such as hydrogen peroxide. These systems include peroxidases, catalases, and superoxide dismutases. A complementary metalloprotein to those that react with oxygen is the oxygen evolving complex present in plants. This system is part of the complex protein machinery that produces oxygen as plants perform photosynthesis.

Myoglobin is a prominent subject in bioinorganic chemistry, with particular attention to the iron-heme complex that is anchored to the protein.

Bioorganometallic chemistry

Bioorganometallic systems feature metal-carbon bonds as structural elements or as intermediates. Bioorganometallic enzymes and proteins include the hydrogenases, FeMoco in nitrogenase, and methylcobalamin. These naturally occurring organometallic compounds. This area is more focused on the utilization of metals by unicellular organisms. Bioorganometallic compounds are significant in environmental chemistry.

Structure of FeMoco, the catalytic center of nitrogenase.

Metals in medicine

A number of drugs contain metals. This theme relies on the study of the design and mechanism of action of metal-containing pharmaceuticals, and compounds that interact with endogenous metal ions in enzyme active sites. The most widely used anti-cancer drug is cisplatin. MRI contrast agent commonly contain gadolinium. Lithium carbonate has been used to treat the manic phase of bipolar disorder. Gold antiarthritic drugs, e.g. auranofin have been commercialized. Carbon monoxide-releasing molecules are metal complexes have been developed to suppress inflammation by releasing small amounts of carbon monoxide. The cardiovascular and neuronal importance of nitric oxide has been examined, including the enzyme nitric oxide synthase. (See also: nitrogen assimilation.) Besides, metallic transition complexes based on triazolopyrimidines have been tested against several parasite strains.

Environmental chemistry

Environmental chemistry traditionally emphasizes the interaction of heavy metals with organisms. Methylmercury has caused major disaster called Minamata disease. Arsenic poisoning is a widespread problem owing largely to arsenic contamination of groundwater, which affects many millions of people in developing countries. The metabolism of mercury- and arsenic-containing compounds involves cobalamin-based enzymes.

Biomineralization

Biomineralization is the process by which living organisms produce minerals, often to harden or stiffen existing tissues. Such tissues are called mineralized tissues. Examples include silicates in algae and diatoms, carbonates in invertebrates, and calcium phosphates and carbonates in vertebrates. Other examples include copper, iron and gold deposits involving bacteria. Biologically-formed minerals often have special uses such as magnetic sensors in magnetotactic bacteria (Fe3O4), gravity sensing devices (CaCO3, CaSO4, BaSO4) and iron storage and mobilization (Fe2O3•H2O in the protein ferritin). Because extracellular iron is strongly involved in inducing calcification, its control is essential in developing shells; the protein ferritin plays an important role in controlling the distribution of iron.

Types of inorganic substances in biology

Alkali and alkaline earth metals

Like many antibiotics, monensin-A is an ionophore that tightly bind Na+ (shown in yellow).

The abundant inorganic elements act as ionic electrolytes. The most important ions are sodium, potassium, calcium, magnesium, chloride, phosphate, and bicarbonate. The maintenance of precise gradients across cell membranes maintains osmotic pressure and pH. Ions are also critical for nerves and muscles, as action potentials in these tissues are produced by the exchange of electrolytes between the extracellular fluid and the cytosol. Electrolytes enter and leave cells through proteins in the cell membrane called ion channels. For example, muscle contraction depends upon the movement of calcium, sodium and potassium through ion channels in the cell membrane and T-tubules.

Transition metals

The transition metals are usually present as trace elements in organisms, with zinc and iron being most abundant. These metals are used as protein cofactors and signalling molecules. Many are essential for the activity of enzymes such as catalase and oxygen-carrier proteins such as hemoglobin. These cofactors are tightly to a specific protein; although enzyme cofactors can be modified during catalysis, cofactors always return to their original state after catalysis has taken place. The metal micronutrients are taken up into organisms by specific transporters and bound to storage proteins such as ferritin or metallothionein when not being used. Cobalt is essential for the functioning of vitamin B12.

Main group compounds

Many other elements aside from metals are bio-active. Sulfur and phosphorus are required for all life. Phosphorus almost exclusively exists as phosphate and its various esters. Sulfur exists in a variety of oxidation states, ranging from sulfate (SO42−) down to sulfide (S2−). Selenium is a trace element involved in proteins that are antioxidants. Cadmium is important because of its toxicity.

Monday, July 25, 2022

Noble metal

From Wikipedia, the free encyclopedia
 

Periodic table extract showing approximately how often each element tends to recognized as a noble metal:
 7  most often (Ru, Rh, Pd, Os, Ir, Pt, Au)  1  often (Ag)  2  sometimes (Cu, Hg)  6  in a limited sense (Tc, Re, As, Sb, Bi, Po)
The thick black line encloses the seven to eight metals most often to often so recognized. Silver is sometimes not recognized as a noble metal on account of its greater reactivity.
* may be tarnished in moist air or corrode in an acidic solution containing oxygen and an oxidant † attacked by sulfur or hydrogen sulfide
§ self-attacked by radiation-generated ozone

A noble metal is ordinarily regarded as a metallic chemical element that is generally resistant to corrosion and is usually found in nature in its raw form. Gold, platinum, and the other platinum group metals (ruthenium, rhodium, palladium, osmium, iridium) are most often so classified. Silver, copper and mercury are less often to sometimes included as noble metals although each of these usually occurs in nature combined with sulfur.

In more specialized fields of study and applications the number of elements counted as noble metals can be smaller or larger. In physics, there are only three noble metals: copper, silver and gold. In dentistry, silver is not always counted as a noble metal since it is subject to corrosion when present in the mouth. In chemistry, the term noble metal is sometimes applied more broadly to any metallic or semimetallic element that does not react with a weak acid and give off hydrogen gas in the process. This broader set includes copper, mercury, technetium, rhenium, arsenic, antimony, bismuth and polonium, as well as gold, the six platinum group metals, and silver.

Meaning and history

While noble metal lists can differ, they tend to cluster around the six platinum group metals (ruthenium, rhodium, palladium, osmium, iridium, platinum) plus gold.

In addition to this term's function as a compound noun, there are circumstances where noble is used as an adjective for the noun metal. A galvanic series is a hierarchy of metals (or other electrically conductive materials, including composites and semimetals) that runs from noble to active, and allows one to predict how materials will interact in the environment used to generate the series. In this sense of the word, graphite is more noble than silver and the relative nobility of many materials is highly dependent upon context, as for aluminium and stainless steel in conditions of varying pH.

The term noble metal can be traced back to at least the late 14th century and has slightly different meanings in different fields of study and application.

Prior to Mendeleev's publication in 1869 of the first (eventually) widely accepted periodic table, Odling published a table in 1864, in which the "noble metals" rhodium, ruthenium, palladium; and platinum, iridium, and osmium were grouped together, and adjacent to silver and gold.

Properties

Abundance of the chemical elements in the Earth's crust as a function of atomic number. The rarest elements (shown in yellow, including the noble metals) are not the heaviest, but are rather the siderophile (iron-loving) elements in the Goldschmidt classification of elements. These have been depleted by being relocated deeper into the Earth's core. Their abundance in meteoroid materials is relatively higher. Tellurium and selenium have been depleted from the crust due to formation of volatile hydrides.

Geochemical

The noble metals are siderophiles (iron-lovers). They tend to sink into the Earth's core because they dissolve readily in iron either as solid solutions or in the molten state. Most siderophile elements have practically no affinity whatsoever for oxygen: indeed, oxides of gold are thermodynamically unstable with respect to the elements.

Copper, silver, gold, and the six platinum group metals are the only native metals that occur naturally in relatively large amounts.[citation needed]

Corrosion resistance

Copper is dissolved by nitric acid and aqueous potassium cyanide.

Ruthenium can be dissolved in aqua regia, a highly concentrated mixture of hydrochloric acid and nitric acid, only when in the presence of oxygen, while rhodium must be in a fine pulverized form. Palladium and silver are soluble in nitric acid, with the solubility of silver being limited by the formation of silver chloride precipitate.

Rhenium reacts with oxidizing acids, and hydrogen peroxide, and is said to be tarnished by moist air. Osmium and iridium are chemically inert in ambient conditions. Platinum and gold can be dissolved in aqua regia. Mercury reacts with oxidising acids.

In 2010, US researchers discovered that an organic "aqua regia" in the form of a mixture of thionyl chloride SOCl2 and the organic solvent pyridine C5H5N achieved "high dissolution rates of noble metals under mild conditions, with the added benefit of being tunable to a specific metal" for example, gold but not palladium or platinum.

Electronic

In physics, the expression "noble metal" is sometimes confined to copper, silver, and gold, since their full d-subshells contribute to what noble character they have. In contrast, the other noble metals, especially the platinum group metals, have notable catalytic applications, arising from their partially filled d-subshells. This is the case with palladium which has a full d-subshell in the atomic state but in condensed form has a partially filled sp band at the expense of d-band occupancy.

The difference in reactivity can be seen during the preparation of clean metal surfaces in an ultra-high vacuum: surfaces of "physically defined" noble metals (e.g., gold) are easy to clean and keep clean for a long time, while those of platinum or palladium, for example, are covered by carbon monoxide very quickly.

Electrochemical

Standard reduction potentials in aqueous solution are also a useful way of predicting the non-aqueous chemistry of the metals involved. Thus, metals with high negative potentials, such as sodium, or potassium, will ignite in air, forming the respective oxides. These fires cannot be extinguished with water, which also react with the metals involved to give hydrogen, which is itself explosive. Noble metals, in contrast, are disinclined to react with oxygen and, for that reason (as well as their scarcity) have been valued for millennia, and used in jewellery and coins.

Electrochemical properties of some metals and metalloids
Element Z G P Reaction SRP(V) EN EA
Gold 79 11 6 Au3+
+ 3 e → Au
1.5 2.54 223
Platinum 78 10 6 Pt2+
+ 2 e → Pt
1.2 2.28 205
Iridium 77 9 6 Ir3+
+ 3 e → Ir
1.16 2.2 151
Palladium 46 10 5 Pd2+
+ 2 e → Pd
0.915 2.2 54
Osmium 76 8 6 OsO
2
+ 4 H+
+ 4 e → Os + 2 H
2
O
0.85 2.2 104
Mercury 80 12 6 Hg2+
+ 2 e → Hg
0.85 2.0 −50
Rhodium 45 9 5 Rh3+
+ 3 e → Rh
0.8 2.28 110
Silver 47 11 5 Ag+
+ e → Ag
0.7993 1.93 126
Ruthenium 44 8 5 Ru3+
+ 3 e → Ru
0.6 2.2 101
Polonium 84 16 6 Po2+
+ 2 e → Po
0.6 2.0 136
Water


H
2
O
+ 4 e +O
2
→ 4 OH
0.4

Copper 29 11 4 Cu2+
+ 2 e → Cu
0.339 2.0 119
Bismuth 83 15 6 Bi3+
+ 3 e → Bi
0.308 2.02 91
Technetium 43 7 6 TcO
2
+ 4 H+
+ 4 e → Tc + 2 H
2
O
0.28 1.9 53
Rhenium 75 7 6 ReO
2
+ 4 H+
+ 4 e → Re + 2 H
2
O
0.251 1.9 6
ArsenicMD 33 15 4 As
4
O
6
+ 12 H+
+ 12 e → 4 As + 6 H
2
O
0.24 2.18 78
AntimonyMD 51 15 5 Sb
2
O
3
+ 6 H+
+ 6 e → 2 Sb + 3 H
2
O
0.147 2.05 101
Z atomic number; G group; P period; SRP standard reduction potential; EN electronegativity; EA electron affinity
✣ traditionally recognized as a noble metal; MD metalloid; ☢ radioactive

The adjacent table lists standard reduction potential in volts; electronegativity (revised Pauling); and electron affinity values (kJ/mol), for some metals and metalloids.

The simplified entries in the reaction column can be read in detail from the Pourbaix diagrams of the considered element in water. Noble metals have large positive potentials; elements not in this table have a negative standard potential or are not metals.

Electronegativity is included since it is reckoned to be, "a major driver of metal nobleness and reactivity".

On account of their high electron affinity values, the incorporation of a noble metal in the electrochemical photolysis process, such as platinum and gold, among others, can increase photoactivity.

Arsenic and antimony are usually considered to be metalloids rather than noble metals. However, physically speaking their most stable allotropes are metallic. Semiconductors, such as selenium and tellurium, have been excluded.

The black tarnish commonly seen on silver arises from its sensitivity to hydrogen sulfide: 2Ag + H2S + 1/2O2 → Ag2S + H2O. Rayner-Canham contends that, "silver is so much more chemically-reactive and has such a different chemistry, that it should not be considered as a 'noble metal'." In dentistry, silver is not regarded as a noble metal due to its tendency to corrode in the oral environment.

The relevance of the entry for water is addressed by Li et al. in the context of galvanic corrosion. Such a process will only occur when:

"(1) two metals which have different electrochemical potentials are...connected, (2) an aqueous phase with electrolyte exists, and (3) one of the two metals has...potential lower than the potential of the reaction (H
2
O
+ 4e +O
2
= 4 OH) which is 0.4 V...The...metal with...a potential less than 0.4 V acts as an anode...loses electrons...and dissolves in the aqueous medium. The noble metal (with higher electrochemical potential) acts as a cathode and, under many conditions, the reaction on this electrode is generally H
2
O
− 4 eO
2
= 4 OH)."

The superheavy elements from hassium (element 108) to livermorium (116) inclusive are expected to be "partially very noble metals"; chemical investigations of hassium has established that it behaves like its lighter congener osmium, and preliminary investigations of nihonium and flerovium have suggested but not definitively established noble behavior. Copernicium's behaviour seems to partly resemble both its lighter congener mercury and the noble gas radon.

Oxides

Oxide melting points, °C
Element I II III IV VI VII
Copper
1326



Ruthenium


d1300
d75+


Rhodium

d1100
?



Palladium
d750 



Silver d200




Rhenium




327
Osmium


d500

Iridium


d1100
?


Platinum


450
d100


Gold

d150


Mercury
d500



Strontium‡
2430



Molybdenum‡



801
d70

AntimonyMD

655


Lanthanum‡

2320


Bismuth‡

817


d = decomposes; if there are two figures, the 2nd is for
the hydrated form; ‡ = not a noble metal; MD = metalloid

As long ago as 1890, Hiorns observed as follows:

"Noble Metals. Gold, Platinum, Silver, and a few rare metals. The members of this class have little or no tendency to unite with oxygen in the free state, and when placed in water at a red heat do not alter its composition. The oxides are readily decomposed by heat in consequence of the feeble affinity between the metal and oxygen."

Smith, writing in 1946, continued the theme:

"There is no sharp dividing line [between 'noble metals' and 'base metals'] but perhaps the best definition of a noble metal is a metal whose oxide is easily decomposed at a temperature below a red heat."
"It follows from this that noble metals...have little attraction for oxygen and are consequently not oxidised or discoloured at moderate temperatures."

Such nobility is mainly associated with the relatively high electronegativity values of the noble metals, resulting in only weakly polar covalent bonding with oxygen. The table lists the melting points of the oxides of the noble metals, and for some of those of the non-noble metals, for the elements in their most stable oxidation states.

Catalytic properties

Many of the noble metals can act as catalysts. For example, platinum is used in catalytic converters, devices which convert toxic gases produced in car engines, such as the oxides of nitrogen, into non-polluting substances.

Gold has many industrial applications; it is used as a catalyst in hydrogenation and the water gas shift reaction.

Bus (computing)

From Wikipedia, the free encyclopedia

Four PCI Express bus card slots (from top to 2nd bottom: ×4, ×16, ×1 and ×16), compared to a 32-bit conventional PCI bus card slot (very bottom)

In computer architecture, a bus (shortened form of the Latin omnibus, and historically also called data highway or databus) is a communication system that transfers data between components inside a computer, or between computers. This expression covers all related hardware components (wire, optical fiber, etc.) and software, including communication protocols.

Early computer buses were parallel electrical wires with multiple hardware connections, but the term is now used for any physical arrangement that provides the same logical function as a parallel electrical busbar. Modern computer buses can use both parallel and bit serial connections, and can be wired in either a multidrop (electrical parallel) or daisy chain topology, or connected by switched hubs, as in the case of Universal Serial Bus (USB).

Background and nomenclature

Computer systems generally consist of three main parts:

An early computer might contain a hand-wired CPU of vacuum tubes, a magnetic drum for main memory, and a punch tape and printer for reading and writing data respectively. A modern system might have a multi-core CPU, DDR4 SDRAM for memory, a solid-state drive for secondary storage, a graphics card and LCD as a display system, a mouse and keyboard for interaction, and a Wi-Fi connection for networking. In both examples, computer buses of one form or another move data between all of these devices.

In most traditional computer architectures, the CPU and main memory tend to be tightly coupled. A microprocessor conventionally is a single chip which has a number of electrical connections on its pins that can be used to select an "address" in the main memory and another set of pins to read and write the data stored at that location. In most cases, the CPU and memory share signalling characteristics and operate in synchrony. The bus connecting the CPU and memory is one of the defining characteristics of the system, and often referred to simply as the system bus.

It is possible to allow peripherals to communicate with memory in the same fashion, attaching adaptors in the form of expansion cards directly to the system bus. This is commonly accomplished through some sort of standardized electrical connector, several of these forming the expansion bus or local bus. However, as the performance differences between the CPU and peripherals varies widely, some solution is generally needed to ensure that peripherals do not slow overall system performance. Many CPUs feature a second set of pins similar to those for communicating with memory, but able to operate at very different speeds and using different protocols. Others use smart controllers to place the data directly in memory, a concept known as direct memory access. Most modern systems combine both solutions, where appropriate.

As the number of potential peripherals grew, using an expansion card for every peripheral became increasingly untenable. This has led to the introduction of bus systems designed specifically to support multiple peripherals. Common examples are the SATA ports in modern computers, which allow a number of hard drives to be connected without the need for a card. However, these high-performance systems are generally too expensive to implement in low-end devices, like a mouse. This has led to the parallel development of a number of low-performance bus systems for these solutions, the most common example being the standardized Universal Serial Bus (USB). All such examples may be referred to as peripheral buses, although this terminology is not universal.

In modern systems the performance difference between the CPU and main memory has grown so great that increasing amounts of high-speed memory is built directly into the CPU, known as a cache. In such systems, CPUs communicate using high-performance buses that operate at speeds much greater than memory, and communicate with memory using protocols similar to those used solely for peripherals in the past. These system buses are also used to communicate with most (or all) other peripherals, through adaptors, which in turn talk to other peripherals and controllers. Such systems are architecturally more similar to multicomputers, communicating over a bus rather than a network. In these cases, expansion buses are entirely separate and no longer share any architecture with their host CPU (and may in fact support many different CPUs, as is the case with PCI). What would have formerly been a system bus is now often known as a front-side bus.

Given these changes, the classical terms "system", "expansion" and "peripheral" no longer have the same connotations. Other common categorization systems are based on the bus's primary role, connecting devices internally or externally, PCI vs. SCSI for instance. However, many common modern bus systems can be used for both; SATA and the associated eSATA are one example of a system that would formerly be described as internal, while certain automotive applications use the primarily external IEEE 1394 in a fashion more similar to a system bus. Other examples, like InfiniBand and I²C were designed from the start to be used both internally and externally.

Internal buses

The internal bus, also known as internal data bus, memory bus, system bus or front-side bus, connects all the internal components of a computer, such as CPU and memory, to the motherboard. Internal data buses are also referred to as local buses, because they are intended to connect to local devices. This bus is typically rather quick and is independent of the rest of the computer operations.

External buses

The external bus, or expansion bus, is made up of the electronic pathways that connect the different external devices, such as printer etc., to the computer.

Address bus

An address bus is a bus that is used to specify a physical address. When a processor or DMA-enabled device needs to read or write to a memory location, it specifies that memory location on the address bus (the value to be read or written is sent on the data bus). The width of the address bus determines the amount of memory a system can address. For example, a system with a 32-bit address bus can address 232 (4,294,967,296) memory locations. If each memory location holds one byte, the addressable memory space is 4 GiB.

Address multiplexing

Early processors used a wire for each bit of the address width. For example, a 16-bit address bus had 16 physical wires making up the bus. As the buses became wider and lengthier, this approach became expensive in terms of the number of chip pins and board traces. Beginning with the Mostek 4096 DRAM, address multiplexing implemented with multiplexers became common. In a multiplexed address scheme, the address is sent in two equal parts on alternate bus cycles. This halves the number of address bus signals required to connect to the memory. For example, a 32-bit address bus can be implemented by using 16 lines and sending the first half of the memory address, immediately followed by the second half memory address.

Typically two additional pins in the control bus -- a row-address strobe (RAS) and the column-address strobe (CAS) -- are used to tell the DRAM whether the address bus is currently sending the first half of the memory address or the second half.

Implementation

Accessing an individual byte frequently requires reading or writing the full bus width (a word) at once. In these instances the least significant bits of the address bus may not even be implemented - it is instead the responsibility of the controlling device to isolate the individual byte required from the complete word transmitted. This is the case, for instance, with the VESA Local Bus which lacks the two least significant bits, limiting this bus to aligned 32-bit transfers.

Historically, there were also some examples of computers which were only able to address words -- word machines.

Memory bus

The memory bus is the bus which connects the main memory to the memory controller in computer systems. Originally, general-purpose buses like VMEbus and the S-100 bus were used, but to reduce latency, modern memory buses are designed to connect directly to DRAM chips, and thus are designed by chip standards bodies such as JEDEC. Examples are the various generations of SDRAM, and serial point-to-point buses like SLDRAM and RDRAM. An exception is the Fully Buffered DIMM which, despite being carefully designed to minimize the effect, has been criticized for its higher latency.

Implementation details

Buses can be parallel buses, which carry data words in parallel on multiple wires, or serial buses, which carry data in bit-serial form. The addition of extra power and control connections, differential drivers, and data connections in each direction usually means that most serial buses have more conductors than the minimum of one used in 1-Wire and UNI/O. As data rates increase, the problems of timing skew, power consumption, electromagnetic interference and crosstalk across parallel buses become more and more difficult to circumvent. One partial solution to this problem has been to double pump the bus. Often, a serial bus can be operated at higher overall data rates than a parallel bus, despite having fewer electrical connections, because a serial bus inherently has no timing skew or crosstalk. USB, FireWire, and Serial ATA are examples of this. Multidrop connections do not work well for fast serial buses, so most modern serial buses use daisy-chain or hub designs.

Network connections such as Ethernet are not generally regarded as buses, although the difference is largely conceptual rather than practical. An attribute generally used to characterize a bus is that power is provided by the bus for the connected hardware. This emphasizes the busbar origins of bus architecture as supplying switched or distributed power. This excludes, as buses, schemes such as serial RS-232, parallel Centronics, IEEE 1284 interfaces and Ethernet, since these devices also needed separate power supplies. Universal Serial Bus devices may use the bus supplied power, but often use a separate power source. This distinction is exemplified by a telephone system with a connected modem, where the RJ11 connection and associated modulated signalling scheme is not considered a bus, and is analogous to an Ethernet connection. A phone line connection scheme is not considered to be a bus with respect to signals, but the Central Office uses buses with cross-bar switches for connections between phones.

However, this distinction‍—‌that power is provided by the bus‍—‌is not the case in many avionic systems, where data connections such as ARINC 429, ARINC 629, MIL-STD-1553B (STANAG 3838), and EFABus (STANAG 3910) are commonly referred to as “data buses” or, sometimes, "databuses". Such avionic data buses are usually characterized by having several equipments or Line Replaceable Items/Units (LRI/LRUs) connected to a common, shared media. They may, as with ARINC 429, be simplex, i.e. have a single source LRI/LRU or, as with ARINC 629, MIL-STD-1553B, and STANAG 3910, be duplex, allow all the connected LRI/LRUs to act, at different times (half duplex), as transmitters and receivers of data.

Bus multiplexing

The simplest system bus has completely separate input data lines, output data lines, and address lines. To reduce cost, most microcomputers have a bidirectional data bus, re-using the same wires for input and output at different times.

Some processors use a dedicated wire for each bit of the address bus, data bus, and the control bus. For example, the 64-pin STEbus is composed of 8 physical wires dedicated to the 8-bit data bus, 20 physical wires dedicated to the 20-bit address bus, 21 physical wires dedicated to the control bus, and 15 physical wires dedicated to various power buses.

Bus multiplexing requires fewer wires, which reduces costs in many early microprocessors and DRAM chips. One common multiplexing scheme, address multiplexing, has already been mentioned. Another multiplexing scheme re-uses the address bus pins as the data bus pins, an approach used by conventional PCI and the 8086. The various "serial buses" can be seen as the ultimate limit of multiplexing, sending each of the address bits and each of the data bits, one at a time, through a single pin (or a single differential pair).

History

Over time, several groups of people worked on various computer bus standards, including the IEEE Bus Architecture Standards Committee (BASC), the IEEE "Superbus" study group, the open microprocessor initiative (OMI), the open microsystems initiative (OMI), the "Gang of Nine" that developed EISA, etc.

First generation

Early computer buses were bundles of wire that attached computer memory and peripherals. Anecdotally termed the "digit trunk", they were named after electrical power buses, or busbars. Almost always, there was one bus for memory, and one or more separate buses for peripherals. These were accessed by separate instructions, with completely different timings and protocols.

One of the first complications was the use of interrupts. Early computer programs performed I/O by waiting in a loop for the peripheral to become ready. This was a waste of time for programs that had other tasks to do. Also, if the program attempted to perform those other tasks, it might take too long for the program to check again, resulting in loss of data. Engineers thus arranged for the peripherals to interrupt the CPU. The interrupts had to be prioritized, because the CPU can only execute code for one peripheral at a time, and some devices are more time-critical than others.

High-end systems introduced the idea of channel controllers, which were essentially small computers dedicated to handling the input and output of a given bus. IBM introduced these on the IBM 709 in 1958, and they became a common feature of their platforms. Other high-performance vendors like Control Data Corporation implemented similar designs. Generally, the channel controllers would do their best to run all of the bus operations internally, moving data when the CPU was known to be busy elsewhere if possible, and only using interrupts when necessary. This greatly reduced CPU load, and provided better overall system performance.

Single system bus

To provide modularity, memory and I/O buses can be combined into a unified system bus. In this case, a single mechanical and electrical system can be used to connect together many of the system components, or in some cases, all of them.

Later computer programs began to share memory common to several CPUs. Access to this memory bus had to be prioritized, as well. The simple way to prioritize interrupts or bus access was with a daisy chain. In this case signals will naturally flow through the bus in physical or logical order, eliminating the need for complex scheduling.

Minis and micros

Digital Equipment Corporation (DEC) further reduced cost for mass-produced minicomputers, and mapped peripherals into the memory bus, so that the input and output devices appeared to be memory locations. This was implemented in the Unibus of the PDP-11 around 1969.

Early microcomputer bus systems were essentially a passive backplane connected directly or through buffer amplifiers to the pins of the CPU. Memory and other devices would be added to the bus using the same address and data pins as the CPU itself used, connected in parallel. Communication was controlled by the CPU, which read and wrote data from the devices as if they are blocks of memory, using the same instructions, all timed by a central clock controlling the speed of the CPU. Still, devices interrupted the CPU by signaling on separate CPU pins.

For instance, a disk drive controller would signal the CPU that new data was ready to be read, at which point the CPU would move the data by reading the "memory location" that corresponded to the disk drive. Almost all early microcomputers were built in this fashion, starting with the S-100 bus in the Altair 8800 computer system.

In some instances, most notably in the IBM PC, although similar physical architecture can be employed, instructions to access peripherals (in and out) and memory (mov and others) have not been made uniform at all, and still generate distinct CPU signals, that could be used to implement a separate I/O bus.

These simple bus systems had a serious drawback when used for general-purpose computers. All the equipment on the bus had to talk at the same speed, as it shared a single clock.

Increasing the speed of the CPU becomes harder, because the speed of all the devices must increase as well. When it is not practical or economical to have all devices as fast as the CPU, the CPU must either enter a wait state, or work at a slower clock frequency temporarily, to talk to other devices in the computer. While acceptable in embedded systems, this problem was not tolerated for long in general-purpose, user-expandable computers.

Such bus systems are also difficult to configure when constructed from common off-the-shelf equipment. Typically each added expansion card requires many jumpers in order to set memory addresses, I/O addresses, interrupt priorities, and interrupt numbers.

Second generation

"Second generation" bus systems like NuBus addressed some of these problems. They typically separated the computer into two "worlds", the CPU and memory on one side, and the various devices on the other. A bus controller accepted data from the CPU side to be moved to the peripherals side, thus shifting the communications protocol burden from the CPU itself. This allowed the CPU and memory side to evolve separately from the device bus, or just "bus". Devices on the bus could talk to each other with no CPU intervention. This led to much better "real world" performance, but also required the cards to be much more complex. These buses also often addressed speed issues by being "bigger" in terms of the size of the data path, moving from 8-bit parallel buses in the first generation, to 16 or 32-bit in the second, as well as adding software setup (now standardised as Plug-n-play) to supplant or replace the jumpers.

However, these newer systems shared one quality with their earlier cousins, in that everyone on the bus had to talk at the same speed. While the CPU was now isolated and could increase speed, CPUs and memory continued to increase in speed much faster than the buses they talked to. The result was that the bus speeds were now very much slower than what a modern system needed, and the machines were left starved for data. A particularly common example of this problem was that video cards quickly outran even the newer bus systems like PCI, and computers began to include AGP just to drive the video card. By 2004 AGP was outgrown again by high-end video cards and other peripherals and has been replaced by the new PCI Express bus.

An increasing number of external devices started employing their own bus systems as well. When disk drives were first introduced, they would be added to the machine with a card plugged into the bus, which is why computers have so many slots on the bus. But through the 1980s and 1990s, new systems like SCSI and IDE were introduced to serve this need, leaving most slots in modern systems empty. Today there are likely to be about five different buses in the typical machine, supporting various devices.

Third generation

"Third generation" buses have been emerging into the market since about 2001, including HyperTransport and InfiniBand. They also tend to be very flexible in terms of their physical connections, allowing them to be used both as internal buses, as well as connecting different machines together. This can lead to complex problems when trying to service different requests, so much of the work on these systems concerns software design, as opposed to the hardware itself. In general, these third generation buses tend to look more like a network than the original concept of a bus, with a higher protocol overhead needed than early systems, while also allowing multiple devices to use the bus at once.

Buses such as Wishbone have been developed by the open source hardware movement in an attempt to further remove legal and patent constraints from computer design.

The Compute Express Link (CXL) is an open standard interconnect for high-speed CPU-to-device and CPU-to-memory, designed to accelerate next-generation data center performance.

Examples of internal computer buses

Parallel

Serial

Examples of external computer buses

Parallel

  • HIPPI High Performance Parallel Interface
  • IEEE-488 (also known as GPIB, General-Purpose Interface Bus, and HPIB, Hewlett-Packard Instrumentation Bus)
  • PC Card, previously known as PCMCIA, much used in laptop computers and other portables, but fading with the introduction of USB and built-in network and modem connections

Serial

Examples of internal/external computer buses

Cooperative

From Wikipedia, the free encyclopedia ...