I am searching an unknown molecules in crude extracts. Already I did LC-MS and Proton NMR. Now I would like to identify compound structure and name of the target compound.
very possible, but it's also depending on the purity, the structural complexity of the compound, the quality of your data (1H NMR resolution, for example). most likely you may need more NMR characterization such as 13C and other 2D NMR in addition to just 1D 1H NMR.
Dear Professor Dr. Bojidarka B. Ivanova. Thank you. Actually I have no enough knowledge about these terminology. I am trying to find allelochemicals from rice. After completed several steps from last 6 month now I am is here. Please share if you have any article on this.
Accounting for the fact that in your RG profile stays 'Agronomy' as professional qualification and taking into consideration the horarium to fundamental natural sciences as well as different curricula to this educational discipline, I have selected the following textbooks/monographs in NMR, MSn and single crystal X-ray diffractions, which to fit relatively well to the topic of your question.
They are organized in the following way: (i) References dealing with physical background; and (ii) References dealing particularly with structural chemistry, excluding/reducing, instrumentation, methods and experimental techniques as well as sample preparation techniques and data processing algorithms. In addition, references (i) are reduced to those having multidisciplinary character, rather then sources devoted to physical fundamentals and background of the methods as phenomenology. The mathematical formalism is also reduced in there references due to reason mentioned above.
NMR:
(a) M. Levitt, Spin-dynamics: basics of nuclear magnetic resonance, 2005, Wiley, West Sussex, pp. 1-686.
From this book you can pay attention to part 1 (Only sub-section 2) - Magnetism; Part 2 - NMR experiment; Excluding parts 3-5, which represent quantum physics, because of, this textbook has been designed to undergraduate students in 'Physics'.
(b) D. Neuhaus, M. Willamson, The nuclear Overhauser effects in structural and conformational analysis, Wiley, 2000, N.Y. pp. 1-619.
From this book only parts 1 and 3, dealing with theoretical background and application of NMR for structural analysis, excluding part 2, which has been devoted to experimental techniques of 2D NMR.
(c) Atta-ur-Rahman, Nuclear magnetic resonance, Springer Verlag, 1986, Berlin Heidelberg, pp. 1-358. In particular, useful to structural analysis of organics.
References (a)-(c) (NMR) exclude solid-state analysis, in general, and NMR of inorganics, metalorganics and organometallics.
X-ray:
(a) C. Whiston, X-ray methods, Wiley, 1987, pp 1-426.
Useful source to obtain a basic recognition (not knowledge) with large set of X-ray methods and their analytical chemical application, in general. So, very adapted multidysciplinary oriented text allowing you to distinguish among various XRD methods.
(b) P. Luger, Modern X-ray analysis on Single Crystal, Walter de Gruyter, Berlin, 1980, pp. 1-312.
It deals with practical application of the method to structural analysis of molecules.
(c) J. Garbarczyk and D. Jones, Organic crystal chemistry, International Union of Crystallography, Oxford Sci. Publ., 1991, Oxford, pp. 1-200.
(d) B. Douglas, S-M. Ho, Structure and Chemistry of Cystalline solids, Springer Verlag, 2006, pp. 1-344.
(e) T. Mak, G-D. Zhou, Crystallography in Modern Chemistry, Wiley, Chichester, 1992, pp. 1-1322.
(f) C. Giacovazzo (Ed.), Fundamentals of Crystallography, International Union of Crystallography, Oxford Sci. Publications, Oxford University Preess, 2002, pp. 1-825.
From this book only chapter 3 (The diffraction of X-ray by crystals), Chapter 6 (Solution and refinment of crystallographic structure); Chapter 8 (Molecules and olecular crystals); And chapter 9 (Protein crystallography), because of the book has been written by crystallographers, and designed to students in 'Mineralogy and crystallography', in general.
MS:
(a) E. de Hoffmann, V. Stroobant, Mass spectrometry principle and application, Wiley, 2009, West Sussex, pp. 1-489.
From this textbook only part 4 (Tandem mass spectrometry) and part 7 (Fragmentation reactions) are associated with structural analysis.
(b) J. Watson, D. Sparkman, Mass spectrometry, Wiley, 2007, London, pp. 1-819.
From this book Chapter 3 (Tandem MS) and Chapter 6 (Fragmentation spectra of classes of compounds)
(c) R. Johnstone, Mass spectrometry for organic chemists, Cambridge University Press, 1972, Cambridge, pp. 1-170.
From this book only chapter 4 (Structural elucidation).
(d) M. Spiteller, G. Spiteller, Massenspektrensammlung von Loesungsmitteln, Verunreinigungen, Saeullenbelegmaterialien und einfachen aliphatischen Verbindungen, Springer Verlag, 1973 (Correlation between MS-spectra (given) structure of 170 organics from hydrocarbons to acids, excluding heterocyclics)
(e) Q. Porter, Mass spectrometry of heterocyclic compounds, Wiley, 1985, pp. 1-964 (Only heterocyclics; MS fragmentation without MS spectra, but only m/z values, however)
References (a)-(e) (MS) exclude structural analysis of inorganics, metalorganics and organometallics, including (bio)macromolecular chemicals.
Thank you for your nice cooperation. I really appreciate your effort for me. Now I am trying to get idea about these. However, I would like to share my NMR and Mass spectrum data with you. If you have time then please reply me.
Hi, Yes it is possible. In addition of the nice comments above, let me share our experiences. If we have data LCMS /HR MS it means, we can predict the molecular ion of target compounds using their adducts, then we can determine the molecular formula using isotope pattern method,, after we predict the mw, molecular formula,and by using our MS MS data, we can search the possible known compounds by using free on line MS data bases such as Metfrag, Metlin, Metfusion, MassBank, Midas and many others. To confirm the predicted structures generally we can use our NMR data.of the isolated compounds, or by comparing our MS data to authentic standards. With LCMS we can have MS directly of our target compounds without any purification. Best regards
For the interpretation of your data, the answer is "Not!".
Firstly, the University is a High Educational Institution, creating new scientific insights into the Universe, which are distributed to the students. This knowledge has broad interdisciplinary and most important fundamental for the science character. Interdisciplinarity, however, is determined by the diversity of the basic sciences. Therefore, the concrete foundations are important (structure of the matter (nuclear structure (physics); Molecular and supramolecular structure (structural chemistry)), laws in physics, and the like). The priority does not include mandatory (or not immediately) application to specific areas such as agriculture, which represents sector of industry; It also belongs to the manufacturing sectors. As an applied research in an industrial manufacturing sector, your field of education is largely based on empirical knowledge.
Simply speaking, the knowlege about structure of the humus (matte) is fundamental, because of it is connected with the knowledge of the Earth. But in your educational plane it is presented as an empirical knowledge. The findings would (And have but within the framework of not explicitly defined period of time) have an industrial contribution, but in general the agricultural production on an industrial scale is not significantly affected by this knowledge. Your training is oriented towards the applied aspect of agriculture as an industry, however. This is the difference between education at University and the Institutions for applied higher learning.
You should bear in mind that for many Countries worldwide, your educational qualification does not meet equivalent to diploma for university education, explicitly. It is explicitly emphasized as a diploma of Higher Educational Institutions, which are called Institutions of "Applied science" for higher learning. Moreover, all educational planes are approved by the Ministry of Education to corresponding Countries as you know as assitant professor. And thus, this is policy in the Higher Education, in general, determining the subsidy to fundamental research and to the applied oriented to the industry one.
In this regard, there is no novelty from a scientific point of view in the fact that you have extracted few unknown as (3D) structure compounds from foods by LC-MS. The compounds can be new to the structural chemistry, but you do not personally have an intellectual contribution to their structure as molecular design and (applied oriented) synthesis. Of course, you can make a contribution with optimization of analytical procedures, for extraction and concentration, which is contribution to "quantitative analytical chemistry", not linked to the "structural analytical chemistry", however. On the other hand, both LC-MS and NMR as analytical instrumentation are fully automated as a process for data collection and sample manipulation. And if you do not have your own intellectual contribution to the structural determination of the data on the basis of these methods, then your work is indeed reduced to a technical work of extraction with already established analytical protocols.
So, in cases like your (i.e. professional qualification 'MSc' in applied science with reduced horarium to fundamental sciences), there is better to apply for PhD position at domestic University (Because of, the agricultural policy is governed by domestic factors) to increase in your qualification so that you can conduct a complete research independently according your qualification.
Such questions had been answered in the past . The answer is no , we do need the other org. chemistry etc techniques to complete our job. the way you are saying , the results will totally be inconclusive & may be wrong as well. So pl adopt proper all analytical techniques to achieve your end result.