DOCSLIB.ORG

Pre-Year 2 Preparation Guide

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

Pre-Year 2 Preparation Guide Don’t spend your whole summer vacation forgetting all of the chemistry you’ve learned …a little bit of preparation will help your performance in Year 2 …a little bit of summer reading will expand your independent learning skills (which employers are very keen on)! 1. Summer Reading List 2. Revision of Year 1 Topics 3. A Quick Guide to (Essential) Differentiation & Integration (6F5Z2007) 4. Symmetry & Basic Crystallography (6F5Z2007) 5. NMR Spectroscopy – Preparation (6F5Z2006) 6. Essential 1st Year Organic Chemistry (6F5Z2006) 7. Biological Processes & Pharm Chem (6F5Z2009) SUMMER READING LIST PREPARATION FOR YEAR 2 Dr. Lindsey J. Munro [email protected] 1 Dr. Lindsey J. Munro [email protected] 2 Summer Reading List Preparing for your 2nd Year To stop you from getting bored in the long, long holidays, here’s a copy of your summer reading list…in case you are near to a library – to help you find out which bits of chemistry that you like! All good preparation for career (& exam) success in the future. Recommended Books for Yrs 2 & 3: We arrange a book pack of the 3 recommended texts which will cover Years 2 & 3 from OUP at a reduced price of ~£122 (20% reduction & the cost works out at ~12-17p / day) – based on 2016. Usually you can purchase these from Portland Bookshop (MMU Student Union) or Blackwell Bookshop “Physical Chemistry” by Atins & de Paula (Newest: 11th edition - 2017) + “Organic Chemistry” by Claydon, Greeves & Warren (Newest: 2nd edition - 2012) + “Inorganic Chemistry” by Weller, Overton, Rourke & Armstrong (Newest: 7th edition - 2018) Chemistry3 will still be a useful introductory textbook – but you will also need the depth of information presented in the other recommended texts. “Maths for Chemistry” will help explain & provide lots of practice questions for the maths that you will encounter in Years 2 & 3. General Comments In general, the following series of books are all good for getting a more in-depth idea about one topic – but I would not recommend that you buy them. They are all well written & light! See if you can find copies in a library. I’ve noted how many copies of each book that there are available in the MMU library – please don’t take out all of these books & keep them sitting in a dark corner for the whole vacation. Just take one book – and try reading it. (NB: Not in one sitting!) Return any books as soon as possible. You might pick a topic that you’ve found especially difficult this year or the subject you’ve liked the best. Revising your notes from this year of anything you’ve found particularly topic is always a good start! Let me know which books you like the best (or least) & if you have any other recommendations. Royal Society of Chemistry (RSC) Tutorial Texts: http://pubs.rsc.org/bookshop/search?searchtext=Tutorial+texts Oxford Chemistry Primers: http://ukcatalogue.oup.com/category/academic/series/chemistry/ocp.do Open University/RSC "The Molecular World": http://www.rsc.org/molecularworld (The OU is particularly good at writing texts that enable you to teach yourself = Key Grad Skill.) Supplementary Book “A Guide to Modern Inorganic Chemistry” by Steven M. Owen & Alan T. Brooker – There are 2 copies in the library – but if you ever find cheap used copies on Amazon or e-bay then I would recommend buying it. Dr. Lindsey J. Munro [email protected] 3 Summer Reading Do not buy these books – just get them from the library 1. Foundations of Organic Chemistry by Hornby & Peach (Oxford Chemistry Primers) - 4 copies - Practice of functional group, nucleophile & electrophile identification - Revise 1st year notes - Revise Chemistry3 (especially if you don’t get one of the copies of the primer) - Highly recommended - essential prior to Year 2 Organic Chemistry in 6F5Z2006 = Core 1 2. “Physical Chemistry: Understanding our Chemical World” by Paul Monk - 11 copies in the library - Written by a former MMU lecturer. - Easy to read guide to physical chemistry – introducing you to key concepts by trying to answer questions about things that we observe in the world around us…like “Why do we sneeze?”, “How is smoke in horror films made?” - Especially Chapters 3, 4 – 10 - Useful for Thermodynamics & Phase Equilibria lectures – Year 2 - 6F5Z2007 = Core 2 - Highly recommended. 3. “Molecular Symmetry & Group Theory” by Alan Vincent - 6 copies (1 – 1977, 5 – 2001) in the library - A unique book that actually gets you to teach yourself a topic in a step-by-step guide. - It gives you a good head-start getting your head around symmetry elements – don’t be put off by the maths…and try building molecules using Scigress if you need help visualizing the structures. - Useful for Symmetry lectures – Year 2 & Spectroscopy lectures - 6F5Z2007 = Core 2 - Highly recommended. 4. d- and f-block chemistry by C. J. Jones (RSC Tutorial Text) - 1 copy in library - Transition metal chemistry lectures – Year 2 - 6F5Z2006 = Core 1 5. “Basic Atomic & Molecular Spectroscopy” by J. Michael Hollas (RSC Tutorial Text) - 1 copy in library - Spectroscopy lectures (Phys. Chem.) – Year 2 - 6F5Z2008 = Analytical Techniques (Core 3) Other libraries – Check!! In the UK the MMU library can issue you with a SCONUL card which allows you to visit (but not borrow) books from all UK university libraries. Dr. Lindsey J. Munro [email protected] 4 REVISION GUIDE PREPARATION FOR YEAR 2 Dr. Lindsey J. Munro [email protected] 5 Dr. Lindsey J. Munro [email protected] 6 Revision Guide Preparation for Year 2 During the long, long vacation you will probably be ready to start doing some thinking and getting ready for your second year. There are lots of good reasons to do this: Your second year marks count towards your final degree classification. When you apply for jobs during your final year, employers will look at these marks to assess whether they should hire you – so make sure they are good!! Many people find the 2nd year of the course a big jump up from the 1st year - therefore, it is important to revise your notes from last year in core topics, since we will assume that you already know & remember the content of these courses, without having to look them up. If you “just” managed to pass the course (anything less than 100%!), then look in particular at topics that you found difficult and think about how you could have improved your performance in both coursework & examinations. Independent study and practising questions on your own are essential elements to developing the problem-solving skills and knowledge required by employers to succeed. Before asking a question, make sure you have searched fully for the answer. Hard work now = Interesting & challenging job later Core 2 (Yr 2) = 6F5Z2007 Essential Preparation Physical + Inorganic Guide to Differentiation & Integration (Separate Section) Essential 2 G Cp - If you don’t know how to deal with mathematical functions such as or dT (or if you T T do vaguely but it makes you want to cry just thinking about it) then working through this simple guide will be your key to success in the Thermochemistry module in CH2112. - Even if you got an A* at A-level you need to be fluent in this mathematics by the start of Year 2 … so yes, you should go through the guide too… - Warning: If you don’t try this guide, you will find the Thermochemistry course more tricky than it really is – it really is just a question of practising so that you are familiar with the content. (Practising = Read / do questions in guide 10 – 30 times … not just once.) - Highly recommended by this year’s 2nd years. Monk & Munro’s “Maths for Chemistry” book (Chapters 14-20) - All exercises in all of these chapters … will help you gain the expertise & proficiency that you will need in the relevant mathematics required for this course & brush up on your independent learning skills as well … which will make your future employers v. happy! Symmetry, Structures of Simple Solids & Basic Crystallography ESSENTIAL REVISION & PREPARATION Guide (Separate Section) - Chapters 3, 6 & 8 – “Inorganic Chemistry” by Weller et al. - Outline of key skills required to practise over vacation - Online Resources - Scigress Modelling Exercises Notes from 6F4Z2004 – Fundamental Chemistry Concepts 2 Thermodynamics & Kinetics (Dr. Edge) - Especially the key principles, equations (memorised) & how to apply these. Dr. Lindsey J. Munro [email protected] 7 Core 1 (Yr 2) = 6F5Z2006 Essential Preparation Organic + Inorganic Review of Organic Chemistry required for 2nd year (Separate Section) - When learning organic chemistry, each new element builds on the foundation of all of the previous knowledge. It is essential that you know how to do the following WITHOUT looking at a text book at the start of the year. You MUST be fluent in the language of organic chemistry before term starts in September: o Name compounds o Identify functional groups, sp2, sp3 carbons, electrophiles & nucleophiles o Curly arrows - Should be able to draw mechanisms (without looking at notes) - Predict products of reactions based on Year 1 knowledge of chemistry o A wide range of reactions (nucleophilic addition, SN1, SN2, E1 and E2 etc.) o Carbonyl group chemistry o Grignard reagents - Overview of each - Additions to the C=O group of Grignard reagents o Reactions of Alkenes & Alkynes – Markovnikov’s rule o Relative stability of carbocations & how that relates to electrophilic additions to alkenes (Markovnikoff & anti-Markovnikoff additions) o Identification of primary, secondary, tertiary & quaternary carbons o R & S for naming enantiomers o Double bond equivalents - Read this review, memorise the key elements now & throughout the term.
Recommended publications
  • GROMACS: Fast, Flexible, and Free

    GROMACS: Fast, Flexible, and Free

    GROMACS: Fast, Flexible, and Free DAVID VAN DER SPOEL,1 ERIK LINDAHL,2 BERK HESS,3 GERRIT GROENHOF,4 ALAN E. MARK,4 HERMAN J. C. BERENDSEN4 1Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Box 596, S-75124 Uppsala, Sweden 2Stockholm Bioinformatics Center, SCFAB, Stockholm University, SE-10691 Stockholm, Sweden 3Max-Planck Institut fu¨r Polymerforschung, Ackermannweg 10, D-55128 Mainz, Germany 4Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, NL-9747 AG Groningen, The Netherlands Received 12 February 2005; Accepted 18 March 2005 DOI 10.1002/jcc.20291 Published online in Wiley InterScience (www.interscience.wiley.com). Abstract: This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simula- tions. The package includes about 100 utility and analysis programs.
  • Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

    Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development

    processes Review Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development Outi M. H. Salo-Ahen 1,2,* , Ida Alanko 1,2, Rajendra Bhadane 1,2 , Alexandre M. J. J. Bonvin 3,* , Rodrigo Vargas Honorato 3, Shakhawath Hossain 4 , André H. Juffer 5 , Aleksei Kabedev 4, Maija Lahtela-Kakkonen 6, Anders Støttrup Larsen 7, Eveline Lescrinier 8 , Parthiban Marimuthu 1,2 , Muhammad Usman Mirza 8 , Ghulam Mustafa 9, Ariane Nunes-Alves 10,11,* , Tatu Pantsar 6,12, Atefeh Saadabadi 1,2 , Kalaimathy Singaravelu 13 and Michiel Vanmeert 8 1 Pharmaceutical Sciences Laboratory (Pharmacy), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland; ida.alanko@abo.fi (I.A.); rajendra.bhadane@abo.fi (R.B.); parthiban.marimuthu@abo.fi (P.M.); atefeh.saadabadi@abo.fi (A.S.) 2 Structural Bioinformatics Laboratory (Biochemistry), Åbo Akademi University, Tykistökatu 6 A, Biocity, FI-20520 Turku, Finland 3 Faculty of Science-Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; [email protected] 4 Swedish Drug Delivery Forum (SDDF), Department of Pharmacy, Uppsala Biomedical Center, Uppsala University, 751 23 Uppsala, Sweden; [email protected] (S.H.); [email protected] (A.K.) 5 Biocenter Oulu & Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7 A, FI-90014 Oulu, Finland; andre.juffer@oulu.fi 6 School of Pharmacy, University of Eastern Finland, FI-70210 Kuopio, Finland; maija.lahtela-kakkonen@uef.fi (M.L.-K.); tatu.pantsar@uef.fi
  • Quantitative Evaluation of Dissociation Mechanisms in Phenolphthalein and the Related Compounds

    Quantitative Evaluation of Dissociation Mechanisms in Phenolphthalein and the Related Compounds

    J. Comput. Chem. Jpn., Vol. 15, No. 1, pp. 13–21 (2016) ©2016 Society of Computer Chemistry, Japan Technical Paper Quantitative Evaluation of Dissociation Mechanisms in Phenolphthalein and the Related Compounds Toshihiko HANAI Health Research Foundation, Research Institute for Production Development 4F, 15 Shimogamo-morimoto-cho, Sakyo-ku, Kyoto 606-0805, Japan e-mail: [email protected] (Received: October 11, 2015; Accepted for publication: April 14, 2016; Online publication: May 6, 2016) Computational chemistry programs were evaluated as aids to teaching qualitative analytical chemistry. Compu- tational chemical calculations can predict absorption spectra, thus enabling the modeling of indicator dissociation mechanisms by different computational chemical programs using a personal computer. An updated MNDO program among 51 programs was found to be the best predictor to explain the dissociation mechanisms of isobenzofuranones and sulfonephthaleins. Unknown dissociation constants were predicted from atomic partial charges instead of Ham- mett's constants. Keywords: Quantitative analysis of dissociation mechanisms, Isobenzofuranone, Sulfonephthalein, Computational chemistry 1 Introduction the absorption wavelength and electron density changes were not well described. The dissociation mechanisms, maximum How to quantitatively teach qualitative analytical chemistry is wavelengths, and electron density maps of isobenzofuranones a very important subject for analytical chemists. Previously, a and sulfonephthaleins were, therefore, evaluated by in silico method to teach molecular interaction mechanisms in chroma- analysis despite the anticipated poor precision. The experimen- tography was quantitatively achieved using molecular mechan- tally measured dissociation of phenolphthalein is described ics and MOPAC programs [1]. Furthermore, the reaction mech- using four dissociation structures, where the ionization of two anisms of highly sensitive detections were also quantitatively phenolic hydroxyl groups converts the neutral molecular form described [2,3].
  • A Comparative Study of the Efficiency of HCV NS3/4A Protease Drugs

    A Comparative Study of the Efficiency of HCV NS3/4A Protease Drugs

    Life Sciences 217 (2019) 176–184 Contents lists available at ScienceDirect Life Sciences journal homepage: www.elsevier.com/locate/lifescie A comparative study of the efficiency of HCV NS3/4A protease drugs against different HCV genotypes using in silico approaches T ⁎ Ahmed A. Ezat , Wael M. Elshemey Biophysics Department, Faculty of Science, Cairo University, 12613 Giza, Egypt ARTICLE INFO ABSTRACT Keywords: Aims: To investigate the efficacy of Direct Acting Antivirals (DAAs) in the treatment of different Hepatitis C HCV Virus (HCV) genotypes. NS3/4A protease Main methods: Homology modeling is used to predict the 3D structures of different genotypes while molecular Molecular docking docking is employed to predict genotype – drug interactions (Binding Mode) and binding free energy (Docking Homology modeling Score). Key findings: Simeprevir (TMC435) and to a lesser degree MK6325 are the best drugs among the studied drugs. The predicted affinity of drugs against genotype 1a is always better than other genotypes. P2–P4 macrocyclic drugs show better performance against genotypes 2, 3 and 5. Macrocyclic drugs are better than linear drugs. Significance: HCV is one of the major health problems worldwide. Until the discovery of DAAs, HCV treatment faced many failures. DAAs target key functional machines of the virus life cycle and shut it down. NS3/4A protease is an important target and several drugs have been designed to inhibit its functions. There are several NS3/4A protease drugs approved by Food and Drug Administration (FDA). Unfortunately, the virus exhibits resistance against these drugs. This study is significant in elucidating that no one drug is able to treat different genotypes with the same efficiency.
  • Parameterizing a Novel Residue

    Parameterizing a Novel Residue

    University of Illinois at Urbana-Champaign Luthey-Schulten Group, Department of Chemistry Theoretical and Computational Biophysics Group Computational Biophysics Workshop Parameterizing a Novel Residue Rommie Amaro Brijeet Dhaliwal Zaida Luthey-Schulten Current Editors: Christopher Mayne Po-Chao Wen February 2012 CONTENTS 2 Contents 1 Biological Background and Chemical Mechanism 4 2 HisH System Setup 7 3 Testing out your new residue 9 4 The CHARMM Force Field 12 5 Developing Topology and Parameter Files 13 5.1 An Introduction to a CHARMM Topology File . 13 5.2 An Introduction to a CHARMM Parameter File . 16 5.3 Assigning Initial Values for Unknown Parameters . 18 5.4 A Closer Look at Dihedral Parameters . 18 6 Parameter generation using SPARTAN (Optional) 20 7 Minimization with new parameters 32 CONTENTS 3 Introduction Molecular dynamics (MD) simulations are a powerful scientific tool used to study a wide variety of systems in atomic detail. From a standard protein simulation, to the use of steered molecular dynamics (SMD), to modelling DNA-protein interactions, there are many useful applications. With the advent of massively parallel simulation programs such as NAMD2, the limits of computational anal- ysis are being pushed even further. Inevitably there comes a time in any molecular modelling scientist’s career when the need to simulate an entirely new molecule or ligand arises. The tech- nique of determining new force field parameters to describe these novel system components therefore becomes an invaluable skill. Determining the correct sys- tem parameters to use in conjunction with the chosen force field is only one important aspect of the process.
  • Kingston University London the Antibiotic Resistance Growth Plate

    Kingston University London the Antibiotic Resistance Growth Plate

    Kingston University London The Antibiotic Resistance Growth Plate (ARGP) as an experimental evolution tool to explore the phenotypic and genotypic mutational pathways underlying the emergence of antimicrobial resistance in Escherichia coli. A thesis submitted in partial fulfilment for the degree of Doctor of Philosophy By Lucky Bonnie Lucia CULLEN Faculty of Science, Engineering and Computing February 2019 Declaration This thesis entitled ‘The Antibiotic Resistance Growth Plate (ARGP)’ as an experimental evolution tool to explore the phenotypic and genotypic mutational pathways underlying the emergence of antimicrobial resistance in Escherichia coli’ is based upon the work conducted in the Faculty of Science, Engineering and Computing at Kingston University London and in collaboration with Dr Philip Aldridge at Newcastle University and Katie Hopkins and Neil Woodford from Public Health England. All the work described is the candidate’s own original work unless otherwise stated. None of the work presented has been submitted for another degree internally or externally. i Acknowledgements At the start of this PhD I had a dream, a dream which could have never been accomplished without the support of many people. Firstly, I would like to express my sincere appreciation to my director of studies Professor Mark Fielder, your provision, guidance and unconditional belief in my potential has contributed significantly to the completion of this thesis. I would also like to acknowledge the overwhelming support received from, Dr Scott Lawton, Camilla Eldridge and Ben Jones, your wealth of knowledge and expertise in the field of evolutionary biology and bioinformatics has assisted greatly in concluding the work within this PhD. I would also like to praise the incredible multidisciplinary support received at Kingston University, specifically that from Dr Gary-Forster Wilkins, Dr Adam Le Gresley, Dr Brian Rooney, Dr James Denholm-Price and Richard Giddens.
  • Conformational Analysis with Scigress

    Conformational Analysis with Scigress

    CONFORMATIONAL ANALYSIS WITH SCIGRESS During this laboratory period you will use two computational chemistry methods to carry out conformational analysis experiments on butane, cyclohexanol and cis-1,3-cyclohexanediol. Mechanics is a method which uses classical Newtonian mechanics to compute the energies of molecules. Bonds are treated as springs and atoms as balls attached to these springs. MOPAC is a method which uses quantum mechanics to calculate the energies of molecules and determine their optimum geometries and other properties; MOPAC is an acronym for Molecular Orbital PACkage Conformational Energy of Butane 1. Build and beautify a molecule of butane. Save your drawing with the name "butane." 2. Highlight (select) the four carbon atoms (in order). All other atoms should be grayed out. Choose Adjust→Dihedral Angle from the menu bar. Select “Define Geometry Label” and “Search”. Apply and then click OK. The workspace containing the butane molecule will reappear with the dihedral angle written in blue across it. The letter S will appear next to the value of the dihedral angle indicating that it is a search label. Re-save the drawing 3. Choose Experiment→New from the menu bar; the experiment dialog box should appear. Choose chemical sample conformations (CAChe 5.0 experiments) from the “Property of” box. Choose optimized map in the “Property” box. Click Start (if an error appears click OK and re-try). 4. Two adjacent windows should appear presenting the results of the calculation. The left window is a plot of potential energy versus dihedral angle for the butane molecule. The graph colors represent the relative energies of the butane molecule with various dihedral angles.
  • Downloaded From: Usage Rights: Creative Commons: Attribution-Noncommercial-No Deriva- Tive Works 4.0

    Downloaded From: Usage Rights: Creative Commons: Attribution-Noncommercial-No Deriva- Tive Works 4.0

    Simbanegavi, Nyevero Abigail (2014) An integrated computational and ex- perimental approach to designing novel nanodevices. Doctoral thesis (PhD), Manchester Metropolitan University. Downloaded from: https://e-space.mmu.ac.uk/620241/ Usage rights: Creative Commons: Attribution-Noncommercial-No Deriva- tive Works 4.0 Please cite the published version https://e-space.mmu.ac.uk AN INTEGRATED COMPUTATIONAL AND EXPERIMENTAL APPROACH TO DESIGNING NOVEL NANODEVICES N. A. SIMBANEGAVI PhD 2014 AN INTEGRATED COMPUTATIONAL AND EXPERIMENTAL APPROACH TO DESIGNING NOVEL NANODEVICES Nyevero Abigail Simbanegavi A thesis submitted in partial fulfilment of the requirements of Manchester Metropolitan University for the degree of Doctor of Philosophy 2014 School of Science and the Environment Division of Chemistry and Environmental Science Manchester Metropolitan University Abstract Small molecules that can organise themselves through reversible bonds to form new molecular structures have great potential to form self-assembling systems. In this study, C60 has been functionalized with components capable of self-assembling via hydrogen bonds in order to form supramolecular structures. Functionalizing the cage not only enhances the solubility of C60 but also alters its electronic properties. In order to analyse the changes in electronic properties of C60 and those of the new derivatives and self-assembled structures, an integrated computational and experimental approach has been used. DNA bases were among the components chosen for functionalizing C60 since these structures are the best example for self-assembly in nature. Experimental routes for novel C60 derivatives functionalised with thymine, adenine, cytosine and guanine have been explored using the Prato reaction. A number of challenges in synthesizing the aldehyde analogues of the DNA bases have been identified, and a number of different solutions have been tested.
  • Molecular Dynamics (MD) for Cancer Control Protocol

    Molecular Dynamics (MD) for Cancer Control Protocol

    Molecular Dynamics (MD) for Cancer control Protocol Claudio Nicolini ( [email protected] ) Claudio Ando Nicolini's Lab, NanoWorld, USA; HC Professor Nanobiotechnology, Lomonosov Moscow State University, Russia; Foreign Member Russian Academy of Sciences; President NWI Fondazione EL.B.A. Nicolini; Editor-in-Chief NWJ, Santa Clara, USA Marine Bozdaganyan Claudio Ando Nicolini's Lab, NanoWorld, USA; Lomonosov Moscow State University (MSU), Moscow, Russia; Fondazione EL.B.A. Nicolini Nicola Luigi Bragazzi Claudio Ando Nicolini's Lab, NanoWorld, USA Philippe Orekhov Claudio Ando Nicolini's Lab, NanoWorld, USA Eugenia Pechkova Claudio Ando Nicolini's Lab, NanoWorld, USA Method Article Keywords: Langmuir-Blodgett (LB)-based crystallography Posted Date: March 15th, 2016 DOI: https://doi.org/10.1038/protex.2016.016 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/13 Abstract In the present protocol, we describe how molecular dynamics \(MD) can be applied for studying Langmuir-Blodgett \(LB)-based crystal proteins. MD can therefore play a major role in nanomedicine, as well as in personalized medicine. Introduction The computer simulation of dynamics in molecular systems is widely used in molecular physics, biotechnology, medicine, chemistry and material sciences to predict physical and mechanical properties of new samples of matter. In the molecular dynamics method there is a polyatomic molecular system in which all atoms are interacting like material points, and behavior of the atoms is described by the equations of classical mechanics. This method allows doing simulations of the system of the order of 106 atoms in the time range up to 1 microsecond.
  • The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme

    The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme

    International Journal of Molecular Sciences Article The First Berberine-Based Inhibitors of Tyrosyl-DNA Phosphodiesterase 1 (Tdp1), an Important DNA Repair Enzyme Elizaveta D. Gladkova 1,2, Ivan V. Nechepurenko 1, Roman A. Bredikhin 1, Arina A. Chepanova 3, Alexandra L. Zakharenko 3, Olga A. Luzina 1 , Ekaterina S. Ilina 3, Nadezhda S. Dyrkheeva 3, Evgeniya M. Mamontova 3, Rashid O. Anarbaev 2,3,Jóhannes Reynisson 4 , Konstantin P. Volcho 1,2,* , Nariman F. Salakhutdinov 1,2 and Olga I. Lavrik 2,3 1 N. N. Vorozhtsov Novosibirsk Institute of Organic Chemistry, Siberian Branch of the Russian Academy of Sciences, 9, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; [email protected] (E.D.G.); [email protected] (I.V.N.); [email protected] (R.A.B.); [email protected] (O.A.L.); [email protected] (N.F.S.) 2 Novosibirsk State University, Pirogova str. 1, Novosibirsk 630090, Russia; [email protected] (R.O.A.); [email protected] (O.I.L.) 3 Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8, Akademika Lavrentieva Ave., Novosibirsk 630090, Russia; [email protected] (A.A.C.); [email protected] (A.L.Z.); [email protected] (E.S.I.); [email protected] (N.S.D.); [email protected] (E.M.M.) 4 School of Pharmacy and Bioengineering, Keele University, Hornbeam Building, Staffordshire ST5 5BG, UK; [email protected] * Correspondence: [email protected] Received: 31 August 2020; Accepted: 26 September 2020; Published: 28 September 2020 Abstract: A series of berberine and tetrahydroberberine sulfonate derivatives were prepared and tested against the tyrosyl-DNA phosphodiesterase 1 (Tdp1) DNA-repair enzyme.
  • Molecular Dynamics Characterization of the Conformational Landscape Of

    Molecular Dynamics Characterization of the Conformational Landscape Of

    See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/290219134 Molecular dynamics characterization of the conformational landscape of small peptides: A series of hands-on collaborative practical sessions for undergraduate students Article in Biochemistry and Molecular Biology Education · January 2016 DOI: 10.1002/bmb.20941 CITATIONS READS 0 82 3 authors: João P G L M Rodrigues Adrien Melquiond Stanford University 32 PUBLICATIONS 489 CITATIONS 30 PUBLICATIONS 311 CITATIONS SEE PROFILE SEE PROFILE Alexandre M J J Bonvin Utrecht University 297 PUBLICATIONS 10,070 CITATIONS SEE PROFILE All in-text references underlined in blue are linked to publications on ResearchGate, Available from: João P G L M Rodrigues letting you access and read them immediately. Retrieved on: 19 September 2016 Molecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A series of hands-on collaborative practical sessions for undergraduate students. João P.G.L.M. Rodrigues1*, Adrien S.J. Melquiond2*, Alexandre M.J.J. Bonvin1* 1. Computational Structural Biology Group, Bijvoet Center for Biomolecular Research, Faculty of Science- Chemistry, Utrecht University, Utrecht, Netherlands. 2. Biomedical genomics, Hubrecht Institute - KNAW & University Medical Center Utrecht, Utrecht, The Netherlands * Corresponding Authors Contact Information: [email protected], [email protected], [email protected] Keywords: protein modelling, molecular dynamics, GROMACS, virtualization, jigsaw teaching Abstract Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community.
  • Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

    Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens

    International Journal of Molecular Sciences Review Application of Various Molecular Modelling Methods in the Study of Estrogens and Xenoestrogens Anna Helena Mazurek 1 , Łukasz Szeleszczuk 1,* , Thomas Simonson 2 and Dariusz Maciej Pisklak 1 1 Chair and Department of Physical Pharmacy and Bioanalysis, Department of Physical Chemistry, Medical Faculty of Pharmacy, University of Warsaw, Banacha 1 str., 02-093 Warsaw Poland; [email protected] (A.H.M.); [email protected] (D.M.P.) 2 Laboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, 91-120 Palaiseau, France; [email protected] * Correspondence: [email protected]; Tel.: +48-501-255-121 Received: 21 July 2020; Accepted: 1 September 2020; Published: 3 September 2020 Abstract: In this review, applications of various molecular modelling methods in the study of estrogens and xenoestrogens are summarized. Selected biomolecules that are the most commonly chosen as molecular modelling objects in this field are presented. In most of the reviewed works, ligand docking using solely force field methods was performed, employing various molecular targets involved in metabolism and action of estrogens. Other molecular modelling methods such as molecular dynamics and combined quantum mechanics with molecular mechanics have also been successfully used to predict the properties of estrogens and xenoestrogens. Among published works, a great number also focused on the application of different types of quantitative structure–activity relationship (QSAR) analyses to examine estrogen’s structures and activities. Although the interactions between estrogens and xenoestrogens with various proteins are the most commonly studied, other aspects such as penetration of estrogens through lipid bilayers or their ability to adsorb on different materials are also explored using theoretical calculations.