Determination of Physical Properties of Molecules PDF

Determination of Physical Properties of Molecules Reference: Martin’s Physical Pharmacy and Pharmaceutical Sciences  An atom consists of a nucleus containing neutrons and protons, with electrons orbiting it. Charged atoms result from an imbalance in electrons and...

Determination of Physical Properties of Molecules Reference: Martin’s Physical Pharmacy and Pharmaceutical Sciences  An atom consists of a nucleus containing neutrons and protons, with electrons orbiting it. Charged atoms result from an imbalance in electrons and protons, leading to ionic interactions. Atomic mass is determined by counting protons and neutrons, and isotopes exist for many elements. Molecules form through interatomic bonding, with molecular structure held together by bonding energy.  Bonding energy depends on electron orbital orientation, overlap, and the nature of the bond. Macromolecules like proteins and polymers may have additional interactions within their structure. The density of the electron cloud around an atom decreases with more bonding. The nature of interatomic bonds can vary due to differences in atomic properties like electronegativity. Additive Properties: Additive properties are those that can be calculated or determined by adding together the contributions of individual components or parts of a system. These properties depend on the sum of the effects or characteristics of each individual component in a mixture or material. Additive properties are typically observed in mixtures or composite materials where the properties of the individual components combine linearly to yield the overall property of the mixture. Examples of additive properties include mass, volume, density, and some thermal properties like specific heat capacity. Constitutive Properties: Constitutive properties are characteristics or parameters that describe how a material responds to external forces or stimuli, such as stress, temperature, or electromagnetic fields. These properties define the relationship between the material's internal state and its external response when subjected to various conditions. Constitutive properties are often represented by mathematical equations or constitutive models that describe the material's behavior under specific circumstances. Examples of constitutive properties include elasticity (describing how a material deforms under stress), thermal conductivity (how heat flows through a material), electrical conductivity (how a material conducts electricity), and magnetic susceptibility (how a material responds to an applied magnetic field). Coulomb’s Law Is a fundamental principle in electrostatics that describes the relationship between the electrostatic force, the charges of two objects, and the distance between them. It quantifies how two charged objects interact with each other due to the presence of electric charge  Different solvents have differing permittivities due to their chemical nature, polar or nonpolar Permitivity - a measure of how much electric flux (electric field lines) can pass through a material. It describes the degree to which a material can be polarized in response to an applied electric field. When no permanent charges exist in molecules but we can measure their polarity by the property we call the DIPOLE MOMENT Dipole Moment A dipole moment is a It is a measure of the property of a molecule overall polarity of the or a system of charges system and quantifies that indicates the the extent to which separation of charges are distributed positive and unevenly, resulting in a negative charges separation of charge. within the system. Dielectric Constant (Relative Permittivity) Dielectric constant ​is a property of materials (like insulators or dielectrics) and describes how these materials respond to an external electric field. It quantifies the ability of a material to be polarized or how easily it allows electric charges to separate within it when subjected to an electric field. Dielectric constant is a measure of the relative permittivity of a material compared to that of a vacuum (or free space). Relationship between Dipole moment and Dielectric Constant Non-polar Molecules When nonpolar molecules like pentane are placed in a suitable solvent between the plates of a charged capacitor, an induced polarization of the molecules can occur When a non-polar molecule is exposed to an external electric field, the negatively charged electrons within the molecule are attracted to the positively charged end of the field, and they move slightly away from the negatively charged end. This shift in electron distribution creates a temporary dipole moment within the molecule. Induced Polarizability A temporarily induced dipole moment is proportional to the field strength of the capacitor and the induced polarizability, αp, which is a characteristic property of the particular molecule. PERMANENT DIPOLE MOMENT OF POLAR MOLECULES In a polar molecule, permanent separation of positive and negative charge regions creates a permanent dipole moment (μ). The difference in electronegativity of atoms in a bond contributes to the permanent dipole moment. The magnitude of μ is independent of any induced dipole and is the vector sum of individual charge moments within the molecule. The unit of μ is the debye (1 debye=10−18 esu cm) esu - Statcoulomb  Maximum dipole In an electric field, moments occur when polar molecules tend molecules are well- to orient themselves aligned with the with negatively electric field, limited charged centers by thermal energy- closer to positively induced molecular charged centers. motion.  The total molar polarization (P) combines induction and permanent dipole effects. Equation (4–6) describes P as a function of dielectric constant (ε), permanent dipole moment (μ), and temperature (T). Dipole moments can be calculated from experimental data on P at different temperatures. Solvents like water with permanent dipoles can interact strongly with solute molecules, influencing solubility and hydration of ions. Symmetry of molecules can be associated with their dipole moments; symmetric molecules like carbon dioxide have no net dipole, while asymmetric ones may have significant dipole moments. Dipole interactions are important in various contexts, including solubility, drug- receptor binding, and the crystalline arrangement of solid materials like ice crystals. Electromagnetic Radiation Electromagnetic radiation is a form of energy characterized by oscillating electric and magnetic fields that propagate through space perpendicular to each other and to the direction of propagation.  These fields are described by sinusoidal waves with characteristics such as amplitude (A) and frequency (ν). Frequency (ν) represents the number of waves passing a fixed point in 1 second, while wavelength (λ) is the distance between two successive wave maxima.  The speed of electromagnetic radiation depends on the medium; in a vacuum, it travels at the speed of light (c = 2.99792 × 10^8 m/sec). The relationship between frequency and wavelength is given by v = c/λ. The wave number (ν) is the reciprocal of the wavelength and is used to describe radiation, particularly because it's proportional to frequency and energy. The electromagnetic spectrum is classified based on wavelength or wave number, with shorter wavelengths corresponding to higher radiant energy. Electromagnetic radiation interactions with matter, primarily through the electric field component, lead to various spectroscopic phenomena, including transmission, reflection, refraction, absorption, and emission. The magnetic component is involved in techniques like electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR). Let us define again Wavelength (λ) Wave number (v bar) Frequency ATOMIC AND MOLECULAR SPECTRA Atoms and molecules have characteristic frequencies at which they absorb electromagnetic radiation. Quantum theory states that these entities can only exist in discrete energy states or electronic states due to the motion of electrons around the nucleus. Absorption of radiant energy occurs in transitions from one energy state (E1) to an upper energy state (E2) in atoms or molecules, resulting in discrete energy values.  The pattern of absorbed frequencies is known as an absorption spectrum, which is produced when radiation of a specific wavelength passes through a sample. The intensity changes in the spectrum are due to electronic excitation. In some cases, electromagnetic radiation can lead to emission when excited species (atoms, ions, or molecules) return to lower energy states, releasing energy as photons (hv). This results in an emission spectrum. Atomic spectra typically consist of lines corresponding to frequencies of specific electronic transition states. Hydrogen’s emission spectrum Molecular Absorption Molecules have quantized vibrational and rotational states in addition to electronic states, making their spectra more complex than atoms. Each type of transition (electronic, vibrational, rotational) involves different energy levels. Electronic transitions typically absorb ultraviolet or visible radiation, vibrational transitions near-infrared, and rotational transitions infrared radiation. Electronic transitions result in broad bands in the UV and visible regions due to concurrent vibrational and rotational changes.  Molecules with resonance structures may absorb longer- wavelength radiation. Microwave and radio wave regions are associated with low-energy transitions involving electron spin (EPR) and nuclear spin (NMR) spectroscopy. These various forms of molecular spectroscopy provide insights into molecular structure and behavior. Ultraviolet and Visible Spectrophotometry Electromagnetic radiation in the UV and visible regions corresponds to the energy levels of electronic transitions in various molecules and ions. Absorbing species are categorized based on the molecular energy levels involved in the electronic transition, which depends on bonding within the molecule. Covalent bonding leads to molecular orbitals, such as sigma (σ) orbitals for single covalent bonds and sigma and pi (π) orbitals for double bonds. Molecular orbital energy levels generally follow a specific order.  Organic molecules absorb UV-Vis light at particular wavelengths depending on the type of electronic transition associated with the absorption. Sigma to sigma-star (σ → σ*) transitions occur at short- wavelength UV radiation (typically 100-150 nm). Molecules with carbonyl groups can undergo n to pi-star (n → π*) or n to sigma-star (n → σ*) transitions, which require lower energy, leading to absorption at longer wavelengths. The region of UV spectra between 270 and 290 nm is associated with carbonyl n to π* electronic transitions in aldehydes and ketones. The parts of a molecule directly linked to UV-Vis absorption, like carbonyl groups, are referred to as chromophores. Absorption spectroscopy relies on measuring transmittance (T) or absorbance (A) using cuvettes with a defined path length (b) and relates absorbance to the concentration (C) of the absorbing substance using Beer's law (A = εbC). Beer's law includes the molar absorptivity (ε), which depends on the specific molecule, solvent, temperature, and wavelength used for analysis. UV-Vis absorption spectra serve as molecular fingerprints, providing information for the identification of compounds. Different functional groups within molecules have unique bonding and electronic structures, resulting in distinct absorption wavelengths. Changes in bonding order or electronic structure alter the UV- Vis spectrum, making it valuable for monitoring various molecular properties, chemical reactions, complexation, and degradation. Absorption spectroscopy is widely used for quantitative analysis due to its applicability to both organic and inorganic systems, sensitivity, selectivity, accuracy, and convenience. Modern spectrophotometers, such as double-beam and diode- array instruments, are coupled to computers for data analysis. Double-beam spectrophotometers use a deuterium lamp as the light source, a monochromator to select wavelengths, and a rotating mirror to direct light through reference and sample cells before detection. Diode-array spectrophotometers have simpler optics and higher radiation throughput, offering rapid scanning capabilities and improved signal-to-noise ratios. Calibration curves generated from standard solutions with known concentrations are commonly used for quantitative analysis. Absorbance spectra can determine specific wavelengths, often absorption maxima, for quantitative measurements.  Spectrophotometers measure all species in a sample even when a single wavelength is selected for detection, which can lead to weaknesses in molecular detection specificity. UV-Vis spectra generated at a specific wavelength may not effectively detect changes in reaction intermediates or multiple species with overlapping absorptions. Spectrophotometers are often used in conjunction with other methods like high-performance liquid chromatography (HPLC) to eliminate species interference by separating compounds before detection. The primary application of spectrophotometry is in quantitative analysis, where the absorbance of chromophores is determined to measure concentrations. Fluorescence Fluorescence is a phenomenon in which a substance absorbs photons (typically from ultraviolet or visible light) and then re-emits those photons at longer wavelengths, usually in the visible or near-infrared range. It is a form of luminescence and occurs when electrons in a molecule or atom are excited to a higher energy state by absorbing photons and then return to their ground state, releasing energy in the form of fluorescent light.  Quantitative Analysis: Fluorescence spectroscopy is a powerful analytical technique for quantitative analysis. The intensity of the emitted fluorescence is directly proportional to the concentration of the fluorescent species. This property is used to determine the concentration of a Properties specific analyte in a sample. Selectivity: Fluorescence can be highly selective of because the emission occurs at specific wavelengths characteristic of the fluorescent molecule. By choosing appropriate excitation and Fluorescen emission wavelengths, researchers can selectively analyze target compounds in complex mixtures. ce Sensitivity: Fluorescence detection is highly sensitive. It can detect even trace amounts of fluorescent substances due to the high signal-to- noise ratio associated with fluorescence emission.  Biomedical Imaging: Fluorescence Labeling: Fluorescence imaging Fluorescent labels or tags can techniques like fluorescence be attached to molecules of microscopy and fluorescence interest (e.g., antibodies, tomography are used for nucleic acids) for tracking and studying biological tissues, visualization. This is widely diagnosing diseases, and used in molecular biology and visualizing cellular processes. cell biology techniques such as For example, fluorescent dyes fluorescence in situ can be used to visualize specific hybridization (FISH) and structures or proteins within immunofluorescence. cells or tissues.  Phosphorescence Phosphorescence is a luminescent phenomenon similar to fluorescence but with some key differences. In both fluorescence and phosphorescence, a substance absorbs photons and then re- emits them at longer wavelengths. However, in fluorescence, the emission is almost instantaneous and occurs as soon as the excitation source is removed. In contrast, phosphorescence involves a delayed emission of photons after the excitation source is removed. This delayed emission is typically longer-lived, lasting from milliseconds to hours or even longer.  Characteristics Delayed Emission: Phosphorescence is characterized by a longer- lived excited state of electrons in a molecule or atom. This delayed emission makes it distinct from fluorescence. Triplet State: Phosphorescence usually involves transitions between electronic energy levels in which electrons occupy the triplet state, which has lower probability of occurring spontaneously compared to the singlet state involved in fluorescence.  Infrared Spectroscopy (IR) spectroscopy is a widely used analytical technique that involves the interaction of infrared radiation with matter to study the vibrational and rotational modes of molecule It is based on the principle that molecules absorb infrared radiation at specific frequencies, which are characteristic of their chemical structure and functional groups  The remaining radiation is transmitted through the Principle: When infrared sample. The absorption radiation with a range of occurs because the energy frequencies is passed of the incoming photons through a sample, some of matches the energy required the radiation is absorbed by to excite the vibrational or the sample. rotational modes of chemical bonds in the molecules.  Molecular Vibrations: Molecules consist of atoms connected by IR spectroscopy primarily focuses chemical bonds, and these bonds on molecular vibrations, which are can vibrate and stretch in various divided into two main categories: ways. Stretching Vibrations: These involve changes in bond lengths, such as stretching or compressing the bonds. Stretching vibrations occur at higher frequencies. Bending Vibrations: These involve changes in bond angles, causing the molecule to bend or flex. Bending vibrations occur at lower frequencies.  Functional Groups: Different types of chemical bonds and functional groups in a molecule exhibit characteristic absorption frequencies in the infrared spectrum. Analyzing these absorption bands allows chemists to identify the presence of specific functional groups, such as carbonyl (C=O), hydroxyl (O-H), amino (N-H), and more.  Spectra: The output of an IR spectrometer is called an IR spectrum. It is a plot of the sample's absorption (or transmittance) as a function of frequency or wavelength. The resulting spectrum displays peaks at specific frequencies, each corresponding to a vibrational or rotational mode. Nuclear Magnetic Resonance (NMR) Nuclear Magnetic Resonance (NMR) spectroscopy is a powerful analytical technique used to study the nuclear properties of certain atoms, particularly hydrogen (protons) and carbon-13 nuclei, in molecules Principle of NMR Spectroscopy: NMR spectroscopy is based on the principle that certain nuclei, such as hydrogen (¹H) and carbon-13 (¹³C), have intrinsic nuclear magnetic moments. When placed in a strong external magnetic field, these nuclei align themselves with the magnetic field. When exposed to radiofrequency (RF) radiation at a specific resonant frequency, the nuclei can absorb energy and undergo a transition from a lower-energy spin state to a higher-energy spin state.  The NMR spectrum is generated by measuring the emitted RF radiation when the excited nuclei return to their lower-energy state. This emitted radiation is detected and used to create a spectrum that provides information about the chemical environment and local structural properties of the nuclei in the sample. Applications of NMR Structure Elucidation: NMR spectroscopy is widely used to determine the structure of organic and inorganic compounds. It provides information about the connectivity of atoms, bond angles, and dihedral angles within molecules. ¹H NMR and ¹³C NMR spectra are commonly used for this purpose. Chemical Composition: NMR spectroscopy can quantify the relative abundances of different nuclei in a sample, helping to determine the chemical composition of a mixture.  Protein and Biomolecule Analysis: Protein NMR is a powerful technique for studying the three-dimensional structures, folding pathways, and dynamics of proteins and other biomolecules. It is crucial in structural biology and drug discovery. Materials Science: NMR spectroscopy is used to study the properties of materials, including polymers, catalysts, and porous materials. It can provide information about composition, structure, and surface properties. Sample Spectra of NMR Electron Paramagnetic Resonance(EPR) Spectroscopy Electron Paramagnetic Resonance (EPR) spectroscopy, also known as Electron Spin Resonance (ESR) spectroscopy, is a powerful analytical technique used to study materials with unpaired electrons, such as free radicals, transition metal complexes, and certain defect centers in solids.  Principle of EPR Spectroscopy: EPR spectroscopy is based on the same fundamental principle as nuclear magnetic resonance (NMR) spectroscopy but focuses on the magnetic properties of unpaired electrons. Unpaired electrons possess a magnetic moment or spin, which interacts with an external magnetic field. When exposed to a microwave radiation source, the energy level of the electrons changes, causing them to undergo transitions between different spin states. Applications Study of Free Radicals Characterization of Transition Metal Complexes Detection of Paramagnetic Species Quality Control and Authentication Refractive Index Refractive index, often denoted as "n," is a fundamental optical property of a substance that describes how light propagates through that material. It quantifies the speed of light in the material relative to its speed in a vacuum. The refractive index is a dimensionless number and is typically symbolized as "n.“ Refractometers are used in the determination of refractive index Refraction Refraction is an optical phenomenon that occurs when light waves change direction as they pass from one transparent medium into another. This change in direction is due to the difference in the speed of light between the two materials. Molar Refraction Molar refraction, also known as the molar refractivity or simply refractivity, is a physical property that quantifies the ability of a substance to refract (bend) light as it passes through it. It is a measure of how the speed of light changes as it travels through a substance. Molar refraction is typically expressed in units of cubic centimeters per mole (cm³/mol). Optical Rotation Electromagnetic radiation comprises two separate, sinusoidal-like wave motions that are perpendicular to one another, an electric wave and a magnetic wave  A source will produce multiple waves of oscillating electromagnetic radiation at any given time, so that multiple electric and magnetic waves are emitted. Passing light through a polarizing prism such as a Nicol prism sorts the randomly distributed vibrations of electric radiation so that only those vibrations occurring in a single plane are passed  Optical rotation, also known as optical activity, is a phenomenon in optics and chemistry that describes the rotation of the plane of polarized light as it passes through certain optically active substances. These substances are chiral Optical Rotation Optical rotation, also known as optical activity, is the phenomenon in which the plane of polarized light rotates when it passes through an optically active substance (chiral compound). Optical rotation is typically measured in degrees (°) and is denoted by the symbol α (alpha). It represents the observed rotation of the plane of polarized light as it passes through a sample of the chiral compound. Specific Rotation Specific rotation is a quantitative measure of the optical rotation exhibited by a chiral substance. It provides a standardized value that is characteristic of the substance. Specific rotation is a mathematical constant associated with a particular chiral compound. It is used to identify and characterize the compound's optical activity. Specific rotation is expressed in degrees per unit length (typically decimeters, dm) per unit concentration (typically grams per milliliter, g/mL). The symbol for specific rotation is also α (alpha).  Standardization: Specific rotation is standardized with respect to path length and concentration. It allows for direct comparisons of optical activity between different samples of the same compound. Summary of Instrumental Methods Method Principle Qualitative Quantitative UV-Vis Absorption of Yes, by Yes, by utilizing Spectrophotome UV or Visible matching Beer-Lambert’s try Light absorption Law and a across Standard Curve wavelengths or Molecular Extinction Coefficient Fluorescence Absorption of Yes Yes, the radiant energy strength of the AND EMISSION fluorescence is OF ENERGY IN A proportional to DIFFERENT the WAVELENGTH concentration Phosphorescenc Similar to Yes Yes e fluorescence, but delayed emission of light Summary of Instrumental Methods Method Principle Qualitative Quantitative Infrared Absorption of IR Yes, used to No Spectroscopy leads to detect (FTIR) movement/excit functional ation of bonds groups Nuclear Placing the Yes, used to No Magnetic compound onto elucidate Resonance a magnetized structures of field and being compounds hit with radio frequency (RF) causes movement of the molecule Electron Similar to NMR Yes No Paramagnetic but focuses Resonance more on unpaired electrons Method Principle Qualitative? Quantitative? Yes, can Measures the measure bending Yes, can identify concentrations (refraction) of substances Refractive Index or purity of a light as it based on their substance passes through refractive index based on a substance refractive index Optical Rotation Measures the Yes, can identify Yes, the degree rotation of chiral molecules of rotation is polarized light or enantiomers proportional to by optically based on the active rotation concentration substances direction and specific rotation Mass Ionizes chemical Yes, used to Yes, by Spectroscopy compounds and identify analyzing ion measures the compounds intensity to mass-to-charge based on their determine the