From my understanding of magnetic shielding, for every atom there should be one numeric value that describes the magnetic shielding.
\n\nwhy then, there are 8 columns decribing the shielding ?\n* XX YX ... XZ YZ ZZ
\n\nhow should I infer the magnetic shielding from those {XX, XY .. ZZ} columns ?
", "messages": [ { "id": "556640", "postDate": "06/20/2019 13:35:59", "content": "From my understanding of magnetic shielding, for every atom there should be one numeric value that describes the magnetic shielding.
\n\nwhy then, there are 8 columns decribing the shielding ?\n* XX YX ... XZ YZ ZZ
\n\nhow should I infer the magnetic shielding from those {XX, XY .. ZZ} columns ?
", "rawMarkdown": "From my understanding of magnetic shielding, for every atom there should be one numeric value that describes the magnetic shielding.\n\nwhy then, there are 8 columns decribing the shielding ?\n* XX YX ... XZ YZ ZZ\n\nhow should I infer the magnetic shielding from those {XX, XY .. ZZ} columns ?", "votes": null }, { "id": "556677", "postDate": "06/20/2019 14:05:04", "content": "It is a tensor think of it as a 3x3 matrix
\n\nmagnetic_shielding_tensors.csv - contains the magnetic shielding tensors for all atoms in the molecules. The first column (molecule_name) contains the molecule name, the second column (atom_index) contains the index of the atom in the molecule, the third to eleventh columns contain the XX, YX, ZX, XY, YY, ZY, XZ, YZ and ZZ elements of the tensor/matrix respectively.
", "rawMarkdown": "It is a tensor think of it as a 3x3 matrix\n\nmagnetic_shielding_tensors.csv - contains the magnetic shielding tensors for all atoms in the molecules. The first column (molecule_name) contains the molecule name, the second column (atom_index) contains the index of the atom in the molecule, the third to eleventh columns contain the XX, YX, ZX, XY, YY, ZY, XZ, YZ and ZZ elements of the tensor/matrix respectively.", "votes": null }, { "id": "556822", "postDate": "06/20/2019 17:59:54", "content": "X,Y,Z are spread across both positive direction and negative direction. And in 3D's, YX = XY but the directions would be twisted, but in the dataset, they are same. You can just use XY,YZ and XZ and ignore other 3 coordinate axis.
", "rawMarkdown": "X,Y,Z are spread across both positive direction and negative direction. And in 3D's, YX = XY but the directions would be twisted, but in the dataset, they are same. You can just use XY,YZ and XZ and ignore other 3 coordinate axis.", "votes": null }, { "id": "556844", "postDate": "06/20/2019 18:37:28", "content": "Ho ok, \nThat helps :) \nThank you !
", "rawMarkdown": "Ho ok, \nThat helps :) \nThank you !", "votes": null }, { "id": "556845", "postDate": "06/20/2019 18:37:51", "content": "Thank you !
", "rawMarkdown": "Thank you !", "votes": null }, { "id": "558748", "postDate": "06/22/2019 21:14:42", "content": "I am no expert, but this might go some way to answering your question:
\n\n\n", "rawMarkdown": "I am no expert, but this might go some way to answering your question:\n> The formal properties of the magnetic shielding are discussed below, but it is important to understand that while many scientists think about the chemical shift or magnetic shielding as a number associated with each resonant nucleus, in reality the shielding is a tensor quantity. This means that the screening of the external magnetic field by the electron density of the molecule depends on the relative orientation of the external magnetic field and the molecule; therefore, the shielding phenomena has to be described by a tensor instead of a scalar number.\n[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058154/#S3title](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058154/#S3title)", "votes": null }, { "id": "559312", "postDate": "06/23/2019 21:54:51", "content": "The formal properties of the magnetic shielding are discussed below, but it is important to understand that while many scientists think about the chemical shift or magnetic shielding as a number associated with each resonant nucleus, in reality the shielding is a tensor quantity. This means that the screening of the external magnetic field by the electron density of the molecule depends on the relative orientation of the external magnetic field and the molecule; therefore, the shielding phenomena has to be described by a tensor instead of a scalar number.\n https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058154/#S3title
\n
Not all the XYs are the same as the YXs. See entry 17 in magnetic_shielding_tensors.csv, for example.
", "rawMarkdown": "Not all the XYs are the same as the YXs. See entry 17 in magnetic\\_shielding\\_tensors.csv, for example.", "votes": null }, { "id": "561469", "postDate": "06/26/2019 13:19:17", "content": "What you often measure experimentally is the trace of the matrix (sum of XX, YY, ZZ), also named the isotropic chemical shift. This is due to the molecules tumbling around in solution, so any information about their individual orientation is averaged out. But since we know the specific orientation in this case, all the tensor elements are given.
", "rawMarkdown": "What you often measure experimentally is the trace of the matrix (sum of XX, YY, ZZ), also named the isotropic chemical shift. This is due to the molecules tumbling around in solution, so any information about their individual orientation is averaged out. But since we know the specific orientation in this case, all the tensor elements are given.", "votes": null }, { "id": "574715", "postDate": "07/14/2019 11:27:10", "content": "I found this slide pack which might be useful (slides 15-17 in particular)\nhttps://web.stanford.edu/class/rad226b/Lectures/Lecture3-2016-Spin-Hamiltonian.pdf
", "rawMarkdown": "I found this slide pack which might be useful (slides 15-17 in particular)\nhttps://web.stanford.edu/class/rad226b/Lectures/Lecture3-2016-Spin-Hamiltonian.pdf", "votes": null } ], "comments": [ { "id": 556677, "author_name": "scirpus", "author_url": "", "post_date": "06/20/2019 14:05:04", "content": "It is a tensor think of it as a 3x3 matrix
\n\nmagnetic_shielding_tensors.csv - contains the magnetic shielding tensors for all atoms in the molecules. The first column (molecule_name) contains the molecule name, the second column (atom_index) contains the index of the atom in the molecule, the third to eleventh columns contain the XX, YX, ZX, XY, YY, ZY, XZ, YZ and ZZ elements of the tensor/matrix respectively.
", "votes": null, "replies": [ { "id": 556845, "author_name": "avivlevi815", "author_url": "", "post_date": "06/20/2019 18:37:51", "content": "Thank you !
", "votes": null, "replies": [] }, { "id": 561469, "author_name": "larsbratholm", "author_url": "", "post_date": "06/26/2019 13:19:17", "content": "What you often measure experimentally is the trace of the matrix (sum of XX, YY, ZZ), also named the isotropic chemical shift. This is due to the molecules tumbling around in solution, so any information about their individual orientation is averaged out. But since we know the specific orientation in this case, all the tensor elements are given.
", "votes": null, "replies": [] } ] }, { "id": 556822, "author_name": "ssameerr", "author_url": "", "post_date": "06/20/2019 17:59:54", "content": "X,Y,Z are spread across both positive direction and negative direction. And in 3D's, YX = XY but the directions would be twisted, but in the dataset, they are same. You can just use XY,YZ and XZ and ignore other 3 coordinate axis.
", "votes": null, "replies": [ { "id": 556844, "author_name": "avivlevi815", "author_url": "", "post_date": "06/20/2019 18:37:28", "content": "Ho ok, \nThat helps :) \nThank you !
", "votes": null, "replies": [] }, { "id": 559312, "author_name": "pietermostert", "author_url": "", "post_date": "06/23/2019 21:54:51", "content": "Not all the XYs are the same as the YXs. See entry 17 in magnetic_shielding_tensors.csv, for example.
", "votes": null, "replies": [] } ] }, { "id": 558748, "author_name": "robertburbidge", "author_url": "", "post_date": "06/22/2019 21:14:42", "content": "I am no expert, but this might go some way to answering your question:
\n\n\n", "votes": null, "replies": [] }, { "id": 574715, "author_name": "anjum48", "author_url": "", "post_date": "07/14/2019 11:27:10", "content": "The formal properties of the magnetic shielding are discussed below, but it is important to understand that while many scientists think about the chemical shift or magnetic shielding as a number associated with each resonant nucleus, in reality the shielding is a tensor quantity. This means that the screening of the external magnetic field by the electron density of the molecule depends on the relative orientation of the external magnetic field and the molecule; therefore, the shielding phenomena has to be described by a tensor instead of a scalar number.\n https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058154/#S3title
\n
I found this slide pack which might be useful (slides 15-17 in particular)\nhttps://web.stanford.edu/class/rad226b/Lectures/Lecture3-2016-Spin-Hamiltonian.pdf
", "votes": null, "replies": [] } ], "raw_markdown_by_id": { "556640": "From my understanding of magnetic shielding, for every atom there should be one numeric value that describes the magnetic shielding.\n\nwhy then, there are 8 columns decribing the shielding ?\n* XX YX ... XZ YZ ZZ\n\nhow should I infer the magnetic shielding from those {XX, XY .. ZZ} columns ?", "556677": "It is a tensor think of it as a 3x3 matrix\n\nmagnetic_shielding_tensors.csv - contains the magnetic shielding tensors for all atoms in the molecules. The first column (molecule_name) contains the molecule name, the second column (atom_index) contains the index of the atom in the molecule, the third to eleventh columns contain the XX, YX, ZX, XY, YY, ZY, XZ, YZ and ZZ elements of the tensor/matrix respectively.", "556822": "X,Y,Z are spread across both positive direction and negative direction. And in 3D's, YX = XY but the directions would be twisted, but in the dataset, they are same. You can just use XY,YZ and XZ and ignore other 3 coordinate axis.", "556844": "Ho ok, \nThat helps :) \nThank you !", "556845": "Thank you !", "558748": "I am no expert, but this might go some way to answering your question:\n> The formal properties of the magnetic shielding are discussed below, but it is important to understand that while many scientists think about the chemical shift or magnetic shielding as a number associated with each resonant nucleus, in reality the shielding is a tensor quantity. This means that the screening of the external magnetic field by the electron density of the molecule depends on the relative orientation of the external magnetic field and the molecule; therefore, the shielding phenomena has to be described by a tensor instead of a scalar number.\n[https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058154/#S3title](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3058154/#S3title)", "559312": "Not all the XYs are the same as the YXs. See entry 17 in magnetic\\_shielding\\_tensors.csv, for example.", "561469": "What you often measure experimentally is the trace of the matrix (sum of XX, YY, ZZ), also named the isotropic chemical shift. This is due to the molecules tumbling around in solution, so any information about their individual orientation is averaged out. But since we know the specific orientation in this case, all the tensor elements are given.", "574715": "I found this slide pack which might be useful (slides 15-17 in particular)\nhttps://web.stanford.edu/class/rad226b/Lectures/Lecture3-2016-Spin-Hamiltonian.pdf" }, "source": "meta" }