#molecular symmetry and group theory

[puffdenlilledragen]

ANYWAY if you want to feel you brain do a stretch i recommend looking into Molecular Symmetry and Group Theory (2nd edition), just the first chapters when it teaches you the flow chart to determine the symmetry group of a molecule. you don't need to know chemistry or maths but it is EXCELLENT training in spatial visualisation of simple 3D objects and it feels so GOOD in the brain!!!!

[chemblrish]

hii how are you? I'm currently studying inorganic chem, mainly coordination compounds but it's proving difficult. I'm unable to fully grasp what's going on. Can you please advise me on coordination compounds and inorganic chem in general? thank you!!

Hi!

Inorganic coordination chem is part of my thesis, you've come to the right place :) Also, I'm going to make this a university-level thing - I didn't study coordination chem in school, so I'm assuming that's the level you expect - but if you actually need advice on studying high school inorganic chem, please let me know!

First, a textbook rec: I studied off Cotton's Basic inorganic chemistry a lot and I liked it. My professor recommended Atkins' Inorganic chemistry too; I admit I didn't use it that much bc I also had some Polish textbooks I found very helpful, but from what I did see, it seemed very comprehensive and in-depth - so if Cotton isn't enough, Atkins might be better for you.

Inorganic chem

orbitals matter: I think it's important to grasp orbitals and hybridization before going any further. This stuff keeps coming up again and again, so if you find yourself struggling with understanding concepts in inorganic chem, I'd suggest making sure you understand atomic and molecular orbitals first.

periodic table trends: please don't memorize them. Please. Understand them. There's a reason why, for example, atomic radii decrease within periods even though both electrons and protons are added as you move to the right (the screening effect - and again, orbitals!). Once more, I liked the way it was explained in Cotton's textbook.

I found flashcards very helpful for studying the properties of the elements and their compounds as that's mostly memorization. Same for HSAB, really.

if your inorganic chem course covers elements of group theory too, here is a website my thesis supervisor told me about :) I think it's pretty great. If you're digging really, really deep into it, Cotton has a whole textbook on group theory in chemistry (Chemical Applications of Group Theory), but I doubt you'd need it for a basic inorganic chem course.

I've also answered an ask on studying chemistry in general - perhaps you'll find it useful too.

Coordination chem

surprise, surprise: ✨ orbitals ✨. Once more, to understand what's going on with coordination compounds, first you need to understand the molecular orbital theory well.

metals oftentimes have a preference for a specific coordination number. Frequently, a whole group will have a preference for the same CN (group 7 ions, for example, prefer CN = 6). That doesn't mean other CNs don't exist, but knowing there's a pattern can be helpful while studying.

coordination numbers aren't totally random. The rules may not be strict and foolproof, but again, there's a general pattern that's worth keeping in mind: bigger ion usually = higher CN (duh?), CNs are usually even (and we still don't really know why that's so! Although it may have to do with geometry and symmetry) and sometimes depend on the charge of the ligand.

crystal field theory. Okay so CFT is really cool, but I see how it can be super confusing too. I'm not sure how deep you have to dig into this stuff for your course, so apologies if I go a little overboard 😅 My advise for studying it would be:

try to visualize the given complex, actually see the position of the ligands in relation to the orbitals

remember: it's all about lowering the energy. That's the core of CFT. Pauli's exclusion principle always, always stands, but CFT tells us coordination compounds are systems that "want to" have the lowest possible energy so bad they'll sometimes break Hund's rule to obtain it

keep in mind CFT is only a model. Some parts of it may not make any sense to you (like the fact it treats all metal - ligand bonds as purely ionic). It just so happens that despite its many simplifications that are obviously not true, CFT still accurately describes many complex compounds

I've had an ask on studying nomenclature, too.

again, I don't know how complex (pun not intended) you need my tips to get, so if you have any specific questions, feel free to hmu :) I'll try my best to explain

[turitolive]

Valence Bond Theory 

Valence Bond Theory is a type of chemical bonding model that is used to predict the bonding behaviour of molecules. This theory is particularly useful when considering the specific interactions that occur between atoms and molecules, and how these interactions ultimately influence the physical and chemical properties of the compound.

In this theory, the chemical bond between atoms is formed when two or more valence electrons are shared between two atoms. The valence electrons are the electrons found in the outermost shell of the atom, and it is these electrons that are most likely to be involved in the process of bonding. 

Valence Bond Theory explains chemical bonding based on the electronic configurations of the atoms present in a molecule. The theory states that atoms share electrons by overlapping of their orbitals so that a new, hybridized orbital is formed from the original atomic orbitals.

When two atoms with parallel spins overlap with each other, the bond formed is called a sigma bond. This bond is stronger than the pi bond, which is formed by atoms with perpendicular spins. Valence Bond Theory helps us understand the bond strength, bond type, and electron distribution in a molecule. 

Postulates of Valence Bond Theory 

The theory is based on several postulates, which include: 

Atomic Orbital Overlap: Covalent bonds are formed by the overlapping of atomic orbitals from different atoms. The overlapping orbitals must have the same symmetry and overlap effectively to allow for the sharing of electrons. 

Electron Pairing: When two atomic orbitals overlap, the electrons within them pair up and occupy the resulting molecular orbital. This pairing of electrons forms a covalent bond between the atoms. 

Conservation of Orbital Symmetry: The symmetry of atomic orbitals is preserved in the process of orbital overlap. Overlapping orbitals must have the same symmetry to ensure proper overlap and bond formation. 

Hybridization: Valence Bond Theory incorporates the concept of hybridization, which suggests that atomic orbitals of different types (such as s, p, d orbitals) can mix or hybridize to form a new set of hybrid orbitals. These hybrid orbitals have specific shapes and orientations that facilitate effective overlap with other atomic orbitals. 

Resonance: Valence Bond Theory also considers the concept of resonance, which arises when a molecule can be represented by multiple Lewis structures with different arrangements of electrons. Resonance structures contribute to the overall electronic structure and bonding in the molecule. 

Types of Orbital Overlap 

Orbital overlap is a term that refers to the interaction between two or more orbitals as they merge to form a chemical bond. The types of orbital overlap are determined by the shape and orientation of the orbitals involved.

There are three main types of orbital overlap: sigma (σ), pi (π), and delta (δ). 

The first type of orbital overlap is sigma (σ) bonding, which occurs when orbitals overlap head on. Sigma bonds are the strongest type of chemical bond formed between atoms and are created by the overlap of s and p orbitals.

This type of overlap results in a linear bond with no orbital nodes, making it the strongest bond between two atoms. Sigmas bonds are the most common types of bonds found in organic chemistry and are responsible for the formation of single bonds in most organic molecules. 

The second type of orbital overlap is pi (π) bonding. P orbital overlap creates π bonds, which are formed by overlapping parallel orbitals. These orbitals have nodal planes perpendicular to the molecular axis. This means that π bonds are weaker than σ bonds because they possess only one nodal plane.

The double bond in alkenes, carbonyl groups, and aromatic compounds results from a π bond between the two atoms. Also, π bonding is responsible for the conductive properties of metals, as the electrons in metal atoms form delocalized π bonds. 

The third type of orbital overlap is delta (δ) bonding. Delta bonds are formed by the overlap of 3 or more orbitals, which can be represented using the D3h point group symmetry. Delta bonds are rare, and only occur in a few compounds such as chromium hexacarbonyl and molybdenum hexacarbonyl.

These compounds have large metal centres with many ligands coordinated to the metal atom, and the bonding is a result of a complex combination of overlapping orbitals. Delta bonds have been of limited practical importance in chemistry but are nonetheless interesting due to the unique bonding arrangement that produces the highly stable compound. 

[sodiumlamp]

This video about imaginary numbers caught my attention, and it turned out to be even better than I expected, drawing a through-line from quadratic equations to the Schrödinger equation, which is extremely fundamental to chemistry and physics. 

Years ago, I tried to study group theory as it relates to molecular symmetry, and in working the problems, I ended up running into the same mathematical principles, usually stuff tied in with Euler’s constant and the golden ratio.   I probably ended up learning more about mathematics than I did about chemistry that year, and I feel like I forgot most of it, but this video illustrates why e and i keeps coming up in anything that has to do with molecular orbitals.   Those are wavefunctions, and Euler’s formula contains both the sine and cosine wave.  

One of these days, I’d really like to study the Schrödinger equation in depth, because it’s always frustrated me how it’s so important when it just looks like a bunch of characters around an equals sign.  I don’t know when I’ll have time to really get into it, but this video gives me some confidence that I can do it.

[studychemistrytopics]

Application of Group Theory in Chemistry

Application of the mathematical theory of groups to the symmetry of inorganic and organic molecule is a powerful method that permits the prediction, classification, and qualitative description of many molecular properties. Most of this information would be unobtainable from first principles because of the difficulties in solving the complicated equations, and, in most cases, very long calculations would be necessary.

In order to obtain equivalent information by other methods. In the particular case of vibrational electromagnetic spectra. Applications of group theory lead to simple methods for the prediction of the number of bands to be found in the infrared and Raman spectra. Therefore shape and electric polarization, and the qualitative description of the normal modes necessary.

This summary will include the tables necessary for the application of group theory to vibrational atomic spectra and instructions on how to use them for molecular gases, liquids, and solutions. A brief introduction to the concepts, definitions, nomenclature, and formulae presented by the group theory, but no theoretical justification of the methods due to complications of equations.

More complete descriptions of the theory underlying such methods, as well as their extensions to molecular crystalline solids and polymers, can be found, at different levels of difficulty.

[tiredbiostudent]

Do you have any tips on how to best study biology??

disclaimer I am the absolute worst person to ask about this but:

��� really depends on the area. for cell bio/genetics/small scale stuff (not my forte at all sfdfsddsk), I would say it’s really important to understand how processes (e.g. cell respiration) work. there’s usually an obnoxious amount of genes, proteins, etc. with painfully similar names so I would also work on making sure you can distinguish which factors operate in which pathways. honestly I find this material really hard and usually overwhelming, but some ways to study could be trying to draw out a cycle or pathway from memory until you have it down, flashcards w protein/gene/etc names, stuff like that.

↠ for things like ecology (which. don’t @ me but is often just a lot of common sense) it might be more memorization based. usually a lot of hierarchies and patterns and things like that, so mind maps might be a good way to synthesize information across multiple topics? really exposing myself here but I have like. never studied for an ecology exam in my life so I can’t offer solid advice on this one sdfjkjdsffjdskj 

↠ for classes like animal diversity/zoology, I found it helpful to create sheets for each phyla/group/etc. with all the key synapomorphies or distinguishing traits and important info- I would say the tricky part of these classes is keeping all the information straight, bc it’s super easy to mix up characteristics between groups (especially w the worm phyla do not get me started). cue cards also worked well! creating tables of main characteristics like tissue level, type of reproduction, symmetry, etc. including all the groups was really effective to organize everything. creating cladograms w key synapomorphies/transitions for each progressing group also helped! lastly I would recommend trying to relate each phyla etc. you learn to animals you know in real life- helps you retain it and also if you’re stuck on a test and can’t remember if like, amphibians have scales or not, you can just think well every frog I know has moist skin so that ain’t it, yk?

↠ for evolution-based classes: really have a good understanding of evolutionary processes and concepts! focus on comprehending the logic behind each theory.  then after you’ve gone over those, relate examples etc. to each of them. also make sure you know how cladograms work (e.g. how to construct one; which two species are most closely related), and memorize the different terms (e.g. plesiomorphy, homology vs. homoplasy, random genetic drift, types of mutations). also try to synthesize the molecular concepts with overarching evolutionary theories- e.g. what kind of mutations or genetic dominance could result in this evolution occurring in this species? if all else fails answer w Darwin, 9 times out of 10 he’s involved somehow.

↠ for courses on plants: know alternation of generations inside OUT. having said that no I still don’t know exactly how it works jdfsdfskhfskd

hope this helped! sorry for having awful studying advice, it’s only because I am awful at studying ‘:) but if you have anymore specific questions I am happy to help out my baby bio students

[mathematicianadda]

CROSS POST FROM R/PHYSICS: My path to learning physics (free access links + math section)

I organized my original post. Also categorized content by topic. And added a math section.

I organized the math section by what I believe to be learning from 'first principals.' This is partially inspired by Schuller's horribly intuitive approach to theoretical physics in his lecture series. That being said, r/math will probably grill me as I might screw up the prerequisite structure or whatever.

Again I've only included texts I have read. So this list is not comprehensive, but I believe it has provided my with a pretty thorough education in elementary mathematics and intermediate - advanced physics.

MATHEMATICS

Logic

Beck - The Art of Proof (PDF) - Prodigious toddler

Lang - Basic Mathematics (PDF) - Biblical

Set theory

Jech - Introduction to Set Theory (PDF) - Undergrad

Number theory

Wilf - Generatingfunctionology (PDF) - Undergrad

Rosen - A classical introduction to modern number theory (PDF) - Undergrad

Algebra

Gelfand - Algebra - Undergrad (PDF) - Undergrad

Artin - Algebra - Undergrad (PDF) - Undergrad

Jacobson - Basic Algebra 2 - Necessary purgatory (PDF) - Grad

Linear Algebra

Strang - Linear Algebra and its Applications (PDF)

Curtis - Abstract linear algebra (NONE) - Undergrad

Greub - Linear algebra and Multilinear algebra (PDF) - Grad

Group theory

Alperin - Groups and Representations (PDF) - Grad

Humphreys - Introduction to Lie Algebras and Representation Theory (PDF) - Grad

Topology

Willard - General topology (NONE) - Grad

Steen - Counterexamples in topology (PDF) - Grad

Geometry

Euclids - The Elements (google) - everyone

Hilbert - Foundations of Geometry (PDF)

Griffiths - Principals of algebraic Geometry (NONE) - Grad

Spivak - A Comprehensive Introduction to Differential Geometry (PDF) - Grad

Kobayashi - Foundations of Differential Geometry (PDF)

Functional analysis

Conway - A Course in Functional Analysis (PDF) - Grad

Kreyszig - Introductory functional analysis with applications - (PDF) - grad

Complex Analysis )

Ahlfors - Complex analysis (PDF) - Grad

Andersson - Topics in complex analysis (PDF) - grad

Calculus

Stewart - Calculus (DIJU) - Undergrad

Spivak - Calculus (PDF) - Undergrad

Spivak - Calculus on manifolds (PDF) - Undergrad

Differential equations

Arnold - Ordinary differential equations (PDF) - Undergrad

Taylor - Partial differential equations (PDF) - Undergrad

Olver - Equivalence, invariants, and symmetry (DIJU) - Grad

Analysis

Rudin - Principles of mathematical analysis (PDF) - Undergrad

Gelbaum - Counterexamples in analysis (PDF) - Undergrad

Katznelson - An introduction to harmonic analysis (DIJU) - Undergrad

Probability

Feller - Introduction to probability theory (DIJU) - Undergrad

PHYSICS

Classical Mechanics:

Kolenkow & Kleppner - An Introduction to Mechanics (PDF) - Undergrad

Taylor - Classical Mechanics (PDF) - Undergrad

Goldstein - Classical Mechanics (PDF) - Grad

Quantum Theory

Griffiths - Introduction to Quantum Mechanics (PDF) - Undergrad

Shankar - Principles of Quantum Mechanics (PDF) - Undergrad

Sakurai - Modern Quantum Mechanics (PDF) - Grad

Heine - Group Theory in Quantum Mechanics (PDF) - Undergrad

Peskin & Schroeder - An Introduction to Quantum Field Theory (PDF) - Undergrad

Srednicki - Quantum Field Theory (PDF) - Grad

Wightman - Spin, Statistics and All That (PDF) - Undergrad

Fujikawa - Path Integrals and Quantum Anomalies (PDF) - Grad

EM theory

Griffiths - Introduction to Electrodynamics (PDF) - Undergrad

Jackson - Classical Electrodynamics (PDF) - The Brita filter of physics

Topics in Theoretical Physics/Mathematical physics

Morse - Methods in Theoretical Physics Vol. 1 & 2 (PDF VOL 1), (PDF VOL 2) - Undergrad

Craig - Hamiltonian Dynamical Systems and Applications (PDF) - Grad

Lawden - Introduction to Tensor Calculus, Relativity & Cosmology (PDF) - Grad

Koks - Explorations in Mathematical Physics (PDF) - Undergrad

Brylinski - Loop Spaces, Characteristic Classes, and Geometric Quantizaiton (PDF) - No-life grad

Guillemin - Symplectic Techniques in Physics (DIJU) - Grad

Struwe - Variational Methods (PDF) - Very grad

Coleman - Aspects of Symmetry (PDF) - Grad

Nakahara - Geometry, Topology and Physics (PDF) - Grad

Schwarz - Topology for Physicists (PDF) - Grad

Statistical mechanics

Schroeder - An Introduction to Thermal Physics (PDF) - Undegrad

Pathria - Statistical Mechanics (PDF) - Grad

Materials/particle physics (sorta)

Omar - Elementary Solid State Physics (PDF) - Undergrad

Philips - Advanced Solid State Physics (PDF) - Undergrad

Feng - Introduction to Condensed Matter Physics (PDF) - '''introduction''' - Grad

Griffiths - Introduction to Elementary particles (PDF) - Undergrad

Computational physics

Klein - Introduction to Computational Physics (PDF) - Undergrad

Thijssen - Computational Physics (PDF) - Grad

Experimental methods

Roe - Probability and Statistics in Experimental Physics (PDF) - Undergrad

Demtroder - Molecular physics (PDF) - Grad (based quantum chemists)

Optics

Smith - Optics and Photonics (PDF) - Undergrad

Fox - Quantum optics (PDF) - Grad

Biophysics

Cotterill - An Introduction to Biophysics (PDF) - Undergrad

Relativity

MTW - Gravitation (PDF) - Biblical

Weinberg - Gravitation & Cosmology (PDF) - Weinberg torture (read his QFT volumes if you're a masochist)

Blagojevic - Gravitation and Gauge Symmetries (PDF) - Grad

Astrophysics

Carroll - Introduction to Modern Astrophysics (PDF) - Undergrad

Collins - Fundamentals of Stellar Astrophysics (PDF) - Grad

Duric - Advanced Astrophysics (PDF) - Grad

submitted by /u/theonlytragon [link] [comments] from math http://bit.ly/2WVXEIL from Blogger http://bit.ly/2NdM6fN

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Acs Study Guide For Organic Chemistry

Acs Organic Chemistry Exam Pdf

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General Chemistry Study Guide Acs

Acs Study Guide For Organic Chemistry Notes

Acs Study Guide For Organic Chemistry Test

Acs-organic-chemistry-study-guide-free-pdf 2/3 Downloaded from happyhounds.pridesource.com on December 12, 2020 by guest Organic 2 this is the best study guide. Green Chemistry Education Resources Books, modules, and multimedia resources. ACS Examinations Institute High quality chemistry assessment materials, including conceptual and laboratory exams, statistical data, student study guides, and more. Service Learning Resources Advice and tips on developing or improving a service learning program in. Descargar baidu pc faster mediafire. Preparing for your ACS examination in organic chemistry: The official guide by Eubanks, I. Dwaine published by American Chemical Society, Division of Chemical Ed (2002). Honestly our prof gave us a practice ACS from an old version and I got like 37/70. Then I proceeded to study from the ACS exam prep book for 1-2 hours a day then took the ACS the next week and scored a 52/70 (around 75%ish) and then with the curve I ended with like a 95% on the test, which our prof also said if we did better on the final, she would replace our lowest test with the ACS (which.

You can purchase Study Guides Online Now: Click Here

Students who are going to be taking an ACS Examinations Institute exam have study materials available in some areas. The Institute is always working to expand this array of study materials. Right now, there are three printed study guides. We also have a variety of practice tests for students.

Preparing for Your ACS Examination in General Chemistry: The Official Guide

(commonly called the General Chemistry Study Guide)

This guide includes 201 pages of information and over 600 problems separated into first-term and second-term general chemistry material. Each section contains 8 chapters of material that also aligns to most general chemistry textbooks for a seamless addition to study materials for students. Each chapter is designed with an introductory section of the material including common representations and where to find this material in a textbook. The second section provides worked examples of typical, multiple choice questions including how the correct answer is determined as well as how the incorrect answers were determined. Also included for each study problem is a listing of the corresponding practice questions that use that concept. The final section is a series of practice problems to test the concepts collectively. The key is provided on a separate page for all study and practice problems.

Chapters in the study guide are:

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First-Term Material:

Atomic Structure

Electronic Structure

Formula Calculations and the Mole

Stoichiometry

Solutions and Aqueous Reactions, Part 1

Heat and Enthalpy

Structure and Bonding

States of Matter

Second-Term Material:

Solutions and Aqueous Reactions, Part 2

Kinetics

Equilibrium

Acids and Bases

Solubility Equilibria

Thermodynamics

Electrochemistry

Nuclear Chemistry

Preparing for Your ACS Examination in Organic Chemistry: The Official Guide

(commonly called the Organic Chemistry Study Guide)

This guide is the newest update to our suite of study materials. A second edition was released in early 2020 with over 240 pages and over 600 unique problems. The guide is organized similarly to the general chemistry guide with a clear separation of first-term and second-term material. Each chapter is organized with study and practice questions where the study questions take you through the problem solving process of key problems explaining the correct process and also explaining the incorrect processes leading to incorrect answers. These study questions are then linked to practice questions where you can work through multiple choice questions and check your answers. Additionally, there are two culminating chapters linking all previous material: Multistep Synthesis and Applications of Organic Chemistry.

Chapters in the study guide are:

Acs Study Guide For Organic Chemistry Reference Sheet

First-Term Material:

Structure: Shape and Stability

Structure: Nomenclature and Functional Groups

Structure: Isomers

Acids and Bases

Nucleophilic Substitutions Reactions

Elimination Reactions

Addition Reactions: Alkenes and Alkynes

Addition Reactions: Alcohols and Ethers

Spectrometry, Spectroscopy, and Spectrophotometry

Radical Reactions

Second-Term Material:

Conjugated Systems and Aromaticity

Aromatic Reactions

Carbonyl Chemistry

Enols and Enolates

Multistep Synthesis

Applications of Organic Chemistry

Preparing for Your ACS Examination in Physical Chemistry: The Official Guide

(commonly called the Physical Chemistry Study Guide) Randy newman allmusic.

This guide includes 126 pages of information in essentially three categories. First, there is a brief explanation of content in physical chemistry. Second, there are example exam items where the question and answers are analyzed (so you can see not only why the correct answer is correct, but also how the other incorrect answers – called distractors – are devised for a multiple-choice item). Finally, there are practice questions for each section.

Content is derived from all areas of Physical Chemistry (Thermodynamics, Quantum Mechanics and Dynamics) and includes:

Thermo – Equations of State

Thermo – Laws of Thermodynamics and State Functions

Thermo – Mathematical Relationships in Thermodynamics

Thermo – Chemical and Phase Equilibria

Dynamics – Kinetic Molecular Theory

Dynamics – Transport Properties

Dynamics – Phenomenological Kinetics

Dynamics – Mechanisms

Dynamics – Reaction Dynamics

Dynamics – Statistical Mechanics

Quantum – Quantum Chemistry: History and Concepts

Quantum – Simple Analytical Quantum Mechanical Systems

Quantum – Modern Quantum Mechanical Problems: Atomic System

Quantum – Symmetry

Quantum – Molecular Orbital Theory

Quantum – Spectral Properties

Quantum – Advanced Topics: Electronic Structure Theory and Spectroscopy

Practice Exams

The Examinations Institute online practice exams – click here for more information. There are two major types of practice exams:

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Tutorial exams providing feedback throughout the test-taking process.

Our newest product, these tutorial exams are designed to provide elaborative feedback as students take the test. Following the submission of each answer to each question, students are shown if they are correct or incorrect with feedback about both their response and the correct process. Following the completion of the test, students receive a report with their performance by question as well as detailed information on similar items from the corresponding study guide. There are currently two tutorial practice exams available:

First-Term General Chemistry

Full-Year Organic Chemistry

Practice exams replicating taking an ACS Exam.

These practice exams are designed to help students practice taking a test in preparation for their standardized exam. While a student works through the questions on the test, they are also asked to respond with their mental effort for each question. Following the completion of the test, students receive a report with their performance by content area, their average mental effort by content area and information on how to use this to target their studies. There are four practice exams available:

Acs Study Guide For Organic Chemistry Notes

First-Term General Chemistry

Full-Year General Chemistry

Full-Year Organic Chemistry

Analytical Chemistry

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Acs Study Guide For Organic Chemistry Test

The writers at StudyOrgo.com are dedicated to providing usefull study materials that are easy to understand. That’s why we created the StudyOrgo.com Organic Chemistry Rapid Review Study Guide, great for Organic Chemistry Midterms and Finals. We have taken all of the beginning topics of Organic Chemistry and have consolidated the important information into this concise, yet comprehensive Study Guide. This guide is infused with a tremendous amount of 'high-yield' information. This means that in addition to providing all of the necessary facts and notes on each topic, we reveal all of the frequently tested key points that are favorites among university classroom exams and standardized exams alike. These are candidly pointed out to guide your studying to focus on the most popular test topics. In addition, we alert you of common student traps and pitfalls. Perhaps the most valuable of gems studded throughout our Study Guide are the tips and shortcuts that help students hone in on how to solve and critically think about organic chemistry. This simply can not be obtained by attempting to sift through the abyss of what most organic chemistry textbooks present.

[biomedgrid]

Biomed Grid | Neurotoxin and Alpha-Neurotoxin Time-Resolved Absorption and Resonance FT-IR and Raman Bio spectroscopy and Density Functional Theory (DFT) Investigation of Vibrionic-Mode Coupling Structure in Vibrational Spectra Analysis

Abstract

α-Neurotoxins are a group of neurotoxic peptides found in the venom of snakes in the families Elapidae and Hydrophiidae. They can cause paralysis, respiratory failure, and death. Members of the three-finger toxin protein family, they are antagonists of post-synaptic nicotinic acetylcholine receptors (nAChRs) in the neuromuscular synapse that bind competitively and irreversibly, preventing synaptic acetylcholine (ACh) from opening the ion channel. Over 100 α-neurotoxins have been identified and sequenced. Parameters such as FT-IR and Raman vibrational wavelengths and intensities for single crystal Neurotoxin and Alpha-Neurotoxin are calculated using density functional theory and were compared with empirical results.

The investigation about vibrational spectrum of cycle dimers in crystal with carboxyl groups from each molecule of acid was shown that it leads to create Hydrogen bounds for adjacent molecules. The current study aimed to investigate the possibility of simulating the empirical values. Analysis of vibrational spectrum of Alpha-Neurotoxin is performed based on theoretical simulation and FT- IR empirical spectrum and Raman empirical spectrum using density functional theory in levels of F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6-31++G**, B3LYP/6-31G and B3LYP6-31-HEG**. Vibration modes of methylene, carboxyl acid and phenyl cycle are separately investigated. The obtained values confirm high accuracy and validity of results obtained from calculations [1-42] (Figure 1).

Figure 1: Molecular structure of Neurotoxin (left) and Alpha–Neurotoxin (right).

Keywords:Vibrionic Structure; Vibrational Spectra Analysis; Density Functional Theory (DFT); Alpha-Neurotoxin; non-Focal Functions of Becke; Correlation Functions of Lee-Yang-Parr; Time-Resolved Absorption and Resonance; FT-IR and Raman Bio spectroscopy

Introduction

α-Neurotoxins are a group of neurotoxic peptides found in the venom of snakes in the families Elapidae and Hydrophiidae. They can cause paralysis, respiratory failure, and death. Members of the three-finger toxin protein family, they are antagonists of post-synaptic nicotinic acetylcholine receptors (nAChRs) in the neuromuscular synapse that bind competitively and irreversibly, preventing synaptic acetylcholine (ACh) from opening the ion channel. Over 100 α- neurotoxins have been identified and sequenced.

Density Functional Theory (DFT) is one of the most powerful calculation methods for electronic structures [5-7]. Numerous results have been previously studied and indicate successful use of these methods [8-10]. The theory is one of the most appropriate methods for simulating the vibrational wavenumbers, molecular structure as well as total energy. It may be useful to initially consider the calculated results by density functional theory using F/6-31G*, HF/6-31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6- 31G, BLYP/6-31++G**, B3LYP/6-31G and B3LYP6-31- HEG** approach [11-16]. It should be noted that calculations are performed by considering one degree of quantum interference as well as polarization effects of 2d orbitals in interaction [17-320].

Details of Calculations

All calculations of molecular orbital in the base of ab are performed by Gaussian 09. In calculation process, the structure of Alpha-Neurotoxin molecule (Figure 2) is optimized and FT- IR and Raman wavenumbers are calculated using F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6- 31++G**, B3LYP/6-31G and B3LYP6-31-HEG** base. All optimized structures are adjusted with minimum energy. Harmonic vibrational wavenumbers are calculated using second degree of derivation to adjust convergence on potential surface as good as possible and to evaluate vibrational energies at zero point. In optimized structures considered in the current study, virtual frequency modes are not observed which indicates that the minimum potential energy surface is correctly chosen. The optimized geometry is calculated by minimizing the energy relative to all geometrical quantities without forcing any constraint on molecular symmetry. Calculations were performed by Gaussian 09.

Figure 2:Different sections of the Neurotoxin (upper) and Alpha– Neurotoxin (lower) [43��93].

The current calculation is aimed to maximize structural optimization using density functional theory. The calculations of density functional theory are performed by F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6- 31++G**, B3LYP/6-31G and B3LYP6-31-HEG** function in which non-focal functions of Becke and correlation functions of Lee-Yang- Parr beyond the Franck-Condon approximation are used. After completion of optimization process, the second order derivation of energy is calculated as a function of core coordination and is investigated to evaluate whether the structure is accurately minimized. Vibrational frequencies used to simulate spectrums presented in the current study are derived from these second order derivatives. All calculations are performed for room temperature of 316 (K).

Vibration Analysis

Analysis of vibrational spectrum of Alpha-Neurotoxin is performed based on theoretical simulation and FT-IR empirical spectrum and Raman empirical spectrum using density functional theory in levels of F/6-31G*, HF/6-31++G**, MP2/6-31G, MP2/6- 31++G**, BLYP/6-31G, BLYP/6-31++G**, B3LYP/6-31G and B3LYP6-31-HEG**. Vibration modes of methylene, carboxyl acid and phenyl cycle are separately investigated. C-H stretching vibrations in single replacement of benzene cycles are usually seen in band range of 3250-3650 cm-1. Weak Raman bands are at 3191 cm-1 and 3207 cm-1. C-C stretching mode is a strong Raman mode at 1211 cm-1. Raman weak band is seen at 1687 cm-1 too. Bending mode of C-H is emerged as a weak mode at 1429 cm-1 and 1205 cm-1 and a strong band at 1289 cm-1 in Raman spectrum. Raman is considerably active in the range of 1250-1650 cm-1 which 1199 cm-1 indicates this issue.

C-H skew-symmetric stretching mode of methylene group is expected at 3189 cm-1 and its symmetric mode is expected at 3000 cm-1. Skew-symmetric stretching mode of CH4 in Alpha- Neurotoxin has a mode in mid-range of Raman spectrum at 3250- 3650 cm-1. When this mode is symmetric, it is at 3099 cm-1 and is sharp. The calculated wavenumbers of higher modes are at 3073 cm-1 and 3096 cm-1 for symmetric and skew-symmetric stretching mode of methylene, respectively.

Scissoring vibrations of CH4 are usually seen at the range of 1530-1590 cm-1 which often includes mid-range bands. Weak bands at 1550 cm-1 are scissoring modes of CH4 in Raman spectrum. Moving vibrations of methylene are usually seen at 1479 cm -1. For the investigated chemical in the current study, these vibrations are at 1349 cm-1 were calculated using density functional theory. Twisting and rocking vibrations of CH4 are seen in Raman spectrum at 925 cm-1 and 1191 cm-1, respectively, which are in good accordance with the results at 907 cm-1 and 1167 cm- 1, respectively. In a non-ionized carboxyl group (COOH), stretching vibrations of carbonyl [C=O] are mainly observed at the range of 1850-1898 cm-1. If dimer is considered as an intact constituent, two stretching vibrations of carbonyl for symmetric stretching are at 1750-1795 cm-1 in Raman spectrum. In the current paper, stretching vibration of carbonyl mode is at 1799 cm-1 which is a mid-range value.

Stretching and bending bands of hydroxyl can be identified by width and band intensity which in turn is dependent on bond length of Hydrogen. In dimer form of Hydrogen bond, stretching band of O-H is of a strong Raman peak at 1377 cm-1 which is due to in-plain metamorphosis mode. Out-of-plain mode of O-H group is a very strong mode of peak at 1056 cm-1 of Raman spectrum. The stretching mode of C-O (H) emerges as a mid-band of Raman spectrum at 1263 cm-1. Lattice vibrations are usually seen at the range of 0-850 cm-1. These modes are induced by rotary and transferring vibrations of molecules and vibrations and are including Hydrogen bond. Bands with low wavenumbers of Hydrogen bond vibrations in FT-IR and Raman spectrum (Figure 3) are frequently weak, width and unsymmetrical. Rotary lattice vibrations are frequently stronger than transferring ones. Intramolecular vibrations with low wavenumbers involving two-bands O-H …O dimer at 99 cm-1, 199 cm-1 and 269 cm-1 are attributed to a rotary moving of two molecules involving in-plain rotation of molecules against each other.

Figure 3:3D Simulation of (a) FT–IR spectrum and (b) Raman spectrum of Alpha–Neurotoxin.

Conclusion and Summary

Calculations of density functional theory using F/6-31G*, HF/6- 31++G**, MP2/6-31G, MP2/6-31++G**, BLYP/6-31G, BLYP/6- 31++G**, B3LYP/6-31G and B3LYP6-31-HEG** levels were used to obtain vibrational wavenumbers and intensities in single crystal of Alpha- Neurotoxin. Investigation and consideration of vibrational spectrum confirm the formation of dimer cycles in the investigated crystal with carboxyl groups from each Hydrogen molecule of acid protected from adjacent molecules. The calculated vibrational spectrum which obtains from calculations of density functional theory is in good accordance with recorded empirical values which indicates successful simulation of the problem. The obtained results indicate that the results obtained from theoretical calculations are valid through comparing with empirical recorded results.

Acknowledgements

Authors are supported by an American International Standards Institute (AISI) Future Fellowship Grant FT1201009373493. We acknowledge Ms. Isabelle Villena for instrumental support and Dr. Michael N. Cocchi for constructing graphical abstract figure. We gratefully acknowledge Prof. Dr. Christopher Brown for proofreading the manuscript.

Read More About this Article:https://biomedgrid.com/fulltext/volume3/neurotoxin-and-alpha-neurotoxin-time-resolved-absorption-and-resonance-ft-ir.000738.php

For more about: Journals on Biomedical Science :Biomed Grid

[pamphletstoinspire]

Catholic Physics - Reflections of a Catholic Scientist - Part 67

Peeling back the onion layers: Gravitational waves detected!

Story with images:

https://www.linkedin.com/pulse/catholic-physics-reflections-scientist-part-67-harold-baines/?published=t

Gravitational waves of a compact binary star by MoocSummers (from Wikimedia Commons) (Caption for linked image)

"Falling in love is not at all the most stupid thing that people do, but gravitation cannot be held responsible for it."Albert Einstein, scribbled on a 1933 letter to him about the effects of gravity on people falling in love.

"Someday, after mastering the winds, the waves, the tides and gravity, we shall harness for God the energies of love, and then, for a second time in the history of the world, man will have discovered fire." Teilhard deChardin

“Gravity is a contributing factor in nearly 73 percent of all accidents involving falling objects. ” Dave Barry

INTRODUCTION

Many of you have read about the recent experimental detection of a gravity waves by LIGO (Laser Interferometer Gravitational-Wave Observatory), another jewel-in-the-crown of empirical confirmations of Einstein's General Relativity theory.  And it came, appropriately, on the 100th anniversary of the publication of that theory.

I'm not going to expound on the science of this fine piece of experimental work or try to give a "horsies-and-duckies" explanation -- that's very well done in the linked publication and in a fine post by Matt Briggs, Gravitational Waves and Discovering Cause, and comments thereto.  Rather, I'm going to use this as an excuse for expounding on what I believe science is all about.  In these arguments, I'll rely on my own 52 years experience as a practicing chemical physicist (or in other environments, biophysicist, medical physicist and even--horrors!--physical chemist).

WHAT PHILOSOPHERS SAY SCIENCE IS ALL ABOUT*

There are two principal schools of the philosophy of science: scientific realism and scientific anti-realism (or scientific empiricism).  The realism school holds that what sciences tells about the universe mirrors an underlying reality.  I've discussed the anti-realism school in another blog post, "Tipping the Sacred Cow of Science", in which I discuss Nancy Cartwright's book, How the Laws of Physics Lie and the work of Bas van Fraassen.  These philosophers hold that scientific theories do NOT mirror reality, but are rules used to "save the appearances", i.e. to give mathematical descriptions useful for prediction, as in the use of Ptolemaic epicycle to predict planetary motions in the sky; to put it another way, science is "descriptive" not "prescriptive".

The only scheme I've found that represents reasonably well how science works is that given by Imre Lakatos, the scientific research programme, which scheme has also been adapted for other disciplines, e.g. theology, economics.  The scheme can be viewed as a hard core of accepted principles (e.g. the Galilean Principle of Relativity that the laws of motion are the same in all inertial frames, or the Second Law of Thermodynamics), surrounded by a layer of theories that confirm or in accord with the core principles and an outer layer of experimental tests confirming or rejecting the outer layer theories.

The theories and auxiliary data in the protective layer are networked to each other and to the core.  For example, the relativistic formulation of black hole growth and radiation is linked to the Second Law of Thermodynamics and to quantum mechanics. (For an interesting view of the Lakatos scheme in other disciplines, do a Google search "images Lakatos scientific research programme".)  The Lakatos scientific research programme does show how science works, but as far as I can see, it does not lay claim to either scientific realism or anti-realism -- it's epistemic, not metaphysical.

WHAT I THINK SCIENCE IS ALL ABOUT**

My view of science is based on much post-retirement reading in the philosophy of science and on my work from 1954 to 1997 in spectoscopy, nmr and MRI -- studies crossing several disciplines -- chemical physics, biophysics, molecular biology, medical physics.  In the ** Note I've given an illustration from my research life of how science works (or should work), but here I'd like to focus on a prime example -- the development of the Standard Model for elementary particle physics.

In an early post (15th April, 2013), God. Symmetry and Beauty I: the Standard Model and the Higgs Boson, I discussed the development of this theory.  I'll summarize here the points relevant to the modus operandi of science and show how they are in accord with the Lakatos model.  First, in the Lakatos outer shell there were experimental findings that did not fit well into any established theory, what was termed the "elementary particle zoo".  Second, two principles in the inner core governed what theories would be acceptable and esthetically satisfying: symmetry and gauge invariance.  An auxiliary theory proposed early on by Higgs, utilizing an auxiliary principle of "symmetry breaking", was developed to enable gauge-invariant theories to be employed and yield mass values for elementary particles.  Some other theories were developed that made predictions that were falsified and so were discarded.  The final icing on the cake was the detection of the Higgs boson by very high energy scattering experiments, thus completing the experimental verification of the Standard Model theory.

GRAVITATIONAL WAVE DETECTION--HOW SCIENCE WORKS**

Gravitational Wave Data, from Caltech Media Assets (scan down to get full description) (Caption for linked image)

LIGO is another example of Super Science, massive experimental enterprises designed to test/confirm fundamental theory, as in the CERN experiments for detecting the Higgs boson.  Did it do so?  Weren't all the other experimental confirmations, listed below, of Einstein's General Relativity theory sufficient?

"the gravitational deflection of light, the perihelion shift of the orbit of Mercury, the gravitational red shift, the frame-dragging effects of Gravity Probe B, and the rate of gravitational-wave energy loss from neutron-star binary pulsars" John G. Cramer, Gravity with 4-Vector Potentials

The answer to that question is no.  Another theory, G4V (Gravity with 4-Vector Potentials -- see link above), has been proposed.  For the properties listed in the quotation above, the G4V theory gives predictions identical to those of Einstein's General Relativity theory.  They differ in the predicted properties of gravity waves by differing in the predicted wave polarizations***.   At the time when this post was written it appears that the observed waves correspond to the Einstein GR predictions.   Thus the experiments will have fulfilled their mission, to decide which theory fits reality better, Einstein's or the G4V.

A THEOLOGICAL PERSPECTIVE

Since this blog is "Reflections of a Catholic Scientist", I should say something about what this means to me, in terms of my faith.  I believe there is an underlying reality revealed partially by science, that as one peals back the layers of the onion, we get closer to the core.  I also believe, along with Bernard d'Espagnat, that we will never know altogether what that core is.  I believe that we will not know that, because the core is God, the Holy Trinity, and God is only known by what he is not.  He cannot be comprehended in His Entirety.

I also believe that God has given us insight to use science to perceive with wonder His Creation.  In the words of Psalm 19a

"The heavens declare the glory of God; and the firmament sheweth his handywork. Psalm 19 (KJV)

and

"What benefactor has enabled you to look out upon the beauty of the sky, the sun in its course, the circle of the moon, the countless number of stars, with the harmony and order that are theirs, like the music of a harp?" St. Gregory of Nazarian, Sermon as quoted in The Office of Readings for 15th February, 2016.

NOTES

*There have been many books and articles written about the philosophy of science.  Some of these contain useful and/or interesting stuff.  Unfortunately many of these philosophers have not done science, and this lack of experience shows in their philosophic work.  I can think of only three who have written both philosophic and scientific papers: Fr. Stanley Jaki, Michael Polyani and Bernard d'Espagnat, all of whom I admire (for different reasons).  

**I want also to illustrate how science works with an example from my own scientific career. So as not to blow my own horn (too much!), I'm going to try to show not only where I succeeded, but where I erred.

A few years into my first academic position at Carnegie Tech (now Carnegie-Mellon University) a graduate student in my research group was facing a road block with his research problem.  A well-established theory was not giving results matching his data. After a lot of thought, it appeared that the gap lay in that higher energy levels of the compound (potassium ferricyanide) he was studying.  Searching the library, I found a publication by Schwinger and Karplus (recalling my earlier graduate course in quantum mechanics) that offered a road to a solution.  After several weeks of intensive devotion I wrote a paper that incorporated density matrix techniques to account for contributions of all electronic levels and submitted it for a publication.  One reviewer pointed out a serious deficiency -- I had neglected to account for mixing of excited states with ground state. I acknowledged he was right, asked him to co-author the paper with me and we collaboratively worked it up for publication.  There is an equation stemming from that work, (Google "Kurland-McGarvey Equation") that is widely enough used in the specialty that it doesn't need footnoting for reference.  So one more small brick in the scientific edifice.

***The polarization of a wave gives the direction of the wave intensity relative to the direction of propagation of the wave.  For example, for light, an electromagnetic radiation wave, the polarization is in a direction perpendicular to the direction of propagation.  For gravity waves, the situation is more complicated: the polarization is a tensor rather than a vector.  (See this link.)

****For some neat videos and pictures, go to the LIGO Lab Gallery.

From a series of articles written by: Bob Kurland - a Catholic Scientist

[analyticsindiam]

Can Machines Learn To Smell: Researchers May Have Cracked The Code

While CNNs provide vision to a machine, RNNs give machines the ability to draw insights out of speech and sound, haptics gives robots a sense of touch, researchers have now brought a new dimension in machines — the ability to smell. While machines have been endowed with the sense of vision, speech, sound and touch thanks to the efforts of researchers for many decades, the concept of smell has eluded the machines. That is to say that humans have been unable to replicate this ability due to their own lack of understanding of olfactory functions. Every aroma is a consequence of interactions between molecules. And, predicting the relationship between a molecule's structure and its odour still remains to be a big challenge. But now researchers are trying to understand the interplay of molecules through quantitative structure-odour relationship (QSOR) modelling. Developments Till Date Till now the representation of molecular structures has been done with the help of graph theory. The way the symmetries and the connections can be defined as edges and vertices has been intuitive for further research into the three-dimensional structure of molecules. The same formulation was exploited a couple of years ago by the researchers at Google Brain in their quest to predict properties of molecules with machine learning.  Making use of the findings and moving forward, today, the researchers have leveraged graph neural networks (GNNs) to predict the olfactory properties of molecules. How Graph Neural Networks Came In Handy?

via Google By viewing atoms as nodes, and bonds as edges, we can interpret a molecule as a graph. These molecular graphs are encoded into a fixed-length vector. The fragments of this molecular graph give a hint of whether an atom or certain functional group exists or not. This is where graph neural networks (GNNs) come into the picture. The researchers say that these GNNs are learnable permutation-invariant transformations on nodes and edges, which produce fixed-length vectors that are further processed by a fully-connected neural network. However, translating the vector-node molecular representation to a graph is not as straightforward as it seems to be. The translation into a graph happens as follows: Every node in the graph is first represented as a vector. For example, the node can be atomic chargeThen, every node is made to pass on its current vector value to its neighbours. An update function then generates a new vector value based on previous steps.This process is then repeated until all of the nodes are summarized into a single vector by summing or averagingThis single vector represents a molecule, which is then passed into a fully connected network The fully connected network gives an output that contains the prediction of molecules and their odour as provided by perfume experts.

Researchers have also found that the learned embeddings from graph neural networks capture  a meaningful odour space representation of the underlying relationship between structure and odour, as demonstrated by a strong performance on two challenging transfer learning tasks. Future Direction Understanding the functioning of olfactory sensory reception in itself is an exciting domain. Odour perception in humans is believed to be the result of the activation of 300-400 different types of olfactory receptors, expressed in millions of olfactory sensory neurons, embedded in a small patch of tissue called the olfactory epithelium.  An aroma invokes many memories. Every fragrance is associated with memory. So it can be safely assumed that deciphering the inner workings of odour-memory association work can uncover the workings of memory itself. From sniffer dogs in airports to wine connoisseurs, the sense of smell permeates into many real-world applications. Since every living and non-living thing can be melted down to the rubrics of chemistry, the use of machine learning for the same might unveil many intricacies of life.  Read the full article

[sciencespies]

Theory reveals the nature of silicon carbide crystals defects

https://sciencespies.com/physics/theory-reveals-the-nature-of-silicon-carbide-crystals-defects/

Theory reveals the nature of silicon carbide crystals defects

by The Henryk Niewodniczanski Institute of Nuclear Physics Polish Academy of Sciences

Silicon carbide crystal model with edge dislocations introduced in places marked in red. A single crystallographic plane is presented at the bottom. The places where electric charges can ‘leak’ to neighboring layers are marked in yellow. Credit: IFJ PAN

More

Imperfections of crystal structure, especially edge dislocations of an elongated nature, deeply modify basic properties of the entire material and, in consequence, drastically limit its applications. Using silicon carbide as an example, physicists from Cracow and Warsaw have shown that even such computationally demanding defects can be successfully examined with atomic accuracy by means of a cleverly constructed, small in size, model.

Mathematics loves perfection. Unfortunately, perfection does not love physical reality. Theoreticians modelling crystals have long tried to include defects in real crystalline structures and predict their impact on the physical properties of materials. The models, based on the results of various experiments, have described changes in the basic properties of a material without explaining the real causes and effects of the occurring phenomena.

A new model of silicon carbide (SiC), built by physicists from the Institute of Nuclear Physics of the Polish Academy of Sciences (IFJ PAN) in Cracow, has allowed them to demonstrate that it is now possible to study crystals ab initio with such complex defects as edge dislocations and to explain their characteristics by processes occurring on an atomic scale. This spectacular result, recently presented at the Multiscale Phenomena in Molecular Matter 2019 conference in Cracow, was achieved by the IFJ PAN physicists in cooperation with the Institute of Fundamental Technological Research of the Polish Academy of Sciences and the Institute of High Pressure Physics of the Polish Academy of Sciences, both located in Warsaw.

“We tried to find the mechanisms responsible at the atomic level for lowering the breakdown voltage in silicon carbide crystals. Our ab initio calculations lead to a qualitative understanding of the problem and contribute to explaining the details of this phenomenon,” says Dr. Jan Lazewski, professor at the IFJ PAN.

Ab initio calculations have now a long history related to Nobel Prize for Walter Kohn and John Pople in 1998 (however to linear crystal defect simulations they have only recently been introduced). This term is used to describe calculations carried out using quantum mechanics equations, supported only by knowledge about the structure of the atom and the symmetry of crystals. There is no direct information from experiments in such models, which means that they can also be used to analyse materials that have never been studied or even synthesized before. Because of relatively substantial complication of the issue, so far ab initio calculations worked, at most, in the case of point defects, related to vacancies (missing atoms or holes in the crystal structure) as well as admixtures introduced into the crystal.

It was not without reason that the Cracow researchers used silicon carbide. The properties of this semiconductor are so interesting that in the past it was even considered a successor to silicon. Its band gap (the barrier the charge has to overcome to get from the valence band to the conduction band and conduct current) is almost three times greater than in silicon, the permissible conduction current density—twice as great, the ability to dissipate heat—more than three times greater, and the cutoff frequency of crystal operation as many as six times greater. In addition, silicon carbide systems can operate at temperatures up to 650 degrees Celsius, while silicon systems already begin to have problems at 120 degrees Celsius. SiC also has a high melting point, it is hard, resistant to acid and radiation. Its disadvantages include above all the price: whilst two-inch silicon wafers cost only a few dollars, the value of similar silicon carbide wafers runs into thousands. Low quality silicon carbide crystals are a popular abrasive material, also used in bulletproof vests and in the brake discs of the world’s most expensive cars, such as Lamborghini or Bugatti. High quality crystals are used to produce mirrors for telescopes and in high voltage devices with high resistance to temperature.

At the atomic level, silicon carbide crystals are composed of many flat layers arranged one on top of each other. Each layer resembles a honeycomb: it consists of hexagonal cells in which the silicon carbide molecules are located vertically in the corners. Each two adjacent layers can be combined in three ways. The multilayer ‘sandwiches’ with different layouts create so-called polytypes, of which there exist more than 250 in the case of silicon carbide. The group from IFJ PAN used the 4H-SiC polymorph.

“When modelling such structures, one of the main problems is computational complexity. A model of pure crystal, devoid of admixtures or dislocations, is characterized by high symmetry and can be calculated even in a few minutes. In order to carry out a calculation for a material with dislocation, we need months working on a high power computer,” emphasizes Dr. Pawel Jochym, professor at the IFJ PAN.

The problems with edge dislocations result from the scale of their influence on the crystal structure of the material. As an illustration, they can be compared to the problem of disguising a gap in a row of tiles on a floor. The gap can be ‘camouflaged’ by moving the tiles of adjacent rows, but the defect will always remain visible. Edge dislocations resulting from the lack of whole lengths or regions of atoms/molecules in individual crystal layers act similarly, affecting the positions of atoms and molecules in many adjacent layers. And since the dislocations can extend over long distances, in practice the disturbances caused by them include the entire crystal.

The most interesting phenomena take place in the dislocation core, i.e. in the vicinity of the edge of the damaged layer of the crystal network. In order to eliminate long-range effects caused by a single dislocation, and thus significantly reduce the number of atoms under consideration, a trick was employed: a second dislocation of the opposite effect was introduced. In this way, the impact of the first dislocation over longer distances was compensated for.

The SiC crystal model consisted of about 400 atoms. The simulations showed that in the layers of crystals, along the edge of the core of the defect, ‘tunnels’ appear in the form of channels with reduced charge density. They lower the potential barrier locally and cause electric charges to ‘leak’ from the valence band. In addition, in the forbidden gap, which in the insulator guarantees a lack of electrical conductivity, conditions appear which reduce its width and effectiveness in limiting the flow of charge. It was shown that these states originate from atoms located in the dislocation core.

“The situation can be compared to a deep, steep ravine that a squirrel is trying to cross. If the bottom of the ravine is empty, the squirrel will not get to the other side. However, if there are a number of trees at the bottom that are high enough, the squirrel can jump over their tops to the other side of the ravine. In the crystal we modelled, the squirrels are the electrical charges, the valence band is one edge of the ravine, the conduction band is the other, and the trees are the aforementioned states associated with the atoms of the dislocation core,” says Prof. Lazewski.

Now that the mechanisms responsible for lowering the threshold of the energy barrier have become known at the atomic level, there is a huge scope for experimentation. The proposed mechanism will have to be verified in order to be able to use it to limit the negative influence of the tested defects. Fortunately, there are already technical possibilities for this.

“The future will verify whether our ideas will be confirmed in their entirety. However, we are confident about the fate of our model and the presented approach to simulating edge dislocations. We already know that the ab initio model has proved its worth in confrontation with certain experimental data,” concludes Prof. Jochym.

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[sciencebulletin]

Electrons break rotational symmetry in exotic low-temp superconductor

Scientists have discovered that the transport of electronic charge in a metallic superconductor containing strontium, ruthenium, and oxygen breaks the rotational symmetry of the underlying crystal lattice. The strontium ruthenate crystal has fourfold rotational symmetry like a square, meaning that it looks identical when turned by 90 degrees (four times to equal a complete 360-degree rotation). However, the electrical resistivity has twofold (180-degree) rotational symmetry like a rectangle. This 'electronic nematicity'—the discovery of which is reported in a paper published on May 4 in the Proceedings of the National Academy of Sciences—may promote the material's 'unconventional' superconductivity. For unconventional superconductors, standard theories of metallic conduction are inadequate to explain how upon cooling they can conduct electricity without resistance (i.e., losing energy to heat). If scientists can come up with an appropriate theory, they may be able to design superconductors that don't require expensive cooling to achieve their near-perfect energy efficiency. "We imagine a metal as a solid framework of atoms, through which electrons flow like a gas or liquid," said corresponding author Ivan Bozovic, a senior scientist and the leader of the Oxide Molecular Beam Epitaxy Group in the Condensed Matter Physics and Materials Science (CMPMS) Division at the U.S. Department of Energy's (DOE) Brookhaven National Laboratory and an adjunct professor in the Department of Chemistry at Yale. "Gases and liquids are isotropic, meaning their properties are uniform in all directions. The same is true for electron gases or liquids in ordinary metals like copper or aluminum. But in the last decade, we have learned that this isotropy doesn't seem to hold in some more exotic metals." Scientists have previously observed symmetry-breaking electronic nematicity in other unconventional superconductors. In 2017, Bozovic and his team detected the phenomenon in a metallic compound containing lanthanum, strontium, copper, and oxygen (LSCO), which becomes superconducting at relatively higher (but still ultracold) temperatures compared to low-temperature counterparts like strontium ruthenate. The LSCO crystal lattice also has square symmetry, with two equal periodicities, or arrangements of atoms, in the vertical and horizontal directions. But the electrons do not obey this symmetry; the electrical resistivity is higher in one direction unaligned with the crystal axes. "We see this kind of behavior in liquid crystals, which polarize light in TVs and other displays," said Bozovic. "Liquid crystals flow like liquids but orient in a preferred direction like solids because the molecules have an elongated rod-like shape. This shape constrains rotation by the molecules when packed close together. Liquids are typically symmetric with respect to any rotation, but liquid crystals break such rotational symmetry, with their properties different in the parallel and perpendicular directions. This is what we saw in LSCO—the electrons behave like an electronic liquid crystal." With this surprising discovery, the scientists wondered whether electronic nematicity existed in other unconventional superconductors. To begin addressing this question, they decided to focus on strontium ruthenate, which has the same crystal structure as LSCO and strongly interacting electrons. At the Kavli Institute at Cornell for Nanoscale Science, Darrell Schlom, Kyle Shen, and their collaborators grew single-crystal thin films of strontium ruthenate one atomic layer at a time on square substrates and rectangular ones, which elongated the films in one direction. These films have to be extremely uniform in thickness and composition—having on the order of one impurity per trillion atoms—to become superconducting. To verify that the crystal periodicity of the films was the same as that of the underlying substrates, the Brookhaven Lab scientists performed high-resolution X-ray diffraction experiments. "X-ray diffraction allows us to precisely measure the lattice periodicity of both the films and the substrates in different directions," said coauthor and CMPMS Division X-ray Scattering Group Leader Ian Robinson, who made the measurements. "In order to determine whether the lattice distortion plays a role in nematicity, we first needed to know if there is any distortion and how much." Bozovic's group then patterned the millimeter-sized films into a "sunbeam" configuration with 36 lines arranged radially in 10-degree increments. They passed electrical current through these lines—each of which contained three pairs of voltage contacts—and measured the voltages vertically along the lines (longitudinal direction) and horizontally across them (transverse direction). These measurements were collected over a range of temperatures, generating thousands of data files per thin film. Compared to the longitudinal voltage, the transverse voltage is 100 times more sensitive to nematicity. If the current flows with no preferred direction, the transverse voltage should be zero at every angle. That wasn't the case, indicating that strontium ruthenate is electronically nematic—10 times more so than LSCO. Even more surprising was that the films grown on both square and rectangular substrates had the same magnitude of nematicity—the relative difference in resistivity between two directions—despite the lattice distortion caused by the rectangular substrate. Stretching the lattice only affected the nematicity orientation, with the direction of highest conductivity running along the shorter side of the rectangle. Nematicity is already present in both films at room temperature and significantly increases as the films are cooled down to the superconducting state. "Our observations point to a purely electronic origin of nematicity," said Bozovic. "Here, interactions between electrons bumping into each other appear to have a much stronger contribution to electrical resistivity than electrons interacting with the crystal lattice, as they do in conventional metals." Going forward, the team will continue to test their hypothesis that electronic nematicity exists in all nonconventional superconductors. "The synergy between the two CMPMS Division groups at Brookhaven was critical to this research," said Bozovic. "We will apply our complementary expertise, techniques, and equipment in future studies looking for signatures of electronic nematicity in other materials with strongly interacting electrons." Provided by: Brookhaven National Laboratory More information: Jie Wu et al. Electronic nematicity in Sr2RuO4. Proceedings of the National Academy of Sciences (2020). DOI: 10.1073/pnas.1921713117 Image: Scientists patterned thin films of strontium ruthenate—a metallic superconductor containing strontium, ruthenium, and oxygen—into the "sunbeam" configuration seen above. They arranged a total of 36 lines radially in 10-degree increments to cover the entire range from 0 to 360 degrees. On each bar, electrical current flows from I+ to I-. They measured the voltages vertically along the lines (between gold contacts 1-3, 2-4, 3-5, and 4-6) and horizontally across them (1-2, 3-4, 5-6). Their measurements revealed that electrons in strontium ruthenate flow in a preferred direction unexpected from the crystal lattice structure. Credit: Brookhaven National Laboratory Read the full article

[omc-juniperpublishers]

Nonlinear Optical Property Of 6'-Amino-5-Fluoro -2-Oxo-3'-Propyl-2'H-Spiro[Indoline-3,4'-Pyrano [2,3-C]Pyrazole]-5'-Carbonitrile- A Theoretical Approach-JuniperPublishers

Journal of Chemistry-JuniperPublishers

                            Abstract

We present a DFT based study of the non-liniear optical property of 6'-Amino-5-fluoro-2-oxo-3'-propyl-2'H-spiro[indoline-3,4'-pyrano[2,3-c] pyrazole]-5'-carbonitrile. The geometry optimization first static hyperpolarizability, dipole moment and polarizability of the compound are performed using B3LYP/6-311+G(d,p) level of theory. The calculated hyperpolarizability, dipole moment and polarizability of the title compound is compared with urea at the same level of theory. The study reveals that the title compound possesses large value than urea hence in general may have potential application in the development of nonlinear optical material.

Keywords: DFT; Hyperpolarizability; Dipole Moment; Polarizability

Abbreviations: DFT: Density Functional Theory; PES: Potential Energy Surface; NLO: Nonlinear Optics

Introduction

The Nonlinear Optics (NLO) of materials was started after the Kerr's observations of quadratic electric field induced changes in the refraction index, known as the Kerr effect [1] in 1875. This was followed by the observation of the Pockel's effect. The organic compounds with large optical nonlinearities have become the focus of current research in view of their potential applications in various photonic technologies, including all optical switching and data processing. Organic molecules that exhibit extended pi conjugation, in particular, show enhanced second order NLO properties. The equilibrium geometry and NLO property of 6'-Amino-5-fluoro-2-oxo-3'-propyl-2'H- spiro[indoline-3,4'-pyrano[2,3-c]pyrazole]-5'-carbonitrile have been calculated by using Density Functional Theory (DFT).

Computational Details

In the present study all the DFT calculations were performed with the help of Gaussian 09 program [2] using a hybrid functional B3LYP and employing 6-311+G (d,p) as a basis set. The geometry of the title compound was fully optimized without any constraint in Potential Energy Surface (PES). The optimized structure of the molecule has been visualized by the use of the Gauss View 5.0 molecular visualization program [3].

Results and Discussion

The optimized geometry of the 6'-Amino-5-fluoro-2-oxo- 3'-propyl-2'W-spiro[indoline-3,4'-pyrano[2,3-c]pyrazole]-5'- carbonitrile is shown in Figure 1 with proper atomic labeling. The compounds that shows asymmetric polarization induced by electron donor and acceptor groups in pi electron conjugated molecules are candidates for electro optic and NLO applications [4] (Figure 1).

Non-linear optical property

The NLO property provides useful information for optical modulation, optical switching and optical logic for the developing new technologies in area of communication. Previously, It has been reported that molecules having conjugated pi electrons are found to possess large values of polarizability [5-8]. The intramolecular charge transfer from electron rich system to electron poor system through a conjugated path can induce a large aberration in both the molecular dipole as well as molecular polarizability. The abnormally high value of hyperpolarizability β, which is a critical parameter of non linear activity of molecular systems, can be presumably linked to intramolecular charge transfer, as a consequence of electron cloud movement through pi conjugated system. The first-order hyperpolarizability (β0) and related properties (μ0 and |α0|) of 6'-Amino-5-fluoro-2- oxo-3'-propyl-2'W-spiro[indoline-3,4'-pyrano[2,3-c]pyrazole]- 5'-carbonitrile have been calculated at the B3LYP/6-311+G (d, p) level of theory. First hyperpolarizability is a third rank tensor of order three that can be described by a 3x3x3 matrix. The 27 components of the order 3 matrix can be reduced to 10 components using the Kleinman Symmetry [9] and it can be presented in the lower tetrahedral format. The components of P0 are defined as the coefficient in the Taylor series expansion of the energy in the external electric field.

The total dipole moment (β0), anisotropy of the polarizability( |α0|), the mean polarizability (Δα ) and the total first hyperpolarizability (β0) using x, y and z components are

Molecule is listed in Table 1. It can be seen that the calculated β0 and μ0 values of title compound are more than the value of urea and are also listed in Table 1. Hence it can be said that the molecule exhibits promising nonlinear optical property (Table 1).

Conclusion

We have performed theoretical study on molecular structure and NLO properties of 6'-Amino-5-fluoro-2-oxo-3'-propyl-2'H- spiro[indoline-3,4'-pyrano[2,3-c]pyrazole]-5'-carbonitrile with the help of density functional theory. Significantly high non linearity is observed in first order molecular hyperpolarizability and polarizability. So this molecule may have potential application in the development of NLO materials.

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A Combined Experimental and Theoretical Study on Vibrational Spectra of 2-Phenylcyclopropan-1-Amine Abstract In this work, a combined experimental and theoretical study on molecular structure, vibrational spectra and natural bond orbital (NBO) analysis of 2-phenylcyclopropan-1-amine (2PCP1A) have been reported. The optimized molecular structure, atomic charges, vibrational frequencies and natural bond orbital analysis of 2PCP1A have been studied by performing DFT/B3LYP/6-31G(d,p),6-311++G(2d,3p)and 6-31G(3df,3pd) levels of theory. The FT-IR, FT-Raman spectra were recorded in the region of 4000–400cm1 and 3500-100cm1 respectively. The harmonic vibrational frequencies were scaled and compared with experimental values. The observed and the calculated frequencies are found to be in good agreement. The UV–visible spectrum was also recorded and compared with the theoretical values. The calculated HOMO and LUMO energies show that charge transfer occurs within the molecule. Natural Population Analysis (NPA) was used for charge determination in the title molecule. Besides, molecular electrostatic potential (MEP), frontier molecular orbitals (FMO) analysis were investigated using theoretical calculations. Keywords: FTIR; FT-Raman; DFT; MEP; NBO; NLO Introduction 2-phenylcyclopropan-1-amine (2PCP1A) compound belongs to the class of organic compounds known as aralkylamines. These are alkylamines in which the alkyl group is substituted at one carbon atom by an aromatic hydrocarbyl group. This monoamine oxidase inhibitor is effective in the treatment of major depression, dysthymic disorder, and atypical depression. It also is useful in panic and phobic disorders. Phenycycloproane and its derivatives are studied by several authors. Influence of Reactant Polarity on the course of (4+2) Cycloadditions was investigated by Sustmann [1]. Density Functional Theory Study of the Cycloaddition Reaction of Furan Derivatives with Masked o-Benzoquinones is carried out by Domingo [2]. Resonance Raman studies of phenylcyclopropane radical cations are studied by Godbout [3]. Weak hydrogen bridges: a systematic theoretical study on the nature and strength of C--H...F--C interactions is done by Kryspin [4]. Lysine demethylase inhibitors for myeloproliferative or lymphoproliferative diseases or disorders are studied by Mathewet [5]. In the present work, harmonic-vibrational frequencies are calculated for 2-phenylcyclopropan-1-amine (2PCP1A) using B3LYP/6-31G(d,p), 6-311++G(2d,3p) and 6-31G(3df,3pd) methods. The calculated spectra of the compound are compared to that of experimentally observed FT-IR and FT-Raman spectra. The redistribution of electron density (ED) in various bonding and antibonding orbitals and E(2) energies have been calculated by natural bond orbital (NBO) analysis by DFT method to give clear evidence of stabilization originating from the hyper conjugation of various intramolecular interactions. The HOMO and LUMO analysis have been used to elucidate information regarding ionization potential (IP), electron affinity (EA), electronegativity (), electrophilicity index (), hardness () and chemical potential () are all correlated. These are all confirming the charge transfer within the molecule and also molecular electrostatic potential (MESP) shows the various electrophilic and nucleophilic region of the title molecule. Experimental The compound under investigation 2PCP1Awas purchased from Aldrich chemicals, USA. The FT-IR spectrum of 2PCP1A was recorded in the region 400-4000 cm1 on IFS 66 V spectrophotometer using KBr pellet technique as shown inFigure 1(b). The FT-Raman spectrum of 2PCP1A has been recorded using 1064 nm line of Nd: YAG laser as excitation wavelength in the region 3500-100cm1on a Thermo Electron Corporation model Nexus 670 spectrophotometer equipped with FT-Raman module accessory as shown in Figure 2(a). The ultraviolet absorption spectra of 2PCP1A were examined in the range 200–400 nm using SHIMADZU UV-1650 PC, UV–VIS recording spectrometer using water as solvent. Computational Details DFT method is very much useful for the Quantum mechanical calculations of energies, geometries and vibrational wave numbers of organic chemical system. The gradient corrected density functional theory (DFT) [6] with the three-parameter hybrid functional Becke3 (B3) [7,8] for the exchange part and the Lee-Yang-Parr (LYP) correlation functional [9], calculations have been carried out in the present investigation, using 6-31G(d.p), 6-311++G(2d,3p) and 6-31G(3df,3pd) basis sets with Gaussian-03 [10] program, invoking gradient geometry optimization [11]. All the parameters were allowed to relax and all the calculations converged to an optimized geometry which corresponds to true energy minima. The optimized structural parameters of 2PCP1A were used for harmonic vibrational frequency calculations resulting in IR and Raman frequencies. The vibrational assignments of the normal modes were made on the basis of the potential energy distribution (PED) calculated by using the VEDA 4 program [12]. Results and Discussion Molecular geometry The first task for the computational work is to determine the optimized geometries of the title compound. The optimized molecular structure of 2PCP1A with the numbering scheme of the atoms is shown in Figure 1(a). The optimized structural parameters such as bond length and bond angles are determined by B3LYP method with 6-31G(d,p),6-311++G(2d,3p) and 6-31G(3df,3pd) as basis sets. The geometry of the molecule is considered by possessing C1 point group symmetry. From the structural data given in Table 1, it is observed that the various benzene ring CC bond distances and the CH bond lengths of title compound are found to be almost the same at all levels of calculations. [Click here to view Large Figure 1] [Click here to view Large Table 1] Vibrational Assignments The molecule 2PCP1A belongs to C1 point group symmetry, and its 57 fundamentals are distributed amongst the symmetry species as, all these modes are found to be active both in the Raman scattering and infrared absorption. The detailed vibrational assignment of fundamental modes of 2PCP1A along with the calculated IR and Raman frequencies and normal mode descriptions (characterized by PED) are reported in Table 2. For visual comparison, the observed and calculated FT-IR and FT-Raman spectra of 2PCP1A at DFT–B3LYP method using 6-31G(d,p), 6-311++G(2d,3p) and 6-31G(3df,3pd) basis sets are shown in Figures 1(b) and 2(a) respectively. The main focus of the present investigation is the proper assignment of the experimental frequencies to the various vibrational modes of 2PCP1A in corroboration with the calculated harmonic vibrational frequencies at B3LYP level using the standard 6-31G(d,p),6-311++G(2d,3p) and 6-31G(3df,3pd) basis sets. Comparison of the frequencies calculated by DFT-B3LYP method with the experimental values reveals the overestimation of the calculated vibrational modes due to neglect of an harmonicity in real system. CH vibrations The aromatic structure shows the presence of CH stretching vibration in the region 3200–3000cm1 which is the characteristic region for the identification of CH stretching vibration [13]. In this region, the bands are not affected appreciably by the nature of the constituents. For our title molecule the bands corresponding to CH stretching vibrations at 3204,3185 and 3172cm1 by DFT methods show excellent agreement with the literature data and also with the band observed in the recorded FT-IR spectrum at 3172cm1 [14,15]. The PED corresponding to this vibration is pure mode of contributing more than 90% as shown in Table 2. Ring Vibrations. Many ring modes are affected by the substitutions in the ring of midodrine. The actual position of these modes are determined not so much by the natural of the substituents but by the form of substitution around the ring system [16]. In our present study the wave number computed 1663, 1662 and 1660cm1 by B3LYP methods are assigned to CC stretching vibrations for the title molecule shows good agreement with recorded spectra. The in-plane and out-of-plane bending vibration are computed by DFT/6-31G(d,p), 6-311++G(2d,3p) and 6-31G(3df,3pd) methods show good agreement with literature [18,19] and recorded spectral data. [Click here to view Large Table 2] [Click here to view Large Figure 2] NH2 Vibrations Primary aliphatic amides absorb in the region 3520-3320cm- 1 [17]. The position of absorption in this region depends upon the degree of hydrogen bonding and the physical state of the sample or the polarity of the solvent. The NH2 asymmetric and symmetric stretching modes are 3568, 3564cm-1 and 3488, 3484cm-1 by B3LYP basis sets, while the experimental values are 3568 and 3566cm-1 in FT-IR and FT-Raman spectrum respectively. They are presented in Table 2. The PED contributions are 100% for stretching mode. NBO Analysis Natural bond analysis gives the accurate possible natural Lewis structure picture of because all orbitals are mathematically chosen to include the highest possible percentage of the electron density. Interaction between both filled and virtual orbital spaces information correctly explained by the NBO analysis could enhance the analysis of intra- and intermolecular interactions. The second order Fock matrix was carried out to evaluate donor (i) and acceptor (j) i.e. donor level bonds to acceptor level bonds interaction in the NBO analysis [18]. The result of interaction is a loss of occupancy from the concentrations of electron NBO of the idealized Lewis structure into an empty non-Lewis orbital. For each donor(i) and acceptor(j), the stabilization energy E(2) associated with the delocalization ij is estimated a where qi is the donor orbital occupancy, εi and εj are diagonal elements and F (i, j) is the off diagonal NBO Fock matrix element. Natural bond orbital analysis is used for investigating charge transfer or conjugative interaction in the molecular systems. Some electron donor orbital, acceptor orbital and the interacting stabilization energy results from the second-order microdisturbance theory are reported [19,20]. The larger E(2) value the more intensive is the interaction between electron donors and acceptors, i.e. the more donation tendency from electron donors to electron acceptors and the greater the extent of conjugation of the whole system [21]. Delocalization of electron density between occupied Lewis-type (bond or lone pair) NBO orbitals and formally unoccupied (antibond or Rydgberg) non-Lewis NBO orbitals correspond to a stabilization donor– acceptor interaction. NBO analysis has been performed on the 2PCP1A molecule at the DFT levels in order to elucidate the intramolecular interaction within the molecule. The intramolecular interaction is formed by the orbital overlap between bonding BD(2)C5C6, BD(2)C9-C10 and antibonding BD*(2)C7-C8, BD*(2)C5-C6 orbital, which results in the intramolecular charge transfer causing stabilization of the system. The second-order perturbation theory of Fock matrix in the NBO analysis shows strong intramolecular hyperconjugative interactions and the results are shown in Table 3. The most important interactions observed are BD(2)C9C10BD*(2)C5-C6 and BD(2)C5-C6BD*(2)C7-C8 and the corresponding energies are 24.30 and 23.78kJ/mol respectively. This larger energy provides the stabilization to the molecular structure. Graphical representation NBO analysis is shown in Figure 2(b). [Click here to view Large Table 3] Molecular Electrostatic Potential (MEP) The MEP is a useful feature to study reactivity given that an approaching electrophile will be attracted to negative regions (where the electron distribution effect is dominant). The importance of MEP lies in the fact that it simultaneously displays molecular size, shape as well as positive, negative and neutral electrostatic potential regions in terms of color grading and is very useful in research of molecular structure with its physicochemical property relationship [22,23]. The resulting surface simultaneously displays molecular size, shape and electrostatic potential value. In the majority of the MEP, while the maximum negative region which preferred site for electrophilic attack indications as red color, the maximum positive region which preferred site for nucleophilic attack symptoms as blue color. The different values of the electrostatic potential at the surface are represented by different colors. Potential increases in the order red < orange < yellow < green < blue. In this study, the color code of the map is in the range between -0.01054a.u. (deepest red) and 0.01054a.u. (deepest blue) in the studied compound, where blue indicates the strongest attraction and red indicates the strongest repulsion. The MEPs of 2PCP1A molecule in 3D plots are represented in Figure 3(a). As can be seen from the MEP map shown in figure, although the regions having the negative potential are over the carbon and nitrogen (the electronegative atoms) and also the regions having the positive potential are over hydrogen atoms localized a maximum positive region. From these results, we can say that the ring, the nitrogen atom and all hydrogen atoms (especially H16 atom) indicate the strongest attraction and C3 and N4 atoms indicate the strongest repulsion. Molecular Orbitals Transport Properties The HOMO-LUMO gap results in a significant degree of electric excitation and charge transfer. In most cases, even in the absence of inversion symmetry, the strongest band in the Raman spectrum is weak in the IR spectrum and vice versa. Changes in the HOMO-LUMO gap by connecting with some noble metal or semiconductor or some other means result in the change of the charge transfer degree, intensity and position of the peak.The HOMO–LUMO gap estimated to be 6.04eV at the B3LYP/6- 31G(d,p) level and the frontier orbitals are illustrated in Figure 3(b).The experimental and theoretical UV–Vis spectra are shown in Figure 4(a). Theoretical and experimental maximum absorption wavelengths and excitation energy are collected in Table 3. The observed peaks were found at 225nm in the water phase. The calculated peaks were found at 227nm in the gas phase. The calculated peaks were thus 2nm higher than the observed peaks, and this error may have been caused by the error of PCM modeling. [Click here to view Large Figure 3] Natural Population Analysis The calculation of atomic charges plays an important role in the application of quantum mechanical calculations to molecular systems [24]. Our interest here is in the comparison of different methods to describe the electron distribution in 2PCP1A as broadly as possible, and assess the sensitivity of the calculated charges to changes in (i) the choice of the basis set and (ii) the choice of the quantum mechanical method. Mulliken charges, calculated by determining the electron population of each atom as defined in the basis functions. The Mulliken charges calculated at different levels basis sets are listed in Table 4. The corresponding Mulliken’s plot with B3LYP different basis sets are shown in Figure 4(b). [Click here to view Large Figure 4] [Click here to view Large Table 4] Global Reactivity and Charge Reactivity Descriptors The other electronic properties as the chemical potential (), electronegativity (), electrophilicity index () and chemical hardness () are given in Table 4. The, and are important tools to study the order of stability of molecular systems. Using HOMO and LUMO energies, the and have been calculated. The chemical hardness and the chemicalpotential are given by the following expression,(IA)/2, (IA)/2. The, which measures the stabilization energy, has been given by the following expression, in terms of electronic chemical potential and the chemical hardness: 2/2 electro negativity (),(IA)/2or where I and A are ionization potential and electron affinity of a molecular system [25-28].M presumably arises from adsorbed molecular water (Table 2). Thermodynamics Properties On the basis of vibrational analysis at B3LYP/6-31G(d,p), 6-311++G(2d,3p) and 6-31G(3df,3pd)levels and several thermodynamic parameters are calculated and are compared in Table 5. The zero point vibration energies (ZPVE) and the entropy, Svib (T) are calculated with B3LYP methods are to the extent of accuracy and the variations in ZPVEs seem to be insignificant. The dipole moment calculated using B3LYP/6- 31G(d,p), 6-311++G(2d,3p) and 6-31G(3df,3pd) basis sets are found. The total energies and the change in the total entropy of2PCP1A at room temperature are found to be marginal. [Click here to view Large Table 5] Conclusion A complete vibrational analysis of 2PCP1A was performed by B3LYP/6-31G(d,p), 6-311++G(2d,3p) and 6-31G(3df,3pd) basis sets. This study demonstrates that the DFT (B3LYP) calculations are powerful approach for understanding the vibrational spectra of the title molecule. FT-IR, FT-Raman and UV-spectral studies of 2PCP1A were carried out. The molecular structure analysis has been performed based on the quantum mechanical approach by DFT calculation. The vibrational modes are assigned on the basis of PED percentage. NBO analysis indicates the strong intramolecular hyperconjugative interaction within the molecule and stability of the molecule. Mulliken charges on 2PCP1A at different levels were calculated and the results discussed. HOMO, LUMO energies and HOMO-LUMO energy gap was also calculated. The maximum absorption peakmax in the UV-Vis spectrum has been observed at 304nm. The MEP map shows that the negative potential sites are on nitrogen and some of the carbon atoms as well as the positive potential sites are on the hydrogen and carbon atoms in the molecule. For more Open Access Journals in Juniper Publishers please click on: https://juniperpublishers.com/ for more details click on the juniper publishers material science

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Author:

Rajni Garg & Randhir Singh

Published in: McGraw Hill Education Release Year: 2015 ISBN: 978-93-83286-90-4 Pages: 1677 Edition: First Edition File Size: 40 MB File Type: pdf Language: English

Description of Inorganic Chemistry

Inorganic chemistry is a dynamic and fascinating field of chemistry growing at a rapid pace in both research and theoretical aspects. The lusty impact of this field has introduced the subject as an essential part of the curricula of all universities. The first edition of Inorganic Chemistry aims to provide the essentials of the subject in an easy and understandable manner. The book is an outcome of the teaching and research experience of the authors so that students can learn concept formulation instead of just rote memorization.  The book is primarily aimed for students at undergraduate (BSc pass and honors) and postgraduate (MSc pass and honors) levels taking inorganic chemistry as a special subject for a one-semester or a full-year course. Inorganic Chemistry book is designed to provide concise information about various aspects of inorganic chemistry that can also be used by students from various fields involving inorganic compounds, such as environmental science, polymer science, industrial chemistry, bioinorganic chemistry, and metallurgy. However, they can skip the irrelevant topics as per their field. Inorganic Chemistry book will also be a source of reference for the students doing BTech courses or taking inorganic chemistry as an ancillary subject. It will also be helpful for the challenging requirements of various competitive exams such as CSIR, SLET, and GATE. The content of the Inorganic Chemistry book has been framed in an easy-to-understand language that would generate interest in the subject. All the chapters provide descriptive information and are enriched with illustrations, comprehensible articles, solved examples, both numerical as well as theoretical, to satisfy the needs of students. At the end of each chapter, a concise summary has been given for quick revision before examinations. The chapters have been enriched with exercises comprising theory-based general questions and objective-type questions to provide an insight into the examination pattern. The book introduces descriptive and illustrative information about structure of atoms and nuclei, radioactivity, chemical bonding, molecular symmetry, structure of solids, redox reactions, non-aqueous solvents, acids and bases, extraction of elements, Periodic Table, chemistry of known elements, coordination chemistry, organometallics, inorganic polymers, bioinorganic chemistry, environmental chemistry and analytical chemistry. Although it is very difficult to include such a vast subject in a single book, a reasonable attempt has been made to cover a variety of important topics. We hope the Inorganic Chemistry book will prove very helpful in providing the complex concepts of inorganic chemistry in an easy way.

Content of Inorganic Chemistry

1. Structure of Atom 1.1 Introduction 1.2 Rutherford Scattering Experiment 1.3 Planck’s Quantum Theory of Radiation 1.4 Photoelectric Effect 1.5 Atomic Spectrum of Hydrogen 1.6 Bohr’s Model of the Atom 1.7 Sommerfeld’s Extension of Bohr’s Atomic Model 1.8 Dual Character of Matter 1.9 Heisenberg’s Uncertainty Principle 1.10 Compton Effect 1.11 Schrodinger Wave Equation 1.12 Quantum Numbers 1.13 Probability Distribution Curves 1.14 Rules for Filling of Orbitals and Electronic Configuration of Elements Summary Solved Examples Exercises 2. Nuclear Chemistry 2.1 Nucleus 2.2 Composition of the Nucleus 2.3 Nuclear Forces 2.4 Nuclear Stability 2.5 Nuclear Models 2.6 Nuclear Reactions 2.7 Radioactivity 2.8 Radioactive Disintegration 2.9 Law of Successive Disintegration: Radioactive Equilibrium 2.10 Soddy-Fajans and Russel Group Displacement Law 2.11 Artificial Radioactivity 2.12 Applications of Radioactive Isotopes Summary Solved Examples Exercises 3. Chemical Bonding 3.1 Introduction 3.2 Ionic Bond or Electrovalent Bond 3.3 Covalent Bond (Lewis-Langmuir Concept) 3.4 Dipole Moment 3.5 Coordinate Covalent Bond or Dative Bond 3.6 Van der Waals’ Forces or Intermolecular Forces 3.7 Hydrogen Bond 3.8 Orbital Overlap Theory 3.9 Molecular Orbital Theory 3.10 Metallic Bond 3.11 Hybridisation 3.12 Sidgwick – Powell Theory 3.13 Valence Shell Electron-pair Repulsion Theory (VSEPR theory) 3.14 Shapes of Some Common Molecules 3.15 Linnett Double Quartet Theory (LDQ Theory)—Modification of Lewis Longmuir Octet Theory 3.16 Resonance Summary Solved Examples Exercises 4. Molecular Symmetry 4.1 Introduction 4.2 Symmetry Element 4.3 Multiplication of Symmetry Operations 4.4 Mathematical Group 4.5 Matrix Representation of Symmetry Operations 4.6 Terms Symbols of Diatomic Molecules 4.7 Applications of Group Theory 4.8 Structure of Solids Summary Solved Examples Exercises 5. Redox Reactions 5.1 Introduction 5.2 Electrochemical Cell 5.3 Kinetics of Redox Reactions 5.4 Redox Reactions in Aqueous Systems 5.5 Diagrammatic Representation of Potential Data Summary Solved Examples Exercises 6. Non-aqueous Solvents 6.1 Introduction 6.2 Classification of Solvents 6.3 Liquid Ammonia 6.4 Liquid Sulphur Dioxide 6.5 Anhydrous Hydrogen Fluoride 6.6 Anhydrous Sulphuric Acid 6.7 Acetic Acid 6.8 Liquid Dinitrogen Tetroxide, N2O4 6.9 Molten Salts and Ionic Liquids 6.10 Concept of Acid-Base 6.11 Acid Strength Behaviour in the Periodic Table Summary Solved Examples Exercises 7. Extraction of Elements 7.1 Introduction 7.2 Occurrence of Elements 7.3 Metallurgy 7.4 Purification of Impure Metals or Refining 7.5 Thermodynamics of the Metallurgy: Ellingham Diagram Summary Solved Examples Exercises 8. Periodic Table and Periodic Properties 8.1 Introduction 8.2 Mendeleev's Periodic Table 8.3 Modern Periodic Law and Periodicity 8.4 Long form of Periodic Table 8.5 Periodic Properties 8.6 Shielding or Screening Effect Summary Solved Examples Exercises 9. Hydrogen and its Compounds 9.1 Introduction 9.2 Position of Hydrogen in the Periodic Table 9.3 Occurrence and Production of Hydrogen 9.4 Physical Properties of Hydrogen 9.5 Chemical Properties of Hydrogen 9.6 Uses of Hydrogen 9.7 Different Forms of Hydrogen 9.8 Spin Isomers of Hydrogen 9.9 Isotopes of Hydrogen 9.10 Compounds of Hydrogen 9.11 Water H2O 9.12 Heavy Water (D2O) Summary Solved Examples Exercises 10. Chemistry of Group 1 Elements 10.1 Introduction 10.2 General Characteristics of Group I Elements 10.3 Chemical Properties of Alkali Metals 10.4 Lithium (Li) 10.5 Sodium (Na) 10.6 Potassium (K) 10.7 Rubidium, Caesium and Francium Summary Solved Examples Exercises 11. Chemistry of Group 2 Elements 11.1 Introduction 11.2 General Characteristics of Group 2 Elements 11.3 Chemical Properties of Alkaline Earth Metals 11.4 Beryllium (Be) 11.5 Magnesium (Mg) 11.6 Calcium (Ca) 11.7 Strontium (Sr) 11.8 Barium (Ba) 11.9 Radium (Ra) 11.10 Portland Cement Summary Solved Examples Exercises 12. Chemistry of Group 13 Elements 12.1 Introduction 12.2 Electronic Structure 12.3 General Physical Properties 12.4 Diagonal Relationship between Boron and Silicon 12.5 Chemical Properties of Group 13 Elements 12.6 Boron 12.7 Aluminum (Al) 12.8 Gallium (Ga) 12.9 Indium and Thallium (Th) 12.10 Comparision of Compounds of Group 13 Elements Summary Solved Examples Exercises 13. Chemistry of Group 14 Elements 13.1 Introduction 13.2 General Properties of Group 14 Elements 13.3 Anomalous Behaviour of Carbon 13.4 Carbon and Silicon—Comparison of Properties 13.5 Carbon 13.6 Silicon (Si) 13.7 Germanium (Ge) 13.8 Tin (Sn) 13.9 Lead (Pb) 13.10 Comparative Account of Compounds of Group 14 Elements Summary Solved Examples Exercises 14. Chemistry of Group 15 Elements 14.1 Introduction 14.1 14.2 General Properties of Group 15 Elements 14.3 Chemical Properties of Group 15 Elements 14.4 Nitrogen (N) 14.5 Phosphorus (P) 14.6 Arsenic (As) 14.7 Antimony (Sb) 14.8 Bismuth (Bi) Summary Solved Examples Exercises 15. Chemistry of Group 16 Elements 15.1 Introduction 15.2 General Properties of Group 16 Elements 15.3 Anomalous Behaviour of Oxygen 15.4 Oxygen (O2 ) 15.5 Sulphur (S2 ) 15.6 Selenium (Se) 15.7 Tellurium (Te) 15.8 Polonium (Po) 15.9 Comparative Account of Compounds of Group 16 Elements Summary Solved Examples Exercises 16. Chemistry of Group 17 Elements 16.1 Introduction 16.2 General Characterisation 16.3 Chemical Properties 16.4 Fluorine (F) 16.5 Chlorine (Cl) 16.6 Bromine (Br) 16.7 Iodine (I) 16.8 Astatine (At) 16.9 Interhalogen Compounds 16.10 Polyhalides 16.11 Pseudohalogens and Pseudohalides Summary Solved Examples Exercises 17. Chemistry of Group 18 Elements 17.1 Introduction 17.2 History and Discovery 17.3 Occurrence and Isolation of Noble Gases 17.4 Uses of Noble Gases 17.5 Physical Properties 17.6 Chemical Properties 17.7 Chemistry of Xenon (Xe) 17.8 Compounds of Krypton (Krf2 ) 17.9 Compounds of Radon (Rn) Summary Solved Examples Exercises 18. Chemistry of d-block Elements 18.1 Introduction 18.2 Classification of d-block Elements 18.3 General Characteristic of d-block Elements Summary Solved Examples Exercises 19. Chemistry of Elements of 3d Series 19.1 Introduction 19.2 Scandium (Sc) 19.3 Titanium (Ti) 19.4 Vanadium (V2 ) 19.5 Chromium (Cr) 19.6 Manganese (Mn) 19.7 Iron (Fe) 19.8 Cobalt (Co) 19.9 Nickel (Ni) 19.10 Copper (Cu) 19.11 Zinc (Zn) Summary Solved Examples Exercises 20. Chemistry of Elements of 4d Series 20.1 Introduction 20.2 Yttrium (Y) 20.3 Zirconium (Zr) 20.4 Niobium (Nb) 20.5 Molybdenum (Mo) 20.6 Technetium (Tc) 20.7 Ruthenium (Ru) 20.8 Rhodium (Rh) 20.9 Palladium (Pd) 20.10 Silver (Ag) 20.11 Cadmium (Cd) Summary Solved Examples Exercises 21. Chemistry of 5d Series 21.1 Introduction 21.2 Hafnium (HF) 21.3 Tantalum (Ta) 21.4 Tungsten (W) 21.5 Rhenium (Re) 21.6 Osmium (Os) 21.7 Iridium (Ir) 21.8 Platinum (Pt) 21.9 Gold (Au) 21.10 Mercury (Hg) Summary Solved Examples Exercises 22. Chemistry of Lanthanides and Actinides 22.1 Introduction 22.2 Lanthanides 22.3 Lanthanum (La) 22.4 Actinides 22.5 Thorium (Th) 22.6 Uranium (U) 22.7 Plutonium (Pu) Summary Solved Examples Exercises 23. Coordination Compounds-I Basics Concepts: Nomenclature and Stereochemistry 23.1 Introduction 23.2 Important Terms 23.3 Rules for Nomenclature of Coordination Compounds 23.4 Rules for Formula of the Coordination Compounds 23.5 Classification of Complexes 23.6 Isomerism Summary Solved Examples Exercises 24. Coordination Compounds— II Theories of Bonding 24.1 Introduction 24.2 Techniques for Study of Complexes 24.3 Theories of Coordination 24.4 Crystal Field Theory (CFT) 24.5 The Ligand Field Theory-Molecular Orbital Theory Summary Solved Examples Exercises 25. Coordination Compounds III: Quantitative Basis of Crystal Field Theory 25.1 Introduction 25.2 Determination of Octahedral Crystal Field Potential 25.3 Determination of Tetragonal Crystal Field Potential 25.4 Determination of Square Planar Crystal-Field Potential 25.5 Determination of Tetrahedral Crystal-Field Potential 25.6 Determination of Cubic Crystal-Field Potential 25.7 Structural and Thermodynamic Effects of Splitting of Orbitals 25.8 Jahn-Teller Effect (Distortion of Geometry) Summary Solved Examples Exercises 26. Coordination Complexes IV: Spectroscopic and Magnetic Properties of Coordination Compounds 26.1 Introduction 26.2 Coupling Schemes 26.3 Energy Terms and the Energy States 26.4 Electronic Spectra of Transition-Metal Compounds 26.5 Orgel Diagrams 26.6 Racah Parameters 26.7 Terms Correlation Diagrams under the Effect of Weak and Strong Field Effects 26.8 Tanabe-Sugano Diagrams (T-S Diagram) 26.9 Charge-Transfer Transitions 26.10 Types of Magnetism Summary Solved Examples Exercises 27. Coordination Compounds – λ The Reaction Mechanisms of Transition-Metal Complexes 27.1 Introduction 27.2 Ligand-substitution Reactions 27.3 Oxidation-reduction Reactions in Coordination Compounds Summary Solved Examples Exercises 28. Complexes of π-Acceptor Ligands 28.1 Introduction 28.2 Complexes of Carbonyls 28.3 Complexes of Nitric Oxide 28.4 Complexes of Phosphines 28.5 Complexes of Cyanide and Isocyanide Ligands Summary Solved Examples Exercises 29. Chemistry of Organometallic Compounds 29.1 Introduction 29.2 Organometallic Compounds of Alkali Metals 29.3 Organometallic Compounds of Alkaline Earth Metals 29.4 Organometallics of Group 13 Elements 29.5 Organometallics of Group 14 Elements 29.6 Organometallics of Group 15 Elements 29.7 Organometallic Compounds of Transition Elements Summary Solved Examples Exercises 30. Metal Clusters 30.1 Introduction 30.2 Polynuclear Compounds of Oxygen and other Chalcogens 30.3 Clusters of p-block Elements other than Chalcogens 30.4 Low-valent Metal Clusters 30.5 High-Valent Metal Clusters or Halide-type Clusters Summary Solved Examples Exercises 31. Inorganic Nomenclature 31.1 Introduction 31.2 General Nomenclature and Formulae of Compounds Solved Examples Exercises 32. Inorganic Polymers 32.1 Introduction 32.2 Classification of Inorganic Polymers 32.3 General Characteristics of Inorganic Polymers 32.4 Important Inorganic Polymers Exercises 33. Bioinorganic Chemistry 33.1 Introduction 33.2 Metalloporphyrins 33.3 Cytochromes 33.4 Peroxidases (Molar Mass ~40,000) 33.5 Catalases 33.6 Ferredoxins 33.7 Metallo-enzymes 33.8 Biological Nitrogen Fixation 33.9 Na-K pump Summary Solved Examples Exercises 34. Pollution 34.1 Introduction 34.2 Air Pollution 34.3 Water Pollution 34.4 Soil Pollution Summary Exercises 35. Analytical Chemistry 35.1 Errors 35.2 Detection and Minimisation of Errors 35.3 Precision 35.4 Ways of Expressing Precision 35.5 Analysis of Data by Using Statistical Techniques 35.6 Detecting Outliers 35.7 Significance Tests 35.8 Significant Figures 35.9 Expressing Error or Accuracy of a Measurement 35.10 Error Propagation in Final Results 35.11 Volumetric Analysis 35.12 Preparation of Standard Solution 35.13 Volumetric Methods Summary Solved Examples Exercises Index