The solution structures of chiral Ti4+ alkoxides. II. The roles of diolate basicity and side-chain binding group polarity

1992 ◽  
Vol 70 (8) ◽  
pp. 2256-2265 ◽  
Author(s):  
Stephen Bianchet ◽  
Pierre G. Potvin
Keyword(s):  
Side Chain ◽  
Resonance Spectroscopy ◽  
Side Chains ◽  
Metal Chelation ◽  
Coupling Constant ◽  
Additional Indication ◽  
Solution Structures ◽  
H Nmr ◽  
Spectral Asymmetry ◽  
Sugar Derivatives

With a view to reproduce the structure in solution of the Katsuki–Sharpless catalyst (the dimeric complex formed by homochiral diisopropyl tartrate with Ti(OiPr)4), five C2-symmetric chiral 2,3-butanediols, related to L-threitol but bearing N-, S-, and P-containing groups at the 1- and 4-positions, were prepared and their reactions with Ti(OiPr)4 were examined by nuclear magnetic resonance spectroscopy. The 1,4-dithioether formed a non-fluxional 2:2 tricyclic complex entirely analogous to those formed by alkylated sugar derivatives. The related disulfone formed a similar complex, but only at low temperatures, probably because of oligomerization at higher temperatures. A symmetric 2:1 complex also formed with excess Ti(OiPr)4, but incompletely and in equilibrium with the 2:2 species. No well-defined complexes were formed with pyrazole or phosphine oxide functionalities. However, in the presence of trifluoroacetic acid (TFA), a 1:2:2 L:Ti:TFA complex was identified with the dimethylpyrazole-containing diol and this resembled the 2:3 complexes formed by tartramides. Generally, the degree of spectral asymmetry and the coupling constant between diolate protons were instrumental in assigning structures and were used to classify all chiral diolate complexes into two groups according to whether or not they exhibited metal chelation and diolate bridging. By comparison of the effects of complexation on the diolate nuclei, a correlation was found between 13C and 1H nmr signal positions and between the pairs of signals in the spectra of asymmetric complexes, except in four cases where metal-bound side-chain groups induced a shielding of the bridging diolate proton. This could serve as an additional indication of metal chelation and diolate bridging and confirmed that nuclei at bridging positions appeared upfield of terminal ones. Noting that all the diols that readily chelated and bridged possessed electron-releasing side chains, while tartrates and tartramides that did not chelate possessed electron-withdrawing side chains, the basicity of the diolate oxygens is considered the most important determinant of structure. Side-chain polarity was instead found to influence whether or not a well-defined complex could form.

NMR and molecular modeling study of active and inactive taxol analogues in aqueous and nonaqueous solution

1994 ◽  
Vol 72 (1) ◽  
pp. 252-260 ◽  
Author(s):  
Howard J. Williams ◽  
A. Ian Scott ◽  
Reiner A. Dieden ◽  
Charles S. Swindell ◽  
Lisa E. Chirlian ◽  
...  
Keyword(s):  
Molecular Modeling ◽  
Water Solution ◽  
Biologically Active ◽  
Side Chain ◽  
Coupling Constant ◽  
Solution Conformation ◽  
Solution Structures ◽  
H Nmr ◽  
Chain Conformations ◽  
Inactive Analog

The conformations of the biologically active taxol analogs Taxotere®, 3R, 4R, and 4S, and the biologically inactive analog 3S were evaluated in CDCl3 and DMSO–water solution using 1H NMR coupling constant and NOESY data and molecular modeling. The solution structures of Taxotere® were very similar to those detected previously for taxol. The A-ring side chain conformations of analogs 3 and 4 could not be defined with the same precision as had been possible for taxol, but the conformational possibilities could be significantly limited by the data. Analogs 3R, 4R, and 4S (but not 3S) can mimic the dominant conformation of taxol in chloroform, but no logical relationship between biological activity and aqueous solution conformation could be detected.

1H and 13C nuclear magnetic resonance and molecular orbital studies of the internal rotational potential and of spin–spin coupling transmission in phenylallene

1995 ◽  
Vol 73 (9) ◽  
pp. 1478-1487 ◽  
Author(s):  
Ted Schaefer ◽  
Scott Kroeker ◽  
David M. McKinnon
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Molecular Orbital ◽  
Coupling Constants ◽  
Spin Coupling ◽  
Side Chain ◽  
Coupling Constant ◽  
H Nmr ◽  
Spin Coupling Constants ◽  
Spin Spin Coupling ◽  
Coupling Mechanisms

The 1H nuclear magnetic resonance spectra of phenylallene, diluted in acetone-d6 and benzene-d6, yield long-range coupling constants over as many as eight formal bonds between the ring and side-chain protons. These are discussed in terms of σ- and π-electron spin–spin coupling mechanisms, which are sensitive to the torsion angle between the allenyl and phenyl fragments. The torsion angle is assessed by means of molecular orbital computations of the internal rotational potential, whose height is calculated as 16.0 kJ/mol at the MP2/6-31G* level of correlation-gradient theory. Comparison with experimental and theoretical internal rotational potentials for styrene suggests that steric repulsions in the planar form of styrene amount to about 4 kJ/mol. In a field of 7.0 T, phenylallene is partially aligned, entailing a positive dipolar coupling constant between the methylene protons, from which absolute signs of the spin–spin coupling constants involving these protons can be inferred. Such coupling constants over seven and eight bonds, to the meta and para protons, are taken as being mediated by the extended π-electron system, providing a measure of π-electron contributions to coupling constants between meta protons and those in side chains (spin correlation). Some coupling constants between protons and 13C nuclei in the side chain, as well as between ring protons and these 13C nuclei, are also discussed in terms of spin coupling mechanisms. Solvent perturbations of one-bond proton–carbon coupling constants in the allenyl group do not follow the usual pattern in which an increase in polarity of the solvent is associated with an increase in the magnitude of the coupling constant. Keywords: 1H NMR, phenylallene; 1H NMR, long-range spin–spin coupling constants in phenylallene; phenylallene, internal rotational potential, molecular orbital computations; molecular orbital calculations, an internal rotational potential in phenylallene.

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.

1H NMR Conformational Studies in Water of Angiotensin II Analogues Modified at the N- and C-Termini: Interactions of the Aromatic Side Chains and Folding of the N-Terminal Domain

1994 ◽  
Vol 59 (11) ◽  
pp. 2523-2532 ◽  
Author(s):  
John Hondrelis ◽  
John Matsoukas ◽  
George Agelis ◽  
Paul Cordopatis ◽  
Ning Zhou ◽  
...  
Keyword(s):  
Shielding Effect ◽  
Resonance Spectroscopy ◽  
Nmr Studies ◽  
Previous Suggestion ◽  
Aminoisobutyric Acid ◽  
H Nmr ◽  
Neutral Ph ◽  
Angiotensin Ii Analogues ◽  
Proton Resonances ◽  
Cosy Nmr

The conformation of [Sar1]angiotensin II in water at neutral pH has been examined by proton magnetic resonance spectroscopy at 400 MHz and in particular by comparing its 1H NMR spectral data with those of analogues modified at positions 1,4 and 6, namely [Sar1,Cha8]ANGII, [Des Asp1,Cha8]ANGII, [Aib1,Tyr(Me)4]ANGII, [Aib1,Tyr(Me)4,Ile8]ANGII, [N-MeAib1,Tyr(Me)4]ANGII, [N-MeAib1,Tyr(Me)4,Ile8]ANGII, ANGIII and [Sar1,Ile8]ANGII. Assignment of all proton resonances in these analogues was made possible by 2D COSY NMR experiments. The H-2 and H-4 protons for the histidine ring in [Sar1]ANGII, ANGII and ANGIII were shielded compared with the same protons in [Sar1,Ile8]ANGII, [Sar1,Cha8]ANGII and [Des Asp1,Cha8]ANGII; this shielding effect was not disturbed upon methylation of the tyrosine hydroxyl and/or replacement of residue 1 (sarcosine or aspartic acid) with aminoisobutyric acid (Aib) or N-methyl aminoisobutyric acid (N-MeAib). These data are consistent with our previous suggestion based on NMR studies in neutral DMSO that a characteristic folded conformation for ANGII previously observed in non-polar solvents can also be detected in water at neutral pH, but to a lesser degree.

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.

scholarly journals Unusual Structural Features in the Adduct of Dirhodium Tetraacetate with Lysozyme

2021 ◽  
Vol 22 (3) ◽  
pp. 1496
Author(s):  
Domenico Loreto ◽  
Giarita Ferraro ◽  
Antonello Merlino
Keyword(s):  
Anticancer Agents ◽  
Structural Features ◽  
Side Chain ◽  
Side Chains ◽  
Valuable Insight ◽  
Experimental Conditions ◽  
Egg White Lysozyme ◽  
Potential Applications ◽  
Model Protein ◽  
Hen Egg White

The structures of the adducts formed upon reaction of the cytotoxic paddlewheel dirhodium complex [Rh2(μ-O2CCH3)4] with the model protein hen egg white lysozyme (HEWL) under different experimental conditions are reported. Results indicate that [Rh2(μ-O2CCH3)4] extensively reacts with HEWL:it in part breaks down, at variance with what happens in reactions with other proteins. A Rh center coordinates the side chains of Arg14 and His15. Dimeric Rh–Rh units with Rh–Rh distances between 2.3 and 2.5 Å are bound to the side chains of Asp18, Asp101, Asn93, and Lys96, while a dirhodium unit with a Rh–Rh distance of 3.2–3.4 Å binds the C-terminal carboxylate and the side chain of Lys13 at the interface between two symmetry-related molecules. An additional monometallic fragment binds the side chain of Lys33. These data, which are supported by replicated structural determinations, shed light on the reactivity of dirhodium tetracarboxylates with proteins, providing useful information for the design of new Rh-containing biomaterials with an array of potential applications in the field of catalysis or of medicinal chemistry and valuable insight into the mechanism of action of these potential anticancer agents.

scholarly journals Synthesis of New Derivatives of BEDT-TTF: Installation of Alkyl, Ethynyl, and Metal-Binding Side Chains and Formation of Tris(BEDT-TTF) Systems

2021 ◽  
Vol 7 (8) ◽  
pp. 110
Author(s):  
Songjie Yang ◽  
Matteo Zecchini ◽  
Andrew Brooks ◽  
Sara Krivickas ◽  
Desiree Dalligos ◽  
...  
Keyword(s):  
Metal Binding ◽  
Tricarboxylic Acid ◽  
Metal Salts ◽  
Side Chain ◽  
Side Chains ◽  
Ethynyl Group ◽  
X Ray ◽  
Transition Metal Salts ◽  
Alkyl Side Chains ◽  
Derivatives Of

The syntheses of new BEDT-TTF derivatives are described. These comprise BEDT-TTF with one ethynyl group (HC≡C-), with two (n-heptyl) or four (n-butyl) alkyl side chains, with two trans acetal (-CH(OMe)2) groups, with two trans aminomethyl (-CH2NH2) groups, and with an iminodiacetate (-CH2N(CH2CO2−)2 side chain. Three transition metal salts have been prepared from the latter donor, and their magnetic properties are reported. Three tris-donor systems are reported bearing three BEDT-TTF derivatives with ester links to a core derived from benzene-1,3,5-tricarboxylic acid. The stereochemistry and molecular structure of the donors are discussed. X-ray crystal structures of two BEDT-TTF donors are reported: one with two CH(OMe)2 groups and with one a -CH2N(CH2CO2Me)2 side chain.

scholarly journals Current Understanding of the Structure, Stability and Dynamic Properties of Amyloid Fibrils

2021 ◽  
Vol 22 (9) ◽  
pp. 4349
Author(s):  
Eri Chatani ◽  
Keisuke Yuzu ◽  
Yumiko Ohhashi ◽  
Yuji Goto
Keyword(s):  
Amyloid Fibrils ◽  
Polypeptide Chain ◽  
Dynamic Properties ◽  
Protein Molecule ◽  
Side Chain ◽  
Structure Stability ◽  
Side Chains ◽  
Precise Control ◽  
Functional Amyloids ◽  
Structural Architecture

Amyloid fibrils are supramolecular protein assemblies represented by a cross-β structure and fibrous morphology, whose structural architecture has been previously investigated. While amyloid fibrils are basically a main-chain-dominated structure consisting of a backbone of hydrogen bonds, side-chain interactions also play an important role in determining their detailed structures and physicochemical properties. In amyloid fibrils comprising short peptide segments, a steric zipper where a pair of β-sheets with side chains interdigitate tightly is found as a fundamental motif. In amyloid fibrils comprising longer polypeptides, each polypeptide chain folds into a planar structure composed of several β-strands linked by turns or loops, and the steric zippers are formed locally to stabilize the structure. Multiple segments capable of forming steric zippers are contained within a single protein molecule in many cases, and polymorphism appears as a result of the diverse regions and counterparts of the steric zippers. Furthermore, the β-solenoid structure, where the polypeptide chain folds in a solenoid shape with side chains packed inside, is recognized as another important amyloid motif. While side-chain interactions are primarily achieved by non-polar residues in disease-related amyloid fibrils, the participation of hydrophilic and charged residues is prominent in functional amyloids, which often leads to spatiotemporally controlled fibrillation, high reversibility, and the formation of labile amyloids with kinked backbone topology. Achieving precise control of the side-chain interactions within amyloid structures will open up a new horizon for designing useful amyloid-based nanomaterials.

scholarly journals Synthesis and antioxidant properties of 2-(3-(hydroxyimino)methyl)-1H-indol-1-yl)acetamide derivatives

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Chandravadivelu Gopi ◽  
Magharla Dasaratha Dhanaraju
Keyword(s):  
Antioxidant Activity ◽  
Condensation Reaction ◽  
Antioxidant Properties ◽  
Side Chain ◽  
Antioxidant Power ◽  
H Nmr ◽  
Antioxidant Agents ◽  
Phenyl Rings ◽  
Ferric Reducing Antioxidant Power ◽  
Ft Ir

Abstract Background The main aim of this work was to synthesise a novel N-(substituted phenyl)-2-(3-(hydroxyimino) methyl)-1H-indol-1-yl) acetamide derivatives and evaluate their antioxidant activity. These compounds were prepared by a condensation reaction between 1H-indole carbaldehyde oxime and 2-chloro acetamide derivatives. The newly synthesised compound structures were characterised by FT-IR, 1H-NMR, mass spectroscopy and elemental analysis. Furthermore, the above-mentioned compounds were screened for antioxidant activity by using ferric reducing antioxidant power (FRAP) and 1,1-diphenyl-2-picrylhydrazyl (DPPH) methods. Result The antioxidant activity result reveals that most of the compounds were exhibiting considerable activity in both methods and the values are very closer to the standards. Among the synthesised compounds, compound 3j, 3a and 3k were shown remarkable activity at low concentration. Conclusion Compounds 3j, 3a and 3k were shown highest activity among the prepared analogues due to the attachment of halogens connected at the appropriate place in the phenyl ring. Hence, these substituted phenyl rings considered as a perfect side chain for the indole nucleus for the development of the new antioxidant agents.

scholarly journals Backbone and nearly complete side-chain chemical shift assignments reveal the human uncharacterized protein CXorf51A as intrinsically disordered

2021 ◽  
Vol 15 (2) ◽  
pp. 441-448
Author(s):  
Christoph Wiedemann ◽  
Kingsley Benjamin Obika ◽  
Sandra Liebscher ◽  
Jan Jirschitzka ◽  
Oliver Ohlenschlãger ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Intrinsically Disordered Protein ◽  
Genome Project ◽  
Side Chain ◽  
Resonance Spectroscopy ◽  
Chemical Shift Assignments ◽  
Uncharacterized Protein ◽  
Protein Coding ◽  
Intrinsically Disordered ◽  
Side Chain Chemical Shift

AbstractEven though the human genome project showed that our DNA contains a mere 20,000 to 25,000 protein coding genes, an unexpectedly large number of these proteins remain functionally uncharacterized. A structural characterization of these “unknown” proteins may help to identify possible cellular tasks. We therefore used a combination of bioinformatics and nuclear magnetic resonance spectroscopy to structurally de-orphanize one of these gene products, the 108 amino acid human uncharacterized protein CXorf51A. Both our bioinformatics analysis as well as the $$^1$$ 1 H, $$^{13}$$ 13 C, $$^{15}$$ 15 N backbone and near-complete side-chain chemical shift assignments indicate that it is an intrinsically disordered protein.

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