Hello;
we have purified a new molecule, a hydroxamic acid, which has demonstrated very remarkable antibacterial activity. we synthesized the molecule itself, but the latter did not demonstrate any bacterial or other activity. How can we explain these observations, stereochemistry, stability?
You say: "we have purified a new molecule" and "we synthesized the molecule itself." Are you sure that you are dealing with the same compound in both cases?
Yurii V Geletii precisely the HPLC peaks for the natural and synthesized molecule seemed the same I don't know if that's enough to say it's the same molecule
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When characterizing organic products, a combination of analytical techniques is often employed to gain a comprehensive understanding of their structure, purity, and properties
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Here's a standard set of techniques commonly used:
1. Spectroscopy
- Nuclear Magnetic Resonance (NMR) Spectroscopy: This is a powerful technique for determining the structure of organic compounds by providing detailed information about the connectivity and environment of atoms, especially hydrogen (¹H NMR) and carbon (¹³C NMR).
- Infrared (IR) Spectroscopy: IR spectroscopy helps identify the functional groups present in a molecule by analyzing the absorption of infrared radiation at characteristic frequencies.
- Ultraviolet-Visible (UV-Vis) Spectroscopy: This technique is particularly useful for detecting and characterizing conjugated systems (alternating double and single bonds) in organic molecules by measuring their absorption of UV-Vis light.
2. Mass spectrometry (MS)
- MS provides information about the molecular weight and the fragmentation pattern of a molecule when it is ionized. This data can be used to confirm the molecular formula and gain insights into the structure.
- Tandem mass spectrometry (MS/MS) techniques can further enhance structural elucidation by providing fragmentation patterns of selected ions, which can help to establish relationships between fragments and pinpoint specific functional groups within a molecule.
3. Chromatography
- Gas Chromatography (GC): GC is ideal for separating volatile organic compounds based on their interaction with a stationary phase and a gaseous mobile phase.
- High-Performance Liquid Chromatography (HPLC): HPLC is used to separate non-volatile or thermally unstable compounds dissolved in a liquid mobile phase, with components separating based on their interaction with the stationary phase.
- Chromatographic techniques are also crucial for assessing the purity of organic compounds, as impurities will manifest as separate peaks on the chromatogram.
4. Elemental analysis
- CHNX Analysis (Combustion Analysis): This technique determines the percentage of carbon (C), hydrogen (H), nitrogen (N), and other heteroatoms (X, such as halogens or sulfur) in an organic compound by combusting the sample and analyzing the resulting gases. This information helps confirm the chemical formula and assess purity.
5. Other techniques
- Melting Point and Boiling Point Determination: Pure organic compounds have specific melting and boiling points, so comparing the measured values with known standards can indicate the purity of a substance.
- X-Ray Crystallography: This technique determines the precise three-dimensional structure of a crystalline organic compound.
Important Note: The specific combination of techniques used will depend on the nature of the organic product, the information required (e.g., structure confirmation, impurity detection, quantification), and the available resources. Utilizing multiple techniques provides orthogonal data and helps build a robust characterization of the compound.
Yurii's comments are very important to your work
In addition,Tell us your protocol. Hydroxamic acid (HA) function as chelators with efficacy based on divalent cation (esp. Fe and less so Mg) affinity vs. siderophores of target microbes. You should ensure the same divalent cations in both preps.
HA's are best vs. fungi as bacterial siderophores - esp. those of Gram negative bacteria - have greater affinity for such critical divalent cations.
Phil Geis Thank you for your response. for my molecule is a very good chelator, I managed to complex it with zinc, iron, cobalt, and even copper. I tested their activities and I had some activity against pseudomenase. E.coli and others, in complexation, the DFT has shown better stability. I have read many articles that specifically talk about Z and E configurations. Even if we synthesize, we need to find the best configuration with the best rotation.
Phil Geis doi:10.1111/lam.12412 in this article all protocol figurate here
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