Molecular geometry

Molecular geometry

Overview
Molecular geometry or molecular structure is the three-dimension
Dimension
In physics and mathematics, the dimension of a space or object is informally defined as the minimum number of coordinates needed to specify any point within it. Thus a line has a dimension of one because only one coordinate is needed to specify a point on it...

al arrangement of the atoms that constitute a molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

. It determines several properties of a substance including its reactivity, polarity
Chemical polarity
In chemistry, polarity refers to a separation of electric charge leading to a molecule or its chemical groups having an electric dipole or multipole moment. Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds. Molecular polarity is dependent on the difference in...

, phase of matter
Phase (matter)
In the physical sciences, a phase is a region of space , throughout which all physical properties of a material are essentially uniform. Examples of physical properties include density, index of refraction, and chemical composition...

, color
Color
Color or colour is the visual perceptual property corresponding in humans to the categories called red, green, blue and others. Color derives from the spectrum of light interacting in the eye with the spectral sensitivities of the light receptors...

, magnetism
Magnetism
Magnetism is a property of materials that respond at an atomic or subatomic level to an applied magnetic field. Ferromagnetism is the strongest and most familiar type of magnetism. It is responsible for the behavior of permanent magnets, which produce their own persistent magnetic fields, as well...

, and biological activity
Biological activity
In pharmacology, biological activity or pharmacological activity describes the beneficial or adverse effects of a drug on living matter. When a drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other...

.

The molecular geometry can be determined by various spectroscopic methods
Spectroscopy
Spectroscopy is the study of the interaction between matter and radiated energy. Historically, spectroscopy originated through the study of visible light dispersed according to its wavelength, e.g., by a prism. Later the concept was expanded greatly to comprise any interaction with radiative...

 and diffraction
Diffraction
Diffraction refers to various phenomena which occur when a wave encounters an obstacle. Italian scientist Francesco Maria Grimaldi coined the word "diffraction" and was the first to record accurate observations of the phenomenon in 1665...

 methods. IR
Infrared spectroscopy
Infrared spectroscopy is the spectroscopy that deals with the infrared region of the electromagnetic spectrum, that is light with a longer wavelength and lower frequency than visible light. It covers a range of techniques, mostly based on absorption spectroscopy. As with all spectroscopic...

, microwave
Rotational spectroscopy
Rotational spectroscopy or microwave spectroscopy studies the absorption and emission of electromagnetic radiation by molecules associated with a corresponding change in the rotational quantum number of the molecule...

 and Raman spectroscopy
Raman spectroscopy
Raman spectroscopy is a spectroscopic technique used to study vibrational, rotational, and other low-frequency modes in a system.It relies on inelastic scattering, or Raman scattering, of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range...

 can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques.
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Encyclopedia
Molecular geometry or molecular structure is the three-dimension
Dimension
In physics and mathematics, the dimension of a space or object is informally defined as the minimum number of coordinates needed to specify any point within it. Thus a line has a dimension of one because only one coordinate is needed to specify a point on it...

al arrangement of the atoms that constitute a molecule
Molecule
A molecule is an electrically neutral group of at least two atoms held together by covalent chemical bonds. Molecules are distinguished from ions by their electrical charge...

. It determines several properties of a substance including its reactivity, polarity
Chemical polarity
In chemistry, polarity refers to a separation of electric charge leading to a molecule or its chemical groups having an electric dipole or multipole moment. Polar molecules interact through dipole–dipole intermolecular forces and hydrogen bonds. Molecular polarity is dependent on the difference in...

, phase of matter
Phase (matter)
In the physical sciences, a phase is a region of space , throughout which all physical properties of a material are essentially uniform. Examples of physical properties include density, index of refraction, and chemical composition...

, color
Color
Color or colour is the visual perceptual property corresponding in humans to the categories called red, green, blue and others. Color derives from the spectrum of light interacting in the eye with the spectral sensitivities of the light receptors...

, magnetism
Magnetism
Magnetism is a property of materials that respond at an atomic or subatomic level to an applied magnetic field. Ferromagnetism is the strongest and most familiar type of magnetism. It is responsible for the behavior of permanent magnets, which produce their own persistent magnetic fields, as well...

, and biological activity
Biological activity
In pharmacology, biological activity or pharmacological activity describes the beneficial or adverse effects of a drug on living matter. When a drug is a complex chemical mixture, this activity is exerted by the substance's active ingredient or pharmacophore but can be modified by the other...

.

Molecular geometry determination


The molecular geometry can be determined by various spectroscopic methods
Spectroscopy
Spectroscopy is the study of the interaction between matter and radiated energy. Historically, spectroscopy originated through the study of visible light dispersed according to its wavelength, e.g., by a prism. Later the concept was expanded greatly to comprise any interaction with radiative...

 and diffraction
Diffraction
Diffraction refers to various phenomena which occur when a wave encounters an obstacle. Italian scientist Francesco Maria Grimaldi coined the word "diffraction" and was the first to record accurate observations of the phenomenon in 1665...

 methods. IR
Infrared spectroscopy
Infrared spectroscopy is the spectroscopy that deals with the infrared region of the electromagnetic spectrum, that is light with a longer wavelength and lower frequency than visible light. It covers a range of techniques, mostly based on absorption spectroscopy. As with all spectroscopic...

, microwave
Rotational spectroscopy
Rotational spectroscopy or microwave spectroscopy studies the absorption and emission of electromagnetic radiation by molecules associated with a corresponding change in the rotational quantum number of the molecule...

 and Raman spectroscopy
Raman spectroscopy
Raman spectroscopy is a spectroscopic technique used to study vibrational, rotational, and other low-frequency modes in a system.It relies on inelastic scattering, or Raman scattering, of monochromatic light, usually from a laser in the visible, near infrared, or near ultraviolet range...

 can give information about the molecule geometry from the details of the vibrational and rotational absorbance detected by these techniques. X-ray crystallography
X-ray crystallography
X-ray crystallography is a method of determining the arrangement of atoms within a crystal, in which a beam of X-rays strikes a crystal and causes the beam of light to spread into many specific directions. From the angles and intensities of these diffracted beams, a crystallographer can produce a...

, neutron diffraction
Neutron diffraction
Neutron diffraction or elastic neutron scattering is the application of neutron scattering to the determination of the atomic and/or magnetic structure of a material: A sample to be examined is placed in a beam of thermal or cold neutrons to obtain a diffraction pattern that provides information of...

 and electron diffraction
Electron diffraction
Electron diffraction refers to the wave nature of electrons. However, from a technical or practical point of view, it may be regarded as a technique used to study matter by firing electrons at a sample and observing the resulting interference pattern...

 can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density. Gas electron diffraction
Gas electron diffraction
Gas electron diffraction is one of the applications of electron diffraction techniques. The target of this method is the determination of the structure of gaseous molecules i.e...

 can be used for small molecules in the gas phase. NMR
NMR
NMR may refer to:Applications of Nuclear Magnetic Resonance:* Nuclear magnetic resonance* NMR spectroscopy* Solid-state nuclear magnetic resonance* Protein nuclear magnetic resonance spectroscopy* Proton NMR* Carbon-13 NMR...

 and FRET methods can be used to determine complementary information including relative distances,

dihedral angles,
angles, and connectivity. Molecular geometries are best determined at low temperature because at higher temperatures the molecular structure is averaged over more accessible geometries (see next section). Larger molecules often exist in multiple stable geometries (conformational isomerism
Conformational isomerism
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted exclusively by rotations about formally single bonds...

) that are close in energy on the potential energy surface
Potential energy surface
A potential energy surface is generally used within the adiabatic or Born–Oppenheimer approximation in quantum mechanics and statistical mechanics to model chemical reactions and interactions in simple chemical and physical systems...

. Geometries can also be computed by ab initio quantum chemistry methods
Ab initio quantum chemistry methods
Ab initio quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term ab initiowas first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excited states of benzene.The background is described by Parr...

 to high accuracy. The molecular geometry can be different as a solid, in solution, and as a gas.

The position of each atom is determined by the nature of the chemical bond
Chemical bond
A chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...

s by which it is connected to its neighboring atoms. The molecular geometry can be described by the positions of these atoms in space, evoking bond length
Bond length
- Explanation :Bond length is related to bond order, when more electrons participate in bond formation the bond will get shorter. Bond length is also inversely related to bond strength and the bond dissociation energy, as a stronger bond will be shorter...

s of two joined atoms, bond angles of three connected atoms, and torsion angles (dihedral angles) of three consecutive bonds.

The influence of thermal excitation


Since the motions of the atoms in a molecule are determined by quantum mechanics, one
must define “motion” in a quantum mechanical way. The overall (external) quantum mechanical motions translation and rotation hardly change the geometry of the molecule. (To some extent rotation influences
the geometry via Coriolis forces and centrifugal distortion
Rotational spectroscopy
Rotational spectroscopy or microwave spectroscopy studies the absorption and emission of electromagnetic radiation by molecules associated with a corresponding change in the rotational quantum number of the molecule...

, but this is negligible for the present discussion.)
A third type of motion is vibration, which is the internal motion of the atoms in a molecule. The molecular vibrations are harmonic (at least to good approximation), which means that the atoms oscillate about their equilibrium, even at the absolute zero of temperature. At absolute zero all atoms are in their vibrational ground state and show zero point quantum mechanical motion, that is, the wavefunction of a single vibrational mode is not a sharp peak, but an exponential of finite width. At higher temperatures the vibrational modes may be thermally excited (in a classical interpretation one expresses this by stating that “the molecules will vibrate faster”), but they oscillate still around the recognizable geometry of the molecule.

To get a feeling for the probability that the vibration of molecule may be thermally excited,
we inspect the Boltzmann factor
Boltzmann distribution
In chemistry, physics, and mathematics, the Boltzmann distribution is a certain distribution function or probability measure for the distribution of the states of a system. It underpins the concept of the canonical ensemble, providing its underlying distribution...

 ,
where is the excitation energy of the vibrational mode, the Boltzmann constant and the absolute temperature. At 298K (25 °C), typical values for the Boltzmann factor are:
0.089 for ΔE = 500 cm−1 ; ΔE = 0.008 for 1000 cm−1 ; 7 10−4 for ΔE = 1500 cm−1. That is, if the excitation energy is 500 cm−1, then about 9 percent of the
molecules are thermally excited at room temperature. The lowest excitation vibrational energy in water is the bending mode (about 1600 cm−1). Thus, at room temperature less than 0.07 percent of all the molecules of a given amount of water will vibrate faster than at absolute zero.

As stated above, rotation hardly influences the molecular geometry. But, as a quantum mechanical motion, it is thermally excited at relatively (as compared to vibration) low temperatures. From a classical point of view it can be stated that more molecules rotate faster at higher temperatures,
i.e., they have larger angular velocity
Angular velocity
In physics, the angular velocity is a vector quantity which specifies the angular speed of an object and the axis about which the object is rotating. The SI unit of angular velocity is radians per second, although it may be measured in other units such as degrees per second, revolutions per...

 and angular momentum
Angular momentum
In physics, angular momentum, moment of momentum, or rotational momentum is a conserved vector quantity that can be used to describe the overall state of a physical system...

. In quantum mechanically language: more eigenstates of higher angular momentum become thermally populated with rising temperatures. Typical rotational excitation energies are on the order of a few cm−1.

The results of many spectroscopic experiments are broadened because they involve an averaging over rotational states. It is often difficult to extract geometries from spectra at high temperatures, because the number of rotational states probed in the experimental averaging increases with increasing temperature. Thus, many spectroscopic observations can only be expected to yield reliable molecular geometries at temperatures close to absolute zero, because at higher temperatures too many higher rotational states are thermally populated.

Bonding


Molecules, by definition, are most often held together with covalent bond
Covalent bond
A covalent bond is a form of chemical bonding that is characterized by the sharing of pairs of electrons between atoms. The stable balance of attractive and repulsive forces between atoms when they share electrons is known as covalent bonding....

s involving single, double, and/or triple bonds, where a "bond" is a shared pair of electrons (the other method of bonding between atoms is called ionic bonding and involves a positive cation
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

 and a negative anion
Ion
An ion is an atom or molecule in which the total number of electrons is not equal to the total number of protons, giving it a net positive or negative electrical charge. The name was given by physicist Michael Faraday for the substances that allow a current to pass between electrodes in a...

).

Molecular geometries can be specified in terms of bond lengths, bond angles and torsional angles. The bond length is defined to be the average distance between the centers of two atoms bonded together in any given molecule. A bond angle is the angle formed between three atoms across at least two bonds. For four atoms bonded together in a chain, the torsional angle
Dihedral angle
In geometry, a dihedral or torsion angle is the angle between two planes.The dihedral angle of two planes can be seen by looking at the planes "edge on", i.e., along their line of intersection...

 is the angle between the plane formed by the first three atoms and the plane formed by the last three atoms.

There exists a mathematical relationship among the bond angles for one central atom and four peripheral atoms (labeled 1 through 4) expressed by the following determinant. This constraint removes one degree of freedom from the choices of (originally) six free bond angles to leave only five choices of bond angles. (Note that the angles , , , and are always zero.)


Molecular geometry is determined by the quantum mechanical
Quantum mechanics
Quantum mechanics, also known as quantum physics or quantum theory, is a branch of physics providing a mathematical description of much of the dual particle-like and wave-like behavior and interactions of energy and matter. It departs from classical mechanics primarily at the atomic and subatomic...

 behavior of the electrons. Using the valence bond approximation
Valence bond theory
In chemistry, valence bond theory is one of two basic theories, along with molecular orbital theory, that were developed to use the methods of quantum mechanics to explain chemical bonding. It focuses on how the atomic orbitals of the dissociated atoms combine to give individual chemical bonds...

 this can be understood by the type of bonds between the atoms that make up the molecule. When atoms interact to form a chemical bond
Chemical bond
A chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...

, the atomic orbitals are said to mix in a process called orbital hybridisation
Orbital hybridisation
In chemistry, hybridisation is the concept of mixing atomic orbitals to form new hybrid orbitals suitable for the qualitative description of atomic bonding properties. Hybridised orbitals are very useful in the explanation of the shape of molecular orbitals for molecules. It is an integral part...

. The two most common types of bonds are Sigma bond
Sigma bond
In chemistry, sigma bonds are the strongest type of covalent chemical bond. They are formed by head-on overlapping between atomic orbitals. Sigma bonding is most clearly defined for diatomic molecules using the language and tools of symmetry groups. In this formal approach, a σ-bond is...

s and Pi bond
Pi bond
In chemistry, pi bonds are covalent chemical bonds where two lobes of one involved atomic orbital overlap two lobes of the other involved atomic orbital...

s. The geometry can also be understood by molecular orbital theory
Molecular orbital theory
In chemistry, molecular orbital theory is a method for determining molecular structure in which electrons are not assigned to individual bonds between atoms, but are treated as moving under the influence of the nuclei in the whole molecule...

 where the electrons are delocalised.

An understanding of the wavelike behavior of electrons in atoms and molecules is the subject of quantum chemistry
Quantum chemistry
Quantum chemistry is a branch of chemistry whose primary focus is the application of quantum mechanics in physical models and experiments of chemical systems...

.

Isomers


Isomer
Isomer
In chemistry, isomers are compounds with the same molecular formula but different structural formulas. Isomers do not necessarily share similar properties, unless they also have the same functional groups. There are many different classes of isomers, like stereoisomers, enantiomers, geometrical...

s are types of molecules that share a chemical formula but have different geometries, resulting in very different properties:
  • A pure substance is composed of only one type of isomer of a molecule (all have the same geometrical structure).

  • Structural isomers
    Structural isomerism
    Structural isomerism, or constitutional isomerism , is a form of isomerism in which molecules with the same molecular formula have bonded together in different orders, as opposed to stereoisomerism. There are multiple synonyms for constitutional isomers.Three categories of constitutional isomers...

     have the same chemical formula but different physical arrangements, often forming alternate molecular geometries with very different properties. The atoms are not bonded (connected) together in the same orders.
    • Functional isomers are special kinds of structural isomers, where certain groups of atoms exhibit a special kind of behavior, such as an ether or an alcohol.

  • Stereoisomers may have many similar physicochemical properties (melting point, boiling point) and at the same time very different biochemical
    Biochemistry
    Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...

     activities. This is because they exhibit a handedness
    Handedness
    Handedness is a human attribute defined by unequal distribution of fine motor skills between the left and right hands. An individual who is more dexterous with the right hand is called right-handed and one who is more skilled with the left is said to be left-handed...

     that is commonly found in living systems. One manifestation of this chirality
    Chirality (chemistry)
    A chiral molecule is a type of molecule that lacks an internal plane of symmetry and thus has a non-superimposable mirror image. The feature that is most often the cause of chirality in molecules is the presence of an asymmetric carbon atom....

     or handedness is that they have the ability to rotate polarized light in different directions.

  • Protein folding
    Protein folding
    Protein folding is the process by which a protein structure assumes its functional shape or conformation. It is the physical process by which a polypeptide folds into its characteristic and functional three-dimensional structure from random coil....

     concerns the complex geometries and different isomers that protein
    Protein
    Proteins are biochemical compounds consisting of one or more polypeptides typically folded into a globular or fibrous form, facilitating a biological function. A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds between the carboxyl and amino groups of...

    s can take.

Types of molecular structure

Main article: VSEPR theory


There are six basic shape types for molecules
  • Linear: In a linear model, atoms are connected in a straight line. The bond angles are set at 180°. A bond angle is very simply the geometric angle between two adjacent bonds. For example, carbon dioxide and nitric oxide
    Nitric oxide
    Nitric oxide, also known as nitrogen monoxide, is a diatomic molecule with chemical formula NO. It is a free radical and is an important intermediate in the chemical industry...

     have a linear molecular shape.
  • Trigonal planar: Just from its name, it can easily be said that molecules with the trigonal planar
    Trigonal planar
    In chemistry, trigonal planar is a molecular geometry model with one atom at the center and three atoms at the corners of a triangle, called peripheral atoms, all in one plane. In an ideal trigonal planar species, all three ligands are identical and all bond angles are 120°. Such species belong to...

     shape are somewhat triangular and in one plane (meaning a flat surface). Consequently, the bond angles are set at 120°. An example of this is boron trifluoride
    Boron trifluoride
    Boron trifluoride is the chemical compound with the formula BF3. This pungent colourless toxic gas forms white fumes in moist air. It is a useful Lewis acid and a versatile building block for other boron compounds.-Structure and bonding:...

    .
  • Bent: Bent or angular molecules have a non-linear shape. A good example is water, or H2O, which has an angle of about 105o A water molecule has two pairs of bonded electrons and two unshared lone pairs.
  • Tetrahedral: Tetra- signifies four, and -hedral relates to a surface, so tetrahedral almost literally means "four surfaces." This is when there are four bonds all on one central atom, with no extra unshared electron
    Electron
    The electron is a subatomic particle with a negative elementary electric charge. It has no known components or substructure; in other words, it is generally thought to be an elementary particle. An electron has a mass that is approximately 1/1836 that of the proton...

     pairs. In accordance with the VSEPR (valence-shell electron pair repulsion theory), the bond angles between the electron bonds are arccos(−1/3) = 109.47°. An example of a tetrahedral molecule is methane
    Methane
    Methane is a chemical compound with the chemical formula . It is the simplest alkane, the principal component of natural gas, and probably the most abundant organic compound on earth. The relative abundance of methane makes it an attractive fuel...

     (CH4).
  • Octahedral: Octa- signifies eight, and -hedral relates to a surface, so octahedral almost literally means "eight surfaces." The bond angle is 90 degrees. An example of an octahedral
    Octahedral molecular geometry
    In chemistry, octahedral molecular geometry describes the shape of compounds where in six atoms or groups of atoms or ligands are symmetrically arranged around a central atom, defining the vertices of an octahedron...

     molecule is sulfur hexafluoride
    Sulfur hexafluoride
    Sulfur hexafluoride is an inorganic, colorless, odorless, and non-flammable greenhouse gas. has an octahedral geometry, consisting of six fluorine atoms attached to a central sulfur atom. It is a hypervalent molecule. Typical for a nonpolar gas, it is poorly soluble in water but soluble in...

     (SF6).
  • Pyramidal: Pyramidal-shaped molecules have pyramid-like shapes
    Pyramid (geometry)
    In geometry, a pyramid is a polyhedron formed by connecting a polygonal base and a point, called the apex. Each base edge and apex form a triangle. It is a conic solid with polygonal base....

    . Unlike the linear
    Linear
    In mathematics, a linear map or function f is a function which satisfies the following two properties:* Additivity : f = f + f...

     and trigonal planar
    Trigonal planar
    In chemistry, trigonal planar is a molecular geometry model with one atom at the center and three atoms at the corners of a triangle, called peripheral atoms, all in one plane. In an ideal trigonal planar species, all three ligands are identical and all bond angles are 120°. Such species belong to...

     shapes but similar to the tetrahedral orientation, pyramidal shapes requires three dimensions in order to fully separate the electrons. Here, there are only three pairs of bonded electrons, leaving one unshared lone pair. Lone pair - bond pair repulsions change the angle from the tetrahedral angle to a slightly lower value. An example is NH3 (ammonia
    Ammonia
    Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...

    ).


VSEPR table


The bond angles in the table below are ideal angles from the simple VSEPR theory, followed by the actual angle for the example given in the following column where this differs. For many cases, such as trigonal pyramidal and bent, the actual angle for the example differs from the ideal angle, but all examples differ by different amounts. For example, the angle in H2S (92°) differs from the tetrahedral angle by much more than the angle for H2O (104.5°) does.
Bonding electron pairs Lone pairs Electron domains (Steric #) Shape Ideal bond angle (example's bond angle) Example Image
2
0
2
linear
180°
CO2
Carbon dioxide
Carbon dioxide is a naturally occurring chemical compound composed of two oxygen atoms covalently bonded to a single carbon atom...

3
0
3
trigonal planar
120°
BF3
Boron trifluoride
Boron trifluoride is the chemical compound with the formula BF3. This pungent colourless toxic gas forms white fumes in moist air. It is a useful Lewis acid and a versatile building block for other boron compounds.-Structure and bonding:...

2
1
3
bent
120° (119°)
SO2
Sulfur dioxide
Sulfur dioxide is the chemical compound with the formula . It is released by volcanoes and in various industrial processes. Since coal and petroleum often contain sulfur compounds, their combustion generates sulfur dioxide unless the sulfur compounds are removed before burning the fuel...

4
0
4
tetrahedral
109.5°
CH4
Methane
Methane is a chemical compound with the chemical formula . It is the simplest alkane, the principal component of natural gas, and probably the most abundant organic compound on earth. The relative abundance of methane makes it an attractive fuel...

3
1
4
trigonal pyramidal
107.5°
NH3
Ammonia
Ammonia is a compound of nitrogen and hydrogen with the formula . It is a colourless gas with a characteristic pungent odour. Ammonia contributes significantly to the nutritional needs of terrestrial organisms by serving as a precursor to food and fertilizers. Ammonia, either directly or...

2
2
4
angular
104.5°
H2O
H2O
H2O is the chemical formula for water and is also used as an abbreviation for the word "water". H2O or H2O It may also refer to:* H2O , a punk band**H2O , their self-titled debut album...

5
0
5
trigonal bipyramidal
90°, 120°, 180°
PCl5
4
1
5
seesaw
180°, 120°, 90° (173.1°, 101.6°)
SF4
Sulfur tetrafluoride
Sulfur tetrafluoride is the chemical compound with the formula SF4. This species exists as a gas at standard conditions. It is a corrosive species that releases dangerous HF upon exposure to water or moisture...

3
2
5
T-shaped
90°, 180° (87.5°, < 180°)
ClF3
Chlorine trifluoride
Chlorine trifluoride is an interhalogen compound with the formula ClF3. This colourless, poisonous, corrosive and very reactive gas condenses to a pale-greenish yellow liquid, the form in which it is most often sold...

2
3
5
linear
180°
XeF2
Xenon difluoride
Xenon difluoride is a powerful fluorinating agent with the chemical formula , and one of the most stable xenon compounds. Like most covalent inorganic fluorides it is moisture sensitive. It decomposes on contact with light or water vapour. Xenon difluoride is a dense, white crystalline solid. It...

6
0
6
octahedral
90°, 180°
SF6
Sulfur hexafluoride
Sulfur hexafluoride is an inorganic, colorless, odorless, and non-flammable greenhouse gas. has an octahedral geometry, consisting of six fluorine atoms attached to a central sulfur atom. It is a hypervalent molecule. Typical for a nonpolar gas, it is poorly soluble in water but soluble in...

5
1
6
square pyramidal
90° (84.8°), 180°
BrF5
Bromine pentafluoride
Bromine pentafluoride, BrF5, is an interhalogen compound and a fluoride of bromine. It is a strong fluorination reagent.It melts at −61.30 °C and boils at 40.25 °C. BrF5 finds use in oxygen isotope analysis. Laser ablation of solid silicates in the presence of bromine pentafluoride releases O2 for...

4
2
6
square planar
90° 180°
XeF4
Xenon tetrafluoride
Xenon tetrafluoride is a chemical compound with chemical formula . It was the first discovered binary compound of a noble gas. It is produced by the chemical reaction of xenon with fluorine, , according to the chemical equation:...

7
0
7
pentagonal bipyramidal
90°, 72°
IF7
Iodine heptafluoride
Iodine heptafluoride, also known as iodine fluoride or even iodine fluoride, is an interhalogen compound with chemical formula IF7. It has an unusual pentagonal bipyramidal structure, as predicted by VSEPR theory...


3D Representations

  • Line or stick - atomic nuclei are not represented, just the bonds as sticks or lines. As in 2D molecular structures of this type, atoms are implied at each vertex.


:{| class=wikitable
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  • Electron density plot - shows the electron density determined either crystallographically
    Crystallography
    Crystallography is the experimental science of the arrangement of atoms in solids. The word "crystallography" derives from the Greek words crystallon = cold drop / frozen drop, with its meaning extending to all solids with some degree of transparency, and grapho = write.Before the development of...

     or using quantum mechanics
    Quantum mechanics
    Quantum mechanics, also known as quantum physics or quantum theory, is a branch of physics providing a mathematical description of much of the dual particle-like and wave-like behavior and interactions of energy and matter. It departs from classical mechanics primarily at the atomic and subatomic...

     rather than distinct atoms or bonds
    |-
    |

    |

    |

    |}>
    • Ball and stick - atomic nuclei are represented by spheres (balls) and the bonds as sticks

    :{| class=wikitable
    |-
    |

    |

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    |}
    • Spacefilling models or CPK models (also an atomic coloring scheme
      CPK coloring
      In chemistry, the CPK coloring is a popular color convention for distinguishing atoms of different chemical elements in molecular models. The scheme is named after the CPK molecular models designed by chemists Robert Corey and Linus Pauling, and improved by Walter Koltun.-History:In 1952, Corey...

       in representations) - the molecule is represented by overlapping spheres representing the atoms


    :{| class=wikitable
    |-
    |

    |

    |

    |

    |}
    • Cartoon - a representation used for proteins where loops, beta sheets, alpha helices are represented diagrammatically and no atoms or bonds are represented explicitly just the protein backbone as a smooth pipe

    |-
    |

    |

    |
    |

    |}>
    The more the amount of lone pairs contained in a molecule the smaller the angles between the atoms of that molecule. The Valence Shell Electron-Pair Repulsion theory VSEPR predicts that lone pairs repel each other thus pushing the different atoms away from them.

    See also

    • VSEPR theory
      VSEPR theory
      Valence shell electron pair repulsion theory is a model in chemistry used to predict the shape of individual molecules based upon the extent of electron-pair electrostatic repulsion. It is also named Gillespie–Nyholm theory after its two main developers...

    • Molecular graphics
      Molecular graphics
      Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device"...

    • Molecular modelling
      Molecular modelling
      Molecular modelling encompasses all theoretical methods and computational techniques used to model or mimic the behaviour of molecules. The techniques are used in the fields of computational chemistry, computational biology and materials science for studying molecular systems ranging from small...

    • Molecular mechanics
      Molecular mechanics
      Molecular mechanics uses Newtonian mechanics to model molecular systems. The potential energy of all systems in molecular mechanics is calculated using force fields...

    • Molecule editor
      Molecule editor
      A molecule editor is a computer program for creating and modifying representations of chemical structures.Molecule editors can manipulate chemical structure representations in either two- or three-dimensions. Two-Dimensional editors generate output used as illustrations or for querying chemical...

    • Molecular design software
      Molecular Design software
      Molecular design software is software for molecular modeling, that provides special support for developing molecular models de novo.In contrast to the usual molecular modeling programs such as the molecular dynamics and quantum chemistry programs, such software directly supports the aspects related...

    • Quantum chemistry
      Quantum chemistry
      Quantum chemistry is a branch of chemistry whose primary focus is the application of quantum mechanics in physical models and experiments of chemical systems...


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