scholarly journals Structure-Activity Relationships of Sandalwood Odorants: Synthesis of a New Campholene Derivative

2010 ◽  
Vol 5 (9) ◽  
pp. 1934578X1000500
Author(s):  
Iris Stappen ◽  
Joris Höfinghoff ◽  
Gerhard Buchbauer ◽  
Peter Wolschann
Keyword(s):  
Structural Changes ◽  
Great Influence ◽  
Complete Loss ◽  
Side Chain ◽  
Side Chains ◽  
Quaternary Carbon ◽  
Structural Modifications ◽  
Structure Activity ◽  
Highly Sensitive ◽  
Sandalwood Odorants

Structural modifications of natural (-)-( Z)-β-santalol have shown that the sandalwood odor impression is highly sensitive, even to small structural changes. Particularly, the substitution of the quaternary carbon is of great influence on the scent. Epi-compounds with side chains in the endo-position possess sandalwood odor in only a few derivatives, whereas modifications at this side chain, as well as modification at the bicyclic ring systems mostly lead to a complete loss of sandalwood fragrance.

Effects of heme modification on oxygen affinity and cooperativity of human adult hemoglobin

2015 ◽  
Vol 19 (01-03) ◽  
pp. 301-307 ◽  
Author(s):  
Tomokazu Shibata ◽  
Eisuke Furuichi ◽  
Kiyohiro Imai ◽  
Akihiro Suzuki ◽  
Yasuhiko Yamamoto
Keyword(s):  
Structural Changes ◽  
Oxygen Affinity ◽  
Side Chain ◽  
Side Chains ◽  
Human Adult ◽  
Alkaline Transition ◽  
Functional Control ◽  
Adult Hemoglobin ◽  
The Relationship ◽  
Heme Cofactor

We substituted strongly electron-withdrawing trifluoromethyl ( CF 3) group(s) as heme side chain(s) of human adult hemoglobin (Hb) to achieve large alterations of the heme electronic structure, in order to elucidate the relationship between the oxygen ( O 2) binding properties of Hb and the electronic properties of heme peripheral side chains. The obtained results were compared with those of similar studies performed on myoglobin (Mb), e.g. (Nishimura R, Matsumoto D, Shibata T, Yanagisawa S, Ogura T, Tai H, Matsuo T, Hirota S, Neya S, Suzuki A, and Yamamoto Y. Inorg. Chem. 2014; 53: 9156–9165). These two proteins shared the common feature of a decrease in O 2 affinity upon the CF 3 substitution(s). Using the P50 value, which is the partial pressure of O 2 required for 50% oxygenation of a protein, and the equilibrium constant ( p K a ) of the "acid-alkaline transition" in the met form of a protein as measures of the O 2 affinity and the electron density of heme Fe atom of the protein, respectively, a linear p K a - log (1/P50) relationship was demonstrated for the Hb and Mb systems. The native Hb, however, deviated from the p K a - log (1/P50) relationship, while the native Mb followed it. These results highlighted the significance of the vinyl side chains of the heme cofactor in the functional control of Hb through tertiary and quaternary structural changes upon the oxygenation of the protein.

scholarly journals Structural Features Defining NF-κB Inhibition by Lignan-Inspired Benzofurans and Benzothiophenes

Biomolecules ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1131
Author(s):  
Toan Dao-Huy ◽  
Simone Latkolik ◽  
Julia Bräuer ◽  
Andreas Pfeil ◽  
Hermann Stuppner ◽  
...  
Keyword(s):  
Significant Influence ◽  
Inhibitory Activity ◽  
Structure Activity Relationship ◽  
Structural Features ◽  
Activity Relationship ◽  
Side Chain ◽  
Side Chains ◽  
Substitution Pattern ◽  
Structure Activity

A series of 2-arylbenzofurans and 2-arylbenzothiophenes was synthesized carrying three different side chains in position five. The synthesized compounds were tested for NF-κB inhibition to establish a structure activity relationship. It was found that both, the side chain in position five and the substitution pattern of the aryl moiety in position two have a significant influence on the inhibitory activity.

scholarly journals Temperature dependant structural changes in thin films of random semifluorinated PMMA copolymers

2013 ◽  
Vol 28 (S2) ◽  
pp. S144-S160 ◽  
Author(s):  
Dieter Jehnichen ◽  
Peter Friedel ◽  
Romy Selinger ◽  
Andreas Korwitz ◽  
Martin Wengenmayr ◽  
...  
Keyword(s):  
Thin Films ◽  
Phase Separation ◽  
Structural Changes ◽  
Bulk Material ◽  
Fluorine Content ◽  
Film Surface ◽  
Phase Behaviour ◽  
Side Chain ◽  
Side Chains ◽  
Polymer Backbone

Semifluorinated (SF) side chain polymers show phase separation between polymer backbone and SF side chains. Due to strong interaction between SF segments the side chains determine the structure behaviour strongly, often resulting in layered structures in which backbones and layers of SF side chains alternate. The interest in this work was directed to find out the dependence of these structures on concentration of SF side chains. Thin films of random copolymers consisting of methylmethacrylate (MMA) and semifluorinated side chain methacrylate (SFMA) segments and with different fluorine content in the perfluoroalkyl side chains (abbreviated as H10F10 and H2F8) were prepared by spin-coating. Phase separation and structure changes were initiated by external subsequent annealing. Corresponding bulk material served as basic information. Generation of ordered structures and variation of film parameters were observed using different X-ray scattering methods (XRR, GIWAXS, and GISAXS). The phase behaviour in bulk is governed by the SF side chain amount and their specific fluorine content which control the self-organization tendency of SF side chains. Additionally, the confinement in thin films generates an orientation of side chains normally to film surface.

scholarly journals Crystallization of dienelactone hydrolase in two space groups: structural changes caused by crystal packing

2014 ◽  
Vol 70 (7) ◽  
pp. 884-889 ◽  
Author(s):  
Joanne L. Porter ◽  
Paul D. Carr ◽  
Charles A. Collyer ◽  
David L. Ollis
Keyword(s):  
Structural Changes ◽  
Crystal Packing ◽  
Side Chain ◽  
Side Chains ◽  
Citrate Buffer ◽  
Space Group ◽  
Space Groups ◽  
Crystal Contacts ◽  
Dienelactone Hydrolase ◽  
Substrate Inhibitor

Dienelactone hydrolase (DLH) is a monomeric protein with a simple α/β-hydrolase fold structure. It readily crystallizes in space groupP212121from either a phosphate or ammonium sulfate precipitation buffer. Here, the structure of DLH at 1.85 Å resolution crystallized in space groupC2 with two molecules in the asymmetric unit is reported. When crystallized in space groupP212121DLH has either phosphates or sulfates bound to the protein in crucial locations, one of which is located in the active site, preventing substrate/inhibitor binding. Another is located on the surface of the enzyme coordinated by side chains from two different molecules. Crystallization in space groupC2 from a sodium citrate buffer results in new crystallographic protein–protein interfaces. The protein backbone is highly similar, but new crystal contacts cause changes in side-chain orientations and in loop positioning. In regions not involved in crystal contacts, there is little change in backbone or side-chain configuration. The flexibility of surface loops and the adaptability of side chains are important factors enabling DLH to adapt and form different crystal lattices.

scholarly journals Prostaglandin receptors on human platelets. Structure-activity relationships of stimulatory prostaglandins

1978 ◽  
Vol 174 (3) ◽  
pp. 921-929 ◽  
Author(s):  
D E MacIntyre ◽  
E W Salzman ◽  
J L Gordon
Keyword(s):  
Human Platelets ◽  
Side Chain ◽  
Similar Response ◽  
Synthetic Analogues ◽  
Induce Platelet Aggregation ◽  
Structural Modifications ◽  
Endogenous Prostaglandin ◽  
Side Chain Conformation ◽  
Dense Bodies ◽  
Structure Activity

1. Synthetic analogues of prostaglandins E2 or F2a (monocyclic bisenoic prostaglandins), like the endogenous prostaglandin endoperoxides (prostaglandins G2 and H2) from platelets, and like synthetic analogues of prostaglandin H2 (bicyclic bisenoic prostaglandins), can induce aggregation of human platelets, although prostaglandins E2 and F2a themselves are inactive. 2. All the prostanoid compounds that induce platelet aggregation release 5-hydroxytryptamine from platelet dense bodies, but do not release beta-N-acetylglucosaminidase from lysosomal granules. Arachidonic acid evokes a similar response. 3. All endoperoxide analogues tested (bicyclic compounds) were powerful platelet stimulants, and all active compounds (whether mono- or bi-cyclid) apparently acted via the same receptor as the endogenous prostaglandin endoperoxides. 4. The nature and stereospecificity of substituents at positions 11 and 15 (or 16) on prostaglandin E2 are critical determinants for platelet-stimulating activity: deoxy substitution at position 11 plus methylation at position 15 (or 16) produces a potent stimulant, particularly if the groups around C-15 are in the S configuration. 5. The effects of these structural modifications are apparently due to, at least in part, a change in side-chain conformation.

scholarly journals Revealing Structural Modifications of Lignin in Acidic γ-Valerolactone-H2O Pretreatment

Polymers ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 116
Author(s):  
Suxiang Li ◽  
Chengke Zhao ◽  
Fengxia Yue ◽  
Fachuang Lu
Keyword(s):  
Structural Changes ◽  
Solvent System ◽  
Side Chain ◽  
Solvent Mixtures ◽  
Aryl Ether ◽  
Structural Modifications ◽  
System A ◽  
Nmr Characterization ◽  
Lignin Model

γ-valerolactone (GVL)/H2O/acid solvent mixtures has been used in chemical pretreatment of lignocellulosic biomass, it was claimed that GVL lignins were structurally close to proto (native) lignins, or having low molecular weight with narrow polydispersity, however, the structural changes of GVL lignins have not been investigated. In this study, β-O-4 (β-aryl ether, GG), β-5 (phenylcoumaran), and β-β (resinol) lignin model compounds were treated by an acidic GVL-H2O solvent system, a promising pretreatment of lignocellulose for biomass utilization, to investigate the structural changes possibly related to the lignin involved. NMR characterization of the products isolated from the treated GG indicated that a phenyl dihydrobenzofuran, having typical C-H correlations at δC/δH 50.74/4.50 and 93.49/4.60 ppm in its HSQC spectrum, was produced from GG. In the pretreatment, the released formaldehyde from GG reacted fast with GG to form a novel 1,3-dioxane intermediate whose characteristic HSQC signals were: δC/δH 94.15–94.48/4.81–5.18 ppm and 80.82–83.34/4.50–4.94 ppm. The β-5 model, dihydrodehydrodiconiferyl alcohol, was converted into phenylcoumarone and stilbene having benzaldehyde that resulted from the allyl alcohol side chain. The β-β model, syringaresinol, was isomerized to form a mixture of syringaresinol, epi-, and dia-syringaresinol although being degraded slightly.

scholarly journals Synthesis of Macrocyclic Hexaoxazole (6OTD) Dimers, Containing Guanidine and Amine Functionalized Side Chains, and an Evaluation of Their Telomeric G4 Stabilizing Properties

2010 ◽  
Vol 2010 ◽  
pp. 1-9 ◽  
Author(s):  
Keisuke Iida ◽  
Masayuki Tera ◽  
Takatsugu Hirokawa ◽  
Kazuo Shin-ya ◽  
Kazuo Nagasawa
Keyword(s):  
Functional Groups ◽  
Dna Sequence ◽  
Activity Relationship ◽  
Potassium Cation ◽  
Side Chain ◽  
Side Chains ◽  
Amine Functionalized ◽  
Structure Activity ◽  
G4 Dna ◽  
Functionalized Side

Structure-activity relationship studies were carried out on macrocyclic hexaoxazole (6OTD) dimers, whose core structure stabilizes telomeric G-quadruplexes (G4). Two new 6OTD dimers having side chain amine and guanidine functional groups were synthesized and evaluated for their stabilizing ability against a telomeric G4 DNA sequence. The results show that the 6OTD dimers interact with the DNA to form 1:1 complexes and stabilize the antiparallel G4 structure of DNA in the presence of potassium cation. The guanidine functionalized dimer displays a potent stabilizing ability of the G4 structure, as determined by using a FRET melting assay (ΔTm=14 °C).

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

scholarly journals Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes

Polymers ◽  
2021 ◽  
Vol 13 (11) ◽  
pp. 1789
Author(s):  
Dmitry Tolmachev ◽  
George Mamistvalov ◽  
Natalia Lukasheva ◽  
Sergey Larin ◽  
Mikko Karttunen
Keyword(s):  
Glutamic Acid ◽  
Chain Length ◽  
Chemical Structure ◽  
Side Chain ◽  
Side Chains ◽  
Side Chain Length ◽  
Polyelectrolyte Brushes ◽  
Grafting Density ◽  
The Difference ◽  
Cellulose Surface

We used atomistic molecular dynamics (MD) simulations to study polyelectrolyte brushes based on anionic α,L-glutamic acid and α,L-aspartic acid grafted on cellulose in the presence of divalent CaCl2 salt at different concentrations. The motivation is to search for ways to control properties such as sorption capacity and the structural response of the brush to multivalent salts. For this detailed understanding of the role of side-chain length, the chemical structure and their interplay are required. It was found that in the case of glutamic acid oligomers, the longer side chains facilitate attractive interactions with the cellulose surface, which forces the grafted chains to lie down on the surface. The additional methylene group in the side chain enables side-chain rotation, enhancing this effect. On the other hand, the shorter and more restricted side chains of aspartic acid oligomers prevent attractive interactions to a large degree and push the grafted chains away from the surface. The difference in side-chain length also leads to differences in other properties of the brush in divalent salt solutions. At a low grafting density, the longer side chains of glutamic acid allow the adsorbed cations to be spatially distributed inside the brush resulting in a charge inversion. With an increase in grafting density, the difference in the total charge of the aspartic and glutamine brushes disappears, but new structural features appear. The longer sides allow for ion bridging between the grafted chains and the cellulose surface without a significant change in main-chain conformation. This leads to the brush structure being less sensitive to changes in salt concentration.

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