my suggestion is as below (which can be wrong but might be helpful)

Yes, it is absolutely possible for phosphoramidite diastereomers to have different Rf values on silica TLC and the same Rf on alumina TLC. Your results are a classic example of how the choice of stationary phase can dramatically alter the outcome of a chromatographic separation, especially for sensitive molecules like phosphoramidites.

The Detailed Analysis

1. Formation of Diastereomers: The Heart of the Matter

Your synthesis is designed to create diastereomers. Here’s why:

• Starting Material Chiral Center: You begin with a secondary chiral alcohol, which you’ve specified has the (S) configuration. This is your first stereocenter.
• New Chiral Center: The phosphorus atom in a phosphoramidite is trivalent and bonded to three different groups (an oxygen from your alcohol, a nitrogen from diisopropylamine, and an oxygen from the cyanoethoxy group). This makes the phosphorus atom a new stereocenter.

The reaction is:

(S)‑R‑OH + Cl‑P(OCH₂CH₂CN)(N(iPr)₂) —[Et₃N, DCM]→ (S)‑R‑O‑P(OCH₂CH₂CN)(N(iPr)₂)

Since the starting chloro(diisopropylamino)-β-cyanoethoxyphosphine is racemic at the phosphorus center, and the reaction conditions are not stereoselective for the phosphorus, you will form two products:

These two products are diastereomers. Diastereomers have different physical properties, including melting points, boiling points, solubilities, and, crucially for chromatography, different interactions with a chiral or even an achiral stationary phase. Therefore, it is expected that you would be able to separate them chromatographically.

2. Behavior on Silica Gel (SiO₂) TLC

Silica gel is the most common stationary phase. Its surface is covered with silanol groups (Si-OH). These groups make the silica surface polar and distinctly acidic.

• Separation of Diastereomers: The two diastereomers, (S, Rp) and (S, Sp), have different three-dimensional shapes. This means that the various polar functional groups (the P-N bond, the ether oxygens, the cyano group -CN) are oriented differently in space relative to the chiral alcohol moiety. One diastereomer might be able to present its most basic/polar sites (like the lone pair on the phosphorus or nitrogen) more readily for hydrogen bonding with the acidic silanol groups. The other diastereomer might have these sites more sterically hindered.The more strongly interacting diastereomer will be retained more on the silica gel, resulting in a lower Rf value. The less strongly interacting diastereomer will elute faster, resulting in a higher Rf value. Your spot with Rf ≈ 0.3 is likely one of your diastereomers (or a mixture of both if they are very close in polarity).
• The Baseline Spot (The “Ghost” in the Machine): This is the most critical observation. Phosphoramidites are notoriously sensitive to acid. The P-N bond is particularly labile. The acidic silanol groups on the surface of the silica gel can catalyze the hydrolysis of your phosphoramidite, especially if there is any trace moisture in your eluent or on the plate.The likely reaction on the silica surface is hydrolysis:

R‑O‑P(OR′)(NR″₂) + H₂O —[SiO₂ (acid catalyst)]→ R‑O‑P(H)(O)(OR′) + HNR″₂

The product formed is an H-phosphonate. H-phosphonates are significantly more polar than the starting phosphoramidite because of the P=O bond and the acidic P-H proton. This highly polar byproduct will have a very strong affinity for the polar silica gel and will not move from the baseline.

• The “Pure” Sample Observation: You noted that after isolating the less polar compound (Rf ≈ 0.3) by flash chromatography, a new TLC of this “pure” fraction still showed a spot on the baseline. This is the smoking gun. It confirms that your phosphoramidite is decomposing on the TLC plate itself to generate the baseline impurity. The same decomposition was likely happening during your flash column chromatography, which also uses silica gel.

3. Behavior on Alumina (Al₂O₃) TLC

Alumina is a different beast. Chromatographic-grade alumina is typically treated to be neutral or slightly basic, although acidic alumina also exists. We will assume you used neutral alumina, which is most common.

• Interaction Mechanism: Neutral alumina’s surface has Lewis acidic sites (Al³⁺) and Lewis basic sites (O²⁻). It is a “harder” Lewis acid/base adsorbent compared to the “harder” proton-donating silica. The interactions are more based on coordination and strong dipole interactions rather than the specific hydrogen bonding of silica.
• Why the Diastereomers Have the Same Rf:Suppressed Decomposition: The neutral or basic nature of the alumina plate prevents the acid-catalyzed hydrolysis of the P-N bond. Therefore, you do not see the formation of the highly polar baseline spot. Your compound is stable during the TLC run. Loss of Selectivity: The specific interactions that allowed silica to differentiate between the two diastereomers (subtle differences in hydrogen bond accessibility) do not exist or are not dominant on the alumina surface. The primary interactions with alumina might be with the cyano group or the phosphate backbone, and these interactions may be sterically identical for both diastereomers. If the part of the molecule that “docks” with the alumina surface is the same for both diastereomers, they will not be separated and will co-elute, appearing as a single spot.
• Why the Rf Value Changed (≈0.3 to ≈0.5): The overall interaction of your molecule with alumina is weaker than with silica in your chosen eluent system (Hex/EtOAc 4:1). This is why the spot moved further up the plate, resulting in a higher Rf value.

A Unified Hypothesis for Your Observations

What to Expect from Your Analyses and Next Steps