Multitechnique Investigation of Conformational Features of Small Molecules: the Case of Methyl Phenyl Sulfoxide (original) (raw)
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Journal of Computational Chemistry, 2009
Interaction energy of the 4-n-pentyloxy-4 -cyanobiphenyl (5OCB) dimer is computed at MP2 level, for many geometrical arrangements using the Fragmentation Reconstruction Method (FRM). DFT calculations are performed for a number of geometries of the monomer. The resulting database is used to parameterize an atomistic intra-and intermolecular force-field suitable for classical bulk simulations. Several structural and dynamical properties in 5OCB isotropic and liquid crystalline phases are computed from molecular dynamics simulation mainly in the NPT ensemble. Lengthy runs (more than 70 ns) and large sample sizes (up to 806 molecules) were used to determine the nematic to isotropic transition temperature up to a precision of few K. Good agreement was found in most of the investigated properties, thus validating the accuracy of the proposed model potential, only derived by quantum mechanical calculations.
Journal of Physical Chemistry A, 1997
The global conformational potentials of 1,2-ethanediol, 1,2-ethanediamine, and 2-aminoethanol (X-CH 2-CH 2-Y; X, Y) OH or NH 2) were obtained at the MP2/6-311+G(2d,p) level by scanning through the dihedral angles of the two functional groups and the carbon-carbon bond with the remaining nuclear coordinates being energy-minimized. It was found that the potentials could be represented by the direct-bond potentials between the adjacent molecular fragments and by the through-space electrostatic potentials between the vicinal and geminal fragments. Here, the through-direct-bond potentials are represented by the conventional three Fourier terms of the internal rotation angles, and the through-space potentials, which include the intramolecular hydrogen bonding between X and Y, are represented by the general functional forms of the electric dipoledipole, dipole-quadrupole, and quadrupole-quadrupole interaction terms. The fitted electrostatic interaction strengths between the X and Y fragments are in good agreement with the predictions of the theoretical molecular fragment dipole and quadrupole moments calculated by the Hirshfeld charge population analysis. Under the present energy decomposition scheme, the intrinsic gauche interactions, which are free of the contribution of the intramolecular H-bonding, could be obtained and correlated with the group electronegativities of X and Y. The potentials were also calculated by the MM3 molecular mechanics method and compared with the present results. With the global conformation potentials, the thermodynamic functions of the molecules and also their individual conformers are calculated and compared with the gas-phase experimental thermodynamic data in the literature.
Journal of Chemical Information and Modeling, 2012
Identification of the global energy minimum conformation of a small molecule can be approached with a range of computational strategies. Smaller sets of compounds can be studied by molecular dynamics methods in explicit water or by ab initio methods. For large compound libraries, conformational search methods can be used. One such method is Monte Carlo sampling, where thousands of random starting conformations for each compound are generated and subsequently minimized using force field methods. To increase the computational efficiency, this type of calculation is performed in vacuo or using a continuum solvent model. The quality of implicit solvent models is currently such that the behavior of most molecules is well modeled. In the case of polar or charged compounds, some issues still linger. There is a tendency to overestimate the electrostatic interaction between charged groups when these are located close to each other in a given conformation. 1,2 For some molecules, the opportunity for such interactions during a conformational search leads to a reported global energy minimum conformation, where these groups form an internal hydrogen bond. Such folded conformations may well exist in solution, in equilibrium with their extended counterparts. This is observed in the case of β-alanine, where NMR data and ab initio calculations demonstrate that the two types of conformations, extended and folded, are both represented in water. 2 It is not a problem that a given method reports the folded conformation, but in the case of β-alanine, the energy difference between the two conformers, as calculated by force field methods, has been reported as high as 20 kcal/mol. 2,3 This indicates that the force field methods may overestimate the stability of the folded conformation. This is most likely caused by the incomplete description of solvation effects by the continuum models, in combination with force field specific effects. Moreover, entropic penalties from introducing an internal hydrogen bond are also not included in the energy minimization methods and are difficult to estimate, even with computationally expensive methods due to sampling issues.
A comparison of conformational energies calculated by several molecular mechanics methods
Journal of Computational Chemistry, 1996
Several commonly used molecular mechanics force fields have been tested for accuracy in conformational energy calculations. Differences in performance between the force fields are discussed for different classes of structures. MMFF93 and force fields based on the MM2 or MM3 functional form are found to perform significantly better than other force fields in the test, with average conformational energy errors around 0.5 kcal/mol. CFF91 also reaches this accuracy for the subset in which fully determined parameters are used, but it doubles the overall error due to use of estimated parameters. Harmonic force fields generally have average errors exceeding 1 kcal/mol. Factors influencing accuracy are identified and discussed. 0 1996 by John Wiley & Sons, Inc. different programs can be run on personal computers or small workstations. The problem today in routine work is not so much how to perform the calculation as what force field to use. A few years ago, two of us participated in a compafison of some of the most popular force fields at that time.' However, the last few years have seen the advent
The force field picture of molecular shape response
International Journal of Quantum Chemistry, 2008
The concept of molecular response that is likely related to an enormous variety of phenomena of chemistry and biochemistry, such as supramolecular catalysts, enzymes reactions, folding, the concept of recognition, sensoring, and drug design, is approached in the present work from both graph theory invoked to rationalize the bonding patterns and from the molecular force field applied to quantify this response. Regarding the need of some supplementary criteria to characterize the chemical bond, we partially focus on the existence of the central C-C bond of syn-1, 6:8,13-biscarbonyl [14]annulene and report its three lower-energy conformers. Some class of triatomic molecules HXY is computationally studied to illustrate the proposed approach to molecular response.
Israel J of Chemistry, 1977
The increasing power of computer simulation experiments for molecular systems is discussed. These include such apparently disparate calculations as Monte Carlo simulation of solvent structure in biological systems, conformational analysis and folding of oligopeptide chains, and lattice-energy calculations and the effect of lattice forces on molecular geometry. All such calculations have in common the requirement of an analytic expression of the energy of the system as a function of the inter- and intramolecular coordinates of interest. The nature and derivation of these force fields and their relation to the spatial electron densities in relevant molecular systems is reviewed. The method of the derivation of intermolecular force fields from crystal data of amides is outlined. It is shown that information which may be obtained from ab-inirio molecular orbital or X-ray diffraction studies, population analysis, and total and difference electron density maps, may be used in conjunction with the crystal data both to verify (or test) assumptions made in the derivation and to help in the formulation of the models on which the analytical expressions for the energy are based. Finally, the relation between intramolecular forces and the electron distribution as represented in difference electron density maps is discussed. Several examples involving carbonyl compounds are presented, in which changes in the molecular geometry, intramolecular forces and vibrational frequencies on protonation and substitution are discussed both in terms of "valence or Urey-Bradley" type interactions and the changes which occur in the difference density maps
The Journal of Organic Chemistry
NMR chemical shifts have been experimentally measured and theoretically estimated for all the carbon atoms of (1R,3S,4S,8S)-p-menthane-3,9-diol in chloroform solution. Theoretical estimations were performed using a combination of molecular dynamics simulations and quantum mechanical calculations. Molecular dynamics simulations were used to obtain the most populated conformations of the (1R,3S:4S,8S)-p-menthane-3,9-diol as well as the distribution of the solvent molecules around it. Quantum mechanical calculations of NMR chemical shifts were performed on the most relevant conformations employing the GIAO-DFT formalism. A special emphasis was put in evaluating the effects of the surrounding solvent molecules. For this purpose, supermolecule calculations were performed on complexes constituted by the solute and n chloroform molecules, where n ranges from 3 to 16. An excellent agreement with experimental data has been obtained following this computational strategy.
Molecular dynamics and interactions in liquids, molecular crystals and molecular complexes
Journal of Molecular Structure, 1978
The itinerant oscillator model for translational stochastic motion in molecular and atomic fluids is developed using a Mori continued fraction representation of the velocity autocorrelation function Cv(t). The initial generalised Langevin equation is solved in terms of the velocity probability density function and the van Hove self correlation function Gs(2,t). These are then compared with their equivalents derived independently from molecular dynamics and experimental sources. In particular Cv(t) is compared with velocity a.c.f's computed from an atom-atom intermolecular potential using molecular dynamics methods for four different interatomic separations. The non-Gaussian characteristics of the p.d.f.'s above are investigated using simulations of a.c.f. '8 of moments of v such as the a.c.f. of kinetic energy. It is concluded that sme form of rotation /translation coupling is needed in order that the initial equation may be made more realistic. 1965 following sane speculations by Prenkel*. Unfortunately, Sears's paper is mathematically uusound, as was pointed out by Damle et all. In this article we shall use a Hori continued fraction representatiou4 of the velocity autocorrelation function, CV(t), to model the:thonaal translations of atoms (and molecules) as described by an initial generalised Langevin equation5. By use of the Mori continued fraction, itinerant oscillation, i.e. molecular or atcmic translations describable by damped oscillations about sme equilibrium position which itself diffuses slowly through the bulk fluid can be followed analytically. The initial equations of motion are based on postulates that the random velocity (v) and force (P) in the system are both Gaussian. This is checked directly against molecular dyuamics results using the recently developed atom-atom algorithm of Tildesley and Streett 6 to compute C"(t) and the a_c.f_ of force (P = A), C,(t); together with-Evans, M-W., 1977, DielectrZc and Related Molecular Processes @hem, Sot. Specialist Per. Rep., London). Vol. 3 (in press).
Crystal Packing, Hydrogen Bonding, and the Effect of Crystal Forces on Molecular Conformation
Accts of Chem Research, 1980
The studies of crystal structures of organic molecules by X-ray and neutron diffraction provide valuable information about the spatial arrangement of the atoms in molecules and the packing of molecules in lattices. In many respects, however, this is just the beginning of the story, rather than the end. Why do these molecules pack in the observed space group? What are the intermolecular forces determining crystal structure? How do crystal forces influence the conformation of flexible molecules? These are some of the fundamental questions which we may now ask, having the wealth of crystal data at our disposal.