Chlorofluorocarbon

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https://en.wikipedia.org/wiki/Chlorofluorocarbon

Chlorofluorocarbons (CFCs) and hydrochlorofluorocarbons (HCFCs) are fully or partly halogenated hydrocarbons that contain carbon (C), hydrogen (H), chlorine (Cl), and fluorine (F), produced as volatile derivatives of methane, ethane, and propane.

The most common representative is dichlorodifluoromethane (R-12). R-12 is also commonly called Freon and is used as a refrigerant. Many CFCs have been widely used as refrigerants, propellants (in aerosol applications), and solvents. Because CFCs contribute to ozone depletion in the upper atmosphere, the manufacture of such compounds has been phased out under the Montreal Protocol, and they are being replaced with other products such as hydrofluorocarbons (HFCs) including R-410A and R-134a.

Structure, properties and production

Main article: Organofluorine chemistry

As in simpler alkanes, carbon in the CFCs bond with tetrahedral symmetry. Because the fluorine and chlorine atoms differ greatly in size and effective charge from hydrogen and from each other, the methane-derived CFCs deviate from perfect tetrahedral symmetry.

The physical properties of CFCs and HCFCs are tunable by changes in the number and identity of the halogen atoms. In general, they are volatile but less so than their parent alkanes. The decreased volatility is attributed to the molecular polarity induced by the halides, which induces intermolecular interactions. Thus, methane boils at −161 °C whereas the fluoromethanes boil between −51.7 (CF₂H₂) and −128 °C (CF₄). The CFCs have still higher boiling points because the chloride is even more polarizable than fluoride. Because of their polarity, the CFCs are useful solvents, and their boiling points make them suitable as refrigerants. The CFCs are far less flammable than methane, in part because they contain fewer C-H bonds and in part because, in the case of the chlorides and bromides, the released halides quench the free radicals that sustain flames.

The densities of CFCs are higher than their corresponding alkanes. In general, the density of these compounds correlates with the number of chlorides.

CFCs and HCFCs are usually produced by halogen exchange starting from chlorinated methanes and ethanes. Illustrative is the synthesis of chlorodifluoromethane from chloroform:

HCCl₃ + 2 HF → HCF₂Cl + 2 HCl

Brominated derivatives are generated by free-radical reactions of hydrochlorofluorocarbons, replacing C-H bonds with C-Br bonds. The production of the anesthetic 2-bromo-2-chloro-1,1,1-trifluoroethane ("halothane") is illustrative:

CF₃CH₂Cl + Br₂ → CF₃CHBrCl + HBr

Applications

CFCs and HCFCs are used in various applications because of their low toxicity, reactivity and flammability. Every permutation of fluorine, chlorine and hydrogen based on methane and ethane has been examined and most have been commercialized. Furthermore, many examples are known for higher numbers of carbon as well as related compounds containing bromine. Uses include refrigerants, blowing agents, aerosol propellants in medicinal applications, and degreasing solvents.

Billions of kilograms of chlorodifluoromethane are produced annually as a precursor to tetrafluoroethylene, the monomer that is converted into Teflon.

Classes of compounds, nomenclature

• Chlorofluorocarbons (CFCs): when derived from methane and ethane these compounds have the formulae CCl_mF_4−m and C₂Cl_mF_6−m, where m is nonzero.
• Hydro-chlorofluorocarbons (HCFCs): when derived from methane and ethane these compounds have the formula CCl_mF_nH_4−m−n and C₂Cl_xF_yH_6−x−y, where m, n, x, and y are nonzero.
• and bromofluorocarbons have formulae similar to the CFCs and HCFCs but also include bromine.
• Hydrofluorocarbons (HFCs): when derived from methane, ethane, propane, and butane, these compounds have the respective formulae CF_mH_4−m, C₂F_mH_6−m, C₃F_mH_8−m, and C₄F_mH_10−m, where m is nonzero.

Numbering system

Main article: Refrigerant § Refrigerants by class and R-number

A special numbering system is to be used for fluorinated alkanes, prefixed with Freon-, R-, CFC- and HCFC-, where the rightmost value indicates the number of fluorine atoms, the next value to the left is the number of hydrogen atoms plus 1, and the next value to the left is the number of carbon atoms less one (zeroes are not stated), and the remaining atoms are chlorine.

Freon-12, for example, indicates a methane derivative (only two numbers) containing two fluorine atoms (the second 2) and no hydrogen (1-1=0). It is therefore CCl₂F₂.

Another equation that can be applied to get the correct molecular formula of the CFC/R/Freon class compounds is this to take the numbering and add 90 to it. The resulting value will give the number of carbons as the first numeral, the second numeral gives the number of hydrogen atoms, and the third numeral gives the number of fluorine atoms. The rest of the unaccounted carbon bonds are occupied by chlorine atoms. The value of this equation is always a three figure number. An easy example is that of CFC-12, which gives: 90+12=102 -> 1 carbon, 0 hydrogens, 2 fluorine atoms, and hence 2 chlorine atoms resulting in CCl₂F₂. The main advantage of this method of deducing the molecular composition in comparison with the method described in the paragraph above is that it gives the number of carbon atoms of the molecule.

Freons containing bromine are signified by four numbers. Isomers, which are common for ethane and propane derivatives, are indicated by letters following the numbers:

Principal CFCs
Systematic name	Common/trivial name(s), code	Boiling point (°C)	Formula
Trichlorofluoromethane	Freon-11, R-11, CFC-11	23.77	CCl3F
Dichlorodifluoromethane	Freon-12, R-12, CFC-12	−29.8	CCl2F2
Chlorotrifluoromethane	Freon-13, R-13, CFC-13	−81	CClF3
Dichlorofluoromethane	R-21, HCFC-21	8.9	CHCl2F
Chlorodifluoromethane	R-22, HCFC-22	−40.8	CHClF2
Chlorofluoromethane	Freon 31, R-31, HCFC-31	−9.1	CH2ClF
Bromochlorodifluoromethane	BCF, Halon 1211, H-1211, Freon 12B1	−3.7	CBrClF2
1,1,2-Trichloro-1,2,2-trifluoroethane	Freon 113, R-113, CFC-113, 1,1,2-Trichlorotrifluoroethane	47.7	Cl2FC-CClF2
1,1,1-Trichloro-2,2,2-trifluoroethane	Freon 113a, R-113a, CFC-113a	45.9	Cl3C-CF3
1,2-Dichloro-1,1,2,2-tetrafluoroethane	Freon 114, R-114, CFC-114, Dichlorotetrafluoroethane	3.8	ClF2C-CClF2
1,1-Dichloro-1,2,2,2-tetrafluoroethane	CFC-114a	3.4	Cl2FC-CF3
1-Chloro-1,1,2,2,2-pentafluoroethane	Freon 115, R-115, CFC-115, Chloropentafluoroethane	−38	ClF2C-CF3
2-Chloro-1,1,1,2-tetrafluoroethane	R-124, HCFC-124	−12	CHFClCF3
1,1-Dichloro-1-fluoroethane	R-141b, HCFC-141b	32	Cl2FC-CH3
1-Chloro-1,1-difluoroethane	R-142b, HCFC-142b	−9.2	ClF2C-CH3
Tetrachloro-1,2-difluoroethane	Freon 112, R-112, CFC-112	91.5	CCl2FCCl2F
Tetrachloro-1,1-difluoroethane	Freon 112a, R-112a, CFC-112a	91.5	CClF2CCl3
1,1,2-Trichlorotrifluoroethane	Freon 113, R-113, CFC-113	48	CCl2FCClF2
1-bromo-2-chloro-1,1,2-trifluoroethane	Halon 2311a	51.7	CHClFCBrF2
2-bromo-2-chloro-1,1,1-trifluoroethane	Halon 2311	50.2	CF3CHBrCl
1,1-Dichloro-2,2,3,3,3-pentafluoropropane	R-225ca, HCFC-225ca	51	CF3CF2CHCl2
1,3-Dichloro-1,2,2,3,3-pentafluoropropane	R-225cb, HCFC-225cb	56	CClF2CF2CHClF

Reactions

The most important reaction of the CFCs is the photo-induced scission of a C-Cl bond:

CCl₃F → CCl₂F^. + Cl^.

The chlorine atom, written often as Cl^., behaves very differently from the chlorine molecule (Cl₂). The radical Cl^. is long-lived in the upper atmosphere, where it catalyzes the conversion of ozone into O₂. Ozone absorbs UV-B radiation, so its depletion allows more of this high energy radiation to reach the Earth's surface. Bromine atoms are even more efficient catalysts; hence brominated CFCs are also regulated.

Impact as greenhouse gases

The warming influence of greenhouse gases in the atmosphere has increased substantially in recent years. The rising presence of carbon dioxide from fossil fuel burning is the largest overall driver. The relatively smaller but significant warming impact from releases of the most abundantly produced CFCs (CFC11 and CFC12) will continue to persist for many further decades into the future.

CFCs were phased out via the Montreal Protocol due to their part in ozone depletion.

The atmospheric impacts of CFCs are not limited to their role as ozone-depleting chemicals. Infrared absorption bands prevent heat at that wavelength from escaping earth's atmosphere. CFCs have their strongest absorption bands from C-F and C-Cl bonds in the spectral region of 7.8–15.3 µm^[9]—referred to as the “atmospheric window” due to the relative transparency of the atmosphere within this region.

The strength of CFC absorption bands and the unique susceptibility of the atmosphere at wavelengths where CFCs (indeed all covalent fluorine compounds) absorb radiation creates a “super” greenhouse effect from CFCs and other unreactive fluorine-containing gases such as perfluorocarbons, HFCs, HCFCs, bromofluorocarbons, SF₆, and NF₃. This “atmospheric window” absorption is intensified by the low concentration of each individual CFC. Because CO₂ is close to saturation with high concentrations and few infrared absorption bands, the radiation budget and hence the greenhouse effect has low sensitivity to changes in CO₂ concentration; the increase in temperature is roughly logarithmic. Conversely, the low concentration of CFCs allow their effects to increase linearly with mass, so that chlorofluorocarbons are greenhouse gases with a much higher potential to enhance the greenhouse effect than CO₂.

Groups are actively disposing of legacy CFCs to reduce their impact on the atmosphere.

According to NASA in 2018, the hole in the ozone layer has begun to recover as a result of CFC bans. However, new research released in 2023 reports an alarming increase in CFCs, pointing to unregulated use in China.

History

Carbon tetrachloride (CCl₄) was used in fire extinguishers and glass "anti-fire grenades" from the late nineteenth century until around the end of World War II. Experimentation with chloroalkanes for fire suppression on military aircraft began at least as early as the 1920s. Freon is a trade name for a group of CFCs which are used primarily as refrigerants, but also have uses in fire-fighting and as propellants in aerosol cans. Bromomethane is widely used as a fumigant. Dichloromethane is a versatile industrial solvent.

The Belgian scientist Frédéric Swarts pioneered the synthesis of CFCs in the 1890s. He developed an effective exchange agent to replace chloride in carbon tetrachloride with fluoride to synthesize CFC-11 (CCl₃F) and CFC-12 (CCl₂F₂).

In the late 1920s, Thomas Midgley Jr. improved the process of synthesis and led the effort to use CFC as a refrigerant to replace ammonia (NH₃), chloromethane (CH₃Cl), and sulfur dioxide (SO₂), which are toxic but were in common use. In searching for a new refrigerant, requirements for the compound were: low boiling point, low toxicity, and to be generally non-reactive. In a demonstration for the American Chemical Society, Midgley flamboyantly demonstrated all these properties by inhaling a breath of the gas and using it to blow out a candle in 1930.

Commercial development and use

During World War II, various chloroalkanes were in standard use in military aircraft, although these early halons suffered from excessive toxicity. Nevertheless, after the war they slowly became more common in civil aviation as well. In the 1960s, fluoroalkanes and bromofluoroalkanes became available and were quickly recognized as being highly effective fire-fighting materials. Much early research with Halon 1301 was conducted under the auspices of the US Armed Forces, while Halon 1211 was, initially, mainly developed in the UK. By the late 1960s they were standard in many applications where water and dry-powder extinguishers posed a threat of damage to the protected property, including computer rooms, telecommunications switches, laboratories, museums and art collections. Beginning with warships, in the 1970s, bromofluoroalkanes also progressively came to be associated with rapid knockdown of severe fires in confined spaces with minimal risk to personnel.

By the early 1980s, bromofluoroalkanes were in common use on aircraft, ships, and large vehicles as well as in computer facilities and galleries. However, concern was beginning to be expressed about the impact of chloroalkanes and bromoalkanes on the ozone layer. The Vienna Convention for the Protection of the Ozone Layer did not cover bromofluoroalkanes as it was thought, at the time, that emergency discharge of extinguishing systems was too small in volume to produce a significant impact, and too important to human safety for restriction.

Regulation

Since the late 1970s, the use of CFCs has been heavily regulated because of their destructive effects on the ozone layer. After the development of his electron capture detector, James Lovelock was the first to detect the widespread presence of CFCs in the air, finding a mole fraction of 60 ppt of CFC-11 over Ireland. In a self-funded research expedition ending in 1973, Lovelock went on to measure CFC-11 in both the Arctic and Antarctic, finding the presence of the gas in each of 50 air samples collected, and concluding that CFCs are not hazardous to the environment. The experiment did however provide the first useful data on the presence of CFCs in the atmosphere. The damage caused by CFCs was discovered by Sherry Rowland and Mario Molina who, after hearing a lecture on the subject of Lovelock's work, embarked on research resulting in the first publication suggesting the connection in 1974. It turns out that one of CFCs' most attractive features—their low reactivity—is key to their most destructive effects. CFCs' lack of reactivity gives them a lifespan that can exceed 100 years, giving them time to diffuse into the upper stratosphere. Once in the stratosphere, the sun's ultraviolet radiation is strong enough to cause the homolytic cleavage of the C-Cl bond. In 1976, under the Toxic Substances Control Act, the EPA banned commercial manufacturing and use of CFCs and aerosol propellants. This was later superseded by broader regulation by the EPA under the Clean Air Act to address stratospheric ozone depletion.

NASA projection of stratospheric ozone, in Dobson units, if chlorofluorocarbons had not been banned. Animated version.

By 1987, in response to a dramatic seasonal depletion of the ozone layer over Antarctica, diplomats in Montreal forged a treaty, the Montreal Protocol, which called for drastic reductions in the production of CFCs. On 2 March 1989, 12 European Community nations agreed to ban the production of all CFCs by the end of the century. In 1990, diplomats met in London and voted to significantly strengthen the Montreal Protocol by calling for a complete elimination of CFCs by 2000. By 2010, CFCs should have been completely eliminated from developing countries as well.

Ozone-depleting gas trends

Because the only CFCs available to countries adhering to the treaty is from recycling, their prices have increased considerably. A worldwide end to production should also terminate the smuggling of this material. However, there are current CFC smuggling issues, as recognized by the United Nations Environmental Programme (UNEP) in a 2006 report titled "Illegal Trade in Ozone Depleting Substances". UNEP estimates that between 16,000–38,000 tonnes of CFCs passed through the black market in the mid-1990s. The report estimated between 7,000 and 14,000 tonnes of CFCs are smuggled annually into developing countries. Asian countries are those with the most smuggling; as of 2007, China, India and South Korea were found to account for around 70% of global CFC production, South Korea later to ban CFC production in 2010. Possible reasons for continued CFC smuggling were also examined: the report noted that many banned CFC producing products have long lifespans and continue to operate. The cost of replacing the equipment of these items is sometimes cheaper than outfitting them with a more ozone-friendly appliance. Additionally, CFC smuggling is not considered a significant issue, so the perceived penalties for smuggling are low. In 2018 public attention was drawn to the issue, that at an unknown place in east Asia an estimated amount of 13,000 metric tons annually of CFCs have been produced since about 2012 in violation of the protocol. While the eventual phaseout of CFCs is likely, efforts are being taken to stem these current non-compliance problems.

By the time of the Montreal Protocol, it was realised that deliberate and accidental discharges during system tests and maintenance accounted for substantially larger volumes than emergency discharges, and consequently halons were brought into the treaty, albeit with many exceptions.

Regulatory gap

While the production and consumption of CFCs are regulated under the Montreal Protocol, emissions from existing banks of CFCs are not regulated under the agreement. In 2002, there were an estimated 5,791 kilotons of CFCs in existing products such as refrigerators, air conditioners, aerosol cans and others. Approximately one-third of these CFCs are projected to be emitted over the next decade if action is not taken, posing a threat to both the ozone layer and the climate. A proportion of these CFCs can be safely captured and destroyed.

Regulation and DuPont

In 1978 the United States banned the use of CFCs such as Freon in aerosol cans, the beginning of a long series of regulatory actions against their use. The critical DuPont manufacturing patent for Freon ("Process for Fluorinating Halohydrocarbons", U.S. Patent #3258500) was set to expire in 1979. In conjunction with other industrial peers DuPont formed a lobbying group, the "Alliance for Responsible CFC Policy," to combat regulations of ozone-depleting compounds. In 1986 DuPont, with new patents in hand, reversed its previous stance and publicly condemned CFCs. DuPont representatives appeared before the Montreal Protocol urging that CFCs be banned worldwide and stated that their new HCFCs would meet the worldwide demand for refrigerants.

Phasing-out of CFCs

Use of certain chloroalkanes as solvents for large scale application, such as dry cleaning, have been phased out, for example, by the IPPC directive on greenhouse gases in 1994 and by the volatile organic compounds (VOC) directive of the EU in 1997. Permitted chlorofluoroalkane uses are medicinal only.

Bromofluoroalkanes have been largely phased out and the possession of equipment for their use is prohibited in some countries like the Netherlands and Belgium, from 1 January 2004, based on the Montreal Protocol and guidelines of the European Union.

Production of new stocks ceased in most (probably all) countries in 1994. However many countries still require aircraft to be fitted with halon fire suppression systems because no safe and completely satisfactory alternative has been discovered for this application. There are also a few other, highly specialized uses. These programs recycle halon through "halon banks" coordinated by the Halon Recycling Corporation to ensure that discharge to the atmosphere occurs only in a genuine emergency and to conserve remaining stocks.

The interim replacements for CFCs are hydrochlorofluorocarbons (HCFCs), which deplete stratospheric ozone, but to a much lesser extent than CFCs. Ultimately, hydrofluorocarbons (HFCs) will replace HCFCs. Unlike CFCs and HCFCs, HFCs have an ozone depletion potential (ODP) of 0. DuPont began producing hydrofluorocarbons as alternatives to Freon in the 1980s. These included Suva refrigerants and Dymel propellants. Natural refrigerants are climate friendly solutions that are enjoying increasing support from large companies and governments interested in reducing global warming emissions from refrigeration and air conditioning.

Phasing-out of HFCs and HCFCs

Hydrofluorocarbons are included in the Kyoto Protocol and are regulated under the Kigali Amendment to the Montreal Protocol due to their very high Global Warming Potential and the recognition of halocarbon contributions to climate change.

On September 21, 2007, approximately 200 countries agreed to accelerate the elimination of hydrochlorofluorocarbons entirely by 2020 in a United Nations-sponsored Montreal summit. Developing nations were given until 2030. Many nations, such as the United States and China, who had previously resisted such efforts, agreed with the accelerated phase out schedule. India successfully phased out HCFCs by 2020.

Properly collecting, controlling, and destroying CFCs and HCFCs

While new production of these refrigerants has been banned, large volumes still exist in older systems and pose an immediate threat to our environment. Preventing the release of these harmful refrigerants has been ranked as one of the single most effective actions we can take to mitigate catastrophic climate change.

Development of alternatives for CFCs

Work on alternatives for chlorofluorocarbons in refrigerants began in the late 1970s after the first warnings of damage to stratospheric ozone were published.

The hydrochlorofluorocarbons (HCFCs) are less stable in the lower atmosphere, enabling them to break down before reaching the ozone layer. Nevertheless, a significant fraction of the HCFCs do break down in the stratosphere and they have contributed to more chlorine buildup there than originally predicted. Later alternatives lacking the chlorine, the hydrofluorocarbons (HFCs) have an even shorter lifetimes in the lower atmosphere. One of these compounds, HFC-134a, were used in place of CFC-12 in automobile air conditioners. Hydrocarbon refrigerants (a propane/isobutane blend) were also used extensively in mobile air conditioning systems in Australia, the US and many other countries, as they had excellent thermodynamic properties and performed particularly well in high ambient temperatures. 1,1-Dichloro-1-fluoroethane (HCFC-141b) has replaced HFC-134a, due to its low ODP and GWP values. And according to the Montreal Protocol, HCFC-141b is supposed to be phased out completely and replaced with zero ODP substances such as cyclopentane, HFOs, and HFC-345a before January 2020.

Among the natural refrigerants (along with ammonia and carbon dioxide), hydrocarbons have negligible environmental impacts and are also used worldwide in domestic and commercial refrigeration applications, and are becoming available in new split system air conditioners. Various other solvents and methods have replaced the use of CFCs in laboratory analytics.

In Metered-dose inhalers (MDI), a non-ozone effecting substitute was developed as a propellant, known as "hydrofluoroalkane."

Applications and replacements for CFCs
Application	Previously used CFC	Replacement
Refrigeration & air-conditioning	CFC-12 (CCl2F2); CFC-11(CCl3F); CFC-13(CClF3); HCFC-22 (CHClF2); CFC-113 (Cl2FCCClF2); CFC-114 (CClF2CClF2); CFC-115 (CF3CClF2);	HFC-23 (CHF3); HFC-134a (CF3CFH2); HFC-507 (a 1:1 azeotropic mixture of HFC 125 (CF3 CHF2) and HFC-143a (CF3CH3)); HFC 410 (a 1:1 azeotropic mixture of HFC-32 (CF2H2) and HFC-125 (CF3CF2H))
Propellants in medicinal aerosols	CFC-114 (CClF2CClF2)	HFC-134a (CF3CFH2); HFC-227ea (CF3CHFCF3)
Blowing agents for foams	CFC-11 (CCl3F); CFC 113 (Cl2FCCClF2); HCFC-141b (CCl2FCH3)	HFC-245fa (CF3CH2CHF2); HFC-365 mfc (CF3CH2CF2CH3)
Solvents, degreasing agents, cleaning agents	CFC-11 (CCl3F); CFC-113 (CCl2FCClF2)	None

Tracer of ocean circulation

Because the time history of CFC concentrations in the atmosphere is relatively well known, they have provided an important constraint on ocean circulation. CFCs dissolve in seawater at the ocean surface and are subsequently transported into the ocean interior. Because CFCs are inert, their concentration in the ocean interior reflects simply the convolution of their atmospheric time evolution and ocean circulation and mixing.

CFC and SF₆ tracer-derived age of ocean water

Chlorofluorocarbons (CFCs) are anthropogenic compounds that have been released into the atmosphere since the 1930s in various applications such as in air-conditioning, refrigeration, blowing agents in foams, insulations and packing materials, propellants in aerosol cans, and as solvents. The entry of CFCs into the ocean makes them extremely useful as transient tracers to estimate rates and pathways of ocean circulation and mixing processes. However, due to production restrictions of CFCs in the 1980s, atmospheric concentrations of CFC-11 and CFC-12 has stopped increasing, and the CFC-11 to CFC-12 ratio in the atmosphere have been steadily decreasing, making water dating of water masses more problematic. Incidentally, production and release of sulfur hexafluoride (SF₆) have rapidly increased in the atmosphere since the 1970s. Similar to CFCs, SF₆ is also an inert gas and is not affected by oceanic chemical or biological activities. Thus, using CFCs in concert with SF₆ as a tracer resolves the water dating issues due to decreased CFC concentrations.

Using CFCs or SF₆ as a tracer of ocean circulation allows for the derivation of rates for ocean processes due to the time-dependent source function. The elapsed time since a subsurface water mass was last in contact with the atmosphere is the tracer-derived age. Estimates of age can be derived based on the partial pressure of an individual compound and the ratio of the partial pressure of CFCs to each other (or SF₆).

Partial pressure and ratio dating techniques

The age of a water parcel can be estimated by the CFC partial pressure (pCFC) age or SF₆ partial pressure (pSF₆) age. The pCFC age of a water sample is defined as:

${\displaystyle pCFC=\frac{[CFC]}{F(T,S)}}$

where [CFC] is the measured CFC concentration (pmol kg⁻¹) and F is the solubility of CFC gas in seawater as a function of temperature and salinity. The CFC partial pressure is expressed in units of 10–12 atmospheres or parts-per-trillion (ppt). The solubility measurements of CFC-11 and CFC-12 have been previously measured by Warner and Weiss Additionally, the solubility measurement of CFC-113 was measured by Bu and Warner and SF₆ by Wanninkhof et al. and Bullister et al. Theses authors mentioned above have expressed the solubility (F) at a total pressure of 1 atm as:

${\displaystyle \ln F=a_1+a_2\left(\frac{100}{T}\right)+a_3\ln \left(\frac{T}{100}\right)+a_4{\left(\frac{T}{100}\right)}^2+S\left[b_1+b_2\left(\frac{T}{100}\right)+b_3\left(\frac{T}{100}\right)\right],}$

where F = solubility expressed in either mol l⁻¹ or mol kg⁻¹ atm⁻¹, T = absolute temperature, S = salinity in parts per thousand (ppt), a₁, a₂, a₃, b₁, b₂, and b₃ are constants to be determined from the least squares fit to the solubility measurements. This equation is derived from the integrated Van 't Hoff equation and the logarithmic Setchenow salinity dependence.

It can be noted that the solubility of CFCs increase with decreasing temperature at approximately 1% per degree Celsius.

Once the partial pressure of the CFC (or SF₆) is derived, it is then compared to the atmospheric time histories for CFC-11, CFC-12, or SF₆ in which the pCFC directly corresponds to the year with the same. The difference between the corresponding date and the collection date of the seawater sample is the average age for the water parcel. The age of a parcel of water can also be calculated using the ratio of two CFC partial pressures or the ratio of the SF₆ partial pressure to a CFC partial pressure.

Safety

According to their material safety data sheets, CFCs and HCFCs are colorless, volatile, non-toxic liquids and gases with a faintly sweet ethereal odor. Overexposure at concentrations of 11% or more may cause dizziness, loss of concentration, central nervous system depression or cardiac arrhythmia. Vapors displace air and can cause asphyxiation in confined spaces. Although non-flammable, their combustion products include hydrofluoric acid and related species. Normal occupational exposure is rated at 0.07% and does not pose any serious health risks.

NOx

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/NOx 

 

This article is about nitrogen oxides produced during combustion. For a more extensive list of nitrogen oxides, see nitrogen oxide. For other meanings of "Nox", see Nox.

In atmospheric chemistry, NO_x is shorthand for nitric oxide (NO) and nitrogen dioxide (NO
₂), the nitrogen oxides that are most relevant for air pollution. These gases contribute to the formation of smog and acid rain, as well as affecting tropospheric ozone.

NO_x gases are usually produced from the reaction between nitrogen and oxygen during combustion of fuels, such as hydrocarbons, in air; especially at high temperatures, such as in car engines. In areas of high motor vehicle traffic, such as in large cities, the nitrogen oxides emitted can be a significant source of air pollution. NO_x gases are also produced naturally by lightning.

NO_x does not include nitrous oxide (N
₂O), a fairly inert oxide of nitrogen that contributes less severely to air pollution, notwithstanding its involvement in ozone depletion and high global warming potential.

NO_y is defined as the sum of NO_x plus the NO_z compounds produced from the oxidation of NO_x which include nitric acid, nitrous acid (HONO), dinitrogen pentoxide (N₂O₅), peroxyacetyl nitrate (PAN), alkyl nitrates (RONO₂), peroxyalkyl nitrates (ROONO₂), the nitrate radical (NO₃), and peroxynitric acid (HNO₄).

Formation and reactions

Because of energy limitations, oxygen and nitrogen do not react at ambient temperatures. But at high temperatures, they undergo an endothermic reaction producing various oxides of nitrogen. Such temperatures arise inside an internal combustion engine or a power station boiler, during the combustion of a mixture of air and fuel, and naturally in a lightning flash.

In atmospheric chemistry, the term NO_x denotes the total concentration of NO and NO₂ since the conversion between these two species is rapid in the stratosphere and troposphere. During daylight hours, these concentrations together with that of ozone are in steady state, also known as photostationary state (PSS); the ratio of NO to NO₂ is determined by the intensity of sunshine (which converts NO₂ to NO) and the concentration of ozone (which reacts with NO to again form NO₂).

In other words, the concentration of ozone in the atmosphere is determined by the ratio of these two species.

${\displaystyle {\text{NO}}_2^{}+\text{h}\nu ⟶\text{NO}+\text{O}{(}^3\text{P}),\lambda <398\text{nm}}$

(1)

${\displaystyle \text{O}{(}^3\text{P})+{\text{O}}_2^{}+\text{M}⟶{\text{O}}_3^{}+\text{M}}$

(2)

${\displaystyle {\text{O}}_3^{}+\text{NO}⟶{\text{NO}}_2^{}+{\text{O}}_2^{}}$

(3)

${\displaystyle \frac{[{\text{NO}}_2^{}]}{[\text{NO}]}=\frac{k_3[{\text{O}}_3^{}]}{j_{{\text{NO}}_2^{}}}}$

(4)

This relationship between NO_x and ozone is also known as the Leighton relationship.

The time τ that is needed to reach a steady state among NO_x and ozone is dominated by reaction (3), which reverses reactions (1)+(2):

${\displaystyle \tau =\frac{1}{k_3[\text{NO}]}}$

(5)

for mixing ratio of NO, [NO] = 10 part per billion (ppb), the time constant is 40 minutes; for [NO] = 1 ppb, 4 minutes.

Formation of smog

When NO_x and volatile organic compounds (VOCs) react in the presence of sunlight, they form photochemical smog, a significant form of air pollution. The presence of photochemical smog increases during the summer when the incident solar radiation is higher. The emitted hydrocarbons from industrial activities and transportation react with NO_x quickly and increase the concentration of ozone and peroxide compounds, especially peroxyacetyl nitrate (PAN).

Children, people with lung diseases such as asthma, and people who work or exercise outside are particularly susceptible to adverse effects of smog such as damage to lung tissue and reduction in lung function.

Formation of nitric acid and acid rain

NO₂ is further oxidized in the gas phase during daytime by reaction with OH

NO₂ + OH (+M) → HNO₃ (+M),

where M denotes a third molecule required to stabilize the addition product. Nitric acid (HNO₃) is highly soluble in liquid water in aerosol particles or cloud drops.

NO₂ also reacts with ozone to form nitrate radical

NO₂ + O₃ → NO₃ + O₂.

During the daytime, NO₃ is quickly photolyzed back to NO₂, but at night it can react with a second NO₂ to form dinitrogen pentoxide.

NO₂ + NO₃ (+M) → N₂O₅ (+M).

N₂O₅ reacts rapidly with liquid water (in aerosol particles or cloud drops, but not in the gas phase) to form HNO₃,

N₂O₅ + H₂O(liq) → 2 HNO₃(aq)

These are thought to be the principal pathways for formation of nitric acid in the atmosphere. This nitric acid contributes to acid rain or may deposit to soil, where it makes nitrate, which is of use to growing plants. The aqueous phase reaction

2 NO₂ + H₂O → HNO₂ + HNO₃

is too slow to be of any significance in the atmosphere.

Sources

Natural sources

Nitric oxide is produced during thunderstorms due to the extreme heating and cooling within a lightning strike. This causes stable molecules such as N₂ and O₂ to convert into significant amounts of NO similar to the process that occurs during high temperature fuel combustion. NO_x from lightning can become oxidized to produce nitric acid (HNO₃), this can be precipitated out as acid rain or deposited onto particles in the air. Elevated production of NO_x from lightning depends on the season and geographic location. The occurrence of lightning is more common over land near the equator in the inter-tropical convergence zone (ITCZ) during summer months. This area migrates slightly as seasons change. NO_x production from lightning can be observed through satellite observations.

Scientists Ott et al. estimated that each flash of lightning on average in the several mid-latitude and subtropical thunderstorms studied turned 7 kg (15 lb) of nitrogen into chemically reactive NO_x. With 1.4 billion lightning flashes per year, multiplied by 7 kilograms per lightning strike, they estimated the total amount of NO_x produced by lightning per year is 8.6 million tonnes. However, NO_x emissions resulting from fossil fuel combustion are estimated at 28.5 million tonnes.

A recent discovery indicated that cosmic ray and solar flares can significantly influence the number of lightning strikes occurring on Earth. Therefore, space weather can be a major driving force of lightning-produced atmospheric NO_x. Atmospheric constituents such as nitrogen oxides can be stratified vertically in the atmosphere. Ott noted that the lightning-produced NO_x is typically found at altitudes greater than 5 km, while combustion and biogenic (soil) NO_x are typically found near the sources at near surface elevation (where it can cause the most significant health effects).

Biogenic sources

Agricultural fertilization and the use of nitrogen fixing plants also contribute to atmospheric NO_x, by promoting nitrogen fixation by microorganisms. The nitrification process transforms ammonia into nitrate. Denitrification is basically the reverse process of nitrification. During denitrification, nitrate is reduced to nitrite, then NO, then N₂O and finally nitrogen. Through these processes, NO_x is emitted to the atmosphere.

A recent study conducted by the University of California Davis found that adding nitrogen fertilizer to soil in California is contributing 25 percent or more to state-wide NO_x pollution levels. When nitrogen fertilizer is added to the soil, excess ammonium and nitrate not used by plants can be converted to NO by microorganisms in the soil, which escapes into the air. NO_x is a precursor for smog formation which is already a known issue for the state of California. In addition to contributing to smog, when nitrogen fertilizer is added to the soil and the excess is released in the form of NO, or leached as nitrate this can be a costly process for the farming industry.

A 2018 study by the Indiana University determined that forests in the eastern United States can expect to see increases in NO_x and in turn, changes in the types of trees which predominate. Due to human activity and climate change, the maples, sassafras, and tulip poplar have been pushing out the beneficial oak, beech, and hickory. The team determined that the first three tree species, maples, sassafras, and tulip poplar, are associated with ammonia-oxidizing bacteria known to "emit reactive nitrogen from soil." By contrast, the second three tree species, oak, beech and hickory, are associated with microbes that "absorb reactive nitrogen oxides," and thus can have a positive impact on the nitrogen oxide component of air quality. Nitrogen oxide release from forest soils is expected to be highest in Indiana, Illinois, Michigan, Kentucky and Ohio.

Industrial sources (anthropogenic sources)

The three primary sources of NO_x in combustion processes:

• thermal NO_x
• fuel NO_x
• prompt NO_x

Thermal NO_x formation, which is highly temperature dependent, is recognized as the most relevant source when combusting natural gas. Fuel NO_x tends to dominate during the combustion of fuels, such as coal, which have a significant nitrogen content, particularly when burned in combustors designed to minimise thermal NO_x. The contribution of prompt NO_x is normally considered negligible. A fourth source, called feed NO_x is associated with the combustion of nitrogen present in the feed material of cement rotary kilns, at between 300 °C and 800 °C, where it is considered a minor contributor.

Thermal

Thermal NO_x refers to NO_x formed through high temperature oxidation of the diatomic nitrogen found in combustion air. The formation rate is primarily a function of temperature and the residence time of nitrogen at that temperature. At high temperatures, usually above 1300 °C (2600 °F), molecular nitrogen (N₂) and oxygen (O₂) in the combustion air dissociate into their atomic states and participate in a series of reactions.

The three principal reactions (the extended Zel'dovich mechanism) producing thermal NO_x are:

N₂+ O ⇌ NO + N

N + O₂ ⇌ NO + O

N + OH${\displaystyle \cdot }$ ⇌ NO + H${\displaystyle \cdot }$

All three reactions are reversible. Zeldovich was the first to suggest the importance of the first two reactions. The last reaction of atomic nitrogen with the hydroxyl radical, ^•HO, was added by Lavoie, Heywood and Keck to the mechanism and makes a significant contribution to the formation of thermal NO_x.

Fuel

It is estimated that transportation fuels cause 54% of the anthropogenic (i.e. human-caused) NO_x. The major source of NO_x production from nitrogen-bearing fuels such as certain coals and oil, is the conversion of fuel bound nitrogen to NO_x during combustion. During combustion, the nitrogen bound in the fuel is released as a free radical and ultimately forms free N₂, or NO. Fuel NO_x can contribute as much as 50% of total emissions through the combusting oil and as much as 80% through the combusting of coal.

Although the complete mechanism is not fully understood, there are two primary pathways of formation. The first involves the oxidation of volatile nitrogen species during the initial stages of combustion. During the release and before the oxidation of the volatiles, nitrogen reacts to form several intermediaries which are then oxidized into NO. If the volatiles evolve into a reducing atmosphere, the nitrogen evolved can readily be made to form nitrogen gas, rather than NO_x. The second pathway involves the combustion of nitrogen contained in the char matrix during the combustion of the char portion of the fuels. This reaction occurs much more slowly than the volatile phase. Only around 20% of the char nitrogen is ultimately emitted as NO_x, since much of the NO_x that forms during this process is reduced to nitrogen by the char, which is nearly pure carbon.

Prompt

Nitrogen oxides are released during manufacturing of nitrogen fertilizers. Though nitrous oxide is emitted during its application, it is then reacted in atmosphere to form nitrogen oxides. This third source is attributed to the reaction of atmospheric nitrogen, N₂, with radicals such as C, CH, and CH₂ fragments derived from fuel, rather than thermal or fuel processes. Occurring in the earliest stage of combustion, this results in the formation of fixed species of nitrogen such as NH (nitrogen monohydride), NCN (diradical cyanonitrene), HCN (hydrogen cyanide), ^•H₂CN (dihydrogen cyanide) and ^•CN (cyano radical) which can oxidize to NO. In fuels that contain nitrogen, the incidence of prompt NO_x is comparatively small and it is generally only of interest for the most exacting emission targets.

Health and environment effects

There is strong evidence that NO_x respiratory exposure can trigger and exacerbate existing asthma symptoms, and may even lead to the development of asthma over longer periods of time. It has also been associated with heart disease, diabetes, birth outcomes, and all-cause mortality, but these nonrespiratory effects are less well-established.

NO_x reacts with ammonia, moisture, and other compounds to form nitric acid vapor and related particles.

NO_x reacts with volatile organic compounds in the presence of sunlight to form ozone. Ozone can cause adverse effects such as damage to lung tissue and reduction in lung function mostly in susceptible populations (children, elderly, asthmatics). Ozone can be transported by wind currents and cause health impacts far from the original sources. The American Lung Association estimates that nearly 50 percent of United States inhabitants live in counties that are not in ozone compliance. In South East England, ground level ozone pollution tends to be highest in the countryside and in suburbs, while in central London and on major roads NO emissions are able to "mop up" ozone to form NO₂ and oxygen.

NO_x also readily reacts with common organic chemicals, and even ozone, to form a wide variety of toxic products: nitroarenes, nitrosamines and also the nitrate radical some of which may cause DNA mutations. Recently another pathway, via NO_x, to ozone has been found that predominantly occurs in coastal areas via formation of nitryl chloride when NO_x comes into contact with salt mist.

The direct effect of the emission of NO_x has positive contribution to the greenhouse effect. Instead of reacting with ozone in Reaction 3, NO can also react with HO₂· and organic peroxyradicals (RO₂·) and thus increase the concentration of ozone. Once the concentration of NO_x exceeds a certain level, atmospheric reactions result in net ozone formation. Since tropospheric ozone can absorb infrared radiation, this indirect effect of NO_x is intensifying global warming.

There are also other indirect effects of NO_x that can either increase or decrease the greenhouse effect. First of all, through the reaction of NO with HO₂ radicals, ^•OH radicals are recycled, which oxidize methane molecules, meaning NO_x emissions can counter the effect of greenhouse gases. For instance, ship traffic emits a great amount of NO_x which provides a source of NO_x over the ocean. Then, photolysis of NO₂ leads to the formation of ozone and the further formation of hydroxyl radicals (·OH) through ozone photolysis. Since the major sink of methane in the atmosphere is by reaction with ^•OH radicals, the NO_x emissions from ship travel may lead to a net global cooling. However, NO_x in the atmosphere may undergo dry or wet deposition and return to land in the form of HNO₃/NO₃⁻. Through this way, the deposition leads to nitrogen fertilization and the subsequent formation of nitrous oxide (N₂O) in soil, which is another greenhouse gas. In conclusion, considering several direct and indirect effects, NO_x emissions have a negative contribution to global warming.

NO_x in the atmosphere is removed through several pathways. During daytime, NO₂ reacts with hydroxyl radicals (·OH) and forms nitric acid (HNO₃), which can easily be removed by dry and wet deposition. Organic peroxyradicals (RO₂·) can also react with NO and NO₂ and result in the formation of organic nitrates. These are ultimately broken down to inorganic nitrate, which is a useful nutrient for plants. During nighttime, NO₂ and NO can form nitrous acid (HONO) through surface-catalyzed reaction. Although the reaction is relatively slow, it is an important reaction in urban areas. In addition, the nitrate radical (NO₃) is formed by the reaction between NO₂ and ozone. At night, NO₃ further reacts with NO₂ and establishes an equilibrium reaction with dinitrogen pentoxide (N₂O₅). Via heterogeneous reaction, N₂O₅ reacts with water vapor or liquid water and forms nitric acid (HNO₃). As mentioned above, nitric acid can be removed through wet and dry deposition and this results in the removal of NO_x from the atmosphere.

Biodiesel and NO_x

Biodiesel and its blends in general are known to reduce harmful tailpipe emissions such as: carbon monoxide; particulate matter (PM), otherwise known as soot; and unburned hydrocarbon emissions. While earlier studies suggested biodiesel could sometimes decrease NO_x and sometimes increase NO_x emissions, subsequent investigation has shown that blends of up to 20% biodiesel in USEPA-approved diesel fuel have no significant impact on NO_x emissions compared with regular diesel. The state of California uses a special formulation of diesel fuel to produce less NO_x relative to diesel fuel used in the other 49 states. This has been deemed necessary by the California Air Resources Board (CARB) to offset the combination of vehicle congestion, warm temperatures, extensive sunlight, PM, and topography that all contribute to the formation of ozone and smog. CARB has established a special regulation for Alternative Diesel Fuels to ensure that any new fuels, including biodiesel, coming into the market do not substantially increase NO_x emissions. The reduction of NO_x emissions is one of the most important challenges for advances in vehicle technology. While diesel vehicles sold in the US since 2010 are dramatically cleaner than previous diesel vehicles, urban areas continue to seek more ways to reduce the formation of smog and ozone. NO_x formation during combustion is associated with a number of factors such as combustion temperature. As such, it can be observed that the vehicle drive cycle, or the load on the engine have more significant impact on NO_x emissions than the type of fuel used. This may be especially true for modern, clean diesel vehicles that continuously monitor engine operation electronically and actively control engine parameters and exhaust system operations to limit NO_x emission to less than 0.2 g/km. Low-temperature combustion or LTC technology may help reduce thermal formation of NO_x during combustion, however a tradeoff exists as high temperature combustion produces less PM or soot and results in greater power and fuel efficiency.

Regulation and emission control technologies

Selective catalytic reduction (SCR) and selective non-catalytic reduction (SNCR) reduce post combustion NO_x by reacting the exhaust with urea or ammonia to produce nitrogen and water. SCR is now being used in ships, diesel trucks and in some diesel cars. The use of exhaust gas recirculation and catalytic converters in motor vehicle engines have significantly reduced vehicular emissions. NO_x was the main focus of the Volkswagen emissions violations.

Other technologies such as flameless oxidation (FLOX) and staged combustion significantly reduce thermal NO_x in industrial processes. Bowin low NO_x technology is a hybrid of staged-premixed-radiant combustion technology with major surface combustion preceded by minor radiant combustion. In the Bowin burner, air and fuel gas are premixed at a ratio greater than or equal to the stoichiometric combustion requirement. Water Injection technology, whereby water is introduced into the combustion chamber, is also becoming an important means of NO_x reduction through increased efficiency in the overall combustion process. Alternatively, the water (e.g. 10 to 50%) is emulsified into the fuel oil before the injection and combustion. This emulsification can either be made in-line (unstabilized) just before the injection or as a drop-in fuel with chemical additives for long-term emulsion stability (stabilized). Excessive water addition facilitates hot corrosion, which is the primary reason why dry low-NO_x technologies are favored today besides the requirement of a more complex system.

Single-molecule real-time sequencing

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Single-molecule_real-time_sequencing 

Single-molecule real-time (SMRT) sequencing is a parallelized single molecule DNA sequencing method. Single-molecule real-time sequencing utilizes a zero-mode waveguide (ZMW). A single DNA polymerase enzyme is affixed at the bottom of a ZMW with a single molecule of DNA as a template. The ZMW is a structure that creates an illuminated observation volume that is small enough to observe only a single nucleotide of DNA being incorporated by DNA polymerase. Each of the four DNA bases is attached to one of four different fluorescent dyes. When a nucleotide is incorporated by the DNA polymerase, the fluorescent tag is cleaved off and diffuses out of the observation area of the ZMW where its fluorescence is no longer observable. A detector detects the fluorescent signal of the nucleotide incorporation, and the base call is made according to the corresponding fluorescence of the dye.

Technology

The DNA sequencing is done on a chip that contains many ZMWs. Inside each ZMW, a single active DNA polymerase with a single molecule of single stranded DNA template is immobilized to the bottom through which light can penetrate and create a visualization chamber that allows monitoring of the activity of the DNA polymerase at a single molecule level. The signal from a phospho-linked nucleotide incorporated by the DNA polymerase is detected as the DNA synthesis proceeds which results in the DNA sequencing in real time.

Template preparation

To prepare the library, DNA fragments are put into a circular form using hairpin adapter ligations.

Phospholinked nucleotide

For each of the nucleotide bases, there is a corresponding fluorescent dye molecule that enables the detector to identify the base being incorporated by the DNA polymerase as it performs the DNA synthesis. The fluorescent dye molecule is attached to the phosphate chain of the nucleotide. When the nucleotide is incorporated by the DNA polymerase, the fluorescent dye is cleaved off with the phosphate chain as a part of a natural DNA synthesis process during which a phosphodiester bond is created to elongate the DNA chain. The cleaved fluorescent dye molecule then diffuses out of the detection volume so that the fluorescent signal is no longer detected.

Zero-Mode Waveguide

The zero-mode waveguide (ZMW) is a nanophotonic confinement structure that consists of a circular hole in an aluminum cladding film deposited on a clear silica substrate.

The ZMW holes are ~70 nm in diameter and ~100 nm in depth. Due to the behavior of light when it travels through a small aperture, the optical field decays exponentially inside the chamber.

The observation volume within an illuminated ZMW is ~20 zeptoliters (20 X 10⁻²¹ liters). Within this volume, the activity of DNA polymerase incorporating a single nucleotide can be readily detected.

Sequencing Performance

Sequencing performance can be measured in read length, accuracy, and total throughput per experiment. PacBio sequencing systems using ZMWs have the advantage of long read lengths, although error rates are on the order of 5-15% and sample throughput is lower than Illumina sequencing platforms.

On 19 Sep 2018, Pacific Biosciences [PacBio] released the Sequel 6.0 chemistry, synchronizing the chemistry version with the software version. Performance is contrasted for large-insert libraries with high molecular weight DNA versus shorter-insert libraries below ~15,000 bases in length. For larger templates average read lengths are up to 30,000 bases. For shorter-insert libraries, average read length are up to 100,000 bases while reading the same molecule in a circle. The latter shorter-insert libraries then yield up to 50 billion bases from a single SMRT Cell.

History

Pacific Biosciences (PacBio) commercialized SMRT sequencing in 2011, after releasing a beta version of its RS instrument in late 2010.

RS and RS II

SMRT Cell for a RS or RS II Sequencer

At commercialization, read length had a normal distribution with a mean of about 1100 bases. A new chemistry kit released in early 2012 increased the sequencer's read length; an early customer of the chemistry cited mean read lengths of 2500 to 2900 bases.

The XL chemistry kit released in late 2012 increased average read length to more than 4300 bases.

On August 21, 2013, PacBio released a new DNA polymerase Binding Kit P4. This P4 enzyme has average read lengths of more than 4,300 bases when paired with the C2 sequencing chemistry and more than 5,000 bases when paired with the XL chemistry. The enzyme’s accuracy is similar to C2, reaching QV50 between 30X and 40X coverage. The resulting P4 attributes provided higher-quality assemblies using fewer SMRT Cells and with improved variant calling. When coupled with input DNA size selection (using an electrophoresis instrument such as BluePippin) yields average read length over 7 kilobases.

On October 3, 2013, PacBio released new reagent combination for PacBio RS II, the P5 DNA polymerase with C3 chemistry (P5-C3). Together, they extend sequencing read lengths to an average of approximately 8,500 bases, with the longest reads exceeding 30,000 bases. Throughput per SMRT cell is around 500 million bases demonstrated by sequencing results from the CHM1 cell line.

On October 15, 2014, PacBio announced the release of new chemistry P6-C4 for the RS II system, which represents the company's 6th generation of polymerase and 4th generation chemistry--further extending the average read length to 10,000 - 15,000 bases, with the longest reads exceeding 40,000 bases. The throughput with the new chemistry was estimated between 500 million to 1 billion bases per SMRT Cell, depending on the sample being sequenced. This was the final version of chemistry released for the RS instrument.

Throughput per experiment for the technology is both influenced by the read length of DNA molecules sequenced as well as total multiplex of a SMRT Cell. The prototype of the SMRT Cell contained about 3000 ZMW holes that allowed parallelized DNA sequencing. At commercialization, the SMRT Cells were each patterned with 150,000 ZMW holes that were read in two sets of 75,000. In April 2013, the company released a new version of the sequencer called the "PacBio RS II" that uses all 150,000 ZMW holes concurrently, doubling the throughput per experiment. The highest throughput mode in November 2013 used P5 binding, C3 chemistry, BluePippin size selection, and a PacBio RS II officially yielded 350 million bases per SMRT Cell though a human de novo data set released with the chemistry averaging 500 million bases per SMRT Cell. Throughput varies based on the type of sample being sequenced. With the introduction of P6-C4 chemistry typical throughput per SMRT Cell increased to 500 million bases to 1 billion bases.

RS Performance

	C1	C2	P4-XL	P5-C3	P6-C4
Average read length bases	1100	2500 - 2900	4300 - 5000	8500	10,000 - 15,000
Throughput per SMRT Cell	30M - 40M	60M - 100M	250M - 300M	350M - 500M	500M - 1B

Sequel

SMRT Cell for a Sequel Sequencer

In September 2015, the company announced the launch of a new sequencing instrument, the Sequel System, that increased capacity to 1 million ZMW holes.

With the Sequel instrument initial read lengths were comparable to the RS, then later chemistry releases increased read length.

On January 23, 2017, the V2 chemistry was released. It increased average read lengths to between 10,000 and 18,000 bases.

On March 8, 2018, the 2.1 chemistry was released. It increased average read length to 20,000 bases and half of all reads above 30,000 bases in length. Yield per SMRT Cell increased to 10 or 20 billion bases, for either large-insert libraries or shorter-insert (e.g. amplicon) libraries respectively.

Pipette tip in an 8M SMRT Cell

On 19 September 2018, the company announced the Sequel 6.0 chemistry with average read lengths increased to 100,000 bases for shorter-insert libraries and 30,000 for longer-insert libraries. SMRT Cell yield increased up to 50 billion bases for shorter-insert libraries.

Sequel Performance

	V2	2.1	6.0
Average read length bases	10,000 - 18,000	20,000 - 30,000	30,000 - 100,000
Throughput per SMRT Cell	5B - 8B	10B - 20B	20B - 50B

8M Chip

In April 2019 the company released a new SMRT Cell with eight million ZMWs, increasing the expected throughput per SMRT Cell by a factor of eight. Early access customers in March 2019 reported throughput over 58 customer run cells of 250 GB of raw yield per cell with templates about 15 kb in length, and 67.4 GB yield per cell with templates in higher weight molecules. System performance is now reported in either high-molecular-weight continuous long reads or in pre-corrected HiFi (also known as Circular Consensus Sequence (CCS)) reads. For high-molecular-weight reads roughly half of all reads are longer than 50 kb in length.

Sequel II High-Molecular-Weight Performance

	Early Access	1.0	2.0
Throughput per SMRT Cell	~67.4 GB	Up to 160 GB	Up to 200 GB

The HiFi performance includes corrected bases with quality above Phred score Q20, using repeated amplicon passes for correction. These take amplicons up to 20kb in length.

Sequel II HiFi Corrected Read Performance

	Early Access	1.0	2.0
Raw reads per SMRT Cell	~250 GB	Up to 360 GB	Up to 500 GB
Corrected reads per SMRT Cell (>Q20)	~25 GB	Up to 36 GB	Up to 50 GB

Application

Single-molecule real-time sequencing may be applicable for a broad range of genomics research.

For de novo genome sequencing, read lengths from the single-molecule real-time sequencing are comparable to or greater than that from the Sanger sequencing method based on dideoxynucleotide chain termination. The longer read length allows de novo genome sequencing and easier genome assemblies. Scientists are also using single-molecule real-time sequencing in hybrid assemblies for de novo genomes to combine short-read sequence data with long-read sequence data. In 2012, several peer-reviewed publications were released demonstrating the automated finishing of bacterial genomes, including one paper that updated the Celera Assembler with a pipeline for genome finishing using long SMRT sequencing reads. In 2013, scientists estimated that long-read sequencing could be used to fully assemble and finish the majority of bacterial and archaeal genomes.

The same DNA molecule can be resequenced independently by creating the circular DNA template and utilizing a strand displacing enzyme that separates the newly synthesized DNA strand from the template. In August 2012, scientists from the Broad Institute published an evaluation of SMRT sequencing for SNP calling.

The dynamics of polymerase can indicate whether a base is methylated. Scientists demonstrated the use of single-molecule real-time sequencing for detecting methylation and other base modifications. In 2012 a team of scientists used SMRT sequencing to generate the full methylomes of six bacteria. In November 2012, scientists published a report on genome-wide methylation of an outbreak strain of E. coli.

Long reads make it possible to sequence full gene isoforms, including the 5' and 3' ends. This type of sequencing is useful to capture isoforms and splice variants.

SMRT sequencing has several applications in reproductive medical genetics research when investigating families with suspected parental gonadal mosaicism. Long reads enable haplotype phasing in patients to investigate parent-of-origin of mutations. Deep sequencing enables determination of allele frequencies in sperm cells, of relevance for estimation of recurrence risk for future affected offspring.

Genome sequencing of endangered species

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

Genome sequencing of endangered species is the application of Next Generation Sequencing (NGS) technologies in the field of conservation biology, with the aim of generating life history, demographic and phylogenetic data of relevance to the management of endangered wildlife.

Background

In the context of conservation biology, genomic technologies such as the production of large-scale sequencing data sets via DNA sequencing can be used to highlight the relevant aspects of the biology of wildlife species for which management actions may be required. This may involve the estimation of recent demographic events, genetic variations, divergence between species and population structure. Genome-wide association studies (GWAS) are useful to examine the role of natural selection at the genome level, to identify the loci associated with fitness, local adaptation, inbreeding, depression or disease susceptibility. The access to all these data and the interrogation of genome-wide variation of SNP markers can help the identification of the genetic changes that influence the fitness of wild species and are also important to evaluate the potential respond to changing environments. NGS projects are expected to rapidly increase the number of threatened species for which assembled genomes and detailed information on sequence variation are available and the data will advance investigations relevant to the conservation of biological diversity.

Methodology

Non-computational methods

The traditional approaches in the preservation of endangered species are captive breeding and the private farming. In some cases those methods led to great results, but some problems still remain. For example, by inbreeding only few individuals, the genetic pool of a subpopulation remains limited or may decrease.

Phylogenetic analysis and gene family estimation

Genetic analyses can remove subjective elements from the determination of the phylogenetic relationship between organisms. Considering the great variety of information provided by living organisms, it is clear that the type of data will affect both the method of treatment and validity of the results: the higher the correlation of data and genotype, the greater is the validity likely to be. The data analysis can be used to compared different sequencing database and find similar sequences, or similar protein in different species. The comparison can be done using informatic software based on alignment to know the divergence between different species and evaluate the similarities.

NGS/Advanced sequencing methodologies

Since whole-genome sequencing is generally very data-intensive, techniques for reduced representation genomic approaches are sometimes used for practical applications. For example, restriction site-associated DNA sequencing (RADseq) and double digest RADseq are being developed. With those techniques researchers can target different numbers of loci. With a statistical and bioinformatic approach scientists can make considerations about big genomes, by just focusing on a small representative part of it.

Statistical and computational methods

While solving biological problems, one encounters multiple types of genomic data or sometimes an aggregate of same type of data across multiple studies and decoding such huge amount of data manually is unfeasible and tedious. Therefore, integrated analysis of genomic data using statistical methods has become popular. The rapid advancement in high throughput technologies allows researchers to answer more complex biological questions enabling the development of statistical methods in integrated genomics to establish more effective therapeutic strategies for human disease.

Genome crucial features

While studying the genome, there are some crucial aspects that should be taken in consideration. Gene prediction is the identification of genetic elements in a genomic sequence. This study is based on a combination of approaches: de novo, homology prediction, and transcription. Tools such as EvidenceModeler are used to merge the different results. Gene structure also have been compared, including mRNA length, exon length, intron length, exon number, and non-coding RNA.

Analysis of repeated sequences has been found useful in reconstructing species divergence timelines.

Application and case studies

Genomic approach in gender determination

In order to preserve a specie, knowledge of the mating system is crucial: scientists can stabilize wild populations through captive breeding, followed by the release in the environment of new individuals.^[3] This task is particularly difficult by considering the species with homomorphic sex chromosomes and a large genome. For example, in the case of amphibians, there are multiple transitions among male and/or female heterogamety. Sometimes even variation of sex chromosomes within amphibian populations of the same specie were reported.

Japanese giant salamander

Japanese giant salamander(Andrias japonicus)

The multiple transitions among XY and ZW systems that occur in amphibians determine the sex chromosome systems to be labile in salamanders populations. By understanding the chromosomal basis of sex of those species, it is possible to reconstruct the phylogenetic history of those families and use more efficient strategies in their conservation.

By using the ddRADseq method scientists found new sex-related loci in a 56 Gb genome of the family Cryptobranchidae. Their results support the hypothesis of female heterogamety of this species. These loci were confirmed through the bioinformatic analysis of presence/absence of that genetic locus in sex-determined individuals. Their sex was established previously by ultrasound, laparoscopy and measuring serum calcium level differences. The determination of those candidate sexual loci was performed so as to test hypotheses of both female heterogamety and male heterogamety. Finally to evaluate the validity of those loci, they were amplified through PCR directly from samples of known-sex individuals. This final step led to the demonstration of female heterogamety of several divergent populations of the family Cryptobranchidae.

Genomic approach in genetic variability

Dryas monkey and golden snub-nosed monkey

Golden snub-nosed monkey (Rhinopithecus roxellana)

A recent study used whole-genome sequencing data to demonstrate the sister lineage between the Dryas monkey and vervet monkey and their divergence with additional bidirectional gene flow approximately 750,000 to approximately 500,000 years ago. With <250 remaining adult individuals, the study showed high genetic diversity and low levels of inbreeding and genetic load in the studied Dryas monkey individuals.

Another study used several techniques such as single-molecule real time sequencing, paired-end sequencing, optical maps, and high-throughput chromosome conformation capture to obtain a high quality chromosome assembly from already constructed incomplete and fragmented genome assembly for the golden snub-nosed monkey. The modern techniques used in this study represented 100-fold improvement in the genome with 22,497 protein-coding genes, of which majority were functionally annotated. The reconstructed genome showed a close relationship between the species and the Rhesus macaque, indicating a divergence approximately 13.4 million years ago.

Genomic approach in preservation

Plants

Plants species identified as PSESP ("plant species with extremely small population") have been the focus of genomic studies, with the aim of determining the most endangered populations. The DNA genome can be sequenced starting from the fresh leaves by doing a DNA extraction. The combination of different sequencing techniques together can be used to obtain a high quality data that can be used to assembly the genome. The RNA extraction is essential for the transcriptome assembly and the extraction process start from stem, roots, fruits, buds and leaves. The de novo genome assembly can be performed using software to optimize assembly and scaffolding. The software can also be used to fill the gaps and reduce the interaction between chromosome. The combination of different data can be used for the identification of orthologous gene with different species, phylogenetic tree construction, and interspecific genome comparisons.

Limits and future perspectives

The development of indirect sequencing methods has to some degree mitigated the lack of efficient DNA sequencing technologies. These techniques allowed researchers to increase scientific knowledge in fields like ecology and evolution. Several genetic markers, more or less well suited for the purpose, were developed helping researchers to address many issues among which demography and mating systems, population structures and phylogeography, speciational processes and species differences, hybridization and introgression, phylogenetics at many temporal scales. However, all these approaches had a primary deficiency: they were all limited only to a fraction of the entire genome so that genome-wide parameters were inferred from a tiny amount of genetic material.

The invention and rising of DNA sequencing methods brought a huge contribution in increasing available data potentially useful to improve the field of conservation biology. The ongoing development of cheaper and high throughput allowed the production of a wide array of information in several disciplines providing conservation biologists a very powerful databank from which was possible to extrapolate useful information about, for example, population structure, genetic connections, identification of potential risks due to demographic changes and inbreeding processes through population-genomic approaches that rely on the detection of SNPs, indel or CNV. From one side of the coin, data derived from high throughput sequencing of whole genomes were potentially a massive advance in the field of species conservation, opening wide doors for future challenges and opportunities. On the other side all these data brought researchers to face two main issues. First, how to process all these information. Second, how to translate all the available information into conservation's strategies and practice or, in other words, how to fill the gap between genomic researches and conservation application.

Unfortunately, there are many analytical and practical problems to consider using approaches involving genome-wide sequencing. Availability of samples is a major limiting factor: sampling procedures may disturb an already fragile population or may have a big impact in individual animals itself putting limitations to samples' collection. For these reasons several alternative strategies where developed: constant monitoring, for example with radio collars, allow us to understand the behavior and develop strategies to obtain genetic samples and management of the endangered populations. The samples taken from those species are then used to produce primary cell culture from biopsies. Indeed, this kind of material allow us to grow in vitro cells, and allow us to extract and study genetic material without constantly sampling the endangered populations. Despite a faster and easier data production and a continuous improvement of sequencing technologies, there is still a marked delay of data analysis and processing techniques. Genome-wide analysis and big genomes studies require advances in bioinformatics and computational biology. At the same time improvements in the statistical programs and in the population genetics are required to make better conservation strategies. This last aspect work in parallel with prediction strategies which should take in consideration all features that determine fitness of a species.