Intermolecular force

Abstract: The Forces between Atoms and Molecules. Principles and Concepts. Historical Perspective. Some Thermodynamic Aspects of Intermolecular Forces. Strong Intermolecular Forces: Covalent and Coulomb Interactions. Interactions Involving Polar Molecules. Interactions Involving the Polarization of Molecules. van der Waals Forces. Repulsive Forces, Total Intermolecular Pair Potentials, and Liquid Structure. Special Interactions. Hydrogen-Bonding, Hydrophobic, and Hydrophilic Interactions. The Forces between Particles and Surfaces. Some Unifying Concepts in Intermolecular and Interparticle Forces. Contrasts between Intermolecular, Interparticle, and Intersurface Forces. van der Waals Forces between Surfaces. Electrostatic Forces between Surfaces in Liquids. Solvation, Structural and Hydration Forces. Steric and Fluctuation Forces. Adhesion. Fluid-Like Structures and Self-Assembling Systems. Micelles, Bilayers, and Biological Membranes. Thermodynamic Principles of Self-Assembly. Aggregation of Amphiphilic Molecules into Micelles, Bilayers, Vesicles, and Biological Membranes. The Interactions between Lipid Bilayers and Biological Membranes. References. Index.

Abstract: We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharmaceutical molecules that are composed of H, C, N, O, S, P, and halogens. It uses a simple functional form and a limited number of atom types, but incorporates both empirical and heuristic models to estimate force constants and partial atomic charges. The performance of GAFF in test cases is encouraging. In test I, 74 crystallographic structures were compared to GAFF minimized structures, with a root-mean-square displacement of 0.26 A, which is comparable to that of the Tripos 5.2 force field (0.25 A) and better than those of MMFF 94 and CHARMm (0.47 and 0.44 A, respectively). In test II, gas phase minimizations were performed on 22 nucleic acid base pairs, and the minimized structures and intermolecular energies were compared to MP2/6-31G* results. The RMS of displacements and relative energies were 0.25 A and 1.2 kcal/mol, respectively. These data are comparable to results from Parm99/RESP (0.16 A and 1.18 kcal/mol, respectively), which were parameterized to these base pairs. Test III looked at the relative energies of 71 conformational pairs that were used in development of the Parm99 force field. The RMS error in relative energies (compared to experiment) is about 0.5 kcal/mol. GAFF can be applied to wide range of molecules in an automatic fashion, making it suitable for rational drug design and database searching.

Abstract: It is shown by an extensive benchmark on molecular energy data that the mathematical form of the damping function in DFT-D methods has only a minor impact on the quality of the results. For 12 different functionals, a standard "zero-damping" formula and rational damping to finite values for small interatomic distances according to Becke and Johnson (BJ-damping) has been tested. The same (DFT-D3) scheme for the computation of the dispersion coefficients is used. The BJ-damping requires one fit parameter more for each functional (three instead of two) but has the advantage of avoiding repulsive interatomic forces at shorter distances. With BJ-damping better results for nonbonded distances and more clear effects of intramolecular dispersion in four representative molecular structures are found. For the noncovalently-bonded structures in the S22 set, both schemes lead to very similar intermolecular distances. For noncovalent interaction energies BJ-damping performs slightly better but both variants can be recommended in general. The exception to this is Hartree-Fock that can be recommended only in the BJ-variant and which is then close to the accuracy of corrected GGAs for non-covalent interactions. According to the thermodynamic benchmarks BJ-damping is more accurate especially for medium-range electron correlation problems and only small and practically insignificant double-counting effects are observed. It seems to provide a physically correct short-range behavior of correlation/dispersion even with unmodified standard functionals. In any case, the differences between the two methods are much smaller than the overall dispersion effect and often also smaller than the influence of the underlying density functional.

Abstract: We present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactions

Abstract: We present the development of a force field for simulation of nucleic acids and proteins. Our approach began by obtaining equilibrium bond lengths and angles from microwave, neutron diffraction, and prior molecular mechanical calculations, torsional constants from microwave, NMR, and molecular mechanical studies, nonbonded parameters from crystal packing calculations, and atomic charges from the fit of a partial charge model to electrostatic potentials calculated by ab initio quantum mechanical theory. The parameters were then refined with molecular mechanical studies on the structures and energies of model compounds. For nucleic acids, we focused on methyl ethyl ether, tetrahydrofuran, deoxyadenosine, dimethyl phosphate, 9-methylguanine-l-methylcytosine hydrogen-bonded complex, 9-methyladenine-l-methylthymine hydrogen-bonded complex, and 1,3-dimethyluracil base-stacked dimer. Bond, angle, torsional, nonbonded, and hydrogen-bond parameters were varied to optimize the agreement between calculated and experimental values for sugar pucker energies and structures, vibrational frequencies of dimethyl phosphate and tetrahydrofuran, and energies for base pairing and base stacking. For proteins, we focused on 4>,'lt maps of glycyl and alanyl dipeptides, hydrogen-bonding interactions involving the various protein polar groups, and energy refinement calculations on insulin. Unlike the models for hydrogen bonding involving nitrogen and oxygen electron donors, an adequate description of sulfur hydrogen bonding required explicit inclusion of lone pairs. There are two fundamental problems in simulating the struc­ tural and energetic properties of molecules: the first is how to choose an analytical been placed E(R) which correctly describes the energy of the system in terms of its 3N degrees of freedom. The second is how the simulation can search or span conforma­ tional space (R) in order to answer questions posed by the scientist interested in the properties of the system. For complex systems, solution to the first problem are an es­ sential first step in attacking the second problem, and thus, considerable effort has been placed in developing analytical functions that are simple enough to allow one to simulate the properties of complex molecules yet accurate enough to obtain meaningful estimates for structures and energies. In the case of the structures and thermodynamic stabilities of saturated hydrocarbons in inert solvents or the gas phase, the first problem has been essentially solved by molecular mechanics ap­ proaches of Allinger, I Ermer and Lifson,2 and their co-workers. However, for polar and ionic molecules in condensed phases, unsolved questions remain as to the best form of the analytical function E(R). In the area of proteins and peptides, seminal work has come from the Scheraga 3 and Lifson 4 schools. The Scheraga group has used both crystal packing (intermolecular) and con­ formational properties of peptides to arrive at force fields ECEPP, UNECEPP, and EPEN for modeling structural and thermodynamic properties of peptides and proteins. Levitt, using the energy refinement software developed in the Lifson group, has proposed a force field for proteins based on calculations on lysozyme,S and Gelin and Karplus have adapted this software along with many parameters from the Scheraga studies to do molecular dynamics