Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics
|
|
- Dayna Waters
- 5 years ago
- Views:
Transcription
1 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Accelerated computational discovery of high-performance materials for organic photovoltaics by means of cheminformatics Roberto livares-amaya a, Carlos Amador-Bedolla a,b, Johannes Hachmann a, ule Atahan-Evrenk a, Roel. ánchez-carrera a, Leslie Vogt a and Alán Aspuru-Guzik a a Department of Chemistry and Chemical Biology, Harvard University, 12 xford t, Cambridge, MA 02138, UA b Facultad de Química, Universidad acional Autónoma de México, México, DF 04510, México aspuru@chemistry.harvard.edu July 1, Molecular Library Generation In cheme 1, we show the set of building blocks. These are used to generate the molecular library. Further details of the molecular library generation will be detailed in a separate publication. 1 2 Descriptors We selected a subset of descriptors available through ChemAxon. The subset selected is shown in Table 1. These descriptors were coded in a program and applied to our huge set of molecules. It should be noted that many descriptors are calculated for each atom of the molecule. In these cases we selected the lowest, the highest and the average value to be used in the calibration and in the prediction. 3 Calibration molecules We selected a set of 50 molecules which have been studied experimentally and results are available. We built molecular formulae from the original papers. For these calculations, aliphatic chains were stripped from the molecular formula. The set of molecules with efficiency parameters measured experimentally, thus used in this study, is shown in Fig. 1 and Fig election of descriptors and results for the calibration molecules Fig. 3, Fig. 4 and Fig. 5 show plots of V oc versus each one of the 33 descriptors, none of them showing an obvious correlation. We used R to perform a multiple linear regression. As could have been expected, 50 experimental data with 33 descriptors make for a very good fit with R-squared of ome of the descriptors are not statistically significant, so we removed the less significant descriptors and ended up with Present Address: Robert Bosch LLC Research and Technology Center, 1 Cambridge Center, Cambridge, MA,
2 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Table 1 The set of descriptors calculated using ChemAxon. 1. Molecular mass 2. logp partition constant octanol/water 3. Ring count 4. Hydrogen bond acceptor atom count in molecule 5. Hydrogen bond donor atom count in molecule 6. Rotatable bond count 7. Molecular polarizability 8. Refractivity 9. van der Waals surface area 10. van der Waals volume 11. Water accesible area calculation (AA) 12. Water accesible area calculation of all atoms with positive partial charge (AA+) 13. Water accesible area calculation of all atoms with negative partial charge (AA-) 14. Water accesible area calculation of all hydrophobic ( q i < 0.125) atoms (AA H) 15. Water accesible area calculation of all polar ( q i >= 0.125) atoms (AA P) 16. Electrophilic localization energy (lowest) 17. Electrophilic localization energy (highest) 18. Electrophilic localization energy (average) 19. Partial charge calculation (lowest) 20. Partial charge calculation (highest) 21. Partial charge calculation (average) 22. Electron density (lowest) 23. Electron density (highest) 24. Electron density (average) 25. teric hindrance (lowest) 26. teric hindrance (highest) 27. teric hindrance (average) 28. rbital electronegativity (sigma) (lowest) 29. rbital electronegativity (sigma) (highest) 30. rbital electronegativity (sigma) (average) 31. rbital electronegativity (pi) (lowest) 32. rbital electronegativity (pi) (highest) 33. rbital electronegativity (pi) (average) a fitting from 20 descriptors (with R-squared of ) all of them significant. Table 2 show results of the fitting. ext, we used the same technique for J sc. Table 3 show results of the fitting. In this case, 18 significant descriptors fit the experimental values with R-squared of Table 4 show results of the fitting of PCE. In this case, 15 significant descriptors fit the experimental values with R-squared of Table 5 show results of the fitting of FF. In this case, 20 significant descriptors fit the experimental values with R-squared of ; not all of them are significant but one has to go to only 12 descriptors to get them all significant and then R-squared drops to This is interpreted as meaning that the fitting for FF is not credible at all, as it may be expected for this morphology based experimental parameter. Table 6 show results of the fitting of the product V oc J sc. The fitting is good with R-squared of and all 20 descriptors are significant. A common test of the calibration of the training set to the descriptors is the leave 1/3 out technique. The whole set of calibration molecules is randomly divided in three subsets: A (17 molecules in this case), B (17 molecules), and C (16 molecules). For V oc, the set of 20 descriptors previously selected is used to fit 2
3 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Table 2 Results for the fitting of V oc to 20 descriptors Estimate td. Error t value Pr(> t ) (Intercept) e-09 *** logp e-09 *** RingCount e-08 *** AcceptorCount e-08 *** RotBondCount e-11 *** Refractivity *** VdWArea e-08 *** VdWVolume e-06 *** AA ** AAH * ElecLocEn(lo) * PartialCh(lo) *** PartialCh(hi) e-06 *** PartialCh(avg) e-08 *** ElecDen(lo) ** ElecDen(avg) e-11 *** terichind(hi) e-06 *** σeleceg(lo) ** σeleceg(hi) * σeleceg(avg) e-07 *** πeleceg(hi) e-07 *** ignif. codes: 0 *** ** 0.01 * Residual standard error: on 29 degrees of freedom (8 observations deleted due to missingness) Multiple R-squared: , Adjusted R-squared: F-statistic: on 20 and 29 DF, p-value: 4.09e-13 separately to the subsets AB (34 molecules), AC (33 molecules) and BC (33 molecules). The coefficients thus obtained are used to predict J sc for the set not used in the fitting (C for AB, for instance). Results are shown in Fig. 6. As can be seen, the prediction of excluded molecules is consistent. We performed the same analysis for J sc results are shown in Fig. 7 and for the product V oc J sc results shown in Fig. 8. 3
4 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Table 3 Results for the fitting of J sc to 18 descriptors Estimate td. Error t value Pr(> t ) (Intercept) e-08 *** logp ** AcceptorCount *** DonorCount *** RotBondCount e-08 *** MolPolarizability ** AA *** AA *** AAH *** AAP *** ElecLocEn(lo) e-08 *** ElecLocEn(avg) e-07 *** ElecDen(lo) *** terichind(hi) e-06 *** σeleceg(lo) *** σeleceg(hi) * σeleceg(avg) e-08 *** πeleceg(hi) * πeleceg(avg) e-07 *** ignif. codes: 0 *** ** 0.01 * Residual standard error: on 31 degrees of freedom (8 observations deleted due to missingness) Multiple R-squared: , Adjusted R-squared: F-statistic: on 18 and 31 DF, p-value: 1.016e-10 References [1] In Preparation,
5 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Table 4 Results for the fitting of %PCE to 15 descriptors Estimate td. Error t value Pr(> t ) (Intercept) e-06 *** RotBondCount e-05 *** Refractivity ** VdWArea ** AA e-05 *** AA e-05 *** AAH e-05 *** AAP e-05 *** ElecLocEn(hi) ** PartCharge(avg) ElecDen(lo) *** terichind(lo) ** σeleceg(hi) * σeleceg(avg) e-09 *** πeleceg(hi) *** πeleceg(avg) * ignif. codes: 0 *** ** 0.01 * Residual standard error: on 33 degrees of freedom (9 observations deleted due to missingness) Multiple R-squared: , Adjusted R-squared: F-statistic: on 15 and 33 DF, p-value: 3.784e-09 5
6 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 e e H H 2 i H 2 i H H H 2 i cheme 1 The thirty basic heterocyclic units used in this study are shown with their Mg chemical handles at the 2,5- or para- position of the five-membered and six-membered ring, respectively. 6
7 i e e Fig. 1 First set of the fifty experimentally characterized molecules (shown here without aliphatic side chains). nce stripped of the aliphatic tails, several molecules are equivalent (6 and 8; 3, 16 and 18; and 48 and 50), but all are retained in the training set. 7 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011
8 i i i i i i i i Fig. 2 econd set of the fifty experimentally characterized molecules (shown here without aliphatic side chains). nce stripped of the aliphatic tails, several molecules are equivalent (6 and 8; 3, 16 and 18; and 48 and 50), but all are retained in the training set. 8 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011
9 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Table 5 Results for the fitting of FF to 20 descriptors. ote that not all of them are significant. Estimate td. Error t value Pr(> t ) (Intercept) MolecMass RingCount ** DonorCount * RotBondCount ** MolPolarizability ** VdWVolume AA * AA * AA * AAP ElecLocEn(lo) ** ElecLocEn(hi) ** ElecLocEn(avg) ** PartialCharge(lo) PartialCharge(avg) ElecDen(hi) ** ElecDen(avg) ** σeleceg(hi) * πeleceg(lo) πeleceg(hi) ignif. codes: 0 *** ** 0.01 * Residual standard error: on 28 degrees of freedom (9 observations deleted due to missingness) Multiple R-squared: , Adjusted R-squared: F-statistic: on 20 and 28 DF, p-value:
10 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Table 6 Results for the fitting of V oc J sc to 20 descriptors Estimate td. Error t value Pr(> t ) (Intercept) e-06 *** MolMass * logp ** AcceptorCount ** DonorCount * RotBondCount e-07 *** Refractivity *** AA ** AA ** AA ** AAP ** ElecLocEn(lo) e-05 *** ElecLocEn(avg) e-06 *** PartCharge(hi) ** ElecDen(lo) *** ElecDen(avg) terichind(hi) *** σeleceg(lo) *** σeleceg(avg) e-06 *** πeleceg(hi) *** πeleceg(avg) e-05 *** ignif. codes: 0 *** ** 0.01 * Residual standard error: on 29 degrees of freedom (8 observations deleted due to missingness) Multiple R-squared: , Adjusted R-squared: F-statistic: on 20 and 29 DF, p-value: 1.427e-08 10
11 value V Mass logp RingCount AccepCount DonorCount RotBondCoun Polariz Refractiv vdwurf vdwvol AA Fig. 3 Experimental values of V oc versus a set of 33 descriptors obtained from ChemAxon for the set of 50 calibration molecules stripped of their aliphatic tails. 11 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011
12 value V AAplus AAminus AAH AAP ElecLocEn ElecLocEn ElecLocEn PartCh PartCh PartCh ElecDen1 Fig. 4 Experimental values of V oc versus a set of 33 descriptors obtained from ChemAxon for the set of 50 calibration molecules stripped of their aliphatic tails. 12 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011
13 value V ElecDen ElecDen terichind terichind terichind rbeleci rbeleci rbeleci rbelecpi rbelecpi rbelecpi3 Fig. 5 Experimental values of V oc versus a set of 33 descriptors obtained from ChemAxon for the set of 50 calibration molecules stripped of their aliphatic tails. 13 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011
14 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Leave 1/3 out validation! experimental! predicted from ABC! predicted from AB! predicted from AC! predicted from BC! Fig. 6 Results of the leave 1/3 out correlation test for V oc. 14
15 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Leave 1/3 out validation! experimental! predicted from ABC! predicted from AB! predicted from AC! predicted from BC! Fig. 7 Results of the leave 1/3 out correlation test for J sc. 15
16 Electronic upplementary Material (EI) for Energy & Environmental cience This journal is The Royal ociety of Chemistry 2011 Leave 1/3 out validation! experimental! predicted from ABC! predicted from AB! predicted from AC! predicted from BC! Fig. 8 Results of the leave 1/3 out correlation test for V oc J sc. 16
Learning Molecular Fingerprints from the Graph Up
Learning Molecular Fingerprints from the Graph Up David Duvenaud, Dougal Maclaurin, Jorge Aguilera-Iparraguirre, Rafael Gómez-Bombarelli, Timothy Hirzel, Alán Aspuru-Guzik, Ryan P. Adams Motivation Want
More informationPatrick: An Introduction to Medicinal Chemistry 5e Chapter 01
Questions Patrick: An Introduction to Medicinal Chemistry 5e 01) Which of the following molecules is a phospholipid? a. i b. ii c. iii d. iv 02) Which of the following statements is false regarding the
More information2014 GCEP Final Report Organic Solar Cells
2014 GCEP Final Report Organic Solar Cells Investigators PIs: Zhenan Bao (Chemical Engineering, Stanford University); Alán Aspuru-Guzik (Chemistry and Chemical Biology, Harvard University); Michael Toney
More information" M A #M B. Standard deviation of the population (Greek lowercase letter sigma) σ 2
Notation and Equations for Final Exam Symbol Definition X The variable we measure in a scientific study n The size of the sample N The size of the population M The mean of the sample µ The mean of the
More informationVirtual Libraries and Virtual Screening in Drug Discovery Processes using KNIME
Virtual Libraries and Virtual Screening in Drug Discovery Processes using KNIME Iván Solt Solutions for Cheminformatics Drug Discovery Strategies for known targets High-Throughput Screening (HTS) Cells
More informationMarvin. Sketching, viewing and predicting properties with Marvin - features, tips and tricks. Gyorgy Pirok. Solutions for Cheminformatics
Marvin Sketching, viewing and predicting properties with Marvin - features, tips and tricks Gyorgy Pirok Solutions for Cheminformatics The Marvin family The Marvin toolkit provides web-enabled components
More informationCOMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS
COMPUTER AIDED DRUG DESIGN (CADD) AND DEVELOPMENT METHODS DRUG DEVELOPMENT Drug development is a challenging path Today, the causes of many diseases (rheumatoid arthritis, cancer, mental diseases, etc.)
More informationCommand-line tools of ChemAxon: tips and tricks
Command-line tools of ChemAxon: tips and tricks György Pirok Solutions for Cheminformatics Command-line interface A command-line interface (CLI) is a mechanism for interacting with a computer operating
More informationIntroduction to Chemoinformatics and Drug Discovery
Introduction to Chemoinformatics and Drug Discovery Irene Kouskoumvekaki Associate Professor February 15 th, 2013 The Chemical Space There are atoms and space. Everything else is opinion. Democritus (ca.
More informationarxiv: v1 [cond-mat.mtrl-sci] 15 Nov 2018
Graph Convolutional Neural Networks for Polymers Property Prediction arxiv:1811.06231v1 [cond-mat.mtrl-sci] 15 Nov 2018 Minggang Zeng Jatin Nitin Kumar Soft Materials, Institute of Materials Research and
More informationExercise 2.4 Molecular Orbital Energy Level Diagrams: Homonuclear Diatomics
Exercise 2.4 Molecular rbital Energy Level Diagrams: Homonuclear Diatomics This exercise assumes that you are familiar with the count and sort algorithm described in Exercise 2.3. The table of atomic orbital
More informationMethods for tautomer enumeration, -searching and -duplicate filtering
Methods for tautomer enumeration, -searching and -duplicate filtering József Szegezdi, Zsolt Mohácsi, Tamás Csizmazia, Szilárd Dóránt, Ákos Papp, György Pirok, Szabolcs Csepregi, Ferenc Csizmadia Solutions
More informationQuantum Chemistry in Nanoscale Environments: Insights on Surface- Enhanced Raman Scattering and Organic Photovoltaics
Quantum Chemistry in Nanoscale Environments: Insights on urface- Enhanced Raman cattering and Organic Photovoltaics The Harvard community has made this article openly available. Please share how this access
More informationElectronic Supplementary Material (ESI) for Molecular BioSystems. This journal is The Royal Society of Chemistry 2015 Table S1. Structures and bioactivitiess ID Structure ACS Registry Number pec50 CoMFA
More informationProtein- Ligand Interactions
Protein- Ligand Interactions Outline Introduction Interm olecular bonding forces Electrostatic or ionic bonds Hydrogen bonds Van der Waals interactions Dipole- dipole and ion- dipole interactions Repulsive
More informationMaterials Informatics: Statistical Modeling in Material Science
Materials Informatics: Statistical Modeling in Material Science Hanoch Senderowitz Bar-Ilan University, Israel Strasbourg Summer School in Cheminformatics, June 2016, Strasbourg, France Presentation Goals
More informationLearning over Molecules: Representations and Kernels
Learning over Molecules: Representations and Kernels Jimmy Sun A thesis submitted in partial fulfillment for the degree of Bachelor of Arts in Computer Science, Chemistry & Physics Harvard College Cambridge,
More informationLecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2-3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions Van der Waals Interactions
More informationExamples: 1. Draw the possible resonance structures for the following covalent compounds: a. O3
AP Chemistry Ms. Ye Name Date Block 1. Draw a Lewis structure for each of these molecules. Identify the molecular shape, hybridization, and bond angles. Determine the total number of valence electrons
More informationQSAR of Microtubule Stabilizing Dictyostatins
QSAR of Microtubule Stabilizing Dictyostatins Kia Montgomery BBSI 2007- University of Pittsburgh Department of Chemistry, Grambling State University Billy Day, Ph.D. Department of Pharmaceutical Sciences,
More informationCHAPTER 6 QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP (QSAR) ANALYSIS
159 CHAPTER 6 QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP (QSAR) ANALYSIS 6.1 INTRODUCTION The purpose of this study is to gain on insight into structural features related the anticancer, antioxidant
More informationStructural biology and drug design: An overview
Structural biology and drug design: An overview livier Taboureau Assitant professor Chemoinformatics group-cbs-dtu otab@cbs.dtu.dk Drug discovery Drug and drug design A drug is a key molecule involved
More informationStatistical concepts in QSAR.
Statistical concepts in QSAR. Computational chemistry represents molecular structures as a numerical models and simulates their behavior with the equations of quantum and classical physics. Available programs
More informationThe MOLECULES of LIFE
The MLEULE of LIFE Physical and hemical Principles olutions Manual Prepared by James Fraser and amuel Leachman hapter 1 From enes to RA and Proteins Problems and olutions and Multiple hoice 1. When two
More informationFractional Factorial Designs
Fractional Factorial Designs ST 516 Each replicate of a 2 k design requires 2 k runs. E.g. 64 runs for k = 6, or 1024 runs for k = 10. When this is infeasible, we use a fraction of the runs. As a result,
More informationHOMOLOGY MODELING. The sequence alignment and template structure are then used to produce a structural model of the target.
HOMOLOGY MODELING Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental
More informationHydrogen Bonding & Molecular Design Peter
Hydrogen Bonding & Molecular Design Peter Kenny(pwk.pub.2008@gmail.com) Hydrogen Bonding in Drug Discovery & Development Interactions between drug and water molecules (Solubility, distribution, permeability,
More informationProblem Set # 1 Solutions CHAPTERS 2 & 3 ATOMIC STRUCTURE AND INTERATOMIC BONDING and THE STRUCTURE OF CRYSTALLINE SOLIDS
Problem Set # Solutions CHAPTERS & ATOMIC STRUCTURE AND INTERATOMIC BONDING and THE STRUCTURE OF CRYSTALLINE SOLIDS Assigned:.7(a),.9,.,.6,.8,.7(a),.7,.9,. (graded problems indicated in bold).7 (a) The
More informationIn silico prediction and experimental evaluation of furanoheliangolide sesquiterpene. lactones as potent agents against Trypanosoma brucei rhodesiense
1 Appendix 2 Supplemental material 3 4 5 In silico prediction and experimental evaluation of furanoheliangolide sesquiterpene lactones as potent agents against Trypanosoma brucei rhodesiense 6 7 Thomas
More informationSpiro-fluorene Based 3D Donor towards Efficient Organic. Photovoltaics
Electronic upplementary Material (EI) for Chemical Communications This journal is The Royal ociety of Chemistry 2012 upporting Information piro-fluorene ased 3D Donor towards Efficient rganic Photovoltaics
More informationElectronic Supplementary Information Effective lead optimization targeted for displacing bridging water molecule
Electronic Supplementary Material (ESI) for Physical Chemistry Chemical Physics. This journal is the Owner Societies 2018 Electronic Supplementary Information Effective lead optimization targeted for displacing
More informationAccelerated Computational Discovery of High-Performance Materials for Organic Photovoltaics by Means of Cheminformatics
Accelerated Computational Discovery of High-Performance Materials for Organic Photovoltaics by Means of Cheminformatics The Harvard community has made this article openly available. Please share how this
More informationNucleophile. Reaction Intermediate. Introduction to Reaction mechanisms. Definitions 2/25/2012
Introduction to Reaction mechanisms Definition A reaction mechanism is the step by step sequence of elementary reactions by which overall chemical change occurs. It is also a detailed description of the
More informationSupplementary information Y-shaped Meal-Free D-π-(A) 2 Sensitizers for High-Performance Dye-Sensitized Solar Cells
Electronic upplementary Material (EI) for Journal of Materials Chemistry A This journal is The Royal ociety of Chemistry 2013 upplementary information Y-shaped Meal-Free D-π-(A) 2 ensitizers for High-Performance
More information1.QSAR identifier 1.1.QSAR identifier (title): QSAR model for Toxicokinetics, Transfer Index (TI) 1.2.Other related models:
QMRF identifier (JRC Inventory): QMRF Title: QSAR model for Toxicokinetics, Transfer Index (TI) Printing Date:16.02.2011 1.QSAR identifier 1.1.QSAR identifier (title): QSAR model for Toxicokinetics, Transfer
More informationLecture Notes D: Molecular Orbital Theory
Lecture Notes D: Molecular Orbital Theory Orbital plotting applet: http://www.mpcfaculty.net/mark_bishop/hybrid_frame.htm Images below from: http://employees.oneonta.edu/viningwj/chem111/hybrids%20and%20pi%20bonding.jpg
More informationAlkyl sulfonyl derivatized PAMAM-G2 dendrimers as nonviral gene delivery vectors with improved transfection efficiencies
upplementary Material (EI) for rganic & Biomolecular Chemistry This journal is (c) The Royal ociety of Chemistry 2010 upplementary Information Alkyl sulfonyl derivatized PAMAM-G2 dendrimers as nonviral
More informationREVIEW element compound atom Neutrons Protons Electrons atomic nucleus daltons atomic number mass number Atomic mass
Domain 2: Matter REVIEW Matter is made up of elements An element is a substance that cannot be broken down to other substances by chemical reactions A compound is a substance consisting of two or more
More informationReaction mechanisms offer us insights into how reactions work / how molecules react with one another.
Introduction 1) Lewis Structures 2) Representing Organic Structures 3) Geometry and Hybridization 4) Electronegativities and Dipoles 5) Resonance Structures (a) Drawing Them (b) Rules for Resonance 6)
More informationChimica Farmaceutica
Chimica Farmaceutica Drug Targets Why should chemicals, some of which have remarkably simple structures, have such an important effect «in such a complicated and large structure as a human being? The answer
More informationStatistics 512: Solution to Homework#11. Problems 1-3 refer to the soybean sausage dataset of Problem 20.8 (ch21pr08.dat).
Statistics 512: Solution to Homework#11 Problems 1-3 refer to the soybean sausage dataset of Problem 20.8 (ch21pr08.dat). 1. Perform the two-way ANOVA without interaction for this model. Use the results
More informationA QSAR study investigating the potential anti-hiv-1 effect of some Acyclovir and Ganciclovir analogs
Issue in Honor of Prof icolò Vivona ARKIVC 2009 (viii) 85-94 A QAR study investigating the potential anti-hiv-1 effect of some Acyclovir and Ganciclovir analogs Anna Maria Almerico,* Marco Tutone, and
More informationLec.1 Chemistry Of Water
Lec.1 Chemistry Of Water Biochemistry & Medicine Biochemistry can be defined as the science concerned with the chemical basis of life. Biochemistry can be described as the science concerned with the chemical
More informationAqueous solutions. Solubility of different compounds in water
Aqueous solutions Solubility of different compounds in water The dissolution of molecules into water (in any solvent actually) causes a volume change of the solution; the size of this volume change is
More informationBiochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015,
Biochemistry,530:,, Introduc5on,to,Structural,Biology, Autumn,Quarter,2015, Course,Informa5on, BIOC%530% GraduateAlevel,discussion,of,the,structure,,func5on,,and,chemistry,of,proteins,and, nucleic,acids,,control,of,enzyma5c,reac5ons.,please,see,the,course,syllabus,and,
More informationInference for Regression Simple Linear Regression
Inference for Regression Simple Linear Regression IPS Chapter 10.1 2009 W.H. Freeman and Company Objectives (IPS Chapter 10.1) Simple linear regression p Statistical model for linear regression p Estimating
More informationR in Linguistic Analysis. Wassink 2012 University of Washington Week 6
R in Linguistic Analysis Wassink 2012 University of Washington Week 6 Overview R for phoneticians and lab phonologists Johnson 3 Reading Qs Equivalence of means (t-tests) Multiple Regression Principal
More informationLogistic Regressions. Stat 430
Logistic Regressions Stat 430 Final Project Final Project is, again, team based You will decide on a project - only constraint is: you are supposed to use techniques for a solution that are related to
More informationSolvent Scales. ε α β α: solvent's ability to act as a hydrogen bond-donor to a solute
Solvent Scales ε α β α: solvent's ability to act as a hydrogen bond-donor to a solute Water 78 1.17 0.47 DMS 47 0.00 0.76 DM 37 0.00 0.76 Methanol 33 0.93 0.66 MPA 29 0.00 1.05 Acetone 21 0.08 0.43 Methylene
More informationCHAPTER 3. Vibrational Characteristics of PTP-1B Inhibitors
CHAPTER 3 Vibrational Characteristics of PTP-1B Inhibitors 3.1 Preface Theoretical Frequency calculations were performed on the molecules chosen in this study. Initially all the geometries were optimized
More informationbcl::cheminfo Suite Enables Machine Learning-Based Drug Discovery Using GPUs Edward W. Lowe, Jr. Nils Woetzel May 17, 2012
bcl::cheminfo Suite Enables Machine Learning-Based Drug Discovery Using GPUs Edward W. Lowe, Jr. Nils Woetzel May 17, 2012 Outline Machine Learning Cheminformatics Framework QSPR logp QSAR mglur 5 CYP
More informationExam Analysis: Organic Chemistry, Midterm 1
Exam Analysis: Organic Chemistry, Midterm 1 1) TEST BREAK DOWN: There are three independent topics covered in the first midterm, which are hybridization, structure and isomerism, and resonance. The test
More informationCHM 115 EXAM #2 Practice
Name CHM 115 EXAM #2 Practice Circle the correct answer. (numbers 1-8, 2.5 points each) 1. Which of the following bonds should be the most polar? a. N Cl b. N F c. F F d. I I e. N Br 2. Choose the element
More informationUsing Bayesian Statistics to Predict Water Affinity and Behavior in Protein Binding Sites. J. Andrew Surface
Using Bayesian Statistics to Predict Water Affinity and Behavior in Protein Binding Sites Introduction J. Andrew Surface Hampden-Sydney College / Virginia Commonwealth University In the past several decades
More informationBiomolecules: lecture 9
Biomolecules: lecture 9 - understanding further why amino acids are the building block for proteins - understanding the chemical properties amino acids bring to proteins - realizing that many proteins
More informationPeriodic Table. 8/3/2006 MEDC 501 Fall
Periodic Table 8/3/2006 MEDC 501 Fall 2006 1 rbitals Shapes of rbitals s - orbital p -orbital 8/3/2006 MEDC 501 Fall 2006 2 Ionic Bond - acl Electronic Structure 11 a :: 1s 2 2s 2 2p x2 2p y2 2p z2 3s
More informationObjectives Simple linear regression. Statistical model for linear regression. Estimating the regression parameters
Objectives 10.1 Simple linear regression Statistical model for linear regression Estimating the regression parameters Confidence interval for regression parameters Significance test for the slope Confidence
More informationLewis Structures and Molecular Shapes
Lewis Structures and Molecular Shapes Drawing Lewis Structures Determine from formula if ionic or covalent Count the electrons If ionic : add valence # to charge if (-), subtract if (+) - = 7+1 electrons;
More informationPolar Bonds and Molecules
Chemistry 1 of 33 Snow covers approximately 23 percent of Earth s surface. Each individual snowflake is formed from as many as 100 snow crystals. The polar bonds in water molecules influence the distinctive
More informationAny of 27 linear and nonlinear models may be fit. The output parallels that of the Simple Regression procedure.
STATGRAPHICS Rev. 9/13/213 Calibration Models Summary... 1 Data Input... 3 Analysis Summary... 5 Analysis Options... 7 Plot of Fitted Model... 9 Predicted Values... 1 Confidence Intervals... 11 Observed
More informationMolecules for organic electronics: intermolecular interactions vs properties
Molecules for organic electronics: intermolecular interactions vs properties Chiara Bertarelli Dipartimento di Chimica, Materiali e Ing. Chimica G. Natta Politecnico di Milano e-mail: chiara.bertarelli@polimi.it
More informationSupporting Information
Electronic Supplementary Material (ESI) for Journal of Materials Chemistry A. This journal is The Royal Society of Chemistry 2018 Supporting Information A minimal non-radiative recombination loss for efficient
More informationSUPPLEMENTARY INFORMATION
doi:10.1038/nature17439 Table S1. Inorganic atom property descriptors used in this study. (C) indicates values computed by us; (M) indicates values obtained directly from Mathematica 10; (M,C) indicates
More informationSupporting Information: Molecular Interfaces for Plasmonic Hot Electron. Photovoltaics
Electronic Supplementary Material (ESI) for Nanoscale. This journal is The Royal Society of Chemistry 2015 Supporting Information: Molecular Interfaces for Plasmonic Hot Electron Photovoltaics F. Pelayo
More informationOther Cells. Hormones. Viruses. Toxins. Cell. Bacteria
Other Cells Hormones Viruses Toxins Cell Bacteria ΔH < 0 reaction is exothermic, tells us nothing about the spontaneity of the reaction Δ H > 0 reaction is endothermic, tells us nothing about the spontaneity
More informationCH.7 Fugacities in Liquid Mixtures: Models and Theories of Solutions
CH.7 Fugacities in Liquid Mixtures: Models and Theories of Solutions The aim of solution theory is to express the properties of liquid mixture in terms of intermolecular forces and liquid structure. The
More informationPlan. Lecture: What is Chemoinformatics and Drug Design? Description of Support Vector Machine (SVM) and its used in Chemoinformatics.
Plan Lecture: What is Chemoinformatics and Drug Design? Description of Support Vector Machine (SVM) and its used in Chemoinformatics. Exercise: Example and exercise with herg potassium channel: Use of
More informationChemistry 110. Bettelheim, Brown, Campbell & Farrell. Ninth Edition
hemistry 110 Bettelheim, Brown, ampbell & Farrell inth Edition Introduction to General, rganic and Biochemistry hapter 16 Amines Amine Molecules are Weak Bases Aliphatic & Aromatic Amines Amines are relatives
More informationQSAR Study of Quinazoline Derivatives as Inhibitor of Epidermal Growth Factor Receptor-Tyrosine Kinase (EGFR-TK)
3rd International Conference on Computation for cience and Technology (ICCT-3) QAR tudy of Quinazoline Derivatives as Inhibitor of Epidermal Growth Factor Receptor-Tyrosine Kinase (EGFR-TK) La de Aman1*,
More informationThe Chemical Basis of Life
The Chemical Basis of Life Chapter 2 Objectives Identify the four elements that make up 96% of living matter. Distinguish between the following pairs of terms: neutron and proton, atomic number and mass
More informationA very brief history of the study of light
1. Sir Isaac Newton 1672: A very brief history of the study of light Showed that the component colors of the visible portion of white light can be separated through a prism, which acts to bend the light
More informationORGANIC - EGE 5E CH. 2 - COVALENT BONDING AND CHEMICAL REACTIVITY
!! www.clutchprep.com CONCEPT: HYBRID ORBITAL THEORY The Aufbau Principle states that electrons fill orbitals in order of increasing energy. If carbon has only two unfilled orbitals, why does it like to
More informationAtomic Structure. Atomic Structure. Atomic Structure. Atomic Structure. Electron Configuration. Electron Configuration
Atomic Electron onfiguration Atomic Electron onfiguration z z z E 3rd SELL 3d 3p 3s y 2p x x y 2p y x y 2p z x 2nd SELL t SELL 2p x y z 2nd SELL 2p x y z y z x Atomic Ground State onfiguration Lowest energy
More informationClass: Dean Foster. September 30, Read sections: Examples chapter (chapter 3) Question today: Do prices go up faster than they go down?
Class: Dean Foster September 30, 2013 Administrivia Read sections: Examples chapter (chapter 3) Gas prices Question today: Do prices go up faster than they go down? Idea is that sellers watch spot price
More informationWater content of flavonoid / cyclodextrin nanoparticles
PLITEHNICA UNIVERSITY F TIMIŞARA - RMANIA Faculty of Industrial Chemistry and Environmental Engineering Water content of flavonoid / cyclodextrin nanoparticles Authors: Daniel I. Hădărugă, Nicoleta G.
More informationAnswer Keys to Homework#10
Answer Keys to Homework#10 Problem 1 Use either restricted or unrestricted mixed models. Problem 2 (a) First, the respective means for the 8 level combinations are listed in the following table A B C Mean
More informationDihedral Angles. Homayoun Valafar. Department of Computer Science and Engineering, USC 02/03/10 CSCE 769
Dihedral Angles Homayoun Valafar Department of Computer Science and Engineering, USC The precise definition of a dihedral or torsion angle can be found in spatial geometry Angle between to planes Dihedral
More informationAssignment 9 Answer Keys
Assignment 9 Answer Keys Problem 1 (a) First, the respective means for the 8 level combinations are listed in the following table A B C Mean 26.00 + 34.67 + 39.67 + + 49.33 + 42.33 + + 37.67 + + 54.67
More informationComputation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge
SUPPORTING INFORMATION Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge Tiejun Cheng, Yuan Zhao, Xun Li, Fu Lin, Yong Xu, Xinglong Zhang, Yan Li and Renxiao
More informationLecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability
Lecture 2 and 3: Review of forces (ctd.) and elementary statistical mechanics. Contributions to protein stability Part I. Review of forces Covalent bonds Non-covalent Interactions: Van der Waals Interactions
More informationSaba Al Fayoumi. Tamer Barakat. Dr. Mamoun Ahram + Dr. Diala Abu-Hassan
1 Saba Al Fayoumi Tamer Barakat Dr. Mamoun Ahram + Dr. Diala Abu-Hassan What is BIOCHEMISTRY??? Biochemistry = understanding life Chemical reactions are what makes an organism (An organism is simply atoms
More informationThe Chemical principles of Coloration
Chapter 2-3 Introduction The Chemical principles of Coloration A single atoms consists of a central core or nucleus which contains numbers of positively charged particles(protons) and uncharged particles(neutrons)
More informationAtomic weight = Number of protons + neutrons
1 BIOLOGY Elements and Compounds Element is a substance that cannot be broken down to other substances by chemical reactions. Essential elements are chemical elements required for an organism to survive,
More informationNavigation in Chemical Space Towards Biological Activity. Peter Ertl Novartis Institutes for BioMedical Research Basel, Switzerland
Navigation in Chemical Space Towards Biological Activity Peter Ertl Novartis Institutes for BioMedical Research Basel, Switzerland Data Explosion in Chemistry CAS 65 million molecules CCDC 600 000 structures
More informationAtomic and molecular interaction forces in biology
Atomic and molecular interaction forces in biology 1 Outline Types of interactions relevant to biology Van der Waals interactions H-bond interactions Some properties of water Hydrophobic effect 2 Types
More informationRapid Learning Center Presenting. Teach Yourself High School Chemistry in 24 Hours.
Rapid Learning Center Chemistry :: Biology :: Physics :: Math Rapid Learning Center Presenting Teach Yourself igh School Chemistry in 24 ours 1/30 http://www.rapidlearningcenter.com Chemical Bonding Rapid
More informationQuiz QSAR QSAR. The Hammett Equation. Hammett s Standard Reference Reaction. Substituent Effects on Equilibria
Quiz Select a method you are using for your project and write ~1/2 page discussing the method. Address: What does it do? How does it work? What assumptions are made? Are there particular situations in
More informationOptimization and Complexity
Optimization and Complexity Decision Systems Group Brigham and Women s Hospital, Harvard Medical School Harvard-MIT Division of Health Sciences and Technology Aim Give you an intuition of what is meant
More informationChapter-2 (Page 22-37) Physical and Chemical Properties of Water
Chapter-2 (Page 22-37) Physical and Chemical Properties of Water Introduction About 70% of the mass of the human body is water. Water is central to biochemistry for the following reasons: 1- Biological
More informationiclicker Question #12A - before lecture Which of the following dotted lines shows a possible hydrogen bond? (A) (B) (C) H
Bio 111 andout for hemistry 4 This handout contains: 1. Today s ilicker Questions 2. The handout for today s lecture. 3. Summary of Basic hemistry Lectures ilicker Question #12A - before lecture Which
More informationWhen intermolecular forces are strong, the atoms, molecules, or ions are strongly attracted to each other, and draw closer together.
INTERMOLECULAR FORCES: THE FORCE BEHIND VARIOUS PROPERTIES WHY? Intermolecular forces are largely responsible for the properties of affinity, solubility, volatility, melting/ boiling point, and viscosity.
More informationRama Abbady. Zina Smadi. Diala Abu-Hassan
1 Rama Abbady Zina Smadi Diala Abu-Hassan (00:00) (10:00) Types of Molecules in the Cell 1. Water Molecules: a large portion of the cell mass is water (70% of total cell mass). 2. Organic molecules (carbon
More informationMolecular Geometry and intermolecular forces. Unit 4 Chapter 9 and 11.2
1 Molecular Geometry and intermolecular forces Unit 4 Chapter 9 and 11.2 2 Unit 4.1 Chapter 9.1-9.3 3 Review of bonding Ionic compound (metal/nonmetal) creates a lattice Formula doesn t tell the exact
More informationInternational Journal of Pure and Applied Researches; Volume 1(1)/2015
Computational tudies and Multivariate Analysis of Global and Local Reactivity Descriptors of Five Membered Heterocycles Molecules by Density Functional Theory (DFT). urendra Babu Department of Chemistry
More informationElements react to attain stable (doublet or octet) electronic configurations of the noble gases.
digitalteachers.co.ug Chemical bonding This chapter teaches the different types and names of bonds that exist in substances that keep their constituent particles together. We will understand how these
More informationAnalysis of a Large Structure/Biological Activity. Data Set Using Recursive Partitioning and. Simulated Annealing
Analysis of a Large Structure/Biological Activity Data Set Using Recursive Partitioning and Simulated Annealing Student: Ke Zhang MBMA Committee: Dr. Charles E. Smith (Chair) Dr. Jacqueline M. Hughes-Oliver
More informationFluorine in Peptide and Protein Engineering
Fluorine in Peptide and Protein Engineering Rita Fernandes Porto, February 11 th 2016 Supervisor: Prof. Dr. Beate Koksch 1 Fluorine a unique element for molecule design The most abundant halogen in earth
More informationIntroduction into Biochemistry. Dr. Mamoun Ahram Lecture 1
Introduction into Biochemistry Dr. Mamoun Ahram Lecture 1 Course information Recommended textbooks Biochemistry; Mary K. Campbell and Shawn O. Farrell, Brooks Cole; 7 th edition Instructors Dr. Mamoun
More informationCorrelation of liquid viscosity with molecular structure for organic compounds using different variable selection methods
Issue in Honor of Professor Dionis Sunko ARKIVOC 2002 (IV) 45-59 Correlation of liquid viscosity with molecular structure for organic compounds using different variable selection methods Bono Lu i, 1*
More information2 The Chemical Context of Life
2 The Chemical Context of Life CAMPBELL BILGY TENT EDITIN Reece Urry Cain Wasserman Minorsky Jackson A Chemical Connection to Biology Biology is the study of life Living organisms and their environments
More information