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Molecular geometry
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{{Use American English|date = March 2019}} {{Short description|Study of the 3D shapes of molecules}} [[Image:Water molecule dimensions.svg|thumb|200px|Geometry of the [[water (molecule)|water molecule]] with values for O-H bond length and for H-O-H bond angle between two bonds]] '''Molecular geometry''' is the [[three-dimensional space|three-dimensional]] arrangement of the [[atom]]s that constitute a [[molecule]]. It includes the general shape of the molecule as well as [[bond length]]s, '''bond angles''', [[torsional angle]]s and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its [[Reactivity (chemistry)|reactivity]], [[Chemical polarity|polarity]], [[Phase (matter)|phase of matter]], [[color]], [[magnetism]] and [[biological activity]].<ref>{{McMurray}}</ref><ref>{{Cotton&Wilkinson6th}}</ref><ref name="article0">{{cite journal|author1=Alexandros Chremos|author2=Jack F. Douglas|title=When does a branched polymer become a particle?|date=2015|journal=J. Chem. Phys.|volume=143|issue=11|pages=111104|doi=10.1063/1.4931483|bibcode=2015JChPh.143k1104C|pmid=26395679|doi-access=free}}</ref> 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 hence [[Transferability (chemistry)|transferable properties]]. == Determination == The molecular geometry can be determined by various [[spectroscopy|spectroscopic methods]] and [[diffraction]] methods. [[Infrared spectroscopy|IR]], [[Rotational spectroscopy|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. [[Gas electron diffraction]] can be used for small molecules in the gas phase. [[nuclear magnetic resonance|NMR]] and [[Förster resonance energy transfer|FRET]] methods can be used to determine complementary information including relative distances,<!-- References for NMR and FRET distances --><ref>[http://dwb.unl.edu/Teacher/NSF/C08/C08Links/pps99.cryst.bbk.ac.uk/projects/gmocz/fret.htm FRET description] {{webarchive|url=https://web.archive.org/web/20080918072755/http://dwb.unl.edu/Teacher/NSF/C08/C08Links/pps99.cryst.bbk.ac.uk/projects/gmocz/fret.htm |date=2008-09-18 }}</ref><ref>{{ cite journal| last1=Hillisch| doi=10.1016/S0959-440X(00)00190-1| first1=A| last2=Lorenz| first2=M| last3=Diekmann| first3=S |title=Recent advances in FRET: distance determination in protein–DNA complexes| pmid=11297928 | journal=Current Opinion in Structural Biology| year=2001| volume=11|issue=2 | pages=201–207}}</ref><ref>{{usurped|1=[https://web.archive.org/web/20081014211053/http://www.fretimaging.org/mcnamaraintro.html FRET imaging introduction]}}</ref> <!-- End References for NMR and FRET distances -->dihedral angles,<!-- References for NMR determination of dihedral angles (through <sup>3</sup>J coupling constants) --><ref>{{usurped|1=[https://web.archive.org/web/20081207031318/http://www.jonathanpmiller.com/Karplus.html obtaining dihedral angles from <sup>3</sup>J coupling constants]}}</ref><ref>[http://www.spectroscopynow.com/FCKeditor/UserFiles/File/specNOW/HTML%20files/General_Karplus_Calculator.htm Another Javascript-like NMR coupling constant to dihedral] {{webarchive|url=https://web.archive.org/web/20051228092336/http://www.spectroscopynow.com/FCKeditor/UserFiles/File/specNOW/HTML%20files/General_Karplus_Calculator.htm |date=2005-12-28 }}</ref> <!-- End references for NMR determination of dihedral angles (through <sup>3</sup>J coupling constants) --> 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 the [[potential energy surface]]. Geometries can also be computed by [[ab initio quantum chemistry methods]] 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]]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]]s of two joined atoms, bond angles of three connected atoms, and [[Torsion of a curve|torsion angles]] ([[dihedral angle]]s) of three [[path graph|consecutive]] bonds. == Influence of thermal excitation == 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 via [[Coriolis force]]s and [[rotational spectroscopy|centrifugal distortion]], but this is negligible for the present discussion.) In addition to translation and rotation, a third type of motion is [[molecular vibration]], which corresponds to internal motions of the atoms such as bond stretching and bond angle variation. The molecular vibrations are [[Quantum harmonic oscillator|harmonic]] (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 show [[Zero point energy|zero point quantum mechanical motion]], so that the wavefunction of a single vibrational mode is not a sharp peak, but approximately a [[Gaussian function]] (the wavefunction for ''n'' = 0 depicted in the article on the [[quantum 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. To get a feeling for the probability that the vibration of molecule may be thermally excited, we inspect the [[Boltzmann distribution|Boltzmann factor]] {{nowrap|''β'' ≡ exp(−{{sfrac|Δ''E''|''kT''}})}}, where Δ''E'' is the excitation energy of the vibrational mode, ''k'' the [[Boltzmann constant]] and ''T'' the absolute temperature. At 298 K (25 °C), typical values for the Boltzmann factor β are: * ''β'' = 0.089{{0}} for Δ''E'' = {{0}}500 cm<sup>−1</sup> * ''β'' = 0.008{{0}} for Δ''E'' = 1000 cm<sup>−1</sup> * ''β'' = 0.0007 for Δ''E'' = 1500 cm<sup>−1</sup>. (The [[Reciprocal length#Measure of energy|reciprocal centimeter]] is an energy unit that is commonly used in [[infrared spectroscopy]]; 1 cm<sup>−1</sup> corresponds to {{val|1.23984e-4|u=eV}}). When an excitation energy is 500 cm<sup>−1</sup>, 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<sup>−1</sup>). 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 [[Boltzmann distribution|thermally populated]] with rising temperatures. Typical rotational excitation energies are on the order of a few cm<sup>−1</sup>. 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]]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]] 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 [[Dihedral angle|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. (The angles ''θ''<sub>11</sub>, ''θ''<sub>22</sub>, ''θ''<sub>33</sub>, and ''θ''<sub>44</sub> are always zero and that this relationship can be modified for a different number of peripheral atoms by expanding/contracting the square matrix.) <math display="block">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}</math> Molecular geometry is determined by the [[quantum mechanics|quantum mechanical]] behavior of the electrons. Using the [[valence bond theory|valence bond approximation]] 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]], the atomic orbitals of each atom are said to combine in a process called [[orbital hybridisation]]. The two most common types of bonds are [[sigma bond]]s (usually formed by hybrid orbitals) and [[pi bond]]s (formed by unhybridized p orbitals for atoms of [[main group element]]s). The geometry can also be understood by [[molecular orbital theory]] where the electrons are delocalised. An understanding of the wavelike behavior of electrons in atoms and molecules is the subject of [[quantum chemistry]]. == Isomers == [[Isomer]]s are types of molecules that share a chemical formula but have difference geometries, resulting in different properties: * A '''pure''' substance is composed of only one type of isomer of a molecule (all have the same geometrical structure). * [[Structural isomerism|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 isomer]]s are special kinds of structural isomers, where certain groups of atoms exhibit a special kind of behavior, such as an ether or an alcohol. * [[Stereoisomer]]s may have many similar physicochemical properties (melting point, boiling point) and at the same time very different [[biochemistry|biochemical]] activities. This is because they exhibit a [[handedness]] that is commonly found in living systems. One manifestation of this [[Chirality (chemistry)|chirality]] or handedness is that they have the ability to rotate polarized light in different directions. * [[Protein folding]] concerns the complex geometries and different isomers that [[protein]]s can take. ==Types of molecular structure== A bond angle is the geometric angle between two adjacent bonds. Some common shapes of simple molecules include: * '''[[Linear molecular geometry|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 molecular geometry|Trigonal planar]]:''' Molecules with the trigonal planar shape are somewhat triangular and in one [[Plane (geometry)|plane (flat)]]. Consequently, the bond angles are set at 120°. For example, [[boron trifluoride]]. * '''[[Bent molecular geometry|Angular]]:''' Angular molecules (also called ''bent'' or ''V-shaped'') have a non-linear shape. For example, water (H<sub>2</sub>O), which has an angle of about 105°. A water molecule has two pairs of bonded electrons and two unshared lone pairs. * '''[[Tetrahedral molecular geometry|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 [[star (graph theory)|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 [[Inverse trigonometric functions|arccos]](−{{sfrac|1|3}}) = 109.47°. For example, [[methane]] (CH<sub>4</sub>) is a tetrahedral molecule. <!-- what about molecules without a central atom, which form a complete graph? --> * '''[[Octahedral molecular geometry|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]] (SF<sub>6</sub>) is an octahedral molecule. * '''[[Trigonal pyramidal molecular geometry|Trigonal pyramidal]]:''' A trigonal pyramidal molecule has a [[Pyramid (geometry)|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.<ref>Miessler G.L. and Tarr D.A. ''Inorganic Chemistry'' (2nd ed., Prentice-Hall 1999), pp.57-58</ref> For example, [[ammonia]] (NH<sub>3</sub>). ===VSEPR table=== {{main|VSEPR theory #AXE method}} The bond angles in the table below are ideal angles from the simple [[VSEPR theory]] (pronounced "Vesper Theory"){{Citation needed|date=November 2021}}, 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 in [[hydrogen sulfide|H<sub>2</sub>S]] (92°) differs from the tetrahedral angle by much more than the angle for [[water (molecule)|H<sub>2</sub>O]] (104.48°) does. {| class="wikitable sortable" style="text-align: center;" |- ! scope="col" | Atoms bonded to <br />central atom ! scope="col" | Lone pairs ! scope="col" | Electron domains <br />(Steric number) ! scope="col" | Shape ! scope="col" | Ideal bond angle <br />(example's bond angle) ! scope="col" | Example ! scope="col" | Image |- | 2 | 0 | 2 | style="text-align: left;" | [[linear molecular geometry|linear]] | 180° | [[carbon dioxide|CO<sub>2</sub>]] | [[Image:Linear-3D-balls.png|50px]] |- | 3 | 0 | 3 | style="text-align: left;" | [[trigonal planar molecular geometry|trigonal planar]] | 120° | [[Boron trifluoride|BF<sub>3</sub>]] | [[Image:Trigonal-3D-balls.png|50px]] |- | 2 | 1 | 3 | style="text-align: left;" | [[Bent molecular geometry|bent]] | 120° (119°) | [[Sulfur dioxide|SO<sub>2</sub>]] | [[Image:Bent-3D-balls.png|50px]] |- | 4 | 0 | 4 | style="text-align: left;" | [[tetrahedral molecular geometry|tetrahedral]] | 109.5° | [[methane|CH<sub>4</sub>]] | [[Image:AX4E0-3D-balls.png|50px]] |- | 3 | 1 | 4 | style="text-align: left;" | [[trigonal pyramidal molecular geometry|trigonal pyramidal]] | 109.5° (106.8°)<ref name="CRC 94th">{{cite book | editor= Haynes, William M. | year = 2013 | title = CRC Handbook of Chemistry and Physics | edition = 94th | publisher = [[CRC Press]] | isbn = 9781466571143|pages=9–26| title-link = CRC Handbook of Chemistry and Physics }}</ref> | [[ammonia|NH<sub>3</sub>]] | [[Image:Pyramidal-3D-balls.png|50px]] |- | 2 | 2 | 4 | style="text-align: left;" | [[Bent molecular geometry|bent]] | 109.5° (104.48°)<ref>{{cite journal|year=1979|last1=Hoy|first1=AR|last2=Bunker|first2=PR|journal=Journal of Molecular Spectroscopy|volume=74|pages=1–8|doi=10.1016/0022-2852(79)90019-5|title=A precise solution of the rotation bending Schrödinger equation for a triatomic molecule with application to the water molecule|issue=1|bibcode=1979JMoSp..74....1H}}</ref><ref>{{cite web |url=http://cccbdb.nist.gov/expangle2.asp?descript=aHOH&all=0 |title=CCCBDB Experimental bond angles page 2 |access-date=2014-08-27 |url-status=dead |archive-url=https://web.archive.org/web/20140903044129/http://cccbdb.nist.gov/expangle2.asp?descript=aHOH&all=0 |archive-date=2014-09-03 }}</ref> | [[H2O|H<sub>2</sub>O]] | [[Image:Bent-3D-balls.png|50px]] |- | 5 | 0 | 5 | style="text-align: left;" | [[trigonal bipyramidal molecular geometry|trigonal bipyramidal]] | 90°, 120° | [[phosphorus pentachloride|PCl<sub>5</sub>]] | [[Image:Trigonal-bipyramidal-3D-balls.png|50px]] |- | 4 | 1 | 5 | style="text-align: left;" | [[seesaw molecular geometry|seesaw]] | ax–ax 180° (173.1°), <br /> eq–eq 120° (101.6°), <br />ax–eq 90° | [[sulfur tetrafluoride|SF<sub>4</sub>]] | [[Image:Seesaw-3D-balls.png|50px]] |- | 3 | 2 | 5 | style="text-align: left;" | [[T-shaped molecular geometry|T-shaped]] | 90° (87.5°), 180° (175°) | [[chlorine trifluoride|ClF<sub>3</sub>]] | [[Image:T-shaped-3D-balls.png|50px]] |- | 2 | 3 | 5 | style="text-align: left;" | [[linear molecular geometry|linear]] | 180° | [[xenon difluoride|XeF<sub>2</sub>]] | [[Image:Linear-3D-balls.png|50px]] |- | 6 | 0 | 6 | style="text-align: left;" | [[octahedral molecular geometry|octahedral]] | 90°, 180° | [[sulfur hexafluoride|SF<sub>6</sub>]] | [[Image:AX6E0-3D-balls.png|50px]] |- | 5 | 1 | 6 | style="text-align: left;" | [[square pyramidal molecular geometry|square pyramidal]] | 90° (84.8°) | [[bromine pentafluoride|BrF<sub>5</sub>]] | [[Image:Square-pyramidal-3D-balls.png|50px]] |- | 4 | 2 | 6 | style="text-align: left;" | [[square planar molecular geometry|square planar]] | 90°, 180° | [[xenon tetrafluoride|XeF<sub>4</sub>]] | [[Image:Square-planar-3D-balls.png|50px]] |- | 7 | 0 | 7 | style="text-align: left;" | [[pentagonal bipyramidal molecular geometry|pentagonal bipyramidal]] | 90°, 72°, 180° | [[iodine heptafluoride|IF<sub>7</sub>]] | [[Image:Pentagonal-bipyramidal-3D-balls.png|50px]] |- | 6 | 1 | 7 | style="text-align: left;" | [[pentagonal pyramidal molecular geometry|pentagonal pyramidal]] | 72°, 90°, 144° | {{chem2|XeOF5-}} | [[Image:Pentagonal-pyramidal-3D-balls.png|50px]] |- | 5 | 2 | 7 | style="text-align: left;" | [[pentagonal planar molecular geometry|pentagonal planar]] | 72°, 144° | [[Tetramethylammonium pentafluoroxenate|{{chem2|XeF5-}}]] | [[Image:Pentagonal-planar-3D-balls.png|50px]] |- | 8 | 0 | 8 | style="text-align: left;" | [[square antiprismatic molecular geometry|square antiprismatic]] | | [[Nitrosonium octafluoroxenate(VI)|{{chem2|XeF8(2-)}}]] | [[Image:Square-antiprismatic-3D-balls.png|50px]] |- | 9 | 0 | 9 | style="text-align: left;" | [[tricapped trigonal prismatic molecular geometry|tricapped trigonal prismatic]] | | [[Potassium nonahydridorhenate|{{chem2|ReH9(2-)}}]] | [[Image:AX9E0-3D-balls.png|50px]] |} The greater the number 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. ==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 |- |<!--col1-->[[Image:Formic-acid-3D-stick.png|center|110px]] |[[Image:L-aspartic-acid-3D-sticks.png|center|110px]] |[[Image:ATP-xtal-3D-sticks.png|center|110px]] |[[Image:Endohedral fullerene.png|center|110px]] |} * '''Electron density plot''' – shows the electron density determined either [[crystallography|crystallographically]] or using [[quantum mechanics]] rather than distinct atoms or bonds. {| class=wikitable |- |[[Image:NorbornylCation ElectronDensity.jpg|center|110px]] |[[Image:WinsteinYellow.jpg|center|110px]] |} * '''Ball and stick''' – atomic nuclei are represented by spheres (balls) and the bonds as sticks. {| class=wikitable |- |<!--col1-->[[Image:Methanol-3D-balls.png|center|110px]] |[[Image:Methanol-graphic.svg|center|110px]] |[[Image:PropyleneGlycol-stickAndBall.png|center|110px]] |[[Image:3LRI SolutionStructureAndBackboneDynamicsOfHumanLong arg3 insulin-Like Growth Factor 1 02.png|center|170px]] |} * [[Spacefilling model]]s or [[CPK model]]s (also an [[CPK coloring|atomic coloring scheme]] in representations) – the molecule is represented by overlapping spheres representing the atoms. {| class=wikitable |- |<!--col1-->[[Image:Methanol.pdb.png|center|110px]] |[[Image:Ubiquitin spheres.png|center|110px]] |[[Image:P-cresol-spaceFilling.png|center|110px]] |[[Image:3GF1 Insulin-Like Growth Factor Nmr 10 01.png|center|170px]] |} * '''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). {| class=wikitable |- |[[Image:Beta-meander1.png|center|110px]] |[[Image:MreB.png|center|110px]] |[[Image:Anthrax toxin protein key motif.svg|center|110px]] |[[Image:8tim TIM barrel.png|center|170px]] |} ==See also== {{commons}} {{Div col|colwidth=20em}} * [[Jemmis mno rules]] * [[Lewis structure]] * [[Molecular design software]] * [[Molecular graphics]] * [[Molecular mechanics]] * [[Molecular modelling]] * [[Molecular symmetry]] * [[Molecule editor]] * [[Polyhedral skeletal electron pair theory]] * [[Quantum chemistry]] * [[Ribbon diagram]] * [[Styx rule]] (for boranes) * [[Topology (chemistry)]] {{Div col end}} ==References== {{Reflist}} ==External links== * [https://web.archive.org/web/20090925191332/http://www.tutor-pages.com/Chemistry/Molecular_Geometry/Polar_Or_Nonpolar.html Molecular Geometry & Polarity Tutorial] 3D visualization of molecules to determine polarity. * [http://www.xtal.iqfr.csic.es/Cristalografia/index-en.html Molecular Geometry using Crystals] 3D structure visualization of molecules using Crystallography. {{MolecularGeometry}}{{Branches of chemistry}}{{Authority control}} {{DEFAULTSORT:Molecular Geometry}} [[Category:Molecular geometry| ]]
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