A general all-atom force field for atomistic simulation of common organic molecules, inorganic small molecules, and polymers was developed using state-of-the-art ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio data, and the van der Waals (vdW) parameters were derived by conducting MD simulations of molecular liquids and fitting the simulated cohesive energies and equilibrium densities to experimental data. The combined parametrization procedure significantly improves the quality of a general force field. Validation studies based on large number of isolated molecules, molecular liquids and molecular crystals, representing 28 molecular classes, show that the present force field enables accurate and simultaneous prediction of structural, conformational, vibrational, and thermophysical properties for a broad range of molecules in isolation and in condensed phases. Detailed results of the parametrization and validation f...

COMPASS: An ab Initio Force-Field Optimized for Condensed-Phase ApplicationsOverview with Details on Alkane and Benzene Compounds

Publisher Summary This chapter deals with the recent developments regarding the description and nature of the conformation of proteins and polypeptides with special reference to the stereochemical aspects of the problem. This chapter considers the parameters that are required for an adequate description of a polypeptide chain. This chapter focuses the attention on what may be called “internal parameters”—that is, those which can be defined in terms of the relationships among atoms or units that form the building blocks of the polypeptide chains. This chapter also provides an account of the mathematical method of utilizing these parameters for calculating the coordinates of all the atoms in a suitable frame of reference, so that all the interatomic distances, and bond angles, can be calculated and their consequences worked out. This chapter observes conformations in amino acids, peptides, polypeptides, and proteins.

Conformation of Polypeptides and Proteins

Anomalous scattering factors Δf′ and Δf″ have been calculated relativistically for Cr, Fe, Cu, Mo, and Ag Kα radiations for the atoms Li through Cf. An interpolation scheme for other wavelengths is included in a separate report. Relativistic calculations of the photoelectric cross section have been made and the integral for the principal contribution to Δf′ has been evaluated numerically without approximation to the form of the cross section‐vs‐energy curve, as has been done in previous calculations. Many of the results are significantly different from previous calculations. Where experimental values exist, agreement for Δf″ is improved. For the rare gases, except for xenon, agreement between Δf′ and experiment is improved. Because of the more rigorous evaluation of Δf′ from cross‐section information, it is presumed that the present Δf′ values are more accurate than previous calculated values. Calculated mass absorption coefficients for the elements are included as incidental information.

Relativistic Calculation of Anomalous Scattering Factors for X Rays

The widespread use of controlled molecular-level motion in key natural processes suggests that great rewards could come from bridging the gap between the present generation of synthetic molecular systems, which by and large rely upon electronic and chemical effects to carry out their functions, and the machines of the macroscopic world, which utilize the synchronized movements of smaller parts to perform specific tasks. This is a scientific area of great contemporary interest and extraordinary recent growth, yet the notion of molecular-level machines dates back to a time when the ideas surrounding the statistical nature of matter and the laws of thermodynamics were first being formulated. Here we outline the exciting successes in taming molecular-level movement thus far, the underlying principles that all experimental designs must follow, and the early progress made towards utilizing synthetic molecular structures to perform tasks using mechanical motion. We also highlight some of the issues and challenges that still need to be overcome.

Synthetic molecular motors and mechanical machines.

Publisher Summary This chapter discusses the maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement (MIR) and multiwavelength anomalous diffraction (MAD) The chapter describes its extension to probability distributions incorporating anomalous diffraction effects, as well as measurement error and nonisomorphism Integrating these distributions in a whole complex plane leads to likelihood functions that can be used for heavy-atom detection and refinement and for producing phase-probability distributions The current implementation of this formalism in the computer program statistical heavy-atom refinement and phasing (SHARP) is also described in the chapter Likelihood functions can be used for the final phasing and calculation of Hendrickson–Lattman coefficients Numerical tests have been performed for three types of common refinements—namely, single isomorphous replacement, multiple isomorphous replacement with anomalous scattering (MIRAS), and MAD—and the results are summarized in the chapter A key feature of SHARP is its ability to refine lack-of-isomorphism parameters along with all the others

[27] Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods

Ammonia and deutero-ammonia have been studied by single-crystal and powder x-ray methods. There are four molecules in the cubic unit cell, and the space group is confirmed to be P2/sub 1/3. The nitrogen parameter obtained by least-squares refinement is equal to 0.0401 for NH/sub 3/ at -102 deg C and the same for ND/sub 3/ at -160 deg C. Cell dimensions, determined by powder methods, are: a = 5.084 A for NH/sub 3/ at -196 deg C, 5.073 A for ND/sub 3/ at -196 deg C, 5.091 A for ND/sub 3/ at -160 deg C, and 5.138 A for NH/sub 3/ at -102 deg C. Each ammonia molecule is involved in six hydrogen bonds of approximate length 3.4 A. A possible assignmert of the hydrogen atoms to these bonds is given. Electron- density maps give evidence of hydrogen positions with coordinates (0.85, 0.14, 0.99), in agreement with this assignment, but with hydrogen off the bond axis, making the H-N-H angles more nearly tetrahedral. (auth)

/pdf/x-ray-study-of-solid-ammonia-3ucga1p45f.pdf

X-ray study of solid ammonia

According to single‐crystal x‐ray diffraction data, crystals of Ce2Mg3(NO3)12·24H2O are rhombohedral, space group R3. The hexagonal cell with a = 11.004±0.006, c = 34.592±0.012 A contains three formula units. Atomic parameters were refined by least squares, and interatomic distances were corrected for thermal motion. The average N–O bond distance in nitrate is 1.26 A. The Ce atoms, on the threefold axis at z = ±0.2497, are each surrounded by 12 oxygen atoms at an average distance of 2.64 A. These oxygen atoms, belonging to six nitrate ions, are at the corners of a somewhat irregular icosahedron. The Mg atoms are of two kinds, located, respectively, at the origin and on the threefold axis at z = ±0.4279. Each Mg atom is surrounded by six water molecules with the oxygen atoms at the corners of an octahedron with an average Mg–O distance of 2.07 A. One‐fourth of the water molecules are not coordinated to cations. Evidence for the hydrogen atom positions from the diffraction data indicates that six of the ei...

/pdf/crystal-structure-of-cerium-magnesium-nitrate-hydrate-26l1ajynpd.pdf

Crystal Structure of Cerium Magnesium Nitrate Hydrate

The structure of vanadyl bisacetylacetonate has been determined from three‐dimensional x‐ray diffraction data. The crystals are triclinic, space group P1, with a=7.53±0.02 A, b=8.23±0.03 A, c=11.24±0.04 A, α=73.0°, β=71.3°, γ=66.6°, Z=2. The structure consists of discrete molecules of VO(C5H7O2)2. Each vanadium atom has five oxygen neighbors at the corners of a rectangular (nearly square) pyramid, with vanadium near its center of gravity. The vanadium‐oxygen distances are 1.56 A to the apex atom (vanadyl oxygen) and 1.96, 1.96, 1.97, and 1.98 A to the others. Other bond distances average 1.28 A for C–O, 1.40 A for C–C (ring), and 1.52 A for C–C (methyl). Standard deviations are 0.01 A for V–O bonds and 0.02 A for C–O and C–C bonds. Each acetylacetone skeleton is planar, and this plane makes an angle of 163° with the plane of the other acetylacetone skeleton of the same molecule.

/pdf/crystal-structure-of-vanadyl-bisacetylacetonate-geometry-of-2aaic8f359.pdf

Crystal Structure of Vanadyl Bisacetylacetonate. Geometry of Vanadium in Fivefold Coordination

LBL-1 0490C, Preprint Submi BIS(PENTAMETHYLCYCLOPENTADIENYL) VATI : CRYSTAL STRUCTURE IUM(II)TETRAHYDROFURAN T, Don Tilley, Helen a Ruben, , Brock Spencer, David H. Templeton April 1 TWO-WEEK LOAN COPY is a Library Copy which may borrowed two weeks. For a personal copy, Tech. Info. Division, Ext. 6782. for the U.S. of under Contract

/pdf/divalent-lanthanide-chemistry-bis-3xwnc9wfcy.pdf

Divalent lanthanide chemistry. Bis (pentamethylcyclopentadienyl) europium(II) and -ytterbium(II) derivatives: crystal structure of bis (pentamethylcyclopentadienyl) (tetrahydrofuran ytterbium(II) -hemitoluene at 176 K

/pdf/the-atomic-parameters-in-the-lanthanum-trifluoride-structure-nydc58tkcp.pdf

David H. Templeton

Papers

X-ray study of solid ammonia

Crystal Structure of Cerium Magnesium Nitrate Hydrate

Crystal Structure of Vanadyl Bisacetylacetonate. Geometry of Vanadium in Fivefold Coordination

Divalent lanthanide chemistry. Bis (pentamethylcyclopentadienyl) europium(II) and -ytterbium(II) derivatives: crystal structure of bis (pentamethylcyclopentadienyl) (tetrahydrofuran ytterbium(II) -hemitoluene at 176 K

The Atomic Parameters in the Lanthanum Trifluoride Structure