Multi-step modeling of liquid crystals using ab initio molecular packing and hybrid quantum mechanics/molecular mechanics simulations

2017 ◽  
Vol 16 (02) ◽  
pp. 1750012 ◽  
Author(s):  
Hang Hu ◽  
Alejandro D. Rey
Keyword(s):  
Molecular Structure ◽  
Quantum Mechanics ◽  
Raman Spectrum ◽  
Liquid Crystals ◽  
Molecular Mechanics ◽  
Crystal Structures ◽  
Molecular Interactions ◽  
Crystal Packing ◽  
Order Parameters ◽  
Molecular Structures

A density functional theory (DFT) based multi-step simulation method is used to characterize the detailed molecular structure and inter/intra- molecular interactions of two benchmark liquid crystals (LC) 5CB, 8CB and a novel tri-biphenyl ring bent core LC material. The method uses hybrid DFT at the B3LYP/6-31G* level to obtain molecular structure and Raman data. These results are fed to a crystal packing simulation to find possible crystal structures. A pico-second quantum mechanics/molecular mechanics (QM/MM) simulation model is built for the selected structures with lower overall energy as well as optimal density. The stabilized crystal structures are then extended into a super cell, heated and simulated using a mixed force field and nano-second molecular dynamics (MD). The described simulation process sequence provides predictions of molecular Raman spectrum, LC density, isotropic depolarization ratio, ratio of differential polarizability, order parameters, molecular structures, and rotating Raman spectrum of the different mesophases. The Raman spectra, order parameters and depolarization ratios all agree well with existing experimental and previous simulation results. The study of the novel tri-biphenyl ring bent core LC system shows that the ratio of differential polarizability depends on intra-molecular interactions. The findings presented in this manuscript contribute to the on-going efforts to establish links between LC molecular structures and their properties, including optical behavior.

scholarly journals Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute–solvent interactions

2014 ◽  
Vol 16 (38) ◽  
pp. 20639-20649 ◽  
Author(s):  
Petr Štěpánek ◽  
Petr Bouř
Keyword(s):  
Amino Acids ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Electronic Spectra ◽  
Aromatic Amino Acids ◽  
Molecular Structures ◽  
Solvent Interactions ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Electronic spectra provide a wealth of information on molecular structures. We demonstrate a very satisfactory agreement between experimental and modeled spectra, as obtained by combined molecular mechanics/quantum mechanics computations for three aromatic amino acids.

Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-based Drug Design and Discovery

2021 ◽  
Vol 21 ◽  
Author(s):  
Prajakta U. Kulkarni ◽  
Harshil Shah ◽  
Vivek K. Vyas
Keyword(s):  
Quantum Mechanics ◽  
Drug Design ◽  
Molecular Mechanics ◽  
Chemical Reactions ◽  
Classical Mechanics ◽  
Molecular Structures ◽  
Protein Crystal ◽  
Structure Based Drug Design ◽  
Structure And Property ◽  
Qsar Models

: Quantum mechanics (QM) is physics based theory which explains the physical properties of nature at the level of atoms and sub-atoms. Molecular mechanics (MM) construct molecular systems through the use of classical mechanics. So, hybrid quantum mechanics and molecular mechanics (QM/MM) when combined together can act as computer-based methods which can be used to calculate structure and property data of molecular structures. Hybrid QM/MM combines the strengths of QM with accuracy and MM with speed. QM/MM simulation can also be applied for the study of chemical process in solutions as well as in the proteins, and has a great scope in structure-based drug design (CADD) and discovery. Hybrid QM/MM also applied to HTS, to derive QSAR models and due to availability of many protein crystal structures; it has a great role in computational chemistry, especially in structure- and fragment-based drug design. Fused QM/MM simulations have been developed as a widespread method to explore chemical reactions in condensed phases. In QM/MM simulations, the quantum chemistry theory is used to treat the space in which the chemical reactions occur; however the rest is defined through molecular mechanics force field (MMFF). In this review, we have extensively reviewed recent literature pertaining to the use and applications of hybrid QM/MM simulations for ligand and structure-based computational methods for the design and discovery of therapeutic agents.

The Raman spectrum and molecular structure of Me3SiOReO3 in the solid, liquid, solution, and gaseous phases

1970 ◽  
Vol 48 (19) ◽  
pp. 3026-3028 ◽  
Author(s):  
D. H. Boal ◽  
G. A. Ozin
Keyword(s):  
Molecular Structure ◽  
Raman Spectrum ◽  
Crystal Packing ◽  
Solid Phase ◽  
Liquid Solution ◽  
The Other ◽  
Non Linear ◽  
Linear Molecules ◽  
Solid Liquid

The Raman spectrum of Me3SiOReO3 is found to be essentially the same in all of the above phases, proving that the non-linear SiORe bridged structure found in the solid phase is retained in the other phases and is not just the result of crystal packing requirements. The interpretation of the spectrum of Me3SiOReO3 is found to be particularly straightforward as the vibrational data can be considered to be intermediate between that of the parent, non-linear molecules (Me3Si)2O and (O3Re)2O. In the present work, assignments for the ReO and SiO bridge stretching modes are proposed.

Theory and Quantitative Predictions

2007 ◽  
Author(s):  
James Wei
Keyword(s):  
Molecular Structure ◽  
Quantum Mechanics ◽  
Schrödinger Equation ◽  
Ab Initio ◽  
Molecular Mechanics ◽  
Equilibrium Position ◽  
Schrodinger Equation ◽  
Single Point ◽  
Absolute Temperature ◽  
Structure And Properties

The purpose of this chapter is to review the theories of molecular structure and property relations, to discuss computational methods for prediction of molecular structure and properties, and to discuss some of the properties that can be predicted by computations. Quantum mechanics is the foundation of molecular structure and properties. The position and energy of the electrons around a molecule are determined by solving the Schrödinger equation for a given set of positions of the nuclei of the atoms. There is a lot of powerful and effective computer software that can be used to calculate many of the properties of an isolated single molecule, especially at zero absolute temperature. The starting point is the construction of the sketch of a molecule by connecting atoms with the appropriate bonds. This qualitative sketch does not need accurate values for the bond lengths and angles. To set up the computation, the investigator specifies one of three computation methods: ab initio, semi-empirical, or molecular mechanics. The first and second methods are based on quantum mechanics about a model of the molecule as a number of negatively charged electrons surrounding a collection of positively charged nuclei. The third option of molecular mechanics is based on classical Newtonian mechanics about a model of the molecule as a number of mechanical bonds linking the atoms together, and these bonds can be stretched and bent according to empirical force fields. When either the Schrödinger equation or the Newtonian equation is solved with the initial spatial distribution of nuclei, in what is called the single-point determination, the binding energy of the molecule is obtained. If we make random perturbations of the positions of the various atoms, and repeat the single-point calculations, we can map the energy levels of the molecule in a neighborhood. The most stable or equilibrium position of the molecule is the one with the lowest energy in the neighborhood, and the search for this equilibrium position of the atoms is called geometry optimization. The most rigorous and accurate method of calculation is the ab initio method, which is also the most demanding in computational time and resources, so that it is most often used for smaller molecules.

Crystal structures of dihydroquercetin 3-acetate and dihydroquercetin 3,3'4',7-tetraacetate: hydrogen bonding in 5-hydroxyflavanones

1999 ◽  
Vol 77 (8) ◽  
pp. 1436-1443 ◽  
Author(s):  
Eberhard Kiehlmann ◽  
Kumar Biradha ◽  
Konstantin V Domasevitch ◽  
Michael J Zaworotko
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Single Crystal ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Heterocyclic Ring ◽  
Molecular Structures ◽  
Crystal Data ◽  
Aromatic Rings ◽  
X Ray

The molecular structures of dihydroquercetin 3-acetate 3 and dihydroquercetin 3,3',4',7-tetraacetate 4 were determined by single crystal X-ray analysis. Comparison of their crystal data with those of 16 known 5-hydroxyflavanones shows intramolecular O(5)-H···O(4)=C hydrogen bonding, preference for nearly perpendicular orientation of the two aromatic rings and preferred sofa conformation of the heterocyclic ring. The major stabilizing force in the crystal packing pattern of 3 is intermolecular hydrogen bonding.Key words: crystal structure, dihydroquercetin, flavanones, hydrogen bonding.

Cinnamamide pharmacophore for anticonvulsant activity: evidence from crystallographic studies

2018 ◽  
Vol 74 (7) ◽  
pp. 782-788 ◽  
Author(s):  
Ewa Żesławska ◽  
Wojciech Nitek ◽  
Henryk Marona ◽  
Agnieszka Gunia-Krzyżak
Keyword(s):  
Crystal Structures ◽  
Anticonvulsant Activity ◽  
Crystal Packing ◽  
Pharmacophore Model ◽  
Molecular Structures ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray ◽  
Intramolecular Hydrogen ◽  
First Time

A number of cinnamamide derivatives possess anticonvulsant activity due to the presence of a number of important pharmacophore elements in their structures. In order to study the correlations between anticonvulsant activity and molecular structure, the crystal structures of three new cinnamamide derivatives with proven anticonvulsant activity were determined by X-ray diffraction, namely (R,S)-(2E)-N-(2-hydroxybutyl)-3-phenylprop-2-enamide–water (3/1), C13H17NO2·0.33H2O, (1), (2E)-N-(1-hydroxy-2-methylpropan-2-yl)-3-phenylprop-2-enamide, C13H17NO2, (2), and (R,S)-(2E)-N-(1-hydroxy-3-methyl-butan-2-yl)-3-phenylprop-2-enamide, C14H19NO2, (3). Compound (1) crystallizes in the space group P\overline{1} with three molecules in the asymmetric unit, whereas compounds (2) and (3) crystallize in the space group P21/c with one and two molecules, respectively, in their asymmetric units. The carbonyl group of (2) is engaged in an intramolecular hydrogen bond with the hydroxy group. This type of interaction is observed for the first time in these kinds of derivatives. A disorder of the substituent at the N atom occurs in the crystal structures of (2) and (3). The crystal packing of all three structures is dominated by a network of O—H...O and N—H...O hydrogen bonds, and leads to the formation of chains and/or rings. Furthermore, the crystal structures are stabilized by numerous C—H...O contacts. We analyzed the molecular structures and intermolecular interactions in order to propose a pharmacophore model for cinnamamide derivatives.

scholarly journals Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes

2015 ◽  
Vol 71 (10) ◽  
pp. 1169-1173 ◽  
Author(s):  
Barbara L. Goldenberg ◽  
Victor G. Young Jr ◽  
George Barany
Keyword(s):  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Crystal Structures ◽  
Crystal Packing ◽  
Molecular Structures ◽  
Protecting Groups ◽  
Asymmetric Unit ◽  
Bond Lengths ◽  
Independent Molecules ◽  
Related Compounds

The present paper reports crystallographic studies on three related compounds that were of interest as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitrogen-protecting groups: (N-methylcarbamoyl)(trichloromethyl)disulfane, C3H4Cl3NOS2, (1), (N-benzylcarbamoyl)(trichloromethyl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenylcarbamoyl)(trichloromethyl)disulfane, C9H8Cl3NOS2, (3). Their molecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent molecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), molecules are linkedviaN—H...O hydrogen bonds forming chains along [110], which are linked by short Cl...Cl and S...O contacts forming sheets parallel to (001). In the crystal of (2), molecules are linkedviaN—H...O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O...Cl contacts forming ribbons along thec-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking.

Molecular Structure and Mesomorphic Properties of Thermotropic Liquid Crystals — I

1983 ◽  
Vol 38 (6) ◽  
pp. 693-697 ◽  
Author(s):  
Maged A. Osman
Keyword(s):  
Molecular Structure ◽  
Liquid Crystals ◽  
Molecular Interactions ◽  
Thermodynamic Stability ◽  
Rigid Core ◽  
Alkyl Chains ◽  
Thermotropic Liquid Crystals ◽  
Mesomorphic Properties

The influence of molecular structure on the mesomorphic properties of thermotropic liquid crystals is discussed. The role of intermolecular attractive and repulsive (steric) forces in determining the packing and consequently the mesomorphic behaviour of the molecules is described. A correlation between the geometry of the rigid core of the molecules and the mesomorphic properties is found. The intermolecular separation strongly influences the thermodynamic stability of the mesophase. Alkyl chains do not only fill in spaces but also take part in the molecular interactions and affect the packing

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