Contents 1 Determination 2 The influence of thermal excitation 3 Bonding 4 Isomers 5 Types of molecular structure 5.1
6 3D representations 7 See also 8 References 9 External links Determination[edit]
The molecular geometry can be determined by various spectroscopic
methods and diffraction methods. IR, microwave and Raman spectroscopy
can give information about the molecule geometry from the details of
the vibrational and rotational absorbance detected by these
techniques. X-ray crystallography, neutron diffraction and electron
diffraction can give molecular structure for crystalline solids based
on the distance between nuclei and concentration of electron density.
β ≡ exp ( − Δ E k T ) displaystyle beta equiv exp left(- frac Delta E kT right) , where Δ E displaystyle Delta E is the excitation energy of the vibrational mode, k displaystyle k the
T displaystyle T the absolute temperature. At 298 K (25 °C), typical values for the Boltzmann factor β are: β = 0.089 for ΔE = 500 cm−1 ; β = 0.008 for ΔE = 1000 cm−1 ; β = 7×10−4 for ΔE = 1500 cm−1. (The reciprocal centimeter is an energy unit that is commonly used in infrared spectroscopy; 1 cm−1 corresponds to 1.23984×10−4 eV). When an excitation energy is 500 cm−1, then about 8.9 percent of the molecules are thermally excited at room temperature. To put this in perspective: 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 at higher temperatures more molecules will rotate faster, which implies that they have higher angular velocity and angular momentum. In quantum mechanical 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[edit] Molecules, by definition, are most often held together with covalent bonds 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 and a negative anion). 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 nuclei 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 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 θ 11 displaystyle theta _ 11 , θ 22 displaystyle theta _ 22 , θ 33 displaystyle theta _ 33 , and θ 44 displaystyle theta _ 44 are always zero and that this relationship can be modified for a different number of peripheral atoms by expanding/contracting the square matrix.) 0 =
cos θ 11 cos θ 12 cos θ 13 cos θ 14 cos θ 21 cos θ 22 cos θ 23 cos θ 24 cos θ 31 cos θ 32 cos θ 33 cos θ 34 cos θ 41 cos θ 42 cos θ 43 cos θ 44
displaystyle 0= begin vmatrix cos theta _ 11 &cos theta _ 12 &cos theta _ 13 &cos theta _ 14 \cos theta _ 21 &cos theta _ 22 &cos theta _ 23 &cos theta _ 24 \cos theta _ 31 &cos theta _ 32 &cos theta _ 33 &cos theta _ 34 \cos theta _ 41 &cos theta _ 42 &cos theta _ 43 &cos theta _ 44 end vmatrix
A pure substance is composed of only one type of isomer of a molecule (all have the same geometrical structure). Structural 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 activities. This is because they exhibit a handedness that
is commonly found in living systems. One manifestation of this
chirality or handedness is that they have the ability to rotate
polarized light in different directions.
Types of molecular structure[edit] A bond angle is the geometric angle between two adjacent bonds. Some common shapes of simple molecules include: Linear: In a linear model, atoms are connected in a straight line. The bond angles are set at 180°. For example, carbon dioxide and nitric oxide have a linear molecular shape. Trigonal planar: Molecules with the trigonal planar shape are somewhat triangular and in one plane (flat). Consequently, the bond angles are set at 120°. For example, boron trifluoride. Bent: Bent or angular molecules have a non-linear shape. For example, water (H2O), which has an angle of about 105°. A water molecule has two pairs of bonded electrons and two unshared lone pairs. Tetrahedral: Tetra- signifies four, and -hedral relates to a face of a solid, so "tetrahedral" literally means "having four faces". This shape is found when there are four bonds all on one central atom, with no extra unshared electron 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°. For example, methane (CH4) is a tetrahedral molecule. Octahedral: Octa- signifies eight, and -hedral relates to a face of a solid, so "octahedral" means "having eight faces". The bond angle is 90 degrees. For example, sulfur hexafluoride (SF6) is an octahedral molecule. Trigonal pyramidal: A trigonal pyramidal molecule has a pyramid-like shape with a triangular base. Unlike the linear and trigonal planar shapes but similar to the tetrahedral orientation, pyramidal shapes require 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 bond angle from the tetrahedral angle to a slightly lower value.[9] For example, ammonia (NH3).
Atoms bonded to
central atom
Lone pairs
2 0 2 linear 180° CO2 3 0 3 trigonal planar 120° BF3 2 1 3 bent 120° (119°) SO2 4 0 4 tetrahedral 109.5° CH4 3 1 4 trigonal pyramidal 109.5 (107.8°) NH3 2 2 4 bent 109.5° (104.48°)[10][11] H2O 5 0 5 trigonal bipyramidal 90°, 120°, 180° PCl5 4 1 5 seesaw ax–ax 180° (173.1°), eq–eq 120° (101.6°), ax–eq 90° SF4 3 2 5 T-shaped 90° (87.5°), 180° (175°) ClF3 2 3 5 linear 180° XeF2 6 0 6 octahedral 90°, 180° SF6 5 1 6 square pyramidal 90° (84.8°) BrF5 4 2 6 square planar 90°, 180° XeF4 7 0 7 pentagonal bipyramidal 90°, 72°, 180° IF7 6 1 7 pentagonal pyramidal 72°, 90°, 144° XeOF5− 5 2 7 planar pentagonal 72°, 144° XeF5− 8 0 8 square antiprismatic XeF82− 9 0 9 tricapped trigonal prismatic ReH92− 3D representations[edit] 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.
Ball and stick – atomic nuclei are represented by spheres (balls) and the bonds as sticks. Spacefilling models or CPK models (also an atomic coloring scheme in representations) – the molecule is represented by overlapping spheres representing the atoms. 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 greater the amount of lone pairs contained in a molecule the smaller the angles between the atoms of that molecule. The VSEPR theory predicts that lone pairs repel each other, thus pushing the different atoms away from them. See also[edit] Wikimedia Commons has media related to Molecular geometry. Jemmis mno rules
Molecular design software
Molecular graphics
Molecular mechanics
Molecular modelling
References[edit] ^ McMurry, John E. (1992), Organic Chemistry (3rd ed.), Belmont: Wadsworth, ISBN 0-534-16218-5 ^ Cotton, F. Albert; Wilkinson, Geoffrey; Murillo, Carlos A.; Bochmann, Manfred (1999), Advanced Inorganic Chemistry (6th ed.), New York: Wiley-Interscience, ISBN 0-471-19957-5 ^ Alexandros Chremos; Jack F. Douglas (2015). "When does a branched polymer become a particle?". J. Chem. Phys. 143: 111104. Bibcode:2015JChPh.143k1104C. doi:10.1063/1.4931483. ^ FRET description Archived 2008-09-18 at the Wayback Machine. ^ Hillisch, A; Lorenz, M; Diekmann, S (2001). "Recent advances in FRET: distance determination in protein–DNA complexes". Current Opinion in Structural Biology. 11 (2): 201–207. doi:10.1016/S0959-440X(00)00190-1. PMID 11297928. ^ FRET imaging introduction Archived 2008-10-14 at the Wayback Machine. ^ obtaining dihedral angles from 3J coupling constants Archived 2008-12-07 at the Wayback Machine. ^ Another Javascript-like NMR coupling constant to dihedral Archived 2005-12-28 at the Wayback Machine. ^ Miessler G.L. and Tarr D.A. Inorganic Chemistry (2nd ed., Prentice-Hall 1999), pp.57-58 ^ Hoy, AR; Bunker, PR (1979). "A precise solution of the rotation bending Schrödinger equation for a triatomic molecule with application to the water molecule". Journal of Molecular Spectroscopy. 74: 1–8. Bibcode:1979JMoSp..74....1H. doi:10.1016/0022-2852(79)90019-5. ^ "Archived copy". Archived from the original on 2014-09-03. Retrieved 2014-08-27. External links[edit] Molecular Geometry & Polarity Tutorial 3D visualization of molecules to determine polarity. Molecular Geometry using Crystals 3D structure visualization of molecules using Crystallography. v t e Molecular geometry Coordination number 2 Linear Bent Coordination number 3 Trigonal planar Trigonal pyramidal T-shaped Coordination number 4 Tetrahedral Square planar Seesaw Coordination number 5 Trigonal bipyramidal Square pyramidal Pentagonal planar Coordination number 6 Octahedral Trigonal prismatic Pentagonal pyramidal Distorted octahedral Coordination number 7 Pentagonal bipyramidal Coordination number 8 Square antiprismatic Coordination number 9 Tricapped trigonal prismatic Capped square antiprismatic Authority control GND: 41703 |