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Synthesis and Conformational Studies of Some Metacyclophane Compounds  [PDF]
Louis Korbla Doamekpor, Vincent Kodzo Nartey, Raphael Kwaku Klake, Takehiko Yamato
International Journal of Organic Chemistry (IJOC) , 2012, DOI: 10.4236/ijoc.2012.22023
Abstract: Various [3.3.3]metacyclophane derivatives were synthesized from 6,15,24-tri-tert-butyl-9,18,27-trimethoxy [3.3.3] metacyclophane-2,11,20-trione 1 using simple chemical reactions. The conformations of the synthesized compounds were studied using mainly solution Proton Nuclear Magnetic Resonance (1H NMR) spectroscopic methods. Two of the synthesized compounds 5, 6, were found to have a partial cone conformation with the third, 4, having the cone conformation. Detailed variable temperature Proton Nuclear Magnetic Resonance studies further confirmed the partialcone conformation for the two products, 5, 6. During the variable temperature nuclear magnetic resonance spectroscopic studies, 6,15,24-tri-tert-butyl-9,18,27-trimethoxy[3.3.3]metacyclophane-2,11,20-triol was found to have a coalescence temperature of about 0?C.
Conformational Study of New AZT Derivatives  [PDF]
M. T. Baumgartner,M. I. Motura,A. B. Pierini,M. C. Bri?ón
Molecules , 2000, DOI: 10.3390/50300409
Abstract: A conformational study of three new AZT derivatives was made by semiempirical methods in order to find a structural correlation between these derivatives and AZT.
A conformational study of proline derivatives
M.E. Kamwaya, F.N. Ngassapa
Bulletin of the Chemical Society of Ethiopia , 2002,
Abstract: From the study of the structures and molecular conformations of a number of proline derivatives, some conclusions were drawn. The widening effect of angle C-C'-N' is caused by steric repulsion between a hydrogen atom at C of the preceding prolyl residue with any other at either C or C of the pyrrolidine ring cis to it. This effect is influenced by the distance between the said hydrogen atoms: the nearer this distance is, the greater is the steric repulsion and the wider is the angle of steric repulsion. The ratio of the angle of steric repulsion to the distance between C and the following C (or C) cis to it is approximately 40 and 41 for peptides with trans and cis configurations, respectively. The torsion angle ranges for 1, 3, 4, and in these derivatives are widened more than usual. The highest vibration, which more often takes place at either the C or C of the pyrrolidine ring, does so not necessarily at the one that is puckered. A -relationship is established, for the determination of -helixity or collageneity, also in small peptides and amino acids that contain proline. The -relationship is versatile and gives about +180o and 180o for the two categories, respectively. The distance between the carbonyl and hydroxyl (or otherwise) terminal end atoms is minimal (2.2 ) and constant, for all peptides. The ratios of the angles at the carbonyl carbons (O'-C'-N') or (O'-C'-O') to this distance is also constant: 56 and 57 for the cis and trans confirgurations, respectively; i.e. a proline O'-C'-N'- (or O'-C'-O')-test, hereinafter called the CT-test, has been established for the determination of cis and trans configurations. It is also established in these proline derivatives, that whereas puckering takes place at C for the CS form, it does so at C for the C2 form. (Received December 10, 2001; revised June 13, 2002) (Bulletin of The Chemical Society of Ethiopia: 2002 16 (2): 199-206)
A conformational study of proline derivatives  [cached]
M.E. Kamwaya,F.N. Ngassapa
Bulletin of the Chemical Society of Ethiopia , 2002,
Abstract: From the study of the structures and molecular conformations of a number of proline derivatives, some conclusions were drawn. The widening effect of angle Cα-C'-N' is caused by steric repulsion between a hydrogen atom at Cα of the preceding prolyl residue with any other at either Cα or Cδ of the pyrrolidine ring cis to it. This effect is influenced by the distance between the said hydrogen atoms: the nearer this distance is, the greater is the steric repulsion and the wider is the angle of steric repulsion. The ratio of the angle of steric repulsion to the distance between Cα and the following Cα (or Cδ) cis to it is approximately 40 and 41 for peptides with trans and cis configurations, respectively. The torsion angle ranges for χ1, χ3, χ 4, θ and φ in these derivatives are widened more than usual. The highest vibration, which more often takes place at either the Cβ or Cγ of the pyrrolidine ring, does so not necessarily at the one that is puckered. A Δ&psi -relationship is established, for the determination of α-helixity or collageneity, also in small peptides and amino acids that contain proline. The Δ&psi-relationship is versatile and gives about +180o and –180o for the two categories, respectively. The distance between the carbonyl and hydroxyl (or otherwise) terminal end atoms is minimal (2.2 ) and constant, for all peptides. The ratios of the angles at the carbonyl carbons (O'-C'-N') or (O'-C'-O') to this distance is also constant: 56 and 57 for the cis and trans confirgurations, respectively; i.e. a proline O'-C'-N'- (or O'-C'-O')-test, hereinafter called the CT-test, has been established for the determination of cis and trans configurations. It is also established in these proline derivatives, that whereas puckering takes place at Cβ for the CS form, it does so at Cγ for the C2 form.
Structural Conformational Study of Eugenol Derivatives Using Semiempirical Methods  [PDF]
Radia Mahboub
Advances in Chemistry , 2014, DOI: 10.1155/2014/490358
Abstract: We investigated the conformational structure of eugenol and eugenyl acetate under torsional angle effect by performing semiempirical calculations using AM1 and PM3 methods. From these calculations, we have evaluated the strain energy of conformational interconversion. To provide a better estimate of stable conformations, we have plotted the strain energy versus dihedral angle. So, we have determined five geometries of eugenol (three energy minima and two transition states) and three geometries of eugenyl acetate (two energy minima and one transition state). From the molecular orbital calculations, we deduce that the optimized trans form by AM1 method is more reactive than under PM3 method. We can conclude that both methods are efficient. The AM1 method allows us to determine the reactivity and PM3 method to verify the stability. 1. Introduction Eugenol (4-allyl-2-methoxyphenol) is a phenylpropene, an allyl chain-substituted guaiacol. It is the main phenolic compound extracted from certain essential oils especially from clove oil, nutmeg, cinnamon, basil, and bay leaf [1–14]. Eugenol is a phenol derivative used in many areas such as perfumes, flavorings agent, and dental materials. It is used as an antiseptic, analgesic, fungicide, bactericide, insecticide, anticarcinogenic, antiallergic, antioxidant, anti-inflammatory, and so forth [15–17]. As derivative, the eugenyl acetate was characterized and its structural properties have investigated by Dos Santos et al. [18, 19]. To our knowledge, a study of the conformational structure as a function of the dihedral angle was not reported. In the present paper, we investigated the conformational structure of eugenol and eugenyl acetate under torsional angle effect by performing semiempirical calculations using AM1 and PM3 methods. From these calculations, we have evaluated the strain energy of conformational interconversion to provide a better estimate of stable conformations. These results can be used to make future applications possible (Figure 1). Figure 1: Conformation structures of cis-eugenol and cis-eugenyl acetate. 2. Methodology Molecular modeling of the optimized eugenol and eugenyl acetate was carried out with the use of an efficient program for molecular mechanics (MM). Calculations are performed for all optimized geometries using AM1 and PM3 methods. The main molecular properties to characterize the geometry structures and the molecular orbital of the eugenyl acetate were calculated and compared. For each method, the geometry of the compound was optimized by using the Polak-Ribiere conjugate gradient
Intramolecular tautomerisation and the conformational variability of some classical mutagens – cytosine derivatives: quantum chemical study  [PDF]
Brovarets’ O. O.,Hovorun D. M.
Biopolymers and Cell , 2011,
Abstract: Aim. To determine the lifetime of the mutagenic cytosine derivatives through the investigation of the physicochemical mechanisms of their intramolecular proton transfer. Methods. Non-empirical quantum chemistry, the analysis of the electron density by means of Bader’s atoms in molecules (AIM) theory and physicochemical kinetics were used. Results. It is shown that the modification of all investigated compounds, except DCyt, prevents their pairing in both mutagenic and canonical tautomeric forms with a base which is an interacting partner. This effect can inhibit their mutagenic potential. It is also established that Watson-Crick tautomeric hypothesis can be formally expanded for the investigated molecules so far as a lifetime of the mutagenic tautomers much more exceeds characteristic time for the incorporation of one nucleotides pair by DNA biosynthesis machinery. It seems that just within the frame of this hypothesis it will be possible to give an adequate explanation of the mechanisms of mutagenic action of N4-aminocytosine, N4-methoxycytosine, N4-hydroxycytosine and N4dehydrocytosine, which have much more energy advantageous imino form in comparison with amino form. Conclusions. For the first time the comprehensive conformational analysis of a number of classical mutagens, namely cytosine derivatives, has been performed using the methods of non-empirical quantum chemistry at the MP2/6-311++G (2df,pd)//B3LYP/6-311++G(d,p) level of theory
Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular Recognition  [PDF]
Yonatan Savir, Tsvi Tlusty
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0000468
Abstract: To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This raises a basic question: Does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target; that is, a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.
Conformational Proofreading: The Impact of Conformational Changes on the Specificity of Molecular Recognition  [PDF]
Yonatan Savir,Tsvi Tlusty
Quantitative Biology , 2010, DOI: 10.1371/journal.pone.0000468.
Abstract: To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve conformational changes. This arises a basic question: does molecular recognition gain any advantage by such conformational changes? By introducing a simple statistical-mechanics approach, we study the effect of conformation and flexibility on the quality of recognition processes. Our model relates specificity to the conformation of the participant molecules and thus suggests a possible answer: Optimal specificity is achieved when the ligand is slightly off target, that is a conformational mismatch between the ligand and its main target improves the selectivity of the process. This indicates that deformations upon binding serve as a conformational proofreading mechanism, which may be selected for via evolution.
Synthesis and conformational analysis of new derivatives of 7-chloro-1,3-dihydro-5-phenyl-2h-1,4-benzodiazepine-2-one  [PDF]
Gholamhassan Imanzadeh,Zahra ArastehFard,Yaser Sadra
Physics , 2011,
Abstract: 1,4-benzodiazepine-2-ones and their derivatives are prominent structures in medicinal chemistry. These biomolecules have wide biological activities and posses therapeutic applications. In this works, we introduce new derivatives of 1,4-benzodiazepine-2-ones which are synthesized using michael addition reaction of 7-chloro- 1,3-dihydro-5-phenyl-2H-1,4-benzodiazepine-2-ones with fumaric esters that matches with green chemistry protocols. The structures of all products are confirmed by FT-IR, 1H-NMR, 13C-NMR and MASS spectroscopy. Since the stereochemistry of 1,4-benzo diazepine-2-ones is important, we study the most stable conformer of one of the products as a model for conformational analysis by hyper chem soft ware and semi empirical AM1 program. Also, using the 1H-NMR spectrum, we investigate the produced diastereomers of one of products as a model.
CONFORMATIONAL ANALYSIS: A REVIEW  [PDF]
Jasmine Uthuppan*1 and Kriti Soni 2
International Journal of Pharmaceutical Sciences and Research , 2013,
Abstract: Conformational analysis is an important step in molecular modeling as it is necessary to reduce time spent in screening of compounds for activity. Most drugs are flexible molecules with the ability to adopt different conformations by means of rotation about single bonds. Conformations play an important role in prediction of not just physico-chemical properties but also the biological activity of the drug. This review details the various methods involved in conformational analysis. The major objective of conformational analysis is to gain insight on conformational characteristic of drugs and also to identify the relation between the role of conformational flexibility and their activity.
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