Enzymatic Activation Of Alkanes Constraints And Prospects Definition

1. Enzymatic Activation Of Alkanes Constraints And Prospects Definition In Hindi
2. Enzymatic Activation Of Alkanes Constraints And Prospects Definition In Science
3. Enzymatic Activation Of Alkanes Constraints And Prospects Definition Math

1. Alkanes are saturated hydrocarbons that are derived from both natural and anthropogenic sources. Due to their apolar C-H σbonds, alkanes are considered to be among the least chemically reactive organic compounds. The activation or functionalization of alkanes is initiated via cleavage of a C-H bond.
2. Effect of Reaction Medium. S N 1 and E1 reactions are most favorable in protic solvents, such as carboxylic acids or alcohols. Neutral or acidic conditions are most common, but sometimes the media are slightly basic. Recall, however, that strongly basic conditions will promote other modes of reactivity, such as the E2 elimination.

An enzyme inhibitor (like Metronidazole) will increase the effects of certain drugs such as alcohol and warfarin. If a patient is taking an enzyme inhibitor or inducer and then stops taking it, the effects of the other drugs they are taking may change.

Abstract

Proteolytic enzymes are crucial for a variety of biological processes in organisms ranging from lower (virus, bacteria, and parasite) to the higher organisms (mammals). Proteases cleave proteins into smaller fragments by catalyzing peptide bonds hydrolysis. Proteases are classified according to their catalytic site, and distributed into four major classes: cysteine proteases, serine proteases, aspartic proteases, and metalloproteases. This review will cover only cysteine proteases, papain family enzymes which are involved in multiple functions such as extracellular matrix turnover, antigen presentation, processing events, digestion, immune invasion, hemoglobin hydrolysis, parasite invasion, parasite egress, and processing surface proteins. Therefore, they are promising drug targets for various diseases. For preventing unwanted digestion, cysteine proteases are synthesized as zymogens, and contain a prodomain (regulatory) and a mature domain (catalytic). The prodomain acts as an endogenous inhibitor of the mature enzyme. For activation of the mature enzyme, removal of the prodomain is necessary and achieved by different modes. The pro-mature domain interaction can be categorized as protein–protein interactions (PPIs) and may be targeted in a range of diseases. Cysteine protease inhibitors are available that can block the active site but no such inhibitor available yet that can be targeted to block the pro-mature domain interactions and prevent it activation. This review specifically highlights the modes of activation (processing) of papain family enzymes, which involve auto-activation, trans-activation and also clarifies the future aspects of targeting PPIs to prevent the activation of cysteine proteases.

Introduction

Cysteine proteases are present in all living organisms. Besides their fundamental functions of catabolism and protein processing, cysteine proteases perform diverse functions (; ). Cysteine proteases of parasites play key role in hemoglobin hydrolysis, blood cell invasion, egress, surface proteins processing (; ; ). In 1937, papain was the first cysteine protease isolated and characterized from Carica papaya (Walsh, 2014). Papain and cathepsins belong to the most abundant family of the cysteine proteases. In mammals, a main group of cysteine proteases is known as lysosomal cathepsins (). The name cathepsin, is derived from the Greek kathepsein (to digest; Willstätter and Bamann, 1929). Bioinformatics analysis reveals that human genome encodes 11 cysteine cathepsins, i.e., the cathepsins B, C, F, H, K, L, O, S, V, X, and W, existing at the sequence level (). Cathepsins and other cysteine proteases from parasites as well as viruses may become good targets for major diseases such as arthritis, osteoporosis, AIDS, immune-related diseases, atherosclerosis, cancer, and for a wide variety of parasitic diseases such as malaria, amebiasis, chagas disease, leishmaniasis, or African sleeping sickness (; ; ; ; ).

In parasitic disease like malaria, cysteine proteases (falcipains) of Plasmodium falciparum specifically involve in hemoglobin degradation, parasite egress, processing surface proteins, therefore, function as a promising new drug targets (; ). P. falciparum expresses four papain-like cysteine proteases named as falcipain-1, 2, 2′ and 3. Falcipain-2 and -3 are the major cysteine proteases of P. falciparum involved in hemoglobin hydrolysis (, ; ; ).

For preventing unwanted protein degradation, like other proteolytic enzymes (serine, aspartic, and metalloproteases), cysteine proteases are also synthesized as inactive precursors (or zymogens). Cysteine protease zymogens contain a prodomain that block access of substrate to the active site (). Besides acting as an endogenous inhibitor (, ), prodomain may have additional roles in protein folding and or intracellular sorting (; ; ). Activation of an enzyme from its zymogen generally takes place within a subcellular compartment or the extracellular environment, in which the particular enzyme performs its biological function. Zymogen conversion may be accomplished by accessory molecules (e.g., trypsinogen convert into trypsin in presence of ca²⁺), by an auto catalytic process with requirement of a significant drop in pH and by other enzymes as in trans-activation (; ). This review highlights the different modes of activation in cysteine proteases and their future aspects.

Cysteine Proteases

Cysteine proteases contain a Cys–His–Asn triad at the active site. A histidine residue, presents in the active site act as proton donor and enhance the nucleophilicity of the cysteine residue (Figure ​Figure11). Nucleophilic cysteine residue attacks to the carbon of the reactive peptide bond, producing the first tetrahedral thioester intermediate in the reaction with release of an amine or amino terminus fragment of the substrate (). This intermediate is stabilized by hydrogen bonding between the substrate oxyanion and a highly conserved glutamine residue. Subsequently, the thioester bond is hydrolyzed to produce a carboxylic acid moiety from the remaining substrate fragment. Based upon a sequence analysis of papain-like cysteine protease family was divided into two distinct subfamilies, cathepsin-L-like and cathepsin-B-like proteases, which can be distinguished by the structure of the prodomain and the mature domain (; ). A third ‘F-like’ group was also proposed based on phylogenetic analyses showing that cathepsins F and W prodomains share a specific sequence pattern, ERFNAQ (). The main difference between the sub-families exists in the sequence of the prodomains and their length (Dieter Bromme, 2011) (Figure ​Figure22). The prodomain of the cathepsin L subfamily (cathepsins L, V, K, S, W, F, and H) contain a prodomain of about 100 residues, with two conserved motifs: a highly conserved ERFNIN and GNFD motifs. An ERFNIN motif is lacking in cathepsin B, C, O, and X. Cathepsin B has a characteristic feature with ‘occluding loop’ which provide carboxydipeptidase activity (). Falcipains, malarial cysteine proteases belongs to cathepsin L-like subfamily. Falcipains, malarial cysteine proteases have some unusual features, including large prodomains, predicted membrane-spanning sequences within the prodomains ().

Structure of the mature domain. Structural representation of cysteine protease with the mature domain (Orange) showing active site residues; Cys, His, and Asn (stick); PBD ID: 3PNR.

Schematic representation of cysteine proteases pro and mature domain. In this schematic representation, cysteine proteases have classified according to their peptidase property and depicted length of the domains.

Zymogen Structure and Mechanism of Inhibition

The mature enzymes or active enzymes of the family share a well-known fold of papain-like which consists of two domains: N-terminal helical domain and a C-terminal β-sheet domain. Catalytic Cys, His, and Asn are contributed by these two domains. These residues are located in the substrate binding cleft (Figure ​Figure11).

The cathepsins B and L are well characterized papain-like enzymes, synthesized as zymogens (; ). The prodomain of cathepsin L (96 amino acids) has an N-terminal globular domain that consist of three α-helices and their connecting loops, an extended structure followed by globular domain which traverse the substrate binding cleft in a reverse orientation (N→C-terminal) with respect to substrate that are cleaved and prevent access to active site. The prodomain and the mature domain interact via many residues (Phe⁵⁶p, Phe⁶³p, phe⁷¹p, Tyr¹⁴⁶, and Tyr¹⁵¹; p stands for prodomain) lying at their interface (). These residues are crucial for the activation of the mature enzyme. In falcipain-2, a mutation at prodomain residue Phe⁶⁰p (equivalent to Phe⁵⁶p of prodomain of cathepsin L) has shown inability to undergo auto-activation at its optimum pH (5.5) (). A conserved Gly⁷⁷p residue helps in bringing the prodomain deep inside the catalytic cleft, in such a way that an oxyanion hole forms a hydrogen bond to Asn⁷⁶p, and indirectly prevent access to catalytic cysteine for the catalysis. The prodomain of cathepsins B has similar fold as procathepsin L, but have some differences such as deletion of 30-residues from the N-terminal makes the prodomain short as compared to procathepsin L, orientation of the helices α2p and α3p are different due to presence of an ‘occluding loop’ a characteristic feature of the cathepsins B subfamily and absence of conserved ERFNIN motif (). Due to presence of an occluding loop, cathepsins B subfamily is able to cleave dipeptide units from the carboxyl-terminal of the substrate (Figure ​Figure33).

Comparison of procathepsin L and B. Structural representation of the procathepsin L (orange) (PDB ID: 1CS8) ERFNIN (red) and GNFD (blue) motifs are shown. The prodomain of cathepsin B (cyan) (PDB ID: 1MIR) with GNFD-motif (blue), occluding loop (purple), and long carboxy terminus (green) are mentioned in the structure.

Although there are differences but both the classes of enzymes have conserved mode of inhibition and share some common features such as interactions between the loop and the conserved hydrophobic residues in the prodomain and a conserved Gly residue near to the catalytic Cys residue. A conserved Gly in the hydrophobic pocket facilitate the C-terminus of the prodomain to push deep into the catalytic cleft and inhibit the catalytic site to perform catalysis. The prodomains exhibit a limited selectivity of inhibition against their related enzymes (). First evidence for prodomains acting as selective inhibitors of cathepsin was seen when recombinant cathepsin L prodomain inhibited cathepsin L with lower Ki (0.088 nM) and cathepsin S with higher Ki (44.6 nM), whereas no inhibition of papain or cathepsin B was observed (). Besides acting as an endogenous inhibitor, prodomain are also involved in some other functions such as refolding and intracellular sorting of the enzyme. Like other papain-family cysteine proteases, prodomain of falcipain-2 is a potent inhibitor of the enzyme (). The C-terminal portion of the prodomain that includes “ERFNIN” and “GNFD” motifs, appear to mediate inhibition in many papain family proteases. The N-terminal portion of the prodomain mediates trafficking of the enzyme to the food vacuole, a site for the hemoglobin digestion (, ). Many studies reported that whole prodomains are involved in correct folding of the enzyme while in falcipain-2 and falcipain-3, only N-terminal motif with 15 amino acid of the mature domain is required for refolding of enzyme (). The C-terminal part of the prodomain is sufficient for falcipains inhibition (; ).

Activation Mechanisms

Once reaching to its specific compartment, processing of the enzyme starts, which include cleavage of the prodomain and activation of the mature enzyme (). In processing of cysteine protease, pH change has great importance. In lysosomes or food vacuoles, enzymes get activated by controlled proteolysis which involves autocatalysis or trans-activation (). Based upon previous studies on procathepsin L, a pH-dependent conversion may start with the disruption of the conserved salt bridges (Asp⁶⁵→Arg²¹ and Gln⁷⁰→Arg³¹) within the prodomain (). Disruption of the salt bridges due to protonation of the carboxylate group at the lower pH could conceivably trigger the disruption of the hydrophobic core of the prodomain, leading to dissociation of the prodomain from the active site, and thereby initiating the process of auto catalytic processing ().

Due to presence of an occluding loop in procathepsin B, mature domain undergoes significant conformation changes during the processing. In contrast, procathepsin L-like papain-family proteases do not have occluding loop, therefore, the mature domain is not expected to undergo significant change during the processing (; ).

Further, structures of other procathepsins provided insight in understanding zymogen activation. The crystal structures of human and rat procathepsin B (; ), human procathepsin L (), human procathepsin K (), and human procathepsin X () showed that the prodomain folds on the surface of the enzyme in an extended conformation and runs through the active-site, in the opposite direction to the substrate, thereby blocking the access of the active site. In the structure of most proenzymes, salt bridges, hydrogen bonding, and hydrophobic interactions within the prodomain and between the pro-mature domains exist. The exception is the structure of cathepsin X, in which the prodomain binds covalently to the mature enzyme with a disulphide bridge between cysteine residue in the prodomain and active site cysteine, thus preventing any auto-activation (). However, it can be processed in vitro under reducing conditions by cathepsin L ().

Processing or zymogen activation of proteases may exhibit via different modes such as auto-activation and trans-activation or both (; ). Auto-catalysis involves the cleavage of prodomain by catalytic site present inside the catalytic cleft of the enzyme under the influence of pH change (). However, trans-activation involve cleavage by the another molecule of the same enzyme or some other proteases that cleave within the residues lying at the junction of the prodomain and the mature domain such as pepsin, aspartic cathepsin D, and legumain/asparaginyl endopeptidase (; ). It is reported that some proteases have unusual kind of activation such as Cathepsin D (). This review further highlights different modes of processing of cysteine protease zymogens.

Activation by Auto-processing

Auto-catalysis is a common mode of activation of cysteine proteases itself from their zymogens under the influence of pH change (acidic pH). The pH has great importance in auto catalytic mode of activation. The pH change triggers the disruption of important interactions between the prodomain and the mature domain, thereby make accessible the cleavage site within the prodomain loop to the active site. An N-terminal prodomain get cleaved off from the whole enzyme by active site and enzyme get activated (Figure ​Figure44).

Model (illustrative) for auto-activation of falcipain-2 (FP2), a malarial cysteine protease. The prodomain of FP2 removed and enzyme get activated under the influence of low pH. Inset shows crucial salt bridges (green-dotted circles) and hydrophobic (purple-dotted circle) interactions are required for auto-activation. Model was generated via Modeler by taking known structures as templates (PDB ID; 3PNR and 1CS8). All figures are prepared using PyMOL.

Early studies suggested that autocatalytic processing is a unimolecular process (; ) and, while others proposed inter-molecular and intra-molecular mechanisms (; ). However, this dilemma has been resolved that the auto-activation of cathepsins is a combination of a unimolecular and a bimolecular process (). For example, procathepsin B possesses a low catalytic activity that is not sufficient to trigger the auto catalytic activation. Low activity of cathepsin B is the result of the prodomain dissociation from the active-site cleft as the first step, which is a unimolecular step (). In the next step, which is bimolecular, this catalytically active cathepsin B molecule processes and activates another procathepsin B molecule in one or more steps. The mature cathepsin B molecules generated in this way then initiate a chain reaction leading to a rapid activation of the remaining procathepsin B molecules. Cysteine proteases based on their cleavage property can be categorized into two groups; endopeptidase and exopeptidase (Table ​Table11). Endopeptidases such as the cathepsins B, H, L, S, and K can be activated by autoactivation, whereas the true exopeptidases, such as the cathepsins C and X, needed endopeptidases, such as the cathepsins L and S (), for their activation (Table ​Table11; Figure ​Figure22) (Dieter Bromme, 2011). Mutational studies of cathepsin K confirmed its mode of activation by autocatalysis. An active site Cys¹³⁹ to Ser mutant of procathepsin K failed to undergo activation but could be processed fully when incubated with wild-type procathepsin K ().

Table 1

Types of cysteine proteases on the basis of cleavage property and their mode of activation.

The activation of cysteine proteases are modulated by the glycosaminoglycans (GAGs) such as sulfated GAGs, heparin, heparan sulfate, and chondroitin sulfates A, B, C, E, and other negatively charged polysaccharides, e.g., dextran sulfate. Various studies have suggested the involvement of GAGs in the in vivo processing of cathepsins (; ). Similarly, GAGs accelerate the auto catalytic activation of cathepsin L and B, including at neutral pH. Studies reported that GAGs interact with cathepsin B via electrostatic interactions, being negatively charged, GAGs interact with the positively charged residues present in the occluding loop of the mature domain and the prodomain of the cathepsin B. GAGs binding induce conformation changes in the prodomain of cathepsin B, which unmask the active site for the catalysis of the other procathepsin B molecules (Figure ​Figure55) (). Further GAGs role in activation of cathepsins was confirmed by the auto-activation of procathepsin S at neutral pH (). However, a recent finding with cathepsin S at high concentration of chondroitin-4-sulfate (C4S) exhibits a decelerating effect of GAGs on activation (). Besides the activation of cysteine proteases, GAGs also have been found to affect both the activity and stability of the mature cysteine cathepsins (; ). Most of the knowledge about the GAGs role in regulation of cathepsins came from the studies of papain. A hyperbolic kinetic profile of cathepsin K in presence of GAGs suggest their interactions outside the active site, may be via allosteric mechanisms (; ).

Mechanism of procathepsin B auto-activation in the presence of glycosaminoglycans (GAGs). GAG molecules bind to the occluding loop and the prodomain of cathepsin B molecule via electrostatic interactions. GAGs binding induce conformational change in procathepsin B (PDB ID: 1MIR), which unmasks the active site and enable the access of procathepsin B molecule.

Cysteine proteases play important role in life cycle of parasitic organism. Parasites also express cathepsin L and B like proteases. Falcipains, well characterized cathepsin L-like cysteine proteases from P. falciparum, synthesize as zymogens and get activated by auto activation in acidic environment (pH 5–5.5). , from our group revealed that prodomain-mature domain of falcipain-2 and falcipain-3 interacts via salt bridges and hydrophobic interactions. Mutagenesis study showed that two salt bridges (Arg¹⁸⁵–Glu²²¹, Glu²¹⁰–Lys⁴⁰³) in falcipain-2, and one salt bridge (Arg²⁰²–Glu²³⁸) in falcipain-3, and hydrophobic interactions present both in falcipain-2 (Phe²¹⁴–Trp⁴⁴⁹Trp ⁴⁵³), and falcipain-3 (Phe²³¹–Trp⁴⁵⁷Trp ⁴⁶¹) also play important roles in the activation of these enzymes (Figure ​Figure44). Mutants were unable to undergo autocatalysis, although, activation can further be achieved by trans-activation ().

Auto activation of cysteine proteases from other parasitic organisms have been proposed by many studies (; ). In vitro study about Fasciola hapatica procathepsin L1 (FhproCL1) demonstrated that auto activation can occur within wide pH range 4.5–7.3 (). Active site mutant of F. hepatica (FhproCL1Gly²⁵) cannot undergo auto-catalytic processing (). Schistosoma mansoni, a parasitic worm causing Schistosomiasis (also known as bilharzia) expresses papain-like cysteine proteases including cathepsins (B1, L1, L3, F, and C) and an aspartic protease (cathepsin D) in the parasite gut, function in an acidic pH environment (; ). A number of reports have shown that both parasite and mammalian cysteine proteases can be auto catalytically activated in vitro from zymogen to mature enzyme by reducing the pH of the solution ().

Activation by Trans-processing

Trans-activation involve cleavage by another molecule of the same enzyme (Figure ​Figure66) or some other proteases that cleave within the residues lying at the junction of prodomain and mature domain such as pepsin, Cathepsin D, and legumain/asparaginyl endopeptidase (Figure ​Figure77) (; ). Cathepsin C and X require an endopeptidase such as cathepsins L or S for their activation. Moreover, cathepsin S prodomain was found to be rapidly degraded by cathepsin L. In contrast to most other cathepsins, cathepsin C was not capable of auto activation, even addition of the mature cathepsin C. This is consistent with procathepsin X, which is also an exopeptidase. Cathepsin X prodomain binds covalently to the mature enzyme with a disulphide bridge between cysteine residues in the prodomain and the active-site cysteine, thus preventing any auto-catalytic processing (). However, it can be processed in vitro under reducing conditions by cathepsin L and S (Figure ​Figure77) (). Falcipains zymogens can be trans-activated by their mature enzymes. In other parasites, cysteine proteases can be trans-activated by their mature enzymes and asparaginyl endopeptidase, a clan CD cysteine protease that cleaves C-terminal to asparginyl (Asn) residues (). Pre-activated wild F. hepatica cathepsin L (FhproCL1) enzyme is able to trans-process (FhproCL1) zymogens at specific cleavage site Leu¹²–Ser^11↓His¹⁰motif and thus increase rate of activation exponentially. Mutational study has shown that alteration of the motif to a Pro¹²–Ser^11↓His¹⁰ prevents or slows down FhproCL1 activation (). A study by Dalton et al. proposed that Schistosome asparaginyl endopeptidase (SmAE) is responsible for trans-processing of the cysteine proteases involved in the hemoglobin degradation in Schistosome (; ). Furthermore, Fasciola hepatica cathepsin B also have preserved asparaginyl endopeptidase-processing site at the pro-mature domain junction and SmAE was also shown to trans-process F. hepatica cathepsin B. Interestingly, the prodomain of O. viverrini cathepsin F (Ov-CF-1) lacks the conserved asparagine residues found in other homologues and could not be trans-processed by Opisthorchis viverrini asparaginyl endopeptidase. However, recent studies shown O. viverrini cathepsin B (Ov-CB-1) is capable of trans-activating cathepsin F (Ov-CF-1) at a specific site between the prodomain and the mature enzyme ().

Model (illustrative) for trans-activation by same enzyme molecule.Trans-activation of the enzyme by other active molecule of same enzyme is shown the figure. Initially, single molecule of enzyme get activated under low pH, thereafter these active molecule further activate the other inactive enzymes and initiate a chain reaction. Model was generated via Modeler by taking known structures as templates (PDB ID; 3PNR and 1CS8).

Model (illustrative) of trans-activation by other enzyme molecule. Procathepsin X (PDB ID: 1DEU) consists covalently linked prodomain (blue). Cathepsin L (violet) (PDB ID: 1CS8) trans-activate procathepsin X by cleaving the prodomain and releasing an active cathepsin X (green).

Activation by Uncommon Mode of Processing

Number of studies reported that both parasite and mammalian cysteine proteases can be auto activated in vitro from zymogen to mature enzyme by reducing the pH of solution (), but some studies reported uncommon mode of activation which involves partial auto-activation followed by full activation by an enzyme.

The schistosome cathepsin B1 (SmCB1) is a unique in terms of activation, as the zymogen does not auto catalytically activate at low pH (; ). Crystal structure of SmCB1 zymogen has solved and revealed another activation trigger which involved sulfate polysaccharides (). The prodomain of the SmCB1 contains a short and unique helix, α-3p which contains Schistosome asparaginyl endopeptidase (SmAE) cleavage site and a heparin-motif (LRRTRRP). A heparin-motif of the prodomain is involved in interaction with the mature enzyme and makes α-3p an ideal point of interaction for sulfated polysaccharides-like dextran sulfate. At low pH, SmCB1 zymogen auto catalytically produces an inactive intermediate clipping off 38 residues of the prodomain, but this does not fully expose the active site. Adding dextran sulfate to the reaction mixture facilitates the pinch off few more residues in the vicinity of substrate binding site, to produce an active intermediate. This finally, leads to processing of SmCB1 to the mature enzyme via trans-activation by SmAE. The binding of sulfated polysaccharides to an intact α-3p heparin-binding motif is required for complete processing of the SmCB1.

Cathepsin-D, an aspartic protease also synthesize as inactive enzyme. The activation of cathepsin-D, an intermediate mechanism had been proposed, i.e., a partial auto-activation followed by a final processing by other enzymes. Studies have shown that the processing of endocytosed procathepsin-D is also independent of its catalytic function and requires cysteine proteases for its activation ().

Discussion

Proteases have been categorized into groups on the basis of the catalytic mechanism used during the hydrolytic process such as cysteine, serine, aspartate, and metalloproteases. For preventing unwanted degradation, cysteine proteases are synthesized as inactive enzymes and removal of the prodomains lead to the activation of the enzymes. Each class has their own mechanism of inhibition and activation. Main concept of inhibition is that prodomain sterically block the pre-formed active site and inhibit the access to the substrate (). Generally zymogens get self-activated in low pH upon reaching to the specific compartments and it is reported that salt bridges plays important role in stabilization of pro-mature domain interactions at neutral pH. Upon reaching to specific compartment, prodomain are removed by autocatalysis or by other enzymes (trans-activation). Auto-activation is most economical mode of conversion since no involvement of other enzymes. However, trans-activation by other enzyme is required to enhance the conversion rate in critical conditions. For example, cathepsins F, a liver fluke (O. viverrini) enzyme, secreted as an inactive zymogen that auto-catalytically processes and activated to a mature enzyme at pH 4.5, but studies shows that it can also be activated via trans-processing by cathepsins B1 at pH 5.5, where it is unable to activate auto-catalytically. Both enzymes (cathepsin B1 and F1) work together to degrade the host tissue and contributing to develop liver-fluke-associated chalangiocarcinoma ().

In vivo studies reported, after removal, prodomains are hydrolyzed and ensure that the activation process is irreversible (; ). Although, in vitro study by showed that the prodomain of falcipain-2 is a potent, competitive, and reversible inhibitor of the active product. Table ​Table22 summarizes the mechanism of inhibition and activation of cysteine proteases.

Table 2

Cysteine protease with their inactivation and activation modes.

The pro-mature domain interactions are categorized in protein–protein interactions (PPIs). Presently, targeting PPIs is an attractive and promising area of research. A special interest in cysteine proteases as targets derives from the recognition that they are critical to the life cycle or pathogenicity of many parasites. This functional diversity is derived from their unique nucleophilicity, adaptability to different substrates, stability in different biological environments, and their regulations. Parasite derived cysteine proteases play key roles in hemoglobin hydrolysis, breakdown of RBC proteins, immunoevasion, enzyme activation, virulence, tissue, and cellular invasion as well as excystment, hatching, and molting (; ). Previous study by showed that the prodomain-mature domain interactions are essential for the auto-activation of the falcipains and their mutation impaired the enzyme ability to undergo activation by autocatalysis. Blocking of such interactions will cease the parasite growth due to inactivity of these proteases. Therefore, designing inhibitors against such interactions are important new targets.

Future Aspects

In this review, we have discussed targeting the cysteine proteases before activation, which may prevent their involvement in various diseases. The possible ways are:

1. Targeting promature domain interactions which are important for the activation.

2. Targeting the residues involved in pH sensing and activation.

Pro-mature domain interactions can be categorized as PPIs. Earlier targeting PPIs were not in trend due to technological hurdles. Studies have demonstrated that small molecules can disrupt the large and complex protein interactions by interacting with interface residues, known as hot-spots (; Pandey, 2013). In a study of a herpes virus protease, researchers developed a small-inhibitor that target to block the interactions of two monomers, and prevent it forming the active dimer interface (). Recently, our group is also focusing on PPIs crucial for activation of enzyme in malarial cysteine proteases. Our earlier reports suggested that salt bridges and hydrophobic interactions between pro-mature domains were crucial for the activation of malarial cysteine proteases (), and disruption of these interactions lead to failure of the activation of enzymes. Therefore, it would be possible to control the growth of the parasites and other harmful organisms by blocking the processing of cysteine proteases. In our lab, we have screened some inhibitors, which are able to block the processing of falcipains and further detail characterization and kinetics of potential inhibitors are underway.

The pH has great importance in activation of zymogens of proteases in specific compartment (). It is very interesting, how pH triggers the activation? Inactive enzyme move through different compartments having varying pH gradient and get activated inside the specific compartment under the influence of pH change. Therefore, it is suggests that there are some sensors residues who can sense the pH change and trigger activation process (). It is reported that folding and activation of furin, a calcium-dependent serine endoprotease, occurs through pH and compartment-specific auto-proteolytic steps. A conserved His⁶⁹ of prodomain act as pH sensor that regulates the compartment-specific cleavages of the prodomain. Although, structural modeling combined with mathematical modeling and molecular dynamic simulations suggested that His⁶⁹ does not contribute directly to the prodomain–enzyme interface. But, rather, triggers movement of a loop region in the prodomain that modulates access to the cleavage site and thus, allows the tight pH regulation of furin activation (; ). Like serine proteases, cysteine proteases also follow the similar mechanism to get activated auto-catalytically under the influence of compartment specific pH change. The cysteine proteases could have pH sensor residue like furin that sense pH change and trigger activation events. Taking this idea, we performed sequence alignment of the prodomain of the cysteine proteases among the organisms including malarial cysteine proteases and found a conserved His residue for further exploring the role as a pH sensor in processing of malarial cysteine proteases. Interestingly, our initial results support that notion that pH sensor also play important role in processing of falcipains. Therefore, disturbing the PPIs and designing inhibitor based on such interactions are futuristic approaches for preventing the pathogenic diseases, and they may have least sensitive to drug resistance.

Author Contributions

SV and KP conceived and designed the review. SV, KP, and RD wrote the review paper.

Conflict of Interest Statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Acknowledgments

We are thankful to University Grant Commission (UGC) for (JRF) junior research fellowship to SV. We are thankful to NIMR and DBT for infrastructural support for pursuing the research work.

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In organic chemistry, an alkane, or paraffin (a historical name that also has other meanings), is an acyclicsaturatedhydrocarbon. In other words, an alkane consists of hydrogen and carbon atoms arranged in a tree structure in which all the carbon–carbon bonds are single.^[1] Alkanes have the general chemical formula C_nH_2n+2. The alkanes range in complexity from the simplest case of methane (CH₄), where n = 1 (sometimes called the parent molecule), to arbitrarily large and complex molecules, like pentacontane (C₅₀H₁₀₂) or 6-ethyl-2-methyl-5-(1-methylethyl) octane, an isomer of tetradecane (C₁₄H₃₀).

IUPAC defines alkanes as 'acyclic branched or unbranched hydrocarbons having the general formula C_nH_2n+2, and therefore consisting entirely of hydrogen atoms and saturated carbon atoms'. However, some sources use the term to denote any saturated hydrocarbon, including those that are either monocyclic (i.e. the cycloalkanes) or polycyclic,^[2] despite their having a different general formula (i.e. cycloalkanes are C_nH_2n).

In an alkane, each carbon atom is sp³-hybridized with 4 sigma bonds (either C–C or C–H), and each hydrogen atom is joined to one of the carbon atoms (in a C–H bond). The longest series of linked carbon atoms in a molecule is known as its carbon skeleton or carbon backbone. The number of carbon atoms may be considered as the size of the alkane.

One group of the higher alkanes are waxes, solids at standard ambient temperature and pressure (SATP), for which the number of carbon atoms in the carbon backbone is greater than about 17.With their repeated –CH₂ units, the alkanes constitute a homologous series of organic compounds in which the members differ in molecular mass by multiples of 14.03 u (the total mass of each such methylene-bridge unit, which comprises a single carbon atom of mass 12.01 u and two hydrogen atoms of mass ~1.01 u each).

Alkanes are not very reactive and have little biological activity. They can be viewed as molecular trees upon which can be hung the more active/reactive functional groups of biological molecules.

The alkanes have two main commercial sources: petroleum (crude oil)^[3] and natural gas.

An alkyl group, generally abbreviated with the symbol R, is a functional group that, like an alkane, consists solely of single-bonded carbon and hydrogen atoms connected acyclically—for example, a methyl or ethyl group.

• 3Nomenclature
• 4Physical properties
  • 4.8Spectroscopic properties
• 5Chemical properties
• 6Occurrence
• 7Production

Structure and classification[edit]

Saturated hydrocarbons are hydrocarbons having only single covalent bonds between their carbons. They can be:

• linear (general formula C
  _nH
  _2n+2) wherein the carbon atoms are joined in a snake-like structure
• branched (general formula C
  _nH
  _2n+2, n > 2) wherein the carbon backbone splits off in one or more directions
• cyclic (general formula C
  _nH
  _2n, n > 3) wherein the carbon backbone is linked so as to form a loop.

According to the definition by IUPAC, the former two are alkanes, whereas the third group is called cycloalkanes.^[1] Saturated hydrocarbons can also combine any of the linear, cyclic (e.g., polycyclic) and branching structures; the general formula is C
_nH
_2n−2k+2, where k is the number of independent loops. Alkanes are the acyclic (loopless) ones, corresponding to k = 0.

Isomerism[edit]

Alkanes with more than three carbon atoms can be arranged in various different ways, forming structural isomers. The simplest isomer of an alkane is the one in which the carbon atoms are arranged in a single chain with no branches. This isomer is sometimes called the n-isomer (n for 'normal', although it is not necessarily the most common). However the chain of carbon atoms may also be branched at one or more points. The number of possible isomers increases rapidly with the number of carbon atoms. For example, for acyclic alkanes:^[4]

• C₁: methane only
• C₂: ethane only
• C₃: propane only
• C₄: 2 isomers: n-butane and isobutane
• C₅: 3 isomers: pentane, isopentane, and neopentane
• C₆: 5 isomers: hexane, 2-methylpentane, 3-methylpentane, 2,2-dimethylbutane, and 2,3-dimethylbutane
• C₁₂: 355 isomers
• C₃₂: 27,711,253,769 isomers
• C₆₀: 22,158,734,535,770,411,074,184 isomers, many of which are not stable.

Branched alkanes can be chiral. For example, 3-methylhexane and its higher homologues are chiral due to their stereogenic center at carbon atom number 3. In addition to the alkane isomers, the chain of carbon atoms may form one or more loops. Such compounds are called cycloalkanes. Stereoisomers and cyclic compounds are excluded when calculating the number of isomers above.

Nomenclature[edit]

The IUPAC nomenclature (systematic way of naming compounds) for alkanes is based on identifying hydrocarbon chains. Unbranched, saturated hydrocarbon chains are named systematically with a Greek numerical prefix denoting the number of carbons and the suffix '-ane'.^[5]

In 1866, August Wilhelm von Hofmann suggested systematizing nomenclature by using the whole sequence of vowels a, e, i, o and u to create suffixes -ane, -ene, -ine (or -yne), -one, -une, for the hydrocarbons C_nH_2n+2, C_nH_2n, C_nH_2n−2, C_nH_2n−4, C_nH_2n−6.^[6] Now, the first three name hydrocarbons with single, double and triple bonds;^[7] '-one' represents a ketone; '-ol' represents an alcohol or OH group; '-oxy-' means an ether and refers to oxygen between two carbons, so that methoxymethane is the IUPAC name for dimethyl ether.

It is difficult or impossible to find compounds with more than one IUPAC name. This is because shorter chains attached to longer chains are prefixes and the convention includes brackets. Numbers in the name, referring to which carbon a group is attached to, should be as low as possible so that 1- is implied and usually omitted from names of organic compounds with only one side-group. Symmetric compounds will have two ways of arriving at the same name.

Linear alkanes[edit]

Straight-chain alkanes are sometimes indicated by the prefix 'n-' (for normal) where a non-linear isomer exists. Although this is not strictly necessary, the usage is still common in cases where there is an important difference in properties between the straight-chain and branched-chain isomers, e.g., n-hexane or 2- or 3-methylpentane. Alternative names for this group are: linear paraffins or n-paraffins.

The members of the series (in terms of number of carbon atoms) are named as follows:

methane

CH₄ – one carbon and 4 hydrogen

ethane

C₂H₆ – two carbon and 6 hydrogen

propane

C₃H₈ – three carbon and 8 hydrogen

butane

C₄H₁₀ – four carbon and 10 hydrogen

pentane

C₅H₁₂ – five carbon and 12 hydrogen

hexane

C₆H₁₄ – six carbon and 14 hydrogen

The first four names were derived from methanol, ether, propionic acid and butyric acid, respectively (hexadecane is also sometimes referred to as cetane). Alkanes with five or more carbon atoms are named by adding the suffix-ane to the appropriate numerical multiplier prefix^[8] with elision of any terminal vowel (-a or -o) from the basic numerical term. Hence, pentane, C₅H₁₂; hexane, C₆H₁₄; heptane, C₇H₁₆; octane, C₈H₁₈; etc. The prefix is generally Greek, however alkanes with a carbon atom count ending in nine, for example nonane, use the Latin prefix non-. For a more complete list, see List of alkanes.

Branched alkanes[edit]

Simple branched alkanes often have a common name using a prefix to distinguish them from linear alkanes, for example n-pentane, isopentane, and neopentane.

IUPAC naming conventions can be used to produce a systematic name.

The key steps in the naming of more complicated branched alkanes are as follows:^[9]

• Identify the longest continuous chain of carbon atoms
• Name this longest root chain using standard naming rules
• Name each side chain by changing the suffix of the name of the alkane from '-ane' to '-yl'
• Number the longest continuous chain in order to give the lowest possible numbers for the side-chains ^[10]
• Number and name the side chains before the name of the root chain
• If there are multiple side chains of the same type, use prefixes such as 'di-' and 'tri-' to indicate it as such, and number each one.
• Add side chain names in alphabetical (disregarding 'di-' etc. prefixes) order in front of the name of the root chain

Saturated cyclic hydrocarbons[edit]

Though technically distinct from the alkanes, this class of hydrocarbons is referred to by some as the 'cyclic alkanes.' As their description implies, they contain one or more rings.

Simple cycloalkanes have a prefix 'cyclo-' to distinguish them from alkanes. Cycloalkanes are named as per their acyclic counterparts with respect to the number of carbon atoms in their backbones, e.g., cyclopentane (C₅H₁₀) is a cycloalkane with 5 carbon atoms just like pentane (C₅H₁₂), but they are joined up in a five-membered ring. In a similar manner, propane and cyclopropane, butane and cyclobutane, etc.

Substituted cycloalkanes are named similarly to substituted alkanes — the cycloalkane ring is stated, and the substituents are according to their position on the ring, with the numbering decided by the Cahn–Ingold–Prelog priority rules.^[8]

Trivial/common names[edit]

The trivial (non-systematic) name for alkanes is 'paraffins'. Together, alkanes are known as the 'paraffin series'. Trivial names for compounds are usually historical artifacts. They were coined before the development of systematic names, and have been retained due to familiar usage in industry. Cycloalkanes are also called naphthenes.

It is almost certain that the term 'paraffin' stems from the petrochemical industry. Branched-chain alkanes are called isoparaffins. The use of the term 'paraffin' is a general term and often does not distinguish between pure compounds and mixtures of isomers, i.e., compounds of the same chemical formula, e.g., pentane and isopentane.

Examples

The following trivial names are retained in the IUPAC system:

• isobutane for 2-methylpropane
• isopentane for 2-methylbutane
• neopentane for 2,2-dimethylpropane.

Physical properties[edit]

All alkanes are colorless.^[11][12] Alkanes with the lowest molecular weights are gasses, those of intermediate molecular weight are liquids, and the heaviest are waxy solids.

Table of alkanes[edit]

Boiling point[edit]

Alkanes experience intermolecular van der Waals forces. Stronger intermolecular van der Waals forces give rise to greater boiling points of alkanes.^[13]

There are two determinants for the strength of the van der Waals forces:

• the number of electrons surrounding the molecule, which increases with the alkane's molecular weight
• the surface area of the molecule

Under standard conditions, from CH₄ to C₄H₁₀ alkanes are gaseous; from C₅H₁₂ to C₁₇H₃₆ they are liquids; and after C₁₈H₃₈ they are solids. As the boiling point of alkanes is primarily determined by weight, it should not be a surprise that the boiling point has almost a linear relationship with the size (molecular weight) of the molecule. As a rule of thumb, the boiling point rises 20–30 °C for each carbon added to the chain; this rule applies to other homologous series.^[13]

A straight-chain alkane will have a boiling point higher than a branched-chain alkane due to the greater surface area in contact, thus the greater van der Waals forces, between adjacent molecules. For example, compare isobutane (2-methylpropane) and n-butane (butane), which boil at −12 and 0 °C, and 2,2-dimethylbutane and 2,3-dimethylbutane which boil at 50 and 58 °C, respectively.^[13] For the latter case, two molecules 2,3-dimethylbutane can 'lock' into each other better than the cross-shaped 2,2-dimethylbutane, hence the greater van der Waals forces.

On the other hand, cycloalkanes tend to have higher boiling points than their linear counterparts due to the locked conformations of the molecules, which give a plane of intermolecular contact.^[14]

Melting points[edit]

The melting points of the alkanes follow a similar trend to boiling points for the same reason as outlined above. That is, (all other things being equal) the larger the molecule the higher the melting point. There is one significant difference between boiling points and melting points. Solids have more rigid and fixed structure than liquids. This rigid structure requires energy to break down. Thus the better put together solid structures will require more energy to break apart. For alkanes, this can be seen from the graph above (i.e., the blue line). The odd-numbered alkanes have a lower trend in melting points than even numbered alkanes. This is because even numbered alkanes pack well in the solid phase, forming a well-organized structure, which requires more energy to break apart. The odd-numbered alkanes pack less well and so the 'looser' organized solid packing structure requires less energy to break apart.^[15]

The melting points of branched-chain alkanes can be either higher or lower than those of the corresponding straight-chain alkanes, again depending on the ability of the alkane in question to pack well in the solid phase: This is particularly true for isoalkanes (2-methyl isomers), which often have melting points higher than those of the linear analogues.

Conductivity and solubility[edit]

Alkanes do not conduct electricity in any way, nor are they substantially polarized by an electric field. For this reason, they do not form hydrogen bonds and are insoluble in polar solvents such as water. Since the hydrogen bonds between individual water molecules are aligned away from an alkane molecule, the coexistence of an alkane and water leads to an increase in molecular order (a reduction in entropy). As there is no significant bonding between water molecules and alkane molecules, the second law of thermodynamics suggests that this reduction in entropy should be minimized by minimizing the contact between alkane and water: Alkanes are said to be hydrophobic in that they repel water.

Their solubility in nonpolar solvents is relatively good, a property that is called lipophilicity. Different alkanes are, for example, miscible in all proportions among themselves.

The density of the alkanes usually increases with the number of carbon atoms but remains less than that of water. Hence, alkanes form the upper layer in an alkane–water mixture.

Molecular geometry[edit]

The molecular structure of the alkanes directly affects their physical and chemical characteristics. It is derived from the electron configuration of carbon, which has four valence electrons. The carbon atoms in alkanes are always sp³-hybridized, that is to say that the valence electrons are said to be in four equivalent orbitals derived from the combination of the 2s orbital and the three 2p orbitals. These orbitals, which have identical energies, are arranged spatially in the form of a tetrahedron, the angle of cos⁻¹(−1/3) ≈ 109.47° between them.

Bond lengths and bond angles[edit]

An alkane molecule has only C–H and C–C single bonds. The former result from the overlap of an sp³ orbital of carbon with the 1s orbital of a hydrogen; the latter by the overlap of two sp³ orbitals on different carbon atoms. The bond lengths amount to 1.09 × 10⁻¹⁰ m for a C–H bond and 1.54 × 10⁻¹⁰ m for a C–C bond.

The spatial arrangement of the bonds is similar to that of the four sp³ orbitals—they are tetrahedrally arranged, with an angle of 109.47° between them. Structural formulae that represent the bonds as being at right angles to one another, while both common and useful, do not correspond with the reality.

Conformation[edit]

The structural formula and the bond angles are not usually sufficient to completely describe the geometry of a molecule. There is a further degree of freedom for each carbon–carbon bond: the torsion angle between the atoms or groups bound to the atoms at each end of the bond. The spatial arrangement described by the torsion angles of the molecule is known as its conformation.

Ethane forms the simplest case for studying the conformation of alkanes, as there is only one C–C bond. If one looks down the axis of the C–C bond, one will see the so-called Newman projection. The hydrogen atoms on both the front and rear carbon atoms have an angle of 120° between them, resulting from the projection of the base of the tetrahedron onto a flat plane. However, the torsion angle between a given hydrogen atom attached to the front carbon and a given hydrogen atom attached to the rear carbon can vary freely between 0° and 360°. This is a consequence of the free rotation about a carbon–carbon single bond. Despite this apparent freedom, only two limiting conformations are important: eclipsed conformation and staggered conformation.

Chloe bay bag serial number. The two conformations, also known as rotamers, differ in energy: The staggered conformation is 12.6 kJ/mol lower in energy (more stable) than the eclipsed conformation (the least stable).

This difference in energy between the two conformations, known as the torsion energy, is low compared to the thermal energy of an ethane molecule at ambient temperature. There is constant rotation about the C–C bond. The time taken for an ethane molecule to pass from one staggered conformation to the next, equivalent to the rotation of one CH₃ group by 120° relative to the other, is of the order of 10⁻¹¹ seconds.

The case of higher alkanes is more complex but based on similar principles, with the antiperiplanar conformation always being the most favored around each carbon–carbon bond. For this reason, alkanes are usually shown in a zigzag arrangement in diagrams or in models. The actual structure will always differ somewhat from these idealized forms, as the differences in energy between the conformations are small compared to the thermal energy of the molecules: Alkane molecules have no fixed structural form, whatever the models may suggest.

Spectroscopic properties[edit]

Virtually all organic compounds contain carbon–carbon, and carbon–hydrogen bonds, and so show some of the features of alkanes in their spectra. Alkanes are notable for having no other groups, and therefore for the absence of other characteristic spectroscopic features of a different functional group like –OH, –CHO, –COOH etc.

Infrared spectroscopy[edit]

The carbon–hydrogen stretching mode gives a strong absorption between 2850 and 2960 cm⁻¹, while the carbon–carbon stretching mode absorbs between 800 and 1300 cm⁻¹. The carbon–hydrogen bending modes depend on the nature of the group: methyl groups show bands at 1450 cm⁻¹ and 1375 cm⁻¹, while methylene groups show bands at 1465 cm⁻¹ and 1450 cm⁻¹. Carbon chains with more than four carbon atoms show a weak absorption at around 725 cm⁻¹.

NMR spectroscopy[edit]

The proton resonances of alkanes are usually found at δ_H = 0.5–1.5. The carbon-13 resonances depend on the number of hydrogen atoms attached to the carbon: δ_C = 8–30 (primary, methyl, –CH₃), 15–55 (secondary, methylene, –CH₂–), 20–60 (tertiary, methyne, C–H) and quaternary. The carbon-13 resonance of quaternary carbon atoms is characteristically weak, due to the lack of nuclear Overhauser effect and the long relaxation time, and can be missed in weak samples, or samples that have not been run for a sufficiently long time.

Mass spectrometry[edit]

Alkanes have a high ionization energy, and the molecular ion is usually weak. The fragmentation pattern can be difficult to interpret, but, in the case of branched chain alkanes, the carbon chain is preferentially cleaved at tertiary or quaternary carbons due to the relative stability of the resulting free radicals. The fragment resulting from the loss of a single methyl group (M − 15) is often absent, and other fragments are often spaced by intervals of fourteen mass units, corresponding to sequential loss of CH₂ groups.

Chemical properties[edit]

Alkanes are only weakly reactive with most chemical compounds. The acid dissociation constant (pK_a) values of all alkanes are estimated to range from 50 to 70, depending on the extrapolation method, hence they are practically inert to bases (see: carbon acids). They are also extremely weak acids, undergoing no observable protonation in pure sulfuric acid (H₀ ~ –12), although superacids that are at least millions of times stronger have been known to protonate them to give hypercoordinate alkanium ions (see: methanium ion). Similarly, they only show reactivity with the strongest of electrophilic reagents (e.g., dioxiranes and salts containing the NF₄⁺ cation). By virtue of their strongly C–H bonds (~100 kcal/mol) and C–C bonds (~90 kcal/mol, but usually less sterically accessible), they are also relatively unreactive toward free radicals, although many electron-deficient radicals will react with alkanes in the absence of other electron-rich bonds (see below). This inertness is the source of the term paraffins (with the meaning here of 'lacking affinity'). In crude oil the alkane molecules have remained chemically unchanged for millions of years.

However redox reactions of alkanes, in particular with oxygen and the halogens, are possible as the carbon atoms are in a strongly reduced condition; in the case of methane, the lowest possible oxidation state for carbon (−4) is reached. Reaction with oxygen (if present in sufficient quantity to satisfy the reaction stoichiometry) leads to combustion without any smoke, producing carbon dioxide and water. Free radical halogenation reactions occur with halogens, leading to the production of haloalkanes. In addition, alkanes have been shown to interact with, and bind to, certain transition metal complexes in C–H bond activation.

Free radicals, molecules with unpaired electrons, play a large role in most reactions of alkanes, such as cracking and reformation where long-chain alkanes are converted into shorter-chain alkanes and straight-chain alkanes into branched-chain isomers.

In highly branched alkanes, the bond angle may differ significantly from the optimal value (109.5°) in order to allow the different groups sufficient space. This causes a tension in the molecule, known as steric hindrance, and can substantially increase the reactivity.

In general, branched alkanes are more thermodynamically stable than their linear isomers. The exact reasons for that have been vigorously debated in the chemical literature and is yet unsettled. Two explanations, stabilization of branched alkanes by electron correlation^[16] and destabilization of linear alkanes by steric replusion have been advanced.^[17] Other explanations include hyperconjugation^[18] and electrostatic effects.^[19] This controversy is also related to the question of whether hyperconjugation is the primary factor governing the stability of alkyl radicals.^[20]

Reactions with oxygen (combustion reaction)[edit]

All alkanes react with oxygen in a combustion reaction, although they become increasingly difficult to ignite as the number of carbon atoms increases. The general equation for complete combustion is:

C_nH_2n+2 + (3/2n + 1/2) O₂ → (n + 1) H₂O + n CO₂

or C_nH_2n+2 + (3n + 1/2) O₂ → (n + 1) H₂O + n CO₂

In the absence of sufficient oxygen, carbon monoxide or even soot can be formed, as shown below:

C_nH_2n+2 + (n + 1/2) O₂ → (n + 1) H₂O + nCO

C_nH_2n+2 + (1/2n + 1/2) O₂ → (n + 1) H₂O + nC

For example, methane:

2 CH₄ + 3 O₂ → 2 CO + 4 H₂O

CH₄ + 3/2 O₂ → CO + 2 H₂O

See the alkane heat of formation table for detailed data.The standard enthalpy change of combustion, Δ_cH^⊖, for alkanes increases by about 650 kJ/mol per CH₂ group. Branched-chain alkanes have lower values of Δ_cH^⊖ than straight-chain alkanes of the same number of carbon atoms, and so can be seen to be somewhat more stable.

Reactions with halogens[edit]

Alkanes react with halogens in a so-called free radical halogenation reaction. The hydrogen atoms of the alkane are progressively replaced by halogen atoms. Free radicals are the reactive species that participate in the reaction, which usually leads to a mixture of products. The reaction is highly exothermic, and can lead to an explosion.

These reactions are an important industrial route to halogenated hydrocarbons. There are three steps:

• Initiation the halogen radicals form by homolysis. Usually, energy in the form of heat or light is required.
• Chain reaction or Propagation then takes place—the halogen radical abstracts a hydrogen from the alkane to give an alkyl radical. This reacts further.
• Chain termination where the radicals recombine.

Experiments have shown that all halogenation produces a mixture of all possible isomers, indicating that all hydrogen atoms are susceptible to reaction. The mixture produced, however, is not a statistical mixture: Secondary and tertiary hydrogen atoms are preferentially replaced due to the greater stability of secondary and tertiary free-radicals. An example can be seen in the monobromination of propane:^[13]

Cracking[edit]

Cracking breaks larger molecules into smaller ones. This can be done with a thermal or catalytic method. The thermal cracking process follows a homolytic mechanism with formation of free-radicals. The catalytic cracking process involves the presence of acidcatalysts (usually solid acids such as silica-alumina and zeolites), which promote a heterolytic (asymmetric) breakage of bonds yielding pairs of ions of opposite charges, usually a carbocation and the very unstable hydrideanion. Carbon-localized free radicals and cations are both highly unstable and undergo processes of chain rearrangement, C–C scission in position beta (i.e., cracking) and intra- and intermolecular hydrogen transfer or hydride transfer. In both types of processes, the corresponding reactive intermediates (radicals, ions) are permanently regenerated, and thus they proceed by a self-propagating chain mechanism. The chain of reactions is eventually terminated by radical or ion recombination.

Isomerization and reformation[edit]

Dragan and his colleague were the first to report about isomerization in alkanes.^[21] Isomerization and reformation are processes in which straight-chain alkanes are heated in the presence of a platinum catalyst. In isomerization, the alkanes become branched-chain isomers. In other words, it does not lose any carbons or hydrogens, keeping the same molecular weight.^[21] In reformation, the alkanes become cycloalkanes or aromatic hydrocarbons, giving off hydrogen as a by-product. Both of these processes raise the octane number of the substance. Butane is the most common alkane that is put under the process of isomerization, as it makes many branched alkanes with high octane numbers.^[21]

Other reactions[edit]

Alkanes will react with steam in the presence of a nickelcatalyst to give hydrogen. Alkanes can be chlorosulfonated and nitrated, although both reactions require special conditions. The fermentation of alkanes to carboxylic acids is of some technical importance. In the Reed reaction, sulfur dioxide, chlorine and light convert hydrocarbons to sulfonyl chlorides. Nucleophilic Abstraction can be used to separate an alkane from a metal. Alkyl groups can be transferred from one compound to another by transmetalation reactions.

Occurrence[edit]

Occurrence of alkanes in the Universe[edit]

Alkanes form a small portion of the atmospheres of the outer gas planets such as Jupiter (0.1% methane, 2 ppm ethane), Saturn (0.2% methane, 5 ppm ethane), Uranus (1.99% methane, 2.5 ppm ethane) and Neptune (1.5% methane, 1.5 ppm ethane). Titan (1.6% methane), a satellite of Saturn, was examined by the Huygens probe, which indicated that Titan's atmosphere periodically rains liquid methane onto the moon's surface.^[22] Also on Titan the Cassini mission has imaged seasonal methane/ethane lakes near the polar regions of Titan. Methane and ethane have also been detected in the tail of the comet Hyakutake. Chemical analysis showed that the abundances of ethane and methane were roughly equal, which is thought to imply that its ices formed in interstellar space, away from the Sun, which would have evaporated these volatile molecules.^[23] Alkanes have also been detected in meteorites such as carbonaceous chondrites.

Occurrence of alkanes on Earth[edit]

Traces of methane gas (about 0.0002% or 1745 ppb) occur in the Earth's atmosphere, produced primarily by methanogenic microorganisms, such as Archaea in the gut of ruminants.^[24]

The most important commercial sources for alkanes are natural gas and oil.^[13] Natural gas contains primarily methane and ethane, with some propane and butane: oil is a mixture of liquid alkanes and other hydrocarbons. These hydrocarbons were formed when marine animals and plants (zooplankton and phytoplankton) died and sank to the bottom of ancient seas and were covered with sediments in an anoxic environment and converted over many millions of years at high temperatures and high pressure to their current form. Natural gas resulted thereby for example from the following reaction:

C₆H₁₂O₆ → 3 CH₄ + 3 CO₂

These hydrocarbon deposits, collected in porous rocks trapped beneath impermeable cap rocks, comprise commercial oil fields. They have formed over millions of years and once exhausted cannot be readily replaced. The depletion of these hydrocarbons reserves is the basis for what is known as the energy crisis.

Methane is also present in what is called biogas, produced by animals and decaying matter, which is a possible renewable energy source.

Alkanes have a low solubility in water, so the content in the oceans is negligible; however, at high pressures and low temperatures (such as at the bottom of the oceans), methane can co-crystallize with water to form a solid methane clathrate (methane hydrate). Although this cannot be commercially exploited at the present time, the amount of combustible energy of the known methane clathrate fields exceeds the energy content of all the natural gas and oil deposits put together. Methane extracted from methane clathrate is, therefore, a candidate for future fuels.

Biological occurrence[edit]

Acyclic alkanes occur in nature in various ways.

Bacteria and archaea

Certain types of bacteria can metabolize alkanes: they prefer even-numbered carbon chains as they are easier to degrade than odd-numbered chains.^[25]

On the other hand, certain archaea, the methanogens, produce large quantities of methane by the metabolism of carbon dioxide or other oxidized organic compounds. The energy is released by the oxidation of hydrogen:

CO₂ + 4 H₂ → CH₄ + 2 H₂O

Methanogens are also the producers of marsh gas in wetlands, and release about two billion tonnes of methane per year^[26]—the atmospheric content of this gas is produced nearly exclusively by them. The methane output of cattle and other herbivores, which can release 30 to 50 gallons per day,^[27] and of termites,^[28] is also due to methanogens. They also produce this simplest of all alkanes in the intestines of humans. Methanogenic archaea are, hence, at the end of the carbon cycle, with carbon being released back into the atmosphere after having been fixed by photosynthesis. It is probable that our current deposits of natural gas were formed in a similar way.^[29]

Fungi and plants

Alkanes also play a role, if a minor role, in the biology of the three eukaryotic groups of organisms: fungi, plants and animals. Some specialized yeasts, e.g., Candida tropicale, Pichia sp., Rhodotorula sp., can use alkanes as a source of carbon or energy. The fungus Amorphotheca resinae prefers the longer-chain alkanes in aviation fuel, and can cause serious problems for aircraft in tropical regions.^[30]

In plants, the solid long-chain alkanes are found in the plant cuticle and epicuticular wax of many species, but are only rarely major constituents.^[31] They protect the plant against water loss, prevent the leaching of important minerals by the rain, and protect against bacteria, fungi, and harmful insects. The carbon chains in plant alkanes are usually odd-numbered, between 27 and 33 carbon atoms in length^[31] and are made by the plants by decarboxylation of even-numbered fatty acids. The exact composition of the layer of wax is not only species-dependent but changes also with the season and such environmental factors as lighting conditions, temperature or humidity.^[31]

More volatile short-chain alkanes are also produced by and found in plant tissues. The Jeffrey pine is noted for producing exceptionally high levels of n-heptane in its resin, for which reason its distillate was designated as the zero point for one octane rating. Floral scents have also long been known to contain volatile alkane components, and n-nonane is a significant component in the scent of some roses.^[32] Emission of gaseous and volatile alkanes such as ethane, pentane, and hexane by plants has also been documented at low levels, though they are not generally considered to be a major component of biogenic air pollution.^[33]

Edible vegetable oils also typically contain small fractions of biogenic alkanes with a wide spectrum of carbon numbers, mainly 8 to 35, usually peaking in the low to upper 20s, with concentrations up to dozens of milligrams per kilogram (parts per million by weight) and sometimes over a hundred for the total alkane fraction.^[34]

Animals

Alkanes are found in animal products, although they are less important than unsaturated hydrocarbons. One example is the shark liver oil, which is approximately 14% pristane (2,6,10,14-tetramethylpentadecane, C₁₉H₄₀). They are important as pheromones, chemical messenger materials, on which insects depend for communication. In some species, e.g. the support beetle Xylotrechus colonus, pentacosane (C₂₅H₅₂), 3-methylpentaicosane (C₂₆H₅₄) and 9-methylpentaicosane (C₂₆H₅₄) are transferred by body contact. With others like the tsetse flyGlossina morsitans morsitans, the pheromone contains the four alkanes 2-methylheptadecane (C₁₈H₃₈), 17,21-dimethylheptatriacontane (C₃₉H₈₀), 15,19-dimethylheptatriacontane (C₃₉H₈₀) and 15,19,23-trimethylheptatriacontane (C₄₀H₈₂), and acts by smell over longer distances. Waggle-dancinghoney bees produce and release two alkanes, tricosane and pentacosane.^[35]

Ecological relations[edit]

One example, in which both plant and animal alkanes play a role, is the ecological relationship between the sand bee (Andrena nigroaenea) and the early spider orchid (Ophrys sphegodes); the latter is dependent for pollination on the former. Sand bees use pheromones in order to identify a mate; in the case of A. nigroaenea, the females emit a mixture of tricosane (C₂₃H₄₈), pentacosane (C₂₅H₅₂) and heptacosane (C₂₇H₅₆) in the ratio 3:3:1, and males are attracted by specifically this odor. The orchid takes advantage of this mating arrangement to get the male bee to collect and disseminate its pollen; parts of its flower not only resemble the appearance of sand bees but also produce large quantities of the three alkanes in the same ratio as female sand bees. As a result, numerous males are lured to the blooms and attempt to copulate with their imaginary partner: although this endeavor is not crowned with success for the bee, it allows the orchid to transfer its pollen,which will be dispersed after the departure of the frustrated male to different blooms.

Enzymatic Activation Of Alkanes Constraints And Prospects Definition In Hindi

Production[edit]

Petroleum refining[edit]

As stated earlier, the most important source of alkanes is natural gas and crude oil.^[13] Alkanes are separated in an oil refinery by fractional distillation and processed into many different products.

Fischer–Tropsch[edit]

The Fischer–Tropsch process is a method to synthesize liquid hydrocarbons, including alkanes, from carbon monoxide and hydrogen. This method is used to produce substitutes for petroleum distillates.

Laboratory preparation[edit]

There is usually little need for alkanes to be synthesized in the laboratory, since they are usually commercially available. Also, alkanes are generally unreactive chemically or biologically, and do not undergo functional group interconversions cleanly. When alkanes are produced in the laboratory, it is often a side-product of a reaction. For example, the use of n-butyllithium as a strong base gives the conjugate acid, n-butane as a side-product:

C₄H₉Li + H₂O → C₄H₁₀ + LiOH

However, at times it may be desirable to make a section of a molecule into an alkane-like functionality (alkyl group) using the above or similar methods. For example, an ethyl group is an alkyl group; when this is attached to a hydroxy group, it gives ethanol, which is not an alkane. To do so, the best-known methods are hydrogenation of alkenes:

RCH=CH₂ + H₂ → RCH₂CH₃(R = alkyl)

Alkanes or alkyl groups can also be prepared directly from alkyl halides in the Corey–House–Posner–Whitesides reaction. The Barton–McCombie deoxygenation^[36][37] removes hydroxyl groups from alcohols e.g.

and the Clemmensen reduction^{[38][39][40][41]} removes carbonyl groups from aldehydes and ketones to form alkanes or alkyl-substituted compounds e.g.:

Applications[edit]

The applications of alkanes depend on the number of carbon atoms. The first four alkanes are used mainly for heating and cooking purposes, and in some countries for electricity generation. Methane and ethane are the main components of natural gas; they are normally stored as gases under pressure. It is, however, easier to transport them as liquids: This requires both compression and cooling of the gas.

Propane and butane are gases at atmospheric pressure that can be liquefied at fairly low pressures and are commonly known as liquified petroleum gas (LPG). Propane is used in propane gas burners and as a fuel for road vehicles,^[42] butane in space heaters and disposable cigarette lighters. Both are used as propellants in aerosol sprays.

From pentane to octane the alkanes are highly volatile liquids. They are used as fuels in internal combustion engines, as they vaporize easily on entry into the combustion chamber without forming droplets, which would impair the uniformity of the combustion. Branched-chain alkanes are preferred as they are much less prone to premature ignition, which causes knocking, than their straight-chain homologues. This propensity to premature ignition is measured by the octane rating of the fuel, where 2,2,4-trimethylpentane (isooctane) has an arbitrary value of 100, and heptane has a value of zero. Apart from their use as fuels, the middle alkanes are also good solvents for nonpolar substances.

Alkanes from nonane to, for instance, hexadecane (an alkane with sixteen carbon atoms) are liquids of higher viscosity, less and less suitable for use in gasoline. They form instead the major part of diesel and aviation fuel. Diesel fuels are characterized by their cetane number, cetane being an old name for hexadecane. However, the higher melting points of these alkanes can cause problems at low temperatures and in polar regions, where the fuel becomes too thick to flow correctly.

Alkanes from hexadecane upwards form the most important components of fuel oil and lubricating oil. In the latter function, they work at the same time as anti-corrosive agents, as their hydrophobic nature means that water cannot reach the metal surface. Many solid alkanes find use as paraffin wax, for example, in candles. This should not be confused however with true wax, which consists primarily of esters.

Alkanes with a chain length of approximately 35 or more carbon atoms are found in bitumen, used, for example, in road surfacing. However, the higher alkanes have little value and are usually split into lower alkanes by cracking.

Some synthetic polymers such as polyethylene and polypropylene are alkanes with chains containing hundreds or thousands of carbon atoms. These materials are used in innumerable applications, and billions of kilograms of these materials are made and used each year.

Environmental transformations[edit]

Alkanes are chemically very inert apolar molecules which are not very reactive as organic compounds. This inertness yields serious ecological issues if they are released into the environment. Due to their lack of functional groups and low water solubility, alkanes show poor bioavailability for microorganisms.^[43]

There are, however, some microorganisms possessing the metabolic capacity to utilize n-alkanes as both carbon and energy sources.^[44] Some bacterial species are highly specialised in degrading alkanes; these are referred to as hydrocarbonoclastic bacteria.^[45]

Hazards[edit]

Methane is flammable, explosive and dangerous to inhale, because it is a colorless, odorless gas, special caution must be taken around methane.^[46] Ethane is also extremely flammable, dangerous to inhale and explosive.^[47] Both of these may cause suffocation.^[46][47] Similarly, propane is flammable and explosive.^[48] It may cause drowsiness or unconsciousness if inhaled.^[48] Butane has the same hazards to consider as propane.^[49]

Alkanes also pose a threat to the environment. Branched alkanes have a lower biodegradability than unbranched alkanes.^[50] However, methane is ranked as the most dangerous greenhouse gas.^[51] Although the amount of methane in the atmosphere is low, it does pose a threat to the environment.^[51]

See also[edit]

Enzymatic Activation Of Alkanes Constraints And Prospects Definition In Science

References[edit]

Enzymatic Activation Of Alkanes Constraints And Prospects Definition Math

1. ^ ^abIUPAC, Compendium of Chemical Terminology, 2nd ed. (the 'Gold Book') (1997). Online corrected version: (2006–) 'alkanes'. doi:10.1351/goldbook.A00222
2. ^'Alkanes'. Chemistry LibreTexts. 28 November 2016.
3. ^Arora, A. (2006). Hydrocarbons (Alkanes, Alkenes And Alkynes). Discovery Publishing House Pvt. Limited. ISBN9788183561426.
4. ^On-Line Encyclopedia of Integer Sequences (sequence A000602 in the OEIS)
5. ^IUPAC, Commission on Nomenclature of Organic Chemistry (1993). 'R-2.2.1: Hydrocarbons'. A Guide to IUPAC Nomenclature of Organic Compounds (Recommendations 1993). Blackwell Scientific. ISBN978-0-632-03488-8. Retrieved 12 February 2007.
6. ^Alkane NomenclatureArchived 2 February 2012 at the Wayback Machine
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