Movatterモバイル変換

[0]ホーム

Jump to content

Molecular geometry

Edit links

From Wikipedia, the free encyclopedia

Study of the 3D shapes of molecules

Geometry of thewater molecule with values for O-H bond length and for H-O-H bond angle between two bonds

Molecular geometry is thethree-dimensional arrangement of theatoms that constitute amolecule. It includes the general shape of the molecule as well asbond lengths,bond angles,torsional angles and any other geometrical parameters that determine the position of each atom.

Molecular geometry influences several properties of a substance including itsreactivity,polarity,phase of matter,color,magnetism andbiological activity.^[1]^[2]^[3] The angles between bonds that an atom forms depend only weakly on the rest of a molecule, i.e. they can be understood as approximately local and hencetransferable properties.

Determination

[edit]

The molecular geometry can be determined by variousspectroscopic methods anddiffraction methods.IR,microwave andRaman 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 andelectron diffraction can give molecular structure for crystalline solids based on the distance between nuclei and concentration of electron density.Gas electron diffraction can be used for small molecules in the gas phase.NMR andFRET methods can be used to determine complementary information including relative distances,^[4]^[5]^[6]dihedral angles,^[7]^[8]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) that are close in energy on thepotential energy surface. Geometries can also be computed byab initio quantum chemistry methods to high accuracy. The molecular geometry can be different as a solid, in solution, and as a gas.^{[citation needed]}

The position of each atom is determined by the nature of thechemical bonds by which it is connected to its neighboring atoms. The molecular geometry can be described by the positions of these atoms in space, evokingbond lengths of two joined atoms, bond angles of three connected atoms, andtorsion angles (dihedral angles) of threeconsecutive bonds.^{[citation needed]}

Influence of thermal excitation

[edit]

Since the motions of the atoms in a molecule are determined by quantum mechanics, "motion" must be defined 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 viaCoriolis forces andcentrifugal distortion, but this is negligible for the present discussion.) In addition to translation and rotation, a third type of motion ismolecular vibration, which corresponds to internal motions of the atoms such as bond stretching and bond angle variation. The molecular vibrations areharmonic (at least to good approximation), and the atoms oscillate about their equilibrium positions, even at the absolute zero of temperature. At absolute zero all atoms are in their vibrational ground state and showzero point quantum mechanical motion, so that the wavefunction of a single vibrational mode is not a sharp peak, but approximately aGaussian function (the wavefunction forn = 0 depicted in the article on thequantum harmonic oscillator). 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.^{[citation needed]}

To get a feeling for the probability that the vibration of molecule may be thermally excited,we inspect theBoltzmann factorβ ≡ exp(−⁠ΔE/kT⁠), where ΔE is the excitation energy of the vibrational mode,k theBoltzmann constant andT the absolute temperature. At 298 K (25 °C), typical values for the Boltzmann factor β are:^{[citation needed]}

β = 0.089 for ΔE =500 cm⁻¹
β = 0.008 for ΔE = 1000 cm⁻¹
β = 0.0007 for ΔE = 1500 cm⁻¹.

(Thereciprocal centimeter is an energy unit that is commonly used ininfrared spectroscopy; 1 cm⁻¹ corresponds to1.23984×10⁻⁴ 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.^{[citation needed]}

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 higherangular velocity andangular momentum. In quantum mechanical language: more eigenstates of higher angular momentum becomethermally 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.^{[citation needed]}

Bonding

[edit]

Molecules, by definition, are most often held together withcovalent bonds involving single, double, and/or triple bonds, where a "bond" is ashared pair of electrons (the other method of bonding between atoms is calledionic bonding and involves a positivecation and a negativeanion).^{[citation needed]}

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, thetorsional angle is the angle between the plane formed by the first three atoms and the plane formed by the last three atoms.^{[citation needed]}

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. (The anglesθ₁₁,θ₂₂,θ₃₃, andθ₄₄ are always zero and that this relationship can be modified for a different number of peripheral atoms by expanding/contracting the square matrix.)^{[citation needed]}

$0={\begin{vmatrix}\cos \theta _{11}&\cos \theta _{12}&\cos \theta _{13}&\cos \theta _{14}\\\cos \theta _{21}&\cos \theta _{22}&\cos \theta _{23}&\cos \theta _{24}\\\cos \theta _{31}&\cos \theta _{32}&\cos \theta _{33}&\cos \theta _{34}\\\cos \theta _{41}&\cos \theta _{42}&\cos \theta _{43}&\cos \theta _{44}\end{vmatrix}}$

Molecular geometry is determined by thequantum mechanical behavior of the electrons. Using thevalence bond approximation this can be understood by the type of bonds between the atoms that make up the molecule. When atoms interact to form achemical bond, the atomic orbitals of each atom are said to combine in a process calledorbital hybridisation. The two most common types of bonds aresigma bonds (usually formed by hybrid orbitals) andpi bonds (formed by unhybridized p orbitals for atoms ofmain group elements). The geometry can also be understood bymolecular orbital theory where the electrons are delocalised.^{[citation needed]}

An understanding of the wavelike behavior of electrons in atoms and molecules is the subject ofquantum chemistry.^{[citation needed]}

Isomers

[edit]

Isomers are types of molecules that share a chemical formula but have difference geometries, resulting in different properties:

Apure substance is composed of only one type of isomer of a molecule (all have the same geometrical structure).^{[citation needed]}
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.^{[citation needed]}
- 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 differentbiochemical activities. This is because they exhibit ahandedness that is commonly found in living systems. One manifestation of thischirality or handedness is that they have the ability to rotate polarized light in different directions.^{[citation needed]}
Protein folding concerns the complex geometries and different isomers thatproteins can take.^{[citation needed]}

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 andnitric oxide have a linear molecular shape.^{[citation needed]}
Trigonal planar: Molecules with the trigonal planar shape are somewhat triangular and in oneplane (flat). Consequently, the bond angles are set at 120°. For example,boron trifluoride.^{[citation needed]}
Angular: Angular molecules (also calledbent orV-shaped) 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.^{[citation needed]}
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 arefour bonds all on one central atom, with no extra unsharedelectron pairs. In accordance with theVSEPR (valence-shell electron pair repulsion theory), the bond angles between the electron bonds arearccos(−⁠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.^{[citation needed]}
Trigonal pyramidal: A trigonal pyramidal molecule has apyramid-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).

VSEPR table

[edit]

Main article:VSEPR theory § AXE method

The bond angles in the table below are ideal angles from the simpleVSEPR theory (pronounced "Vesper Theory")^{[citation needed]}, 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, and examples differ by different amounts. For example, the angle inH₂S (92°) differs from the tetrahedral angle by much more than the angle forH₂O (104.48°) does.

Atoms bonded to central atom	Lone pairs	Electron domains (Steric number)	Shape	Ideal bond angle (example's bond angle)	Example
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° (106.8°)^[10]	NH₃
2	2	4	bent	109.5° (104.48°)^[11]^[12]	H₂O
5	0	5	trigonal bipyramidal	90°, 120°	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°	XeOF−5
5	2	7	pentagonal planar	72°, 144°	XeF−5
8	0	8	square antiprismatic		XeF2−8
9	0	9	tricapped trigonal prismatic		ReH2−9

The greater the number of lone pairs contained in a molecule, the smaller the angles between the atoms of that molecule. TheVSEPR theory predicts that lone pairs repel each other, thus pushing the different atoms away from them.

3D representations

[edit]

Line orstick – 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.

Electron density plot – shows the electron density determined eithercrystallographically or usingquantum mechanics rather than distinct atoms or bonds.

Ball and stick – atomic nuclei are represented by spheres (balls) and the bonds as sticks.

Spacefilling models orCPK models (also anatomic coloring scheme in representations) – the molecule is represented by overlapping spheres representing the atoms.

Cartoon – a representation used for proteins where loops, beta sheets, and alpha helices are represented diagrammatically and no atoms or bonds are explicitly represented (e.g. the protein backbone is represented as a smooth pipe).

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 (11): 111104.Bibcode:2015JChPh.143k1104C.doi:10.1063/1.4931483.PMID 26395679.
^FRET description Archived 2008-09-18 at theWayback 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
^obtaining dihedral angles from³J coupling constants
^Another Javascript-like NMR coupling constant to dihedral Archived 2005-12-28 at theWayback Machine
^Miessler G.L. and Tarr D.A.Inorganic Chemistry (2nd ed., Prentice-Hall 1999), pp.57-58
^Haynes, William M., ed. (2013).CRC Handbook of Chemistry and Physics (94th ed.).CRC Press. pp. 9–26.ISBN 9781466571143.
^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):1–8.Bibcode:1979JMoSp..74....1H.doi:10.1016/0022-2852(79)90019-5.
^"CCCBDB Experimental bond angles page 2". Archived fromthe original on 2014-09-03. Retrieved2014-08-27.

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
VSEPR theory Coordination number
Coordination number 2	Linear Bent
Coordination number 3	Trigonal planar Trigonal pyramidal T-shaped
Coordination number 4	Tetrahedral Seesaw Square planar
Coordination number 5	Trigonal bipyramidal Square pyramidal Pentagonal planar
Coordination number 6	Octahedral Trigonal prismatic Pentagonal pyramidal
Coordination number 7	Pentagonal bipyramidal Capped octahedral Capped trigonal prismatic
Coordination number 8	Square antiprismatic Dodecahedral Bicapped trigonal prismatic Cubic
Coordination number 9	Tricapped trigonal prismatic Capped square antiprismatic
Category

v t e Branches ofchemistry
Glossary of chemical formulae List of biomolecules List of inorganic compounds Periodic table
Analytical	Calorimetry Characterization Chromatography GC HPLC Crystallography Electroanalytical methods Elemental analysis Instrumental chemistry Mass spectrometry EI ICP MALDI Separation process Spectroscopy IR Raman UV-Vis NMR Titration Wet chemistry
Theoretical	Computational chemistry Mathematical chemistry Molecular modelling Molecular mechanics Molecular dynamics Molecular geometry VSEPR theory Quantum chemistry
Physical	Chemical kinetics Chemical physics Molecular physics Chemical thermodynamics Cryochemistry Electrochemistry Spectroelectrochemistry Photoelectrochemistry Equilibrium chemistry Femtochemistry Interface and colloid science Micromeritics Mechanochemistry Microwave chemistry Photochemistry Sonochemistry Spectroscopy Spin chemistry Structural chemistry Surface science Thermochemistry
Inorganic	Ceramic chemistry Cluster chemistry Coordination chemistry Magnetochemistry Organometallic chemistry Organolanthanide chemistry Solid-state chemistry
Organic	Dynamic covalent chemistry Enantioselective synthesis Fullerene chemistry Organic reactions Organic synthesis Petrochemistry Physical organic chemistry Polymer chemistry Retrosynthetic analysis Stereochemistry Alkane stereochemistry Total synthesis /Semisynthesis
Biological	Biochemistry Molecular biology Cell biology Bioinorganic chemistry Bioorganic chemistry Bioorganometallic chemistry Biophysical chemistry Chemical biology Bioorthogonal chemistry Clinical chemistry Medicinal chemistry Pharmacology Neurochemistry
Interdisciplinarity	Nuclear chemistry Radiochemistry Radiation chemistry Actinide chemistry Cosmochemistry /Astrochemistry /Stellar chemistry Geochemistry Biogeochemistry Photogeochemistry Environmental chemistry Atmospheric chemistry Ocean chemistry Clay chemistry Carbochemistry Food chemistry Carbohydrate chemistry Food physical chemistry Agricultural chemistry Soil chemistry Chemistry education Amateur chemistry General chemistry Clandestine chemistry Forensic chemistry Forensic toxicology Post-mortem chemistry Nanochemistry Supramolecular chemistry Chemical synthesis Green chemistry Click chemistry Combinatorial chemistry Biosynthesis Chemical engineering Stoichiometry Materials science Metallurgy Ceramic engineering Polymer science
See also	History of chemistry Nobel Prize in Chemistry Timeline of chemistry of element discoveries "The central science" Chemical reaction Catalysis Chemical element Chemical compound Atom Molecule Ion Chemical substance Chemical bond Alchemy Quantum mechanics
Category Commons Portal WikiProject