Theoretical Analysis of the Base Stacking in DNA: Choice of the Force Field and a Comparison with the Oligonucleotide Crystal Structures

1993 ◽  
Vol 11 (2) ◽  
pp. 277-292 ◽  
Author(s):  
Jiřrí Šponer ◽  
Jaroslav Kypr
Keyword(s):  
Theoretical Analysis ◽  
Force Field ◽  
Crystal Structures ◽  
Base Stacking

Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods

2016 ◽  
Vol 72 (4) ◽  
pp. 460-476 ◽  
Author(s):  
Anders Broo ◽  
Sten O. Nilsson Lill
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Crystal Structures ◽  
Density Functional ◽  
Geometry Optimization ◽  
Field Methods ◽  
Functional Theory ◽  
Ranking List ◽  
Drug Molecules ◽  
New Type

A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.

Intermolecular Force-Field Parameters for Boron Hydrides

1998 ◽  
Vol 54 (1) ◽  
pp. 41-49 ◽  
Author(s):  
D. E. Williams ◽  
D. Gao
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Crystal Structures ◽  
Weighted Least Squares ◽  
Minimum Energy ◽  
Structural Parameter ◽  
Exponential Dependence ◽  
Monoclinic Space Group ◽  
Boron Hydrides ◽  
Force Field Parameters

Intermolecular atom–atom force-field parameters of the (exp-6-1) type for B and H atoms in boron hydrides were determined. They were obtained by full-weighted least-squares minimization of 116 forces in 15 observed crystal structures of boranes, the heat of sublimation of B10H14 and data from ab initio wavefunction calculations for diborane. Net atomic charges were obtained by fitting them to molecular electric potentials calculated from ab initio wavefunctions. Charges of terminal hydrogens were usually negative and those of bridging hydrogens usually positive. Repulsion-energy calculations for the B2H6 dimer provided the exponential dependence of H...H repulsion. Using the resulting force field, minimum-energy crystal structures were found with structural parameter values close to those of the observed structures. For diborane, energy minimization beginning with randomly oriented molecules placed initially in an 8 × 8 × 8 body-centered orthogonal cell led to the observed crystal structure and monoclinic space group.

scholarly journals An optimized intermolecular force field for hydrogen-bonded organic molecular crystals using atomic multipole electrostatics

2016 ◽  
Vol 72 (4) ◽  
pp. 477-487 ◽  
Author(s):  
Edward O. Pyzer-Knapp ◽  
Hugh P. G. Thompson ◽  
Graeme M. Day
Keyword(s):  
Force Field ◽  
Crystal Structures ◽  
Force Fields ◽  
Molecular Crystals ◽  
Intermolecular Force ◽  
Organic Molecular Crystals ◽  
Organic Solid ◽  
Lattice Energies ◽  
Validation Set ◽  
Unit Cell Dimensions

We present a re-parameterization of a popular intermolecular force field for describing intermolecular interactions in the organic solid state. Specifically we optimize the performance of the exp-6 force field when used in conjunction with atomic multipole electrostatics. We also parameterize force fields that are optimized for use with multipoles derived from polarized molecular electron densities, to account for induction effects in molecular crystals. Parameterization is performed against a set of 186 experimentally determined, low-temperature crystal structures and 53 measured sublimation enthalpies of hydrogen-bonding organic molecules. The resulting force fields are tested on a validation set of 129 crystal structures and show improved reproduction of the structures and lattice energies of a range of organic molecular crystals compared with the original force field with atomic partial charge electrostatics. Unit-cell dimensions of the validation set are typically reproduced to within 3% with the re-parameterized force fields. Lattice energies, which were all included during parameterization, are systematically underestimated when compared with measured sublimation enthalpies, with mean absolute errors of between 7.4 and 9.0%.

Synthesis, crystal structures, photoluminescence, magnetic and antioxidant properties, and theoretical analysis of Zn(ii) and Cu(ii) complexes of an aminoalcohol ligand supported by benzoate counter anions

2019 ◽  
Vol 43 (2) ◽  
pp. 622-633 ◽  
Author(s):  
Mantasha I. ◽  
M. Shahid ◽  
Musheer Ahmad ◽  
Rahisuddin Rahisuddin ◽  
Rizwan Arif ◽  
...  
Keyword(s):  
Dna Binding ◽  
Theoretical Analysis ◽  
Crystal Structures ◽  
Antioxidant Properties

Two photoluminescent Zn(ii) and Cu(ii) complexes are designed, characterized and assessed for DNA binding and antioxidant properties.

Crystal structures and conformations of 1-α-D-xylofuranosylcytosine and its protonated form (HCl salt)

1981 ◽  
Vol 59 (2) ◽  
pp. 238-245 ◽  
Author(s):  
Michael L. Post ◽  
Carol P. Huber ◽  
George I. Birnbaum ◽  
David Shugar
Keyword(s):  
Hydrogen Bonding ◽  
Crystal Structures ◽  
Direct Method ◽  
Intramolecular Hydrogen Bonding ◽  
Protonated Form ◽  
X Ray Diffraction ◽  
Base Stacking ◽  
Torsion Angles ◽  
Cell Parameters ◽  
Intramolecular Hydrogen

The structures of 1-α-D-xylofuranosylcytosine, C9H13N3O5 (1), and its hydrochloride salt, C9H13N3O5•HCl (1•HCl), have been determined by X-ray diffraction from diffractometer data, using direct method techniques. Both compounds crystallize in the orthorhombic system with Z = 4. Space group and cell parameters are, for 1: P21212, a = 18.706, b = 8.127, c = 7.007 Å; and for 1 HCl::P21212, a = 16.800, b = 8.045, c = 8.897 Å. Refinement by block-diagonal least-squares calculations gave a final R of 0.033 on 873 reflections and 0.034 on 914 reflections for 1 and 1 HCl, respectively. The glycosyl torsion angles are in the anti domain, χCN = −25.1° (1) and −28.6° (1•HC1), and the sugar puckers are nearly pure [Formula: see text] and 3E (1•HCl) forms. The C(4′)—C(5′) rotamer is trans–gauche in both cases. No intramolecular hydrogen bonding occurs in the xylofuranosyl rings. Lattice packing in the crystal structures occurs via intermolecular hydrogen bonding, with base stacking in pairs about one of the 2-fold axes for the neutral form, and with no base-stacking interactions for the protonated form. The biological implications of the structure and conformation of α-nucleosides are examined.

Study on the Pressure Distribution on Solid-Plug Conveying of Centrifugal Extruder

2013 ◽  
Vol 690-693 ◽  
pp. 2928-2932
Author(s):  
Jing Zhao ◽  
Shi Jie Wang ◽  
Xiao Ren Lv
Keyword(s):  
Theoretical Analysis ◽  
Force Field ◽  
Pressure Distribution ◽  
Influencing Factors ◽  
Centrifugal Force ◽  
Structural Parameters ◽  
Rotation Velocity ◽  
Centrifugal Force Field

In this paper, a new polymer process machine--- centrifugal extruder is introduced. The performance of centrifugal extruder had been studied by theoretical analysis. The analysis shows that the centrifugal force field can provide the solid-plug conveying pressure sufficiently and stably, which can prove the industry practicability of centrifugal extrude. By further discussion, it shows that the important influencing factors on the pressure comprise the structural parameters of the rotors and the rotation velocity.

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