Aggregations of Atoms: Giving Matter Properties

in work

some parts are explorative and need to be checked

Currently (May 2021) a loose collection of topics, how atoms arrange to form matter. Mainly topics relevant for other part of this page are discussed. The topics are sketchy and incomplete. Long-term goal: Description how atomic elements arrange to form inorganic or organic matter.

Content

• Content
• Summary
  • Summary Principles
  • Summary Changes in Intermolecular Binding Patterns
• Principles
  • Nuclear-Physical Topics
  • Chemical Topics
  • Physical Topics
• Intermolecular Bindings give Matter Structure and State
  • States of Matter
  • Units for States of Matter
  • Binding Patterns
• Changes in intermolecular Bindings
  • Condensation and Evaporation
  • Efflorescence and Deliquescence
• References
  • References Efflorescence and Deliquescence
• History and Relation of Biology, Chemistry and Physics

Summary

Summary Principles

Atoms are specified by their atomic core which consists of protons and neutrons. Changing of atomic cores is a topic of nuclear physics. In chemistry atomic cores and so the number of protons and neutrons is constant. The charged protons determine the possible electron configurations which in turn determine the chemical properties of an atom. Under normal conditions atoms have a stable electron configuration. Stable electron configuration usually follow the octet rule [of thumb]: 8 electrons on the outermost electron shell. The electron configuration can change by:

• taking up electrons or giving electrons away => charged particles =: ions
• sharing electrons => atoms coupled together by electron bonds =: molecules

Molecules, ions and inert elements are called generalized molecules. These and tiny particles built from them interact through intermolecular forces. These intermolecular forces determine how matter arranged and what properties it has:

• Intermolecular forces inducing fixed positions give raise to solid bodies with a fixed shaped.
• Intermolecular forces with constant distances give raise to fluids.
• In absence of intermolecular forces matter is gaseous.

Within a substance different intermolecular forces can act, especially when the substance consists of different materials. The intermolecular forces depend on the setting: temperature and all the substances present.

Summary Changes in Intermolecular Binding Patterns

Changes in the temperature or the mixture of substances influence the intermolecular forces, which can result in state transitions:

• solid <=> liquid (freezing <= and melting =>)
• liquid <=> gaseous (condensation <= and evaporation =>)
• solid <=> gaseous (sublime =>)

Particles which can absorb water are called hygroscopic. These can growth or shrink in humid respectively in dry air.

Evaporation can lead to over saturation of a solution and cause the organic or inorganic materials to crystallize. This process is called efflorescence and is reverse to deliquescence. Deliquescence is when particles absorb water and become solute therein.

Principles

Nuclear-Physical Topics

Atomic Core

An atomic core consists of protons and neutrons.

• The combination of protons and neutrons determines how stable the atomic core is. Unstable atomic cores decay and emit radiation (radioactive decay).
• The charged protons determine the interactions with the electrons.

Chemical Topics

Atom

An atomic core surrounded by electrons.

The number of electrons associated with an atom varies. In neutral charge it matches the number of protons. The atomic cores however can neither be broken nor be transformed through chemical reactions (by definition of chemical reactions). The number of protons determines how the forces on the electrons and thus the electron configurations. The possible electron configuration in turn determine how atoms react, which is the core of chemistry. Atoms with a specified proton number thus are called chemical elements:

Chemical Element

An atom of a specified proton number or a aggregation of such atoms.

Chemical elements are grouped into metallic and non-metallic. The metallic usually release electrons to achieve a stable electron configuration and the non-metallic usually take or share electrons.

Chemical Reaction

A chemical reaction is when atoms change their electron configuration.

• Electrons can move between atoms => Change of charge = Ionization
• Electrons can be shared between specific atoms => Molecules

Two or more atoms which are bound together by sharing electrons in an electron bond are called molecule:

Molecule

Atoms bound together through electron bonds.

Physical Topics

Atoms achieve locally stable electron configuration by chemical reactions. The resulting chemical products then are the units which to form matter.

Generalized Molecule

Physical Unit

A particle with a constant electron configuration is denoted as generalized molecule or physical unit.

The idea is that a generalized molecule is a constant for physical transformations such as solute, state transition, crystallization and can only be changed by chemical reactions.

• Regarding classical mechanics and thermodynamics a generalized molecule is the unit of motion.
• Molecules can only be changed trough chemical reactions but not through physical processes (except)

Examples of generalized molecules:

• Chemical molecules such as H2O, CH4 or proteins when atoms achieved a stable electron configuration by sharing elements.
• The inert elements such as helium (He) or argon (Ar) which already have a complete outer electron shell.
• Ions with a complete outer electron shell e.g. the units of salt which are Na+ and Cl-. They can be arrange fixed forming a salt crystal or be dissolved in water where each Na+ and Cl- is surrounded by water dipoles such that opposite charges match.

Generalized molecules interact through intermolecular forces.

Intermolecular Forces

Intermolecular forces are between generalized molecules. Intermolecular forces are due to electric forces between positive and negative part of molecules.

Generalized molecules can be charged in two ways:

• Statically charged particles:
  • Dipoles => Dipole force (H-Bridge in the case of dipoles involving H)
  • Ions => Ion binding
  • Dipoles and Ions => Dipole Forces
• Dynamically charged particles
  • Mainly large molecules (generalized molecules but the induced forces at naturally occurring temperatures are only relevant for large molecules). => Van der Waals Forces

Intermolecular Bindings give Matter Structure and State

in work and incomplete and partly explorative

States of Matter

Solid = stable in shape

Liquid = changeable shape but constant volume

Gas = changeable shape and upon pressure the volume changes

Units for States of Matter

What is solid, liquid or gaseous can vary depending on the task of interest. Examples:

• Millet, salt or sugar can measured - using the changeable shape - in measure jug or a spoon and thus behave fluid like for this task. Although solid at small scale, when considered at large scale the small particles are free to move respect to each other giving them a liquid behavior for the measuring quantities used for cooking. To measure very small amounts (in the order of a single grain) however, the behavior becomes that of a solid: the single grains have a constant shape and are indivisible. Similarly for sieves, it depends on the how fine grained the sieve is whether substances flow through as liquids or are hold back as solids.
• Water between 0 and 100 degrees behaves fluid. However if zooming down to recognize single molecules, ‘fluid’ water is a collection of tiny ‘sort of ice’ particles which move freely respect to each other.
• An aerosol behaves like a gas mixture. However the particles, which are ‘dissolved’ in the air, are not gaseous at the microscopic level but fluid (tiny water droplets in the air) or solid (e.g. dust, soot particles).

=> For macroscopic states, the interactions of microscopic particles are important and not the microscopic structure of the particles.

State Defining Units

State defining units or just state-units are particles whose interacting patters determine the state of matter.

• The smallest state defining units are generalized molecules which determine the microscopic structure of matter.
• The matter of interest should consists of many units such that the behavior of the unit particles behave stochastically for the task of interest.

Binding Patterns

Bindings inducing Constant Positions

The units cannot move respect to each other without breaking the bindings. -> Solid matter

Examples: Salts (ion bindings), Ice (hydrogen bonds)

Bindings inducing Constant Distances

The units move freely but at constant distance respect to each other. -> Liquid

Example:

• Generalized molecules interact through intramolecular forces (which are minimized at a certain distance). The average distance between molecules is constant but the molecules move freely with respect to each other.

No Bindings

The units fly around freely and only interact upon collision. => Gas

Examples: Air (mixture of different generalized molecules flying around. The molecules are N2, O2, H2O, CO2, …)

Changes in intermolecular Bindings

Condensation and Evaporation

Evaporation

The process when molecules from a liquid escape the intramolecular binding to move into the gaseous phase.

Condensation

The process when particles move from gaseous to liquid.

Condeva Equilibrium of a Particle

The condeva equilibrium is the state where the rates of evaporation and condensation are equal for particles consisting of specific substances.

The condeva equilibrium is used on this page only. There may exist a concept like this under a different name in literature.

At the condeva equilibrium the particles stay constant in size. For a given substance there is specific relative humidity at which particles of the substance are in the condeva equilibrium:

Condeva Humidity of a Particle

The condeva humidity for a particle of a given substance is the humidity (can be given relative or absolute) at which the particles of the substance are in the condeva equilibrium.

• The condeva humidity of particle depends on its substances and their arrangement.
• By definition the condensation and evaporation rates are equal at the condeva humidity thus the particles neither growth nor shrink.
• If the droplets consist of pure water, the condeva humidity is a relative humidity of 100% which is called the critical point. If the relative humidity is above 100% the water condensates and near instant a relative humidity of 100% is reached => pure water particles either are evaporating or they are the critical point = condeva equilibrium of pure water.

Efflorescence and Deliquescence

Efflorescence

Efflorescence (derived from fluorspar/fluorite which is the salt calcium fluoride) is the process dissolved matter falls out and crystallizes.

Usually efflorescence happens because of evaporation of water out of a solution but other mechanism to remove water are possible to such as other substances which absorb water.

Example: When enough water evaporates from a sodium chloride (common salt) solution, the sodium chloride crystallizes into many tiny crystals which all reflect light (white color).

Efflorescent Humidity

The efflorescent humidity-point for a homogenous solution is the humidity at which the solute crystallizes due to evaporation of water.

Notes:

• The efflorescent humidity depends on the solution e.g. proteins, salts and fatty acids in a solution are determinants of its efflorescent humidity.
• For a solution containing different solutes not all solutes may crystallize at the same humidity. Thus the efflorescent point is cannot be given as a single humidity value for the entire solution.
• For respiratory tract fluids it is about 30 to 40%.

  The efflorescent humidity is likely lower for upper respiratory tract fluids than for LRT fluids since URT fluids are more hydrophilic [to confirm and cite]. Guess: about 40% for LRT fluids and about 30% for URT fluids.

Deliquescence

Deliquescence (= de ‘down’ + liquescere ‘become liquid’) is the process when solid matter goes into solution.

1. Deliquescence for salts is usually due to absorption of water.
2. Deliquescence is opposite to efflorescence for the adsorption of water.
3. For organic substance decay can yield deliquescence.
4. Ice-blocks in the sea become deliquescent upon melting.

In chemistry deliquescence usually only is used in the sense of 2. but not for 3. and 4..

Deliquescence Humidity

The deliquescence humidity is the humidity at which a substance absorbs enough water such that it dissolves in the water.

The deliquescence humidity is always greater equal than the efflorescence humidity. Usually much greater except if there are ‘contact crystals’. Contact crystals can serve as a starting ground for crystals to build i.e. they seed crystal formation. Seeding crystals cause the efflorescence humidity to increase, even close to the deliquescence is possible. Typical values are 40% for the efflorescence humidity and 80% for the deliquescence humidity. With seeding crystals the efflorescence humidity can increase close to 80%. These behavior is shown and described in Fig. 3 in the work of Davis et al.

Seed Crystal

A crystal which acts as nucleolus for crystallization.

References

References Efflorescence and Deliquescence

Summary Davis

Contact efflorescence as a pathway for crystallization of atmospherically relevant particles Ryan D. Davis, Sara Lance, Joshua A. Gordon, Shuichi B. Ushijima, Margaret A. Tolbert Proceedings of the National Academy of Sciences Dec 2015, 112 (52) 15815-15820; https://doi.org/10.1073/pnas.1522860113

in work

Appendix

History and Relation of Biology, Chemistry and Physics

Historically biology, chemistry and physics evolved as separate scientific disciplines with the tasks:

• Biology: Observing and describing living organisms.
• Chemistry: the successor of alchemy (the transmutation of metals from greek al=the and khēmia=transmuting metals). Chemistry is about transmuting and disassembling substances.
• Physics: Movements and forces on solid objects. Early handed down descriptions and experiments were done by Archimedes and Galileo. Newton mathematically described the observed planetary motions as the movement of objects rotating around the sun subject to gravity. From that point on physics dealt with distance forces influencing the acceleration of objects. This approach turned out to describe many phenomena in nature.

Concepts from physics (movements of particles, behavior of waves, forces and related concepts) can be used to model/explain nearly every phenomena observed. The underlying mechanism of chemical reactions are explained by the behavior of the outer electron shells of atoms which in turn can be described by quantum mechanics. Mostly these underlying mechanisms can be abstracted away however and chemistry describes how atoms react with each other. Molecular biology in turn is the chemistry of molecules only occurring in the context of life forms. The building block of life can be described by molecular biology. Life forms, which are complex constructs huge numbers of these building blocks, show phenomena that are often best described by abstracting away the building blocks. So physics, chemistry and biology describe different parts of nature.

Physical, chemical and biological are used here as follows:

• Physics

  Physics is about the behavior of particles and bodies and how they interact with each other to change their movements and states. The behavior of particle systems (many particles which interact) is often easier/only doable by considering the entity and not single particles.

• Chemistry

  Chemistry describes reactions of substances. Chemical reaction = changes in the electron arrangement of the outer electron shells.

• Biology

  • Classical Biology studies life-forms including their relations, their behavior and habitats.
  • Molecular biology is essentially the chemistry occurring in the context of life forms: Reactions and participating substances occurring only in the context of life forms on earth e.g. complex organic molecules and their reactions.