Abstract
Molecular mechanics (MM) rests on a view of molecules as balls held together by springs. The potential energy of a molecule can be written as the sum of terms involving bond stretching, angle bending, dihedral angles and nonbonded interactions. Giving these terms explicit mathematical forms constitutes devising a forcefield, and giving actual numbers to the constants in the forcefield constitutes parameterizing the field. An example is given of the devising and parameterization of an MM forcefield. Calculations on biomolecules is a very important application of MM, and the pharmaceutical industry designs new drugs with the aid of MM. Organic synthesis now makes considerable use of MM, which enables chemists to estimate which products are likely to be favored and to devise more realistic routes to a target molecule. In molecular dynamics MM is used to generate the forces acting on molecules and hence to calculate their motions.
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Notes
- 1.
Frank H. Westheimer, born Baltimore, Maryland, 1912. Ph.D. Harvard 1935. Professor University of Chicago, Harvard. Died 2007.
- 2.
Edward D. Hughes, born Wales, 1906. Ph.D. University of Wales, D.Sc. University of London. Professor, London. Died 1963.
- 3.
Christopher K. Ingold, born London 1893. D.Sc. London 1921. Professor Leeds, London. Knighted 1958. Died London 1970.
- 4.
Paul von R. Schleyer, born Cleveland, Ohio, 1930. Ph.D. Harvard 1957. Professor Princeton; institute codirector and professor University of Erlangen-Nürnberg, 1976–1998. Professor University of Georgia.
- 5.
Norman L. Allinger, born Rochester New York, 1930. Ph.D. University of California at Los Angeles, 1954. Professor Wayne State University, University of Georgia.
References
General references to molecular mechanics: (a) Rappe AK, Casewit CL (1997) Molecular mechanics across chemistry. University Science Books, Sausalito, CA; website http://www.chm.colostate.edu/mmac. (b) Leach AR (2001) Molecular modelling, principles and applications, 2nd edn. Prentice Hall, Essex (UK), chapter 4. (c) Burkert U, Allinger NL (1982) Molecular mechanics, ACS Monograph 177. American Chemical Society, Washington, DC. (d) Allinger NL (1976) Calculation of molecular structures and energy by force methods. In: Gold V, Bethell D (eds) Advances in physical organic chemistry, vol 13. Academic, New York. (e) Clark T (1985) A handbook of computational chemistry. Wiley, New York. (f) Levine IN (2000) Quantum chemistry, 5th edn. Prentice-Hall, Engelwood Cliffs, NJ, pp 664–680. (g) Issue no. 7 of Chem Rev (1993), 93. (h) Conformational energies: Pettersson I, Liljefors T (1996) In: Reviews in Computational Chemistry, vol 9, Lipkowitz KB, Boyd DB (eds) VCH Weinheim. (i) Inorganic and organometallic compounds: Landis CR, Root DM, Cleveland T (1995) In: Reviews in Computational Chemistry, vol 6, Lipkowitz KB, Boyd DB (eds) VCH Weinheim. (j) Parameterization: Bowen JP, Allinger NL (1991) Reviews in Computational Chemistry, vol 6, Lipkowitz KB, Boyd DB (eds) VCH Weinheim
MM history: (a) References 1. (b) Engler EM, Andose JD, Schleyer PvR (1973) J Am Chem Soc 95:8005 and references therein. (c) Molecular mechanics up to the end of 1967 is reviewed in detail in: Williams JE, Stang PJ, Schleyer PvR (1968) Ann Rev Phys Chem 19:531
(a) Westheimer FH, Mayer JE (1946) J Chem Phys 14:733. (b) Hill TL (1946) J Chem Phys 14:465. (c) Dostrovsky I, Hughes ED, Ingold CK (1946) J Chem Soc 173. (d) Westheimer FH (1947) J Chem Phys 15:252
(a) Ma B, Lii J-H, Chen K, Allinger NL (1997) J Am Chem Soc 119:2570 and references therein. (b) In an MM4 study of amines, agreement with experiment was generally good: Chen K-H, Lii J-H, Allinger NL (2007) J Comp Chem 28:2391. (c) Five papers, using MM4, on Alcohols, ethers, carbohydrates, and related compounds. J Comp Chem 24 (2003): Allinger NL, Chen K-H, Lii J-H, Durkin KA, 1447; Lii J-H, Chen K-H, Durkin A, Allinger NL, 1473; Lii J-H, Chen K-H, Grindley TB, Allinger NL, 1490; Lii J-H, Chen K-H, Allinger NL, 1504; (2004) J Phys Chem A 108; Lii J-H, Chen K-H, Allinger NL, 3006
(a) Information on and references to molecular mechanics programs may be found in references 1 and the website of reference 1a. (b) For papers on the popular Merck Molecular Force Field and the MM4 forcefield (and information on some others) see the issue of J Comp Chem 17 (1996)
The force constant is defined as the proportionality constant in the equation force = k x extension(of length or angle), so integrating force with respect to extension to get the energy (= force x extension) needed to stretch the bond gives E = (k/2)(extension)2, i.e. k = force constant = 2k stretch (or 2k bend)
(a) A brief discussion and some parameters: Atkins PW (1994) Physical chemistry, 5th edn. Freeman, New York, pp 772, 773; it is pointed out here that e−r/σ is actually a much better representation of the compressive potential than is r−12. (b) Moore WJ (1972) Physical chemistry, 4th edn. Prentice-Hall, New Jersey, p 158 (From Hirschfelder JO, Curtis CF, Bird RB (1954) Molecular theory of gases and liquids. Wiley, New York). Note that our k nb is called 4ε here and must be multiplied by 8.31/1000 to convert it to our units of kJ mol−1
Infrared spectroscopy: Silverstein RM, Bassler GC, Morrill TC (1981) Spectrometric identification of organic compounds, 4th edn. Wiley, New York, Chapter 3
Different methods of structure determination give somewhat different results; this is discussed in reference 4(a) and in: (a) Ma B, Lii J-H, Schaefer HF, Allinger NL (1996) J Phys Chem 100:8763 and (b) Domenicano A, Hargittai I (eds) (1992) Accurate molecular structures. Oxford Science, New York
To properly parameterize a molecular mechanics forcefield by calculations only high-level ab initio (or density functional) calculations would actually be used, but this does not affect the principle being demonstrated
Reference 1b, section 4.8
MM3: Allinger NL, Yuh YH, Lii J-H (1989) J Am Chem Soc 111:8551. The calculation was performed with MM3 as implemented in Spartan (reference 15)
Eksterowicz JE, Houk KN (1993) Chem Rev 93:2439
Smith MB, March J (2000) March’s advanced organic chemistry. Wiley, New York, pp 284–285
Spartan is an integrated molecular mechanics, ab initio and semiempirical program with an input/output graphical interface. It is available in UNIX workstation and PC versions: Wavefunction Inc., http://www.wavefun.com, 18401 Von Karman, Suite 370, Irvine CA 92715, USA. As of mid-2009, the latest version of Spartan was Spartan 09. The name arises from the simple or “Spartan” user interface.
Ref. [1c], pp 182–184
Gundertofte K, Liljefors T, Norby P-O, Pettersson I (1996) J Comp Chem 17:429
Comparison of various forcefields for geometry (and vibrational frequencies): Halgren TA (1996) J Comp Chem 17:553
The Merck force field (ref. [18]) often gives geometries that are satisfactory for energy calculations (i.e. for single-point energies, no geometry optimization with the quantum mechanical method) with quantum mechanical methods; this could be very useful for large molecules: Hehre WJ, Yu J, Klunzinger PE (1997) A guide to molecular mechanics and molecular orbital calculations in Spartan. Wavefunction Inc., Irvine, CA, chapter 4
Halgren TA (1996) J Comp Chem 17:490
Nicklaus MC (1997) J Comp Chem 18:1056; the difference between CHARMM and CHARMm is explained here
(a) www.amber.ucsf.edu/amber/amber.html (b) Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179 (c) Barone V, Capecchi G, Brunel Y, Andries M-LD, Subra R (1997) J Comp Chem 18:1720
(a) Field MJ, Bash PA, Karplus M (1990) J Comp Chem 11:700. (b) Bash PA, Field MJ, Karplus M (1987) J Am Chem Soc 109: 8092
Singh UC, Kollman P (1986) J Comp Chem 7:718
(a) Reference 1b, chapter 10. (b) Höltje H-D, Folkers G (1996) Molecular modelling, applications in medicinal chemistry. VCH, Weinheim, Germany. (c) van de Waterbeemd H, Testa B, Folkers G (eds) (1997) Computer-assisted lead finding and optimization. VCH, Weinheim, Germany
(a) Reference 1b,chapter 6. (b) Karplus M, Putsch GA (1990) Nature 347:631. (c) Brooks III CL, Case DA (1993) Chem Rev 93:2487. (d) Eichinger M, Grubmüller H, Heller H, Tavan P (1997) J Comp Chem 18:1729. (e) Marlow GE, Perkyns JS, Pettitt BM (1993) Chem Rev 93:2503. (f) Aqvist J, Warshel A (1993) Chem Rev 93:2523
Reference 1b, pp 410–456
Lipkowitz KB, Peterson MA (1993) Chem Rev 93:2463
(a) Saunders M (1991) Science 253:330. (b) See too Dodziuk H, Lukin O, Nowinski KS (1999) Polish J Chem 73:299
(a) Hehre WJ, Radom L, Schleyer pvR, Pople JA (1986) Ab initio Molecular Orbital Theory. Wiley, New York (b) M.D. Harmony, V.W. Laurie, R.L. Kuczkowski, R.H. Schwenderman, D.A. Ramsay, F.J. Lovas, W.H. Lafferty, A.G. Makai, Molecular Structures of Gas-Phase Polyatomic Molecules Determined by Spectroscopic Methods”, J. Physical and Chemical Reference Data, 1979, 8, 619–721 (c) Huang J, Hedberg K (1989) J Am Chem Soc 111:6909
Lii J-H, Allinger NL (1992) J Comp Chem 13:1138. The MM3 program can be bought from Tripos Associates of St. Louis, Missouri
Nevins N, Allinger NL (1996) J Comp Chem 17:730 and references therein
Lipkowitz KB (1995) J Chem Ed 72:1070
(a) Wiberg K (1996) Angew Chem Int Ed Engl 25:312. (b) Issue no. 5 of Chem Rev, 1989, 89. (c) Inagaki S, Ishitani Y, Kakefu T (1994) J Am Chem Soc 116:5954. (d) Nagase S (1995) Acc Chem Res 28:469. (e) Gronert S, Lee JM (1995) J Org Chem 60:6731. (f) Sella A, Basch H, Hoz S (1996) J Am Chem Soc 118:416. (g) Grime S (1996) J Am Chem Soc 118:1529. (h) Balaji V, Michl J (1988) Pure Appl Chem 60:189. (i) Wiberg KB, Ochterski JW (1997) J Comp Chem 18:108
Seeman JI (1983) Chem Rev 83:83
Added in press:
Handley CM, Popelier PLA (2010) The use of neural networks used to devise forcefields. J Phys Chem A 114:3371
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Appendices
Easier Questions
-
1.
What is the basic idea behind molecular mechanics?
-
2.
What is a forcefield?
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3.
What are the two basic approaches to parameterizing a forcefield?
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4.
Why does parameterizing a forcefield for transition states present special problems?
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5.
What is the main advantage of MM, generally speaking, over the other methods of calculating molecular geometries and relative energies?
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6.
Why is it not valid in all cases to obtain the relative energies of isomers by comparing their MM strain energies?
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7.
What class of problems cannot be dealt with by MM?
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8.
Give four applications for MM. Which is the most widely used?
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9.
MM can calculate the values (cm−1) of vibrational frequencies, but without “outside assistance” it can’t calculate their intensities. Explain.
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10.
Why is it not valid to calculate a geometry by some slower (e.g. ab initio) method, then use that geometry for a fast MM frequency calculation?
Harder Questions
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1.
One big advantage of molecular mechanics over other methods of calculating geometries and relative energies is speed. Does it seem likely that continued increases in computer speed could make MM obsolete?
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2.
Do you think it is possible (in practical terms? In principle?) to develop a forcefield that would accurately calculate the geometry of any kind of molecule?
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3.
What advantages or disadvantages are there to parameterizing a forcefield with the results of “high-level” calculations rather than the results of experiments?
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4.
Would you dispute the suggestion that no matter how accurate a set of MM results might be, they cannot provide insight into the factors affecting a chemical problem, because the “ball and springs” model is unphysical?
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5.
Would you agree that hydrogen bonds (e.g. the attraction between two water molecules) might be modelled in MM as weak covalent bonds, as strong van der Waals or dispersion forces, or as electrostatic attractions? Is any one of these three approaches to be preferred in principle?
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6.
Replacing small groups by “pseudoatoms” in a forcefield (e.g. CH3 by an “atom” about as big) obviously speeds up calculations. What disadvantages might accompany this simplification?
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7.
Why might the development of an accurate and versatile forcefield for inorganic molecules be more of a challenge than for organic molecules?
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8.
What factor(s) might cause an electronic structure calculation (e.g. ab initio or DFT) to give geometries or relative energies very different from those obtained from MM?
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9.
Compile a list of molecular characteristics/properties that cannot be calculated purely by MM.
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10.
How many parameters do you think a reasonable forcefield would need to minimize the geometry of 1,2-dichloroethane?
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Lewars, E.G. (2011). Molecular Mechanics. In: Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-3862-3_3
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