nmrproject/Report/refs.bib

@article{ORCA,
	author = {Neese,F.},
	title = {The ORCA program system},
	journal = {WIRES Comput. Molec. Sci.},
	volume = {2},
	number = {1},
	pages = {73-78},
	DOI = {10.1002/wcms.81},
	year = {2012},
	type = {journal Article}
}
@article{DFTORCA,
	author = {Neese, F. and Wennmohs, F. and Becker, U. and Riplinger, C.},
	title = {The ORCA quantum chemistry program package},
	journal = {The Journal of Chemical Physics},
	volume = {152},
	number = {22},
	pages = {224108},
	year = {2020},
	month = {06},
	abstract = {In this contribution to the special software-centered issue, the ORCA program package is described. We start with a short historical perspective of how the project began and go on to discuss its current feature set. ORCA has grown into a rather comprehensive general-purpose package for theoretical research in all areas of chemistry and many neighboring disciplines such as materials sciences and biochemistry. ORCA features density functional theory, a range of wavefunction based correlation methods, semi-empirical methods, and even force-field methods. A range of solvation and embedding models is featured as well as a complete intrinsic to ORCA quantum mechanics/molecular mechanics engine. A specialty of ORCA always has been a focus on transition metals and spectroscopy as well as a focus on applicability of the implemented methods to “real-life” chemical applications involving systems with a few hundred atoms. In addition to being efficient, user friendly, and, to the largest extent possible, platform independent, ORCA features a number of methods that are either unique to ORCA or have been first implemented in the course of the ORCA development. Next to a range of spectroscopic and magnetic properties, the linear- or low-order single- and multi-reference local correlation methods based on pair natural orbitals (domain based local pair natural orbital methods) should be mentioned here. Consequently, ORCA is a widely used program in various areas of chemistry and spectroscopy with a current user base of over 22 000 registered users in academic research and in industry.},
	issn = {0021-9606},
	doi = {10.1063/5.0004608},
	url = {https://doi.org/10.1063/5.0004608},
	eprint = {https://pubs.aip.org/aip/jcp/article-pdf/doi/10.1063/5.0004608/16740678/224108_1_online.pdf},
}

@book{bender2006foundations,
	title={Foundations of Combinatorics with Applications},
	author={Bender, E. A. and Williamson, S. G.},
	year={2006},
	publisher={Dover Publications},
	address={Mineola, NY},
	edition={Dover},
	pages={468},
	isbn={978-0486446035},
	note={ISBN-10: 0-486-44603-4}
}
@book{Graphtheory,
	title = {Graphentheorie : eine anwendungsorientierte Einführung},
	series = {Mathematik-Studienhilfen},
	author = {Tittmann, P.},
	address = {München},
	publisher = {Hanser},
	year = {2019},
	edition = {3., aktualisierte Auflage},
	url = {https://doi.org/10.3139/9783446465039},
	url = {https://www.hanser-elibrary.com/doi/book/10.3139/9783446465039},
}
@article{andersenhyperflow,
	author = {Andersen, J. L. and Flamm, C. and Merkle, D. and Stadler, P. F.},
	title = {Chemical Transformation Motifs—Modelling Pathways as Integer Hyperflows},
	year = {2019},
	issue_date = {March-April 2019},
	publisher = {IEEE Computer Society Press},
	address = {Washington, DC, USA},
	volume = {16},
	number = {2},
	issn = {1545-5963},
	url = {https://doi.org/10.1109/TCBB.2017.2781724},
	doi = {10.1109/tcbb.2017.2781724},
	abstract = {We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and hyperedges to reactions. Pathways are modelled as integer hyperflows and we expand the network model by detailed routing constraints. In contrast to the more traditional approaches like Flux Balance Analysis or Elementary Mode analysis we insist on integer-valued flows. While this choice makes it necessary to solve possibly hard integer linear programs, it has the advantage that more detailed mechanistic questions can be formulated. It is thus possible to query networks for general transformation motifs, and to automatically enumerate optimal and near-optimal pathways. Similarities and differences between our work and traditional approaches in metabolic network analysis are discussed in detail. To demonstrate the applicability of the mathematical framework to real-life problems we first explore the design space of possible non-oxidative glycolysis pathways and show that recent manually designed pathways can be further optimized. We then use a model of sugar chemistry to investigate pathways in the autocatalytic formose process. A graph transformation-based approach is used to automatically generate the reaction networks of interest.},
	journal = {IEEE/ACM Trans. Comput. Biol. Bioinformatics},
	month = apr,
	pages = {510–523},
	numpages = {14}
}
@book{ocwiley,
	author    = {Peter, K. and Vollhardt, C.  and Schore, N. E. },
	title     = {Organische Chemie},
	publisher = {Wiley-VCH},
	year      = {2020},
	isbn      = {978-3-527-34582-3},
}
@phdthesis{andersenphd,
	title        = {Analysis of Generative Chemistries},
	author       = {Andersen, J. L.  },
	year         = 2015,
	month        = {September},
	address      = {Leipzig, DE},
	note         = {Available at \url{    https://nbn-resolving.org/urn:nbn:de:bsz:15-qucosa-202723}},
	school       = {Universität Leipzig},
	type         = {PhD thesis}
}
@book{equilibrium,
	title={Principles of organic synthesis},
	author={Norman, R. OC},
	year={2017},
	publisher={Routledge}
}
@article{lewisrep,
	author = {Packer, J. E. and Woodgate, S. D.},
	title = {Lewis structures, formal charge, and oxidation numbers: A more user-friendly approach},
	journal = {Journal of Chemical Education},
	volume = {68},
	number = {6},
	pages = {456-456},
	year = {1991},
	month = {06},
	abstract = {This paper presents a set of rules for writing Lewis structures requiring only the ability to add, subtract, count, and know the number of valence electrons of neutral atoms.},
	issn = {0021-9584},
	doi = {10.1021/ed068p456},
	url = {https://doi.org/10.1021/ed068p456},
	eprint = {https://pubs.acs.org/jceda8/article-pdf/68/6/456/416109/ed068p456.pdf},
}
@article{hypergraphpath,
	author = {Krieger, S. and Kececioglu, J.},
	title ={Shortest Hyperpaths in Directed Hypergraphs for Reaction Pathway Inference},
	
	journal = {Journal of Computational Biology},
	volume = {30},
	number = {11},
	pages = {1198-1225},
	year = {2023},
	doi = {10.1089/cmb.2023.0242},
	
	URL = { 
	
	
	https://journals.sagepub.com/doi/abs/10.1089/cmb.2023.0242
	
	
	},
	eprint = { 
	
	
	https://journals.sagepub.com/doi/pdf/10.1089/cmb.2023.0242
	
	
	}
	,
	abstract = { Signaling and metabolic pathways, which consist of chains of reactions that produce target molecules from source compounds, are cornerstones of cellular biology. Properly modeling the reaction networks that represent such pathways requires directed hypergraphs, where each molecule or compound maps to a vertex, and each reaction maps to a hyperedge directed from its set of input reactants to its set of output products. Inferring the most likely series of reactions that produces a given set of targets from a given set of sources, where for each reaction its reactants are produced by prior reactions in the series, corresponds to finding a shortest hyperpath in a directed hypergraph, which is NP-complete.We give the first exact algorithm for general shortest hyperpaths that can find provably optimal solutions for large, real-world, reaction networks. In particular, we derive a novel graph-theoretic characterization of hyperpaths, which we leverage in a new integer linear programming formulation of shortest hyperpaths that for the first time handles cycles, and develop a cutting-plane algorithm that can solve this integer linear program to optimality in practice. Through comprehensive experiments over all of the thousands of instances from the standard Reactome and NCI-PID reaction databases, we demonstrate that our cutting-plane algorithm quickly finds an optimal hyperpath—inferring the most likely pathway—with a median running time of under 10 seconds, and a maximum time of less than 30 minutes, even on instances with thousands of reactions. We also explore for the first time how well hyperpaths infer true pathways, and show that shortest hyperpaths accurately recover known pathways, typically with very high precision and recall.Source code implementing our cutting-plane algorithm for shortest hyperpaths is available free for research use in a new tool called Mmunin. }
}
@ARTICLE{chordlesscycle,
	author = {{Silva Dias}, E. and {Castonguay}, D. and {Longo}, H. and {Abdala Rfaei Jradi}, W.},
	title = "{Efficient Enumeration of Chordless Cycles}",
	journal = {arXiv e-prints},
	keywords = {Computer Science - Data Structures and Algorithms, Computer Science - Discrete Mathematics},
	year = 2013,
	month = sep,
	eid = {arXiv:1309.1051},
	pages = {arXiv:1309.1051},
	doi = {10.48550/arXiv.1309.1051},
	archivePrefix = {arXiv},
	eprint = {1309.1051},
	primaryClass = {cs.DS},
	adsurl = {https://ui.adsabs.harvard.edu/abs/2013arXiv1309.1051S},
	adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}
@inbook{ilp,
	author = {Chen, D.-S. and Batson, R. G. and Dang, Y.},
	publisher = {John Wiley and Sons, Ltd},
	isbn = {9781118166000},
	title = {Linear Programming—Fundamentals},
	booktitle = {Applied Integer Programming},
	doi = {https://doi.org/10.1002/9781118166000},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/9781118166000},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/9781118166000},
	year = {2009},
	keywords = {traveling salesman problem, Hamiltonian paths, machine sequencing problems, vehicle Routing, genome sequencing},
}
@article{petrinets,
	author = {Peterson, J. L.},
	title = {Petri Nets},
	year = {1977},
	issue_date = {Sept. 1977},
	publisher = {Association for Computing Machinery},
	address = {New York, NY, USA},
	volume = {9},
	number = {3},
	issn = {0360-0300},
	url = {https://doi.org/10.1145/356698.356702},
	doi = {10.1145/356698.356702},
	journal = {ACM Comput. Surv.},
	month = sep,
	pages = {223–252},
	numpages = {30}
}
@phdthesis{petri1962kommunikation,
	author       = {Petri, C. A.},
	title        = {Kommunikation mit Automaten},
	school       = {Technische Universit{"a}t Darmstadt},
	year         = {1962},
	address      = {Darmstadt, Germany},
	type         = {Dissertation}
}
@book{atkinsdft,
	abstract = {This text unravels those fundamental physical principles which explain how all matter behaves. It takes us from the foundations of quantum mechanics, through quantum models of atomic, molecular, and electronic structure, and on to discussions of spectroscopy, and the electronic and magnetic properties of molecules.},
	author = {Atkins, P. W. and Friedman, R. S.},
	address = {Oxford},
	booktitle = {Molecular quantum mechanics},
	edition = {5th ed. / Peter Atkins and Ronald Friedman.},
	isbn = {9780199541423},
	keywords = {Quantum chemistry ; Science},
	language = {eng},
	publisher = {Oxford University Press},
	title = {Molecular quantum mechanics },
	year = {2011},
}
@misc{mod,
	title={A Software Package for Chemically Inspired Graph Transformation}, 
	author={J. L. Andersen and C. Flamm and D. Merkle and P. F. Stadler},
	year={2016},
	eprint={1603.02481},
	archivePrefix={arXiv},
	primaryClass={cs.FL},
	url={https://arxiv.org/abs/1603.02481}, 
}
@inproceedings{networkx,
	abstract = {NetworkX is a Python language package for exploration
	and analysis of networks and network algorithms.
	The core package provides data structures
	for representing many types of networks, or graphs,
	including simple graphs, directed graphs, and graphs
	with parallel edges and self-loops. The nodes in NetworkX
	graphs can be any (hashable) Python object
	and edges can contain arbitrary data; this flexibility
	makes NetworkX ideal for representing networks
	found in many different scientific fields.
	In addition to the basic data structures many graph
	algorithms are implemented for calculating network
	properties and structure measures: shortest paths,
	betweenness centrality, clustering, and degree distribution
	and many more. NetworkX can read and
	write various graph formats for easy exchange with
	existing data, and provides generators for many
	classic graphs and popular graph models, such as
	the Erdos-Renyi, Small World, and Barabasi-Albert
	models.
	The ease-of-use and flexibility of the Python programming
	language together with connection to the
	SciPy tools make NetworkX a powerful tool for scientific
	computations. We discuss some of our recent
	work studying synchronization of coupled oscillators
	to demonstrate how NetworkX enables research in
	the field of computational networks.},
	added-at = {2008-09-24T13:11:32.000+0200},
	address = {Pasadena, CA USA},
	author = {Hagberg, A. A. and Schult, D. A. and Swart, P. J.},
	biburl = {https://www.bibsonomy.org/bibtex/272096c6553d7057409fe78ca698eb332/mschuber},
	booktitle = {Proceedings of the 7th Python in Science Conference},
	editor = {Varoquaux, Ga\"el and Vaught, Travis and Millman, Jarrod},
	interhash = {7a78aca0e0e5adfc4d7e882e4635435f},
	intrahash = {72096c6553d7057409fe78ca698eb332},
	keywords = {2008 analysis network python tool},
	pages = {11 - 15},
	timestamp = {2008-09-24T13:11:32.000+0200},
	title = {Exploring Network Structure, Dynamics, and Function using NetworkX},
	url = {http://conference.scipy.org/proceedings/SciPy2008/paper_2/},
	year = 2008
}
@article{rdkit,
	added-at = {2017-04-11T06:11:47.000+0200},
	author = {Landrum, G.},
	biburl = {https://www.bibsonomy.org/bibtex/28d01fceeccd6bf2486e47d7c4207b108/salotz},
	description = {Release 2016_09_4 (Q3 2016) Release · rdkit/rdkit},
	interhash = {ee9a4ddeff3121aa622cf35709fa6e21},
	intrahash = {8d01fceeccd6bf2486e47d7c4207b108},
	keywords = {chemoinformatics drug-design pharmacophores software},
	timestamp = {2017-04-11T06:11:47.000+0200},
	title = {RDKit: Open-Source Cheminformatics Software},
	url = {https://github.com/rdkit/rdkit/releases/tag/Release_2016_09_4},
	year = 2016
}
@article{avogadro,
	author={Hanwell, M. D.
	and Curtis, D. E.
	and Lonie, D. C.
	and Vandermeersch, T.
	and Zurek, E.
	and Hutchison, G. R.},
	title={Avogadro: an advanced semantic chemical editor, visualization, and analysis platform},
	journal={Journal of Cheminformatics},
	year={2012},
	month={Aug},
	day={13},
	volume={4},
	number={1},
	pages={17},
	abstract={The Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.},
	issn={1758-2946},
	doi={10.1186/1758-2946-4-17},
	url={https://doi.org/10.1186/1758-2946-4-17}
}
@article{nmrbin,
	title = {A novel spectra similarity measure},
	journal = {Chemometrics and Intelligent Laboratory Systems},
	volume = {85},
	number = {1},
	pages = {1-8},
	year = {2007},
	issn = {0169-7439},
	doi = {https://doi.org/10.1016/j.chemolab.2005.10.002},
	url = {https://www.sciencedirect.com/science/article/pii/S0169743905001620},
	author = {L. Bodis and A. Ross and E. Pretsch},
	keywords = {Spectra comparison, NMR spectra, Quality control},
	abstract = {A new method is described for calculating the similarity degree of two spectra. Its performance is optimized with similar, computer-generated 1H NMR spectra. The method is compared with a recently proposed local cross-correlation method. Using a test set, its power to discriminate between related and unrelated 1H NMR spectra is better than with the cross-correlation method. Better results are also obtained when comparing measured spectra of a database with the corresponding estimated ones or with estimated spectra of randomly assigned structures. Although, so far, it has only been tested with 1H NMR spectra, due to the generality of the approach, the novel procedure can be applied to comparing other spectra or patterns as well.}
}
@misc{gurobi,
	author = {{Gurobi Optimization, LLC}},
	title = {{Gurobi Optimizer Reference Manual}},
	year = {2026},
	url = {https://www.gurobi.com}
}
@Article{caffeinesynth,
	AUTHOR = {Lin, Z. and Wei, J. and Hu, Y. and Pi, D. and Jiang, M. and Lang, T.},
	TITLE = {Caffeine Synthesis and Its Mechanism and Application by Microbial Degradation, A Review},
	JOURNAL = {Foods},
	VOLUME = {12},
	YEAR = {2023},
	NUMBER = {14},
	ARTICLE-NUMBER = {2721},
	URL = {https://www.mdpi.com/2304-8158/12/14/2721},
	PubMedID = {37509813},
	ISSN = {2304-8158},
	ABSTRACT = {Caffeine is a metabolite derived from purine nucleotides, typically accounting for 2–5 Percent of the dry weight of tea and 1–2 Percent of the dry weight of coffee. In the tea and coffee plants, the main synthesis pathway of caffeine is a four-step sequence consisting of three methylation reactions and one nucleosidase reaction using xanthine as a precursor. In bacteria, caffeine degradation occurs mainly through the pathways of N-demethylation and C-8 oxidation. However, a study fully and systematically summarizing the metabolism and application of caffeine in microorganisms has not been established elsewhere. In the present study, we provide a review of the biosynthesis, microbial degradation, gene expression, and application of caffeine microbial degradation. The present review aims to further elaborate the mechanism of caffeine metabolism by microorganisms and explore the development prospects in this field.},
	DOI = {10.3390/foods12142721}
}
@Article{vanillinesynth,
	AUTHOR = {Tazon, A. W. and Awwad, F. and Meddeb-Mouelhi, F. and Desgagné-Penix, I.},
	TITLE = {Biotechnological Advances in Vanillin Production: From Natural Vanilla to Metabolic Engineering Platforms},
	JOURNAL = {BioChem},
	VOLUME = {4},
	YEAR = {2024},
	NUMBER = {4},
	PAGES = {323--349},
	URL = {https://www.mdpi.com/2673-6411/4/4/17},
	ISSN = {2673-6411},
	ABSTRACT = {Vanillin, an aromatic aldehyde, is one of the most popular flavors worldwide, extensively used in the food, cosmetics, pharmaceutical, and agrochemical industries. Despite its widespread use, less than 1 Percent of the total vanillin production is natural, with the majority being synthesized chemically. While chemical synthesis can help to meet the growing demand for vanillin, a strong market trend has rapidly developed for products created from natural ingredients, including natural vanillin. Given the labor-intensive process of extracting vanillin from vanilla pods, there is a critical need for new metabolic engineering platforms to support the biotechnological production of nature-identical vanillin. This review highlights the significance of vanillin in various markets, its diverse applications, and the current state of bio-engineered production using both prokaryotic and eukaryotic biological systems. Although recent advancements have demonstrated successful vanillin production through biocatalytic approaches, our focus was to provide a current and innovative overview of vanillin bioengineering across various host systems with special consideration placed on microalgae, which are emerging as promising platforms for vanillin production through metabolic engineering. The use of these systems to support the biotechnological production of vanillin, while leveraging the photosynthetic capabilities of microalgae to capture CO2 and convert it into biomass, can significantly reduce the overall carbon footprint.},
	DOI = {10.3390/biochem4040017}
}
@article{xanthinnmr,
	author = {Benoit, R. L. and Fréchette, M.},
	title = {Protonation of hypoxanthine, guanine, xanthine, and caffeine},
	journal = {Canadian Journal of Chemistry},
	volume = {63},
	number = {11},
	pages = {3053-3056},
	year = {1985},
	doi = {10.1139/v85-506},
	URL = { 
	https://doi.org/10.1139/v85-506
	},
	eprint = { 
	https://doi.org/10.1139/v85-506
	}
	,
	abstract = { The protonation equilibria of three hydroxypurines, hypoxanthine, guanine, and xanthine, and of related caffeine have been studied by 1H and 13C nmr and uv spectroscopies in aqueous sulfuric or perchloric acids. The results have been interpreted on the basis of the excess acidity method. The values and the protonation sites are discussed and comparisons are made with results of recent theoretical calculations. }
}
@article{manyxanthinesnmr,
	author = {Mueller, C. E. and Shi, D. and Manning, M., Jr. and Daly, J. W.},
	title = {Synthesis of paraxanthine analogs (1,7-disubstituted xanthines) and other xanthines unsubstituted at the 3-position: structure-activity relationships at adenosine receptors},
	journal = {Journal of Medicinal Chemistry},
	volume = {36},
	number = {22},
	pages = {3341-3349},
	year = {1993},
	month = {10},
	issn = {0022-2623},
	doi = {10.1021/jm00074a015},
	url = {https://doi.org/10.1021/jm00074a015},
	eprint = {https://pubs.acs.org/jmcmar/article-pdf/36/22/3341/7236147/jm00074a015.pdf},
}
@article{7xanthinnmr,
	author = {Jayantha, B. and Zhang, S. and Summers, R. M. and Mendis, G. P. and Jayakody, L. N.},
	title = {Engineered Pseudomonas putida monoculture system for green synthesis of 7-methylxanthine},
	journal = {Green Chemistry},
	volume = {27},
	number = {37},
	pages = {11365-11379},
	year = {2025},
	month = {10},
	abstract = { 7-Methylxanthine (7-MX) is a clinically proven safe drug to treat myopia. The chemical synthesis of 7-MX is hindered due to low specificity, demanding sustainable biological production using renewable, cost-effective feedstocks. To this end, we systematically engineered robust P. putida EM42 to produce 7-MX using caffeine and glycerol in minimal salt media. Removing the transcriptional repressor (glpR), genome integration of heterologous N-demethylase and its reductase, ndmABD, and overexpression of native fdhA to balance the redox cofactors enabled the selective conversion of caffeine to 7-MX with 100\% yield. We discovered a native transporter, PP\_RS18750, that efficiently takes up caffeine, facilitating the conversion in glycerol-containing media. We achieved 9.2 ± 0.42 g L−1 of 7-MX in a 3-L bioreactor by process-level optimization, the highest titer reported to date. Our techno-economic analysis indicates that this novel engineered monoculture approach can produce pharmaceutical-grade 7-MX commercially for \$328 per kg, with remarkably low E-factor and Process Mass Intensity (PMI) values, demonstrating the sustainable green valorization of caffeine into high-value methylated xanthine. },
	issn = {1463-9262},
	doi = {10.1039/d5gc02883c},
	url = {https://doi.org/10.1039/d5gc02883c},
	eprint = {https://pubs.rsc.org/gc/article-pdf/27/37/11365/10400487/d5gc02883c.pdf},
}
@article{theobrominnoMenmr,
	author = {Bouzková, K. and Babinský, M. and Novosadová, L. and Marek, R.},
	title = {Intermolecular Interactions in Crystalline Theobromine
	as Reflected in Electron Deformation Density and 13C NMR
	Chemical Shift Tensors},
	journal = {Journal of Chemical Theory and Computation},
	volume = {9},
	number = {6},
	pages = {2629-2638},
	year = {2013},
	month = {06},
	abstract = {An understanding of the role of intermolecular
	interactions in
	crystal formation is essential to control the generation of diverse
	crystalline forms which is an important concern for pharmaceutical
	industry. Very recently, we reported a new approach to interpret the
	relationships between intermolecular hydrogen bonding, redistribution
	of electron density in the system, and NMR chemical shifts (Babinský
	et al. J. Phys. Chem. A, 2013, 117, 497). Here, we employ this approach to characterize
	a full set of crystal interactions in a sample of anhydrous theobromine
	as reflected in 13C NMR chemical shift tensors (CSTs).
	The important intermolecular contacts are identified by comparing
	the DFT-calculated NMR CSTs for an isolated theobromine molecule and
	for clusters composed of several molecules as selected from the available
	X-ray diffraction data. Furthermore, electron deformation density
	(EDD) and shielding deformation density (SDD) in the proximity of
	the nuclei involved in the proposed interactions are calculated and
	visualized. In addition to the recently reported observations for
	hydrogen bonding, we focus here particularly on the stacking interactions.
	Although the principal relations between the EDD and CST for hydrogen
	bonding (HB) and stacking interactions are similar, the real-space
	consequences are rather different. Whereas the CHX
	hydrogen bonding influences predominantly and significantly the in-plane
	principal component of the 13C CST perpendicular to the
	HB path and the CH hydrogen bonding modulates
	both in-plane components of the carbonyl 13C CST, the stacking
	modulates the out-of-plane electron density resulting in weak deshielding
	(2–8 ppm) of both in-plane principal components of the CST
	and weak shielding (ca. 5 ppm) of the out-of-plane component.
	The hydrogen-bonding and stacking interactions may add to or subtract
	from one another to produce total values observed experimentally.
	On the example of theobromine, we demonstrate the power of this approach
	to identify and classify the intermolecular forces that govern the
	packing motifs in crystals and modulate the NMR CSTs.},
	issn = {1549-9618},
	doi = {10.1021/ct400209b},
	url = {https://doi.org/10.1021/ct400209b},
	eprint = {https://pubs.acs.org/jctcce/article-pdf/9/6/2629/8808212/ct400209b.pdf},
}
@article{theobrominnmr,
	author = {Thevis, M. and Opfermann, G. and Krug, O. and Schänzer, W.},
	title = {Electrospray ionization mass spectrometric characterization and quantitation of xanthine derivatives using isotopically labelled analogues: an application for equine doping control analysis},
	journal = {Rapid Communications in Mass Spectrometry},
	volume = {18},
	number = {14},
	pages = {1553-1560},
	doi = {https://doi.org/10.1002/rcm.1518},
	url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/rcm.1518},
	eprint = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/rcm.1518},
	abstract = {Abstract Isotope-dilution mass spectrometry has been employed successfully in numerous fields of analytical chemistry enabling the establishment of fast and reliable procedures. In equine sports, xanthine derivatives such as caffeine and theobromine are prohibited, and doping control laboratories analyze horse urine specimens regarding these illicit performance-enhancing drugs. Theobromine has to exceed a threshold level of 2 μg/mL, hence a robust and reliable quantitation is required. Stably deuterated theobromine and caffeine were synthesized by the reaction of xanthine or theobromine with iodomethane-d3 in the presence of N-methyl-N-trimethylsilyltrifluoroacetamide or potassium carbonate in acetonitrile, respectively. Both compounds were characterized by nuclear magnetic resonance spectroscopy and electrospray ionization tandem mass spectrometry, and a robust and fast assay for the qualitative and quantitative analysis of theobromine in equine urine samples was validated. Urine specimens were extracted by means of solid-phase extraction cartridges, and concentrated extracts were analyzed by liquid chromatography interfaced to a triple-quadrupole mass spectrometer. In addition, the dissociation behavior of deuterated analogues to caffeine and theobromine allowed proposals for fragmentation routes of xanthine derivatives after atmospheric pressure ionization and collisionally activated dissociation. Copyright C 2004 John Wiley and Sons, Ltd.},
	year = {2004}
}
@article{cinamnmr,
	title = {A comparative vibrational and NMR study of cis-cinnamic acid polymorphs and trans-cinnamic acid},
	journal = {Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy},
	volume = {57},
	number = {3},
	pages = {513-519},
	year = {2001},
	issn = {1386-1425},
	doi = {https://doi.org/10.1016/S1386-1425(00)00401-7},
	url = {https://www.sciencedirect.com/science/article/pii/S1386142500004017},
	author = {K. Hanai and A. Kuwae and T. Takai and H. Senda and K.-K. Kunimoto},
	keywords = {-Cinnamic acid, -Cinnamic acid, Polymorphism, IR/Raman spectra, NMR spectra},
	abstract = {The IR and Raman spectra of the two polymorphic forms (58°- and 68°-forms) of cis-cinnamic acid were measured, and the spectral differences discussed on the basis of the crystal structures of the two forms. The IR bands related to the COOH group differ in the frequencies and band shape, reflecting differences in the hydrogen bonding between the two modifications. These spectra were compared with those of trans-cinnamic acid. The IR, Raman, and NMR spectra of the isotopic compounds, including the deuterated and 13C analogs of the cis and trans acids, were also recorded in the solid state and in solution to confirm the spectral assignments.}
}
@article{mcoumnmr,
	author = {Nakazawa, T. and Ohsawa, K.},
	title = {Metabolism of Rosmarinic Acid in Rats},
	journal = {Journal of Natural Products},
	volume = {61},
	number = {8},
	pages = {993-996},
	year = {1998},
	month = {08},
	abstract = {The urine of rats administered rosmarinic acid (7) orally contained seven metabolites, which
	were identified as trans-caffeic acid 4-O-sulfate (1), trans-m-coumaric acid 3-O-sulfate (2), trans-ferulic acid 4-O-sulfate (3), trans-caffeic acid (4), m-hydroxyphenylpropionic acid (5), trans-m-coumaric acid (6), and unchanged rosmarinic acid (7) by spectroscopic and chemical data. The
	total cumulative amount of 1−7 excreted in the urine 48 h after the oral administration of
	rosmarinic acid was approximately 31.8 Percent of the dose administered. On the other hand, the
	metabolites attributed to rosmarinic acid could not be found in the bile. Orally administered
	rosmarinic acid may thus be concluded to be excreted in the urine rather than in the bile, with
	cleavage of ester bonds, selective para-dehydroxylation, methylation, and sulfate-conjugation.
	Metabolites 2, 3, 5, and 6 were also detected in the plasma. },
	issn = {0163-3864},
	doi = {10.1021/np980072s},
	url = {https://doi.org/10.1021/np980072s},
	eprint = {https://pubs.acs.org/jnprdf/article-pdf/61/8/993/13045095/np980072s.pdf},
}
@article{pcoumnmr,
	author = {Świsłocka, R. and Kowczyk-Sadowy, M. and Kalinowska, M. and Lewandowski, W.},
	title = {Spectroscopic (FT-IR, FT-Raman, 1H and 13C NMR) and theoretical studies of p-coumaric acid and alkali metal p-coumarates},
	journal = {Journal of Spectroscopy},
	volume = {27},
	number = {1},
	pages = {546146},
	keywords = {p-Coumaric acid, alkali metal p-coumarates, IR, Raman, NMR spectra},
	doi = {https://doi.org/10.3233/SPE-2012-0568},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.3233/SPE-2012-0568},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.3233/SPE-2012-0568},
	abstract = {The evaluation of the electronic charge distribution in metal complexes enables more precise interpretation of mechanism by which particular metal ions affect biochemical properties of ligands [J. Inorg. Biochem. 99 (2005), 1407–1423, J. Mol. Struct. 919 (2009), 284–289]. In this paper we investigated the influence of alkali metal cations (lithium, sodium, potassium, rubidium and cesium) on the electronic structure of p-coumaric acid (p-CA). It allowed to observe the systematic changes in the spectra of investigated complexes depending on the position of the element in the periodic table. p-Coumaric acid is a derivative of cinnamic acid that occurs in several plant species. Li, Na, K, Rb and Cs p-coumarates were synthesized and the experimental and theoretical FT-IR, FT-Raman, 1H and 13C NMR spectra of p-coumaric acid and its salts were registered and analyzed. The structures, atomic charges, infrared and NMR spectra of p-coumaric acid and Li, Na, K salts were calculated by B3LYP/6-311++G** method.},
	year = {2012}
}
@article{aldhnmr,
	author = {Kuan, F.-H. and Inoue, Y. and Chûjô, R.},
	title = {Structure and molecular dynamics of solid-state inclusion complexes of cyclodextrin and permethylated cyclodextrin with benzaldehyde studied by high-resolution CP/MAS13C NMR},
	journal = {Journal of inclusion phenomena},
	volume = {4},
	number = {3},
	pages = {281–290},
	doi = {https://doi.org/10.1007/BF00658002},
	eprint = {https://link.springer.com/article/10.1007/BF00658002},
	abstract = {The structure and molecular dynamics of the benzaldehyde inclusion-complexes with alpha-andbeta-cyclodextrins and permethylated alpha-cyclodextrin in the solid state have been studied by high-resolution cross-polarization/magic angle sample-spinning13C NMR spectroscopy. It is shown that the guest benzaldehyde molecule undergoes motion in the host cyclodextrin cavity and the rate of motion depend on the cavity size. In the alpha-cyclodextrin complex, compared to beta-and permethylated alpha-cyclodextrin complexes, the benzaldehyde motion is severely restricted, but under high-vacuum benzaldehyde is released more easily from the cavity.},
	year = {1986}
}
@Article{caffacdnmr,
	AUTHOR = {Yu, J. and Xie, J. and Sun, M. and Xiong, S. and Xu, Ch. and Zhang, Z. and Li, M. and Li, C. and Lin, L.},
	TITLE = {Plant-Derived Caffeic Acid and Its Derivatives: An Overview of Their NMR Data and Biosynthetic Pathways},
	JOURNAL = {Molecules},
	VOLUME = {29},
	YEAR = {2024},
	NUMBER = {7},
	ARTICLE-NUMBER = {1625},
	URL = {https://www.mdpi.com/1420-3049/29/7/1625},
	PubMedID = {38611904},
	ISSN = {1420-3049},
	ABSTRACT = {In recent years, caffeic acid and its derivatives have received increasing attention due to their obvious physiological activities and wide distribution in nature. In this paper, to clarify the status of research on plant-derived caffeic acid and its derivatives, nuclear magnetic resonance spectroscopy data and possible biosynthetic pathways of these compounds were collected from scientific databases (SciFinder, PubMed and China Knowledge). According to different types of substituents, 17 caffeic acid and its derivatives can be divided into the following classes: caffeoyl ester derivatives, caffeyltartaric acid, caffeic acid amide derivatives, caffeoyl shikimic acid, caffeoyl quinic acid, caffeoyl danshens and caffeoyl glycoside. Generalization of their 13C-NMR and 1H-NMR data revealed that acylation with caffeic acid to form esters involves acylation shifts, which increase the chemical shift values of the corresponding carbons and decrease the chemical shift values of the corresponding carbons of caffeoyl. Once the hydroxyl group is ester, the hydrogen signal connected to the same carbon shifts to the low field (1.1~1.6). The biosynthetic pathways were summarized, and it was found that caffeic acid and its derivatives are first synthesized in plants through the shikimic acid pathway, in which phenylalanine is deaminated to cinnamic acid and then transformed into caffeic acid and its derivatives. The purpose of this review is to provide a reference for further research on the rapid structural identification and biofabrication of caffeic acid and its derivatives.},
	DOI = {10.3390/molecules29071625}
}
@article{mhydaldhnmr,
	author = {Mart, H. and Sökmen, T. and Yürük, H.},
	title = {The synthesis and thermal properties of oligo-3-hydroxybenzaldehyde synthesized by oxidative polycondensation},
	journal = {Journal of Applied Polymer Science},
	volume = {101},
	number = {2},
	pages = {892-897},
	keywords = {oxidative polycondensation, polyaromatics, polyphenols, oligomers},
	doi = {https://doi.org/10.1002/app.23537},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/app.23537},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/app.23537},
	abstract = {Abstract Polymerization of 3-hydroxybenzaldehyde was investigated by oxidative polycondensation (OP) method. No polycondensation reaction was observed both in acidic (in CH3COOH) and organic (in THF) media. Polycondensation was carried out with hydrogenperoxide (H2O2) in an aqueous alkaline medium at 90°C. The product was characterized by 1H NMR, 13C NMR, FTIR, UV–vis, and elemental analysis. The number average molecular weight, mass average molecular weight, and polydispersity index values of O-3HBA were found to be 3600, 8000 g mol−1, and 2.22, respectively. The product (O-3HBA) with reactive aldehyde and hydroxyl group was soluble in most polar organic solvents and was composed of phenylene units. Thermal properties of the oligomer were investigated by thermogravimetric analyses under an air atmosphere. The weight loss of O-3HBA was found to be 5 and 50 Percent at 231 and >1000C, respectively. The carboneous residue of the O-3HBA was 54 Percent at 1000C. C 2006 Wiley Periodicals, Inc. J Appl Polym Sci 101: 892–897, 2006},
	year = {2006}
}
@article{phydaldhnmr,
	author = {Jha, A. and  Kumar, B.R.  and Kumar Ch, R.},
	title = {Synthesized Novel Schiff Base of 4-Hydroxybenzaldehyde with Anilines for Optoelectronic
	Applications},
	journal = {SSRN Preprint Server},
	pages = {46},
	keywords = {Schiff base, Spectral studies, Computational studies, Energy gap, Refractive index.},
	url = {https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4934411},
	abstract = {Optical materials organic in nature are leading materials exhibiting semiconducting properties is trend of present technology in optical and electronic applications. Active organic materials of Schiff bases  are of vital importance in terms of their molecular properties, band gap, refractive index and dielectric operated at room temperature than compared to inorganic materials at elevated temperatures during synthesis. The present article focuses on the development of thin films with the synthesis of Schiff base of  4-hydroxy benzaldehydes and substituted anilines using the green synthesis method. The formation of the Schiff base compounds was confirmed with spectroscopic methods with shifts in wavenumbers in infrared spectra, transition with optical band gap with ultraviolet spectra and chemical environment with chemical shifts using proton NMR. Powdered XRD provide information of structure, composition and crystalline proximity of the synthesized Schiff base compounds. Optical properties refractive index and dielectric constant were attributed with spectroscopic ellipsometer. Computational studies were performed using the Gaussian 16 package with the B3LYP method basis set 6-311++ for all molecular compounds to confirm the molecular structures, optimized geometry, and electronic and optical properties. The insights of these properties are best visualized in terms of quantum mechanical descriptors responsible due to changes in electron density. Studies of these Schiff base compounds with nitro groups proved to exhibit optical properties and as an excellent organic semiconducting material with an energy gap of 3.08 eV; refractive index of 2.074, and dielectric constant of 4.303. },
	year = {2024}
}
@article{mphydaldhnmr,
	author = {N. Syafni and D. Putra and D. Arbain},
	title = {3,4-DIHYDROXYBENZOIC ACID AND 3,4-DIHYDROXYBENZALDEHYDE FROM THE FERN  Trichomanes chinense  L.; ISOLATION, ANTIMICROBIAL AND ANTIOXIDANT PROPERTIES},
	journal = {Indonesian Journal of Chemistry},
	volume = {12},
	number = {3},
	year = {2012},
	keywords = {Trichomanes chinense L.; 3,4-dihydroxybenzoic acid; 3,4-dihydroxybenzaldehyde; antioxidant; antimicrobial},
	abstract = {3,4-dihydroxybenzoic acid (1) and 3,4-dihydroxybenzaldehyde (2) have been isolated from ethyl acetate fraction of methanolic fractions of leaves, stems and roots of the fern Trichomanes chinense L. (Hymenophyllaceae). These two compounds also showed significant antioxidant using DPPH and antimicrobial activities using the disc diffusion assay.},
	issn = {2460-1578},	pages = {273--278},	doi = {10.22146/ijc.21342},
	url = {https://journal.ugm.ac.id/ijc/article/view/21342}
}
@article{heavyateff1,
	author = {Lodewyk, M. W. and Siebert, M. R. and Tantillo, D. J.},
	title = {Computational Prediction of 1H and 13C Chemical Shifts: A Useful Tool for Natural Product, Mechanistic, and Synthetic Organic Chemistry},
	journal = {Chemical Reviews},
	volume = {112},
	number = {3},
	pages = {1839-1862},
	year = {2012},
	month = {03},
	issn = {0009-2665},
	doi = {10.1021/cr200106v},
	url = {https://doi.org/10.1021/cr200106v},
	eprint = {https://pubs.acs.org/chreay/article-pdf/112/3/1839/8644981/cr200106v.pdf},
}
@article{heavyatef2,
	author = {Jonas, E. and Kuhn, S. and Schlörer, N.},
	title = {Prediction of chemical shift in NMR: A review},
	journal = {Magnetic Resonance in Chemistry},
	volume = {60},
	number = {11},
	pages = {1021-1031},
	keywords = {chemical shift prediction, graph neural network, machine learning, NMR},
	doi = {https://doi.org/10.1002/mrc.5234},
	url = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/abs/10.1002/mrc.5234},
	eprint = {https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/pdf/10.1002/mrc.5234},
	abstract = {Abstract Calculation of solution-state NMR parameters, including chemical shift values and scalar coupling constants, is often a crucial step for unambiguous structure assignment. Data-driven (sometimes called empirical) methods leverage databases of known parameter values to estimate parameters for unknown or novel molecules. This is in contrast to popular ab initio techniques that use detailed quantum computational chemistry calculations to arrive at parameter estimates. Data-driven methods have the potential to be considerably faster than ab inito techniques and have been the subject of renewed interest over the past decade with the rise of high-quality databases of NMR parameters and novel machine learning methods. Here, we review these methods, their strengths and pitfalls, and the databases they are built on.},
	year = {2022}
}
@article{nmrbinsize,
	author = {Schripsema, J.},
	title = {Similarity and differential NMR spectroscopy in metabolomics: application to the analysis of vegetable oils with 1H and 13C NMR},
	journal = {Metabolomics},
	volume = {15},
	number = {39},
	pages = {1573-3890},
	doi = {https://doi.org/10.1007/s11306-019-1502-9},
	abstract = {In NMR based metabolomics there is a need for tools to easily compare spectra and to extract the maximum of information from the data.},
	year = {2019}
}
@article{olefinmetathese,
	author = {Connon, S. J. and Blechert, S.},
	title = {Recent Developments in Olefin Cross-Metathesis},
	journal = {Angewandte Chemie International Edition},
	volume = {42},
	number = {17},
	pages = {1900-1923},
	keywords = {cross-metathesis, homogeneous catalysis, olefins, ring-opening metathesis, synthetic methods},
	doi = {https://doi.org/10.1002/anie.200200556},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.200200556},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.200200556},
	abstract = {Abstract Among the many types of transition-metal-catalyzed CC bond-forming reactions, olefin metathesis has come to the fore in recent years owing to the wide range of transformations that are possible with commercially available and easily handled catalysts. Consequently, olefin metathesis is now widely considered as one of the most powerful synthetic tools in organic chemistry. Until recently the intermolecular variant of this reaction, cross-metathesis, had been neglected despite its potential. With the evolution of new catalysts, the selectivity, efficiency, and functional-group compatibility of this reaction have improved to a level that was unimaginable just a few years ago. These advances, together with a better understanding of the mechanism and catalyst–substrate interactions, have brought us to a stage where more and more researchers are employing cross-metathesis reactions in multistep procedures and in the synthesis of natural products. The recent inclusion of alkynes and hindered bicyclic olefins as viable substrates for bimolecular metathesis coupling, the discovery of enantioselective cross-metathesis and cross-metathesis in water, and the successful marriage of metathesis and solid-phase organic synthesis has further widened the scope of this versatile reaction.},
	year = {2003}
}
@article{dielsalder,
	author = {Sauer, J. and Wiest, H. and Mielert, A.},
	title = {Eine Studie der DIELS-ALDER-Reaktion, I. Die Reaktivität von Dienophilen gegenüber Cyclopentadien und 9.10-Dimethyl-anthracen},
	journal = {Chemische Berichte},
	volume = {97},
	number = {11},
	pages = {3183-3207},
	doi = {https://doi.org/10.1002/cber.19640971129},
	url = {https://chemistry-europe.onlinelibrary.wiley.com/doi/abs/10.1002/cber.19640971129},
	eprint = {https://chemistry-europe.onlinelibrary.wiley.com/doi/pdf/10.1002/cber.19640971129},
	abstract = {Abstract Die Additionsgeschwindigkeiten verschiedener Dienophile an Cyclopentadien und 9.10-Dimethyl-anthracen werden in wasserfreiem Dioxan als Solvens durch kinetische Messungen ermittelt und in Hinsicht auf den Mechanismus der DIELS-ALDER-Reaktion diskutiert.},
	year = {1964}
}
@article{ringstrain,
	author = {Wiberg, K. B.},
	title = {The Concept of Strain in Organic Chemistry},
	journal = {Angewandte Chemie International Edition in English},
	volume = {25},
	number = {4},
	pages = {312-322},
	keywords = {Strained molecules},
	doi = {https://doi.org/10.1002/anie.198603121},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/anie.198603121},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/anie.198603121},
	abstract = {Abstract “Die Ringschließung ist offenbar diejenige Erscheinung, welche am meisten über die räumliche Anordnung der Atome Auskunft geben kann. Wenn eine Kette von 5 und 6 Gliedern sich leicht, eine von weniger oder mehr Gliedern sich schwierig oder auch gar nicht schließen läßt, so müssen dafür offenbar räumliche Gründe vorhanden sein.… Die vier Valenzen des Kohlenstoffatoms wirken in den Richtungen, welche den Mittelpunkt der Kugel mit den Tetraederecken verbinden, und welche miteinander einen Winkel von 109°28′ machen. Die Richtung der Anziehung kann eine Ablenkung erfahren, die jedoch eine mit der Größe der Letzteren wachsende Spannung zur Folge hat,”[ Ring formation is evidently the reaction that can provide the most important information on the spatial arrangement of atoms. Steric reasons should explain the observation that 5- or 6-membered chain undergoes ready closure, whereas a shorter or longer chain undergoes difficult or no closure.… The four valences of the carbon atom act in the directions that connect the center of a sphere with the corners of a tetrahedron and form angles of 109 Degree 28′ with one another. The direction of the attraction can deviate, but this in increasing strain as the sizes of the latter increase. ] This is the quintessence of the “ring-strain theory” formulated by Adolf von Baeyer over one hundred years ago. Although it is today only one facet of the many aspects of strain theory, it has repeatedly stimulated experimental and theoretical chemists. Among the most spectacular of the recent successes in synthetic chemistry are the syntheses of tetra-tert-butyltetrahedrane and [1.1.1]propellane. The reasons for the great stability of these two highly strained compounds are completely different. The experimental findings as well as the results of theoretical analysis by means of molecular mechanics and ab initio calculations have contributed decisively to our present state of knowledge of the structure, energy, and reactivity of organic compounds.},
	year = {1986}
}
@article{ilpmot,
	title = {Inference of chemical reaction networks using mixed integer linear programming},
	journal = {Computers and Chemical Engineering},
	volume = {90},
	pages = {31-43},
	year = {2016},
	issn = {0098-1354},
	doi = {https://doi.org/10.1016/j.compchemeng.2016.04.019},
	url = {https://www.sciencedirect.com/science/article/pii/S0098135416301156},
	author = {Willis, M. J.  and von Stosch, M. },
	keywords = {Chemical reaction network, Structural optimization, Kinetic fitting, Mixed-integer-linear programming},
	abstract = {The manual determination of chemical reaction networks (CRN) and reaction rate equations is cumbersome and becomes workload prohibitive for large systems. In this paper, a framework is developed that allows an almost entirely automated recovery of sets of reactions comprising a CRN using experimental data. A global CRN structure is used describing all feasible chemical reactions between chemical species, i.e. a superstructure. Network search within this superstructure using mixed integer linear programming (MILP) is designed to promote sparse connectivity and can integrate known structural properties using linear constraints. The identification procedure is successfully demonstrated using simulated noisy data for linear CRNs comprising two to seven species (modelling networks that can comprise up to forty two reactions) and for batch operation of the nonlinear Van de Vusse reaction. A further case study using real experimental data from a biodiesel reaction is also provided.}
}
@article{nmrsimml,
	author = {Rowlands, J. B. and Jonsson, L. and Goodman, J. M. and Howe, P. W. A. and Czechtizky, W. and Leek, T. and Lewis, R. J.},
	title = {Towards automatically verifying chemical structures: the powerful combination of 1H NMR and IR spectroscopy},
	journal = {Chemical Science},
	volume = {16},
	number = {45},
	pages = {21590-21599},
	year = {2025},
	month = {12},
	abstract = { Human interpretation of spectroscopic data remains key to confirming newly synthesised chemical structures. Whilst there have been advances in automated spectral interpretation, the false positive and false negative rates remain too high to replace human interpretation. One approach, Automated Structure Verification (ASV), scores observed nuclear magnetic resonance (NMR) spectra against predicted NMR spectra. We describe a method to extend this approach to infrared (IR) spectra and apply it alongside proton NMR spectra to distinguish between a challenging set of 99 similar isomer pairs. Based on relative scores, we classify each as correct, incorrect or unsolved. Our results show that IR can be used as an efficient automated method to distinguish similar isomers with an accuracy close to that of proton NMR. We further introduce a method to combine NMR and IR results and show that the combination significantly outperforms either technique alone. At a true positive rate of 90\%, unsolved pairs are reduced to 0–15\% using NMR and IR together compared to 27–49\% using individual techniques alone. At a true positive rate of 95 Percent, they are reduced to 15–30\% from 39–70\%. These results are a significant step towards efficient automated structure verification based on easily measured spectroscopy data. },
	issn = {2041-6520},
	doi = {10.1039/d5sc06866e},
	url = {https://doi.org/10.1039/d5sc06866e},
	eprint = {https://pubs.rsc.org/sc/article-pdf/16/45/21590/1904936/d5sc06866e.pdf},
}
@article{nmrquant,
	title = {Quantitative 1H NMR spectroscopy},
	journal = {TrAC Trends in Analytical Chemistry},
	volume = {35},
	pages = {5-26},
	year = {2012},
	issn = {0165-9936},
	doi = {https://doi.org/10.1016/j.trac.2012.02.007},
	url = {https://www.sciencedirect.com/science/article/pii/S0165993612000702},
	author = {S. K. Bharti and R. Roy},
	keywords = {Calibration-curve method, Electronic referencing, Metabolomics, NMR spectroscopy, Nuclear magnetic resonance (NMR), Pharmaceutical analysis, Quantitative NMR (qNMR), Referencing technique, Standard-addition method, Validation},
	abstract = {This review illustrates the need to use nuclear magnetic resonance (NMR) spectroscopy for the quantitative analysis of small molecules in their crude forms and in mixtures. We provide the basic concepts of quantitative NMR (qNMR), a brief description of important acquisition and processing parameters responsible for obtaining high-quality, reproducible NMR spectra in order to maximize accuracy, and the latest referencing techniques used for quantitative analysis. We also describe methods that are used for quantitative analysis including calibration-curve and standard-addition methods. Further, we briefly address validation of qNMR spectroscopy and its major applications in various scientific disciplines.}
}
@article{cheminformatics,
	author = {Wegner, J. K. and Sterling, A. and Guha, R. and Bender, A. and Faulon, J.-L. and Hastings, J. and O'Boyle, N. and Overington, J. and Van Vlijmen, H. and Willighagen, E.},
	title = {Cheminformatics},
	year = {2012},
	issue_date = {November 2012},
	publisher = {Association for Computing Machinery},
	address = {New York, NY, USA},
	volume = {55},
	number = {11},
	issn = {0001-0782},
	url = {https://doi.org/10.1145/2366316.2366334},
	doi = {10.1145/2366316.2366334},
	abstract = {Open-source chemistry software and molecular databases broaden the research horizons of drug discovery.},
	journal = {Commun. ACM},
	month = nov,
	pages = {65–75},
	numpages = {11}
}
@article{cheminformatics2,
	author = {Chen, H. and Kogej, T. and Engkvist, O.},
	title = {Cheminformatics in Drug Discovery, an Industrial Perspective},
	journal = {Molecular Informatics},
	volume = {37},
	number = {9-10},
	pages = {1800041},
	keywords = {Cheminformatics, Machine Learning, Library Design, High-Throughput Screening},
	doi = {https://doi.org/10.1002/minf.201800041},
	url = {https://onlinelibrary.wiley.com/doi/abs/10.1002/minf.201800041},
	eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1002/minf.201800041},
	abstract = {Abstract Cheminformatics has established itself as a core discipline within large scale drug discovery operations. It would be impossible to handle the amount of data generated today in a small molecule drug discovery project without persons skilled in cheminformatics. In addition, due to increased emphasis on “Big Data”, machine learning and artificial intelligence, not only in the society in general, but also in drug discovery, it is expected that the cheminformatics field will be even more important in the future. Traditional areas like virtual screening, library design and high-throughput screening analysis are highlighted in this review. Applying machine learning in drug discovery is an area that has become very important. Applications of machine learning in early drug discovery has been extended from predicting ADME properties and target activity to tasks like de novo molecular design and prediction of chemical reactions.},
	year = {2018}
}