Fragmentation Pattern In Mass Spectrometry

 Fragmentation Pattern In Mass Spectrometry

Mass Spectrometry

In order to determine the mass-to-charge ratio (m/z) of one or more molecules in a sample, mass spectrometry is a valuable analytical instrument. The precise molecular weight of the sample's constituent parts can frequently be determined using these measures as well.

Fragmentation in mass spectrometry is the dissociation of energetically unstable molecular ions created when molecules pass through an instrument's ionization chamber. A molecule's fragments result in a distinctive pattern in the mass spectrum.

A recent study has concentrated on the fragmentation that happens during tandem mass spectrometry investigations since this information makes molecular identification easier.

Fragmentation

Fragmentation is a sort of chemical dissociation in which an electron is removed from a molecule, resulting in ionization. Ionization is brought on by the removal of electrons from sigma bonds, pi bonds, or nonbonding orbitals. This can happen by the bond's homolytic cleavage, homolysis, heterolytic cleavage, or heterolysis. The fragmentation process is influenced by relative bond energy and the capacity for advantageous cyclic transition states. Stevenson's Rule outlines the primary fragmentation mechanisms.

Simple bond cleavage reactions and rearrangement reactions are two major groups of bond cleavage patterns.

Fragmentation pattern

Fragmentation reactions

Simple reactions that cleave bonds

The majority of organic molecules proceed via simple bond cleavage reactions, which involve direct bond cleavage. Among the many different kinds of straightforward bond cleavage reactions are sigma bond cleavage, radical site-initiated fragmentation, and charge site-initiated fragmentation.

Cleavage of the sigma bond

The most frequent occurrence of sigma bond breakage is found in molecules that can create stable cations like saturated alkanes, secondary, and tertiary carbocations. When an alpha electron is taken away, this happens. As the C-C bond lengthens and deteriorates, fragmentation results. At this location, fragmentation yields both charged and neutral fragments.

Alpha Fission

Site-initiated radical fragmentation, Homolytic cleavage

Sigma bond cleavage can also occur on radical cations that are not ionized. Alcohols, ethers, ketones, esters, amines, alkenes, and aromatic compounds with a carbon linked to the ring are examples of substances where this is frequently seen. A radical on a heteroatom or an unsaturated functional group is present in the cation. The radical ion's significant propensity for electron pairing acts as the catalyst for fragmentation. When the radical and an odd electron from bonds next to the radical move to create a bond with the heteroatom or unsaturated functional group, this is known as cleavage. This cleavage, sometimes referred to as homolytic bond cleavage or -cleavage, occurs when the sigma bond breaks.

Heterolytic Cleavage

The inductive impact of the charge site in radical cations is what propels fragmentation that is triggered by the charge site. The charge-bearing atom receives electrons from the bond next to it, which causes the charge to become neutral and shift to a different location. This process is an illustration of heterolytic bond cleavage and is also known as inductive cleavage.

McLafferty Rearrangement reactions

Rearrangement reactions are fragmentation reactions that create new bonds and an intermediate structure prior to cleavage. The McLafferty rearrangement/-hydrogen rearrangement is one of the most researched rearrangement reactions. This happens when radical cations, such as ketones, aldehydes, carboxylic acids, esters, amides, olefins, and phenylalkanes, have unsaturated functional groups. The functional group will initially receive -hydrogen during this reaction, and the intermediate will then undergo -bond cleavage.  

McLafferty Rearrangement

Fragmentation Rules

1. The straight chain compound has the highest relative height of the molecular ion peak, which then falls.

2. In a homologous series, the relative height of the molecular ion peak often declines as molecular weight increases. The apparent exception is fatty esters.

3.Cleavage occurs preferentially at alkyl-substituted carbon atoms; the more substituted, the higher the likelihood of cleavage. This results from tertiary carbocations being more stable than secondary carbocations, which are more stable than primary carbocations.

Tertiary > Secondary >Primary> Methyl Group

4. The molecular ion is stabilized by double bonds, cyclic structures, and particularly aromatic (or heteroaromatic) rings, which raises the likelihood of their appearance.

5. The resonance-stabilized allylic carbocation is produced by double bonds, which favor allylic cleavage. Due to the ready migration of the double bond, this rule does not apply to simple alkenes, but it does apply to cycloalkenes.

Allylic carbon

The allylic carbon is connected to a carbon atom, which is doubly bound to another carbon atom. The allylic carbon atom is represented by the asterisk in the generic formula for allyl, which is R-CH2-CH=CH2. In contrast to the vinyl group, the allylic carbon atom is sp3 hybridised since it formed a single covalent bond with CH=CH2.

6.Alkyl side chains typically disappear from saturation rings at the bond. This is essentially an exception to branching (rule 3). The ring fragment usually retains its positive charge. A retro Diels-Alder reaction can occur in an unsaturated ring.

7. Cleavage at the bond to the ring in alkyl-substituted aromatic compounds is very likely to result in the resonance-stabilized benzyl ion or, more likely, the tropylium ion. See diagram below.

8. The charge is frequently left on the fragment containing the heteroatom, whose nonbonding electrons offer resonance stabilization, when the C-C bonds close to it break. See below in picture.

9. Cleavage is frequently accompanied by rearrangement and the removal of tiny, stable, neutral molecules such alcohols, mercaptans, olefins, water, ammonia, hydrogen cyanide, hydrogen sulphide, or carbon monoxide.

Nitrogen Rule

Any molecule (with all paired electrons) containing an odd number of nitrogen atoms will have an odd nominal mass, according to the nitrogen rule. The integer mass of an atom, ion, or molecule made up exclusively of the most stable isotope is known as the nominal mass (s).

This rule is used when molecules have only carbon, Nitrogen, Hydrogen, Oxygen, and Halogen atoms.

Here below are examples that are helpful for understanding the Nitrogen rule, you will be able to find out the molecular formula of the unknown compound by using this rule.

Compounds containing an even or odd number of nitrogen atoms their molecular weight will also be even or odd respectively. Even or no nitrogen atom in molecules means its molecular weight will be even.  

History, Classification and Formation of Liquid Crystals

 History, Classification and Formation of Liquid Crystals

History, Classification and Formation of Liquid Crystals

The word "crystal" originates from the Greek word krystallos, which is a synonym for ice and literally means "coldness drawn together."

Liquid crystals

Some substances don't melt into ordinary liquids right away; instead, they go through a stage that flows like a liquid yet resembles a solid in many ways. The material is a liquid crystal at this stage. It retains some of the crystalline solid's organized structure, which is the most prevalent kind of solid.

When substances are heated to their melting temperatures, the majority of them instantly transform from solids to liquids. When a substance in a crystalline solid reaches its melting point, all the forces that keep the substance's crystal structure are normally dismantled at once, allowing the substance's molecules to move around freely and pass by one another.

There are two or more steps to the melting process that occur at various temperatures for compounds that turn into liquid crystals. Some of the forces governing the structure of these substances are substantially stronger than others when they are solid.

History of Liquid crystals

In 1850 W. Heintz take stearin and heat it, he noticed two temperatures one at 52°C convert to cloudy liquid form and at 62°C stearin becomes clear liquid. The phase between solid and liquid form of stearin is called as liquid crystal or mesosphere.

While researching carrot cholesteryl benzoate in 1888, Austrian botanist Friedrich Reinitzer made the unintentional discovery of liquid crystals. When Reinitzer heated cholesteryl benzoate, he discovered that it had two melting points. It initially melted around 294°F (145°C) and changed into a hazy fluid. It altered once more at 353°F (179°C), but this time it became a transparent liquid. He also noticed that the substance reflected polarised light and had the ability to change the direction of polarization of light.

Classification of Liquid crystals

There are various LC phase types, and these can be identified by the way they look (such as textures). Because molecules in one region of the material, or "domain," are all orientated in the same direction, but in other regions, they are all oriented differently, the opposing textures result. A LC state of matter may not always exist in Liquid Crystal materials (just as water may be ice or water vapor).

Classification of Liquid Crystals

a) On the bases of mode of formation

Lyotropic liquid crystals

The majority of solids can also be converted to liquids by being dissolved in another liquid. As with most melting, this transition from the solid to the dissolved state usually happens in a single step, but for some compounds, it happens in multiple steps. The dissolving liquid can more easily pass through the layers of connected molecules formed by these substances than it can through the layers' individual molecules. The solid's ordered structure partially collapses when the layers become separated from one another in this fashion, creating a hazy fluid known as a lyotropic liquid crystal. Lyotropic LCs show phase transitions that depend on solvent molecule concentration and temperature (typically water).

Thermotropic liquid crystals

These are created by heating solids. When the temperature changes, thermotropic LCs show a phase transition into the LC phase. A polarised light beam can spin its axis as it passes through some liquid crystals. This feature is lost in the presence of a weak electric field.

b) On the basis of arrangement of particles

Between the crystalline (solid) and isotropic (liquid) states of matter, there is a separate phase known as the liquid crystal state. Depending on the level of order present in the material, there are numerous different types of liquid crystal states.

Nematic LC

In the Nematic liquid crystal phase, molecules tend to point in the same direction despite having no positional order. Particles moves randomly in liquid crystal as shown in figure.

Smectic LC

The Greek word for soap is where the word "smectic" comes from. The thick, slick material that is frequently discovered in the bottom of a soap dish is actually a sort of smectic liquid crystal, which clarifies the origin of this seemingly equivocal substance. Another different mesophase of liquid crystal solids is the smectic state. In contrast to the Nematic, molecules in this phase exhibit a degree of translational order. The molecules in the smectic state continue to organize themselves in layers or planes while maintaining the general orientational order of nematics. Separate planes are seen to flow past one another, and motion is limited to inside these planes. The smectic state is more "solid-like" than the nematic because of the enhanced order.

One layer of particles slides other layer or layer exchange simply (see fig below), they show properties that are in between liquids and solids.

Cholestic LC

A form of chiral liquid crystal having a helical structure is called a cholesteric liquid crystal. Chiral nematic liquid crystals are another name for cholesteric liquid crystals. While the molecules in cholesteric liquid crystals are twisted and chiral in arrangement, they organize in layers with no positional ordering within layers and a director axis that varies with layers.

Because colour will reflect when the pitch, or the separation between layers with the same orientation, is about equal to the wavelength of the colour, cholesteric liquid crystals are coloured. When we press, heat, or cool cholesteric liquid crystals, we observe colour variations due to this shift in pitch.

No movement of particles occurs, they only vibrate at their own positions (see fig, below) and their properties are more closely related to solids.

 

Nematic, Sematic and Cholestic LC

Liquid crystals Formation

Compounds having long, thin molecules that have specific atom groupings give rise to liquid crystals. These groups give the molecules their stiff, rod-like shape, which makes them strongly attract one another when they are arranged against each other.

Properties of liquid crystals

A kind of substance called liquid crystal (LC) has properties that fall somewhere between those of solid crystals and those of regular liquids. A liquid crystal, for instance, may flow like a liquid while having molecules that resemble crystals.

Solid like properties

Anisotropy

Optical activity

Particle arrangement

Liquid like properties

Surface tension

Viscosity

Fluidity

Uses

These substances are employed in liquid crystal displays (LCDs) found in many electrical items in thin layers. LCDs are frequently found in flat-screen televisions, computer monitors, cell phones, portable electronic games, digital camera viewfinders, and clocks and calculators.

Both natural and manmade applications serve as good examples of LCs. In living systems, lyotropic LCs are abundant; the tobacco mosaic virus, as well as numerous proteins and cell membranes, are LCs. In the domain of minerals, LCs include clays, soap solutions, and numerous related detergents. Liquid crystals are widely used in liquid crystal displays.

What Are Liquids & Forces Inside Liquids

 What Are Liquids & Forces Inside Liquids

What are Liquids

The term "liquid" can be used to describe both a substance's kind and its physical state. For instance, water is the most prevalent liquid on Earth.

A form of matter known as a liquid has unique characteristics that make it less stiff than a solid but more rigid than a gas. Unlike a solid, which has a defined shape, a liquid can flow. In contrast, a liquid takes on the shape of the container it is kept in. A liquid does not expand to fill the container like a gas does, despite the fact that this is comparable to a gas. Water, oil, alcohol, and mercury are a few examples of liquids that can be found at room temperature, which is roughly 20 degrees Celsius or 68 degrees Fahrenheit. Liquids can differ greatly from one another. For instance, olive oil pours more slowly than vinegar because it is heavier and thicker and hence weights more.

Physical properties of liquids
Cohesion

The intermolecular forces that hold molecules together cause the molecular components of a liquid to attract one another to varying degrees. Surface tension, which is what keeps water in droplets together or allows a pin to float on the surface, is a sign of cohesion.

Adhesion

 Depending on the type of liquid and the other component, there can be variable degrees of attractive forces between them. This explains why water adheres to surfaces differently depending on their composition, such as glass versus plastic. Adhesion also explains capillary action, which is when liquid tends to rise slender tubes or other porous materials, such as when a nurse uses a small glass tube to draw blood from a patient.

Volume

Despite taking on the shape of its container, liquid retains a largely constant volume. Unless vaporization or evaporation is affecting the volume, a modest change in pressure or temperature may only slightly modify the volume.

Compressibility

 Liquids are held together by strong intermolecular forces in a manner similar to that of solids, resulting in a relatively incompressible substance—another characteristic that distinguishes liquids from gases.

Variability

A liquid doesn't have a set form. It behaves similarly to gas in that it molds itself to the shape of the container it is held in, but unlike gas, it does not expand to fill the container.

Flowability

One of a liquid's fundamental properties is its capacity to flow. Its viscosity, which changes according on molecular size and intermolecular interactions, determines how much it flows, though. Because of its greater molecular structure, motor oil, for instance, has a far higher viscosity than water. As a result, motor oil moves much more slowly than water.

Evaporation

A liquid's molecular components frequently clash with one another or the container because of how much movement they undergo. These collisions result in the transfer of energy between molecules. Intermolecular forces are mainly in charge of the physical properties of the substance. Surface tension can be broken when enough energy is delivered to the liquid's surface, leading to the liquid evaporating. 

Forces inside liquids

Most important forces are intermolecular forces. The compacted states of matter are caused by intermolecular forces. Intermolecular forces, which hold the particles that make up solids and liquids together, have an impact on a number of the physical characteristics of matter in these two forms.

Intermolecular Forces

A force that attracts the protons or positive parts of one molecule to the electrons or negative parts of another molecule is known as an intermolecular force. A substance's various physical and chemical properties are influenced by this force. The strength of an object's intermolecular forces determines its boiling point; the higher the intermolecular forces, the higher the boiling point. We can compare the intermolecular forces between different substances by comparing their boiling points. This is so that these intermolecular forces can be broken and the liquid can be transformed into vapour using the heat that the substance absorbs at its boiling point.

Between molecules that have hydrogen bound to a strongly electronegative atom, such as O, N, or F, hydrogen bonds are very potent dipole-dipole interactions. Van der Waals forces and hydrogen bonds are examples of electrostatic intermolecular forces. Intermolecular interactions, which hold molecules to one another in liquids and hold polyatomic ions together, are weaker than intramolecular interactions, which hold the atoms within molecules together. Intermolecular contacts alter to cause transitions from the solid to liquid or from the liquid to gas phases, but intramolecular interactions are unaffected. Dipole-dipole interactions, London dispersion forces (commonly referred to as van der Waals forces), and hydrogen bonds are the three main types of intermolecular interactions.

Factors affecting intermolecular forces

The following interactions affect intermolecular forces:

a) Dipole-Dipole Forces

Polar molecules are attracted to one another through dipole-dipole interactions. Due to variations in the electronegativity of the atoms involved in a covalent connection, polar molecules contain permanent dipoles. One molecule's partially positive portion will gravitate toward another molecule's partially negative component. Simply we say that these forces are present between polar molecules.

Example: In HCl molecules, dipole-dipole interactions take place. Chlorine obtains a partial negative charge because it is relative more electronegative than hydrogen (whereas hydrogen acquires a partial positive charge). The HCl molecules then engage in a dipole-dipole interaction.

 b) Dipole Induced Dipole Forces or Debye Forces

Ion-induced dipole interactions are comparable to these interactions. The key distinction is that non-polar molecules are converted into induced dipoles by the proximity of polar molecules. Present between polar or permanent dipole and non-polar molecules, for example mixture of Ne and HCL

c) London Dispersion Forces or Instantaneous Dipole-Induced Dipole Forces

Discovered by German Physicist Fritz London in 1930. It has a limited range of operation and is the weakest force. The flow of electrons causes this type of force, which produces transient positive and negative charged areas. These forces present between non polar molecules.

d) Interactions between Ion-Dipoles

With the exception of the fact that they happen between ions and polar molecules, these interactions are comparable to dipole-dipole interactions. For example: The polar H2O molecules are drawn to the sodium and chloride ions in the beaker when NaCl and water are combined there. The size of the dipole moment affects how strong this interaction is, size and charge of an ion; the size of the polar molecule

e) Dipole Interactions Induced by Ions

In this kind of interaction, an ion that is put close to a non-polar molecule causes it to become polarised. Once charged, the non-polar molecules exhibit induced dipole behaviour. Ion-induced dipole interaction is the name given to this interaction between an ion and an induced dipole.

f) Hydrogen Bonding

Intermolecular forces tend to be exceptionally strong in molecules having hydrogen atoms bound to electronegative atoms like O, N, and F (and to a much lesser extent Cl and S). These lead to boiling temperatures that are significantly higher than those found for compounds where London dispersion forces predominate. With regard to the covalent hydrides of elements in groups 14–17. Group 14 contains the heavier constituents of methane as well as a sequence of boiling temperatures that rise gradually with molar mass. Nonpolar molecules, for which London dispersion forces are the only intermolecular forces, are predicted to follow this pattern (boiling point increases with molecular mass). As opposed to what their molar weights would suggest, the hydrides of the lightest members of groups 15–17 have boiling points that are almost higher than 100°C. 

Intramolecular forces

Ionic bond

This bond is created when all of the valence electrons are completely transferred between the atoms. It is a kind of chemical connection that produces two ions with opposing charges. In ionic bonding, the nonmetal takes the lost electrons to form a negatively charged anion while the metal loses them to become a positively charged cation.

Covalent bond

Atoms that share a similar electronegativities—the affinity or desire for electrons—form a covalent connection. Both atoms share electrons in order to achieve octet configuration and become more stable because they have equivalent affinities for electrons and neither has a propensity to donate them.

When the electronegativity difference between the linked atoms is smaller than 0.5, a nonpolar covalent bond is created between the same atoms or atoms with extremely similar electronegativities.

When atoms with marginally differing electronegativities share electrons, a polar covalent link is created. Between 0.5 and 1.9 electronegativity are different between linked atoms.

HF, O-H in water, and hydrogen chloride are all example of polar covalent bonds.

Metallic bond

This kind of covalent bonding only happens between metal atoms, and it allows the valence electrons to freely travel around the crystal structure. This link is created by the attraction of the fixed positively charged metal ions and the moving electrons, often known as the "sea of electrons." Samples of pure elemental metals, like gold or aluminium, or alloys, like brass or bronze, include metallic bonds. Freely moving electrons oscillate and emit photons of light, which is what gives metals their reflecting quality. They also allow metals to efficiently conduct heat and energy.

Difference between Intermolecular and Intramolecular forces