scholarly journals Cocrystals of Ethenzamide With 2-Nitrobenzoic Acid - Conformational Analysis, MD Simulations And DFT Investigations

2021 ◽  
Author(s):  
Y. Sheena Mary ◽  
Y. Shyma Mary ◽  
Razieh Razavi
Keyword(s):  
Hydrogen Bond ◽  
Conformational Analysis ◽  
Crystal Engineering ◽  
Energy Charge ◽  
Thermodynamic Characteristics ◽  
Md Simulations ◽  
Pharmaceutical Chemistry ◽  
Nitrobenzoic Acid ◽  
Wide Range ◽  
Stability Energy

Abstract In crystal engineering and pharmaceutical chemistry, cocrystals have a wide range of applications. Ethenzamide (EA) is found to form cocrystal with 2-nitrobenzoic acid (NBA). Geometry properties like stability energy, charge distribution, bond length, electronic properties and thermodynamic characteristics have been analyzed. The C-H…O hydrogen bond involves C-H of EA and oxygen of NBA. Configuration with the angle, N3-C4-C5-C6 gives the lowest energy conformation. Partition coefficient value suggests that EA-NBA has pharmaceutics behavior. RMSD values show the simulation’s relative stability and the complexes, remained stable throughout.

A Hydrogen Bond Between Linear Tetrapyrrole and Conserved Aspartate Causes the Far-Red Shifted Absorption of Phytochrome Photoreceptors

2020 ◽  
Author(s):  
Egle Maximowitsch ◽  
Tatiana Domratcheva
Keyword(s):  
Hydrogen Bond ◽  
Light Adaptation ◽  
Positive Charge ◽  
Pyrrole Ring ◽  
Md Simulations ◽  
Spectral Shift ◽  
Specific Domain ◽  
Study Guides ◽  
Rational Engineering ◽  
Tuning Mechanism

Photoswitching of phytochrome photoreceptors between red-absorbing (Pr) and far-red absorbing (Pfr) states triggers light adaptation of plants, bacteria and other organisms. Using quantum chemistry, we elucidate the color-tuning mechanism of phytochromes and identify the origin of the Pfr-state red-shifted spectrum. Spectral variations are explained by resonance interactions of the protonated linear tetrapyrrole chromophore. In particular, hydrogen bonding of pyrrole ring D with the strictly conserved aspartate shifts the positive charge towards ring D thereby inducing the red spectral shift. Our MD simulations demonstrate that formation of the ring D–aspartate hydrogen bond depends on interactions between the chromophore binding domain (CBD) and phytochrome specific domain (PHY). Our study guides rational engineering of fluorescent phytochromes with a far-red shifted spectrum.

Pharmaceutical Co-Crystals - Design, Development and Applications

2020 ◽  
Vol 10 (3) ◽  
pp. 169-184
Author(s):  
Rachna Anand ◽  
Arun Kumar ◽  
Arun Nanda
Keyword(s):  
Physicochemical Properties ◽  
Crystal Engineering ◽  
Pharmacological Action ◽  
Physicochemical Characteristics ◽  
Research Area ◽  
Dissolution Profile ◽  
Design Development ◽  
Drug Molecule ◽  
Wide Range ◽  
Major Factors

Background: Solubility and dissolution profile are the major factors which directly affect the biological activity of a drug and these factors are governed by the physicochemical properties of the drug. Crystal engineering is a newer and promising approach to improve physicochemical characteristics of a drug without any change in its pharmacological action through a selection of a wide range of easily available crystal formers. Objective: The goal of this review is to summarize the importance of crystal engineering in improving the physicochemical properties of a drug, methods of design, development, and applications of cocrystals along with future trends in research of pharmaceutical co-crystals. Co-crystallization can also be carried out for the molecules which lack ionizable functional groups, unlike salts which require ionizable groups. Conclusion: Co-crystals is an interesting and promising research area amongst pharmaceutical scientists to fine-tune the physicochemical properties of drug materials. Co-crystallization can be a tool to increase the lifecycle of an older drug molecule. Crystal engineering carries the potential of being an advantageous technique than any other approach used in the pharmaceutical industry. Crystal engineering offers a plethora of biopharmaceutical and physicochemical enhancements to a drug molecule without the need of any pharmacological change in the drug.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

scholarly journals Conformational analysis and intramolecular interactions in monosubstituted phenylboranes and phenylboronic acids

2013 ◽  
Vol 9 ◽  
pp. 1127-1134 ◽  
Author(s):  
Josué M Silla ◽  
Rodrigo A Cormanich ◽  
Roberto Rittner ◽  
Matheus P Freitas
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Conformational Analysis ◽  
Conformational Equilibrium ◽  
Intramolecular Hydrogen Bonding ◽  
Intramolecular Interactions ◽  
Coupling Constant ◽  
Intramolecular Hydrogen ◽  
Phenylboronic Acids ◽  
Electron Donation

A 1 TS J F,H(O) coupling pathway, dictated by a hydrogen bond, in some 2-fluorobenzoic acids has been observed, while such an interaction does not occur in 2-fluorophenol. Thus, this work reports the conformational analysis of 2-fluorophenylboronic acid (1), in order to evaluate a possible intramolecular OH∙∙∙F hydrogen bond in comparison to an nF→pB interaction, which mimics the quantum nF→σ*OH hydrogen bond that would be expected in 2-fluorophenol. 2-Fluorophenylborane (3), which does not experience hydrogen bonding, was used to verify whether nF→pB interaction governs the conformational equilibrium in 1 due to a predominant OH∙∙∙F hydrogen bond or to other effects. A series of 2-X-phenylboranes (X = Cl, Br, NH2, PH2, OH and SH) were further computationally analyzed to search for electron donors to boron, capable of influencing the conformational equilibrium. Overall, the intramolecular OH∙∙∙F hydrogen bond in 1 is quite stabilizing and dictates the 1 h J F,H(O) coupling constant. Moreover, electron donation to the empty p orbital of boron (for noncoplanar BH2 moiety relative to the phenyl ring) is also significantly stabilizing for the NH2 and PH2 derivatives, but not enough to make the corresponding conformers appreciably populated, because of steric effects and the loss of πCC→pB resonance. Thus, the results found earlier for 2-fluorophenol about the lack of intramolecular hydrogen bonding are now corroborated.

scholarly journals Inhibiting myosin-ATPase reveals a dynamic range of mitochondrial respiratory control in skeletal muscle

2011 ◽  
Vol 437 (2) ◽  
pp. 215-222 ◽  
Author(s):  
Christopher G. R. Perry ◽  
Daniel A. Kane ◽  
Chien-Te Lin ◽  
Rachel Kozy ◽  
Brook L. Cathey ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Dynamic Range ◽  
Energy Charge ◽  
Respiratory Control ◽  
Basic Research ◽  
Dependent Manner ◽  
Atpase Inhibitor ◽  
Wide Range ◽  
The Impact

Assessment of mitochondrial ADP-stimulated respiratory kinetics in PmFBs (permeabilized fibre bundles) is increasingly used in clinical diagnostic and basic research settings. However, estimates of the Km for ADP vary considerably (~20–300 μM) and tend to overestimate respiration at rest. Noting that PmFBs spontaneously contract during respiration experiments, we systematically determined the impact of contraction, temperature and oxygenation on ADP-stimulated respiratory kinetics. BLEB (blebbistatin), a myosin II ATPase inhibitor, blocked contraction under all conditions and yielded high Km values for ADP of >~250 and ~80 μM in red and white rat PmFBs respectively. In the absence of BLEB, PmFBs contracted and the Km for ADP decreased ~2–10-fold in a temperature-dependent manner. PmFBs were sensitive to hyperoxia (increased Km) in the absence of BLEB (contracted) at 30 °C but not 37 °C. In PmFBs from humans, contraction elicited high sensitivity to ADP (Km<100 μM), whereas blocking contraction (+BLEB) and including a phosphocreatine/creatine ratio of 2:1 to mimic the resting energetic state yielded a Km for ADP of ~1560 μM, consistent with estimates of in vivo resting respiratory rates of <1% maximum. These results demonstrate that the sensitivity of muscle to ADP varies over a wide range in relation to contractile state and cellular energy charge, providing evidence that enzymatic coupling of energy transfer within skeletal muscle becomes more efficient in the working state.

scholarly journals Equation of state for rhodium at high pressures

2021 ◽  
Vol 2057 (1) ◽  
pp. 012118
Author(s):  
K V Khishchenko
Keyword(s):  
Experimental Data ◽  
Numerical Simulation ◽  
Equation Of State ◽  
Internal Energy ◽  
Specific Volume ◽  
High Pressures ◽  
Thermodynamic Characteristics ◽  
Wide Range ◽  
Hydrodynamic Processes

Abstract An equation of state has been developed for rhodium in a wide range of changes in the specific volume and internal energy. The results of calculations of the thermodynamic characteristics of this metal are presented in comparison with the available experimental data at high pressures. This equation of state can be used in the numerical simulation of hydrodynamic processes under intense impulse influences on matter.

scholarly journals Role of pK a in establishing the crystal structures of six hydrogen-bonded compounds of 4-methylquinoline with different isomers of chloro- and nitro-substituted benzoic acids

2021 ◽  
Vol 77 (11) ◽  
Author(s):  
Hiroyuki Ishida
Keyword(s):  
Hydrogen Bond ◽  
Shape Index ◽  
Benzoic Acids ◽  
Quinoline Ring ◽  
Nitrobenzoic Acid ◽  
Layer Structures ◽  
Acid And Base ◽  
Short Hydrogen Bond ◽  
Substituted Benzoic Acids ◽  
Hydrogen Bonded

The structures of the six hydrogen-bonded 1:1 compounds of 4-methylquinoline (C10H9N) with chloro- and nitro-substituted benzoic acids (C7H4ClNO4), namely, 4-methylquinolinium 2-chloro-4-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (I), 4-methylquinoline–2-chloro-5-nitrobenzoic acid (1/1), C10H9N·C7H4ClNO4, (II), 4-methylquinolinium 2-chloro-6-nitrobenzoate, C10H9.63N0.63+·C7H3.37ClNO4 0.63−, (III), 4-methylquinolinium 3-chloro-2-nitrobenzoate, C10H9.54N0.54+·C7H3.46ClNO4 0.54−, (IV), 4-methylquinolinium 4-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, (V), and 4-methylquinolinium 5-chloro-2-nitrobenzoate, C10H10N+·C7H3ClNO4 −, have been determined at 185–190 K. In each compound, the acid and base molecules are linked by a short hydrogen bond between a carboxy (or carboxylate) O atom and an N atom of the base. The O...N distances are 2.5652 (14), 2.556 (3), 2.5485 (13), 2.5364 (13), 2.5568 (13) and 2.5252 (11) Å, respectively, for compounds (I)–(VI). In the hydrogen-bonded acid–base units of (III) and (IV), the H atoms are each disordered over two positions with O site:N site occupancies of 0.37 (3):0.63 (3) and 0.46 (3):0.54 (4), respectively, for (III) and (IV). The H atoms in the hydrogen-bonded units of (I), (V) and (VI) are located at the N-atom site, while the H atom in (II) is located at the O-atom site. In all the crystals of (I)–(VI), π–π stacking interactions between the quinoline ring systems and C—H...O hydrogen bonds are observed. Similar layer structures are constructed in (IV)–(VI) through these interactions together with π–π interactions between the benzene rings of the adjacent acid molecules. A short Cl...Cl contact and an N—O...π interaction are present in (I), while a C—H...Cl hydrogen bond and a π–π interaction between the benzene ring of the acid molecule and the quinoline ring system in (II), and a C—H...π interaction in (III) are observed. Hirshfeld surfaces for the title compounds mapped over d norm and shape index were generated to visualize the weak intermolecular interactions.

A threefold interpenetrated two-dimensional zinc(II) supramolecular architecture based on 3-nitrobenzoic acid and 4,4′-bipyridine

2016 ◽  
Vol 72 (2) ◽  
pp. 128-132 ◽  
Author(s):  
Long Tang ◽  
Ji-Jiang Wang ◽  
Feng Fu ◽  
Sheng-Wen Wang ◽  
Qi-Rui Liu
Keyword(s):  
Coordination Polymers ◽  
Crystal Engineering ◽  
Critical Factor ◽  
Building Blocks ◽  
Zigzag Chain ◽  
Great Success ◽  
Supramolecular Architecture ◽  
Two Dimensional ◽  
Hydrothermal Conditions ◽  
Nitrobenzoic Acid

With regard to crystal engineering, building block or modular assembly methodologies have shown great success in the design and construction of metal–organic coordination polymers. The critical factor for the construction of coordination polymers is the rational choice of the organic building blocks and the metal centre. The reaction of Zn(OAc)2·2H2O (OAc is acetate) with 3-nitrobenzoic acid (HNBA) and 4,4′-bipyridine (4,4′-bipy) under hydrothermal conditions produced a two-dimensional zinc(II) supramolecular architecture,catena-poly[[bis(3-nitrobenzoato-κ2O,O′)zinc(II)]-μ-4,4′-bipyridine-κ2N:N′], [Zn(C7H4NO4)2(C10H8N2)]nor [Zn(NBA)2(4,4′-bipy)]n, which was characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis and single-crystal X-ray diffraction analysis. The ZnIIions are connected by the 4,4′-bipy ligands to form a one-dimensional zigzag chain and the chains are decorated with anionic NBA ligands which interact further through aromatic π–π stacking interactions, expanding the structure into a threefold interpenetrated two-dimensional supramolecular architecture. The solid-state fluorescence analysis indicates a slight blue shift compared with pure 4,4′-bipyridine and HNBA.

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